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Sample records for genetic models mineralization

  1. Mouse models for pseudoxanthoma elasticum: genetic and dietary modulation of the ectopic mineralization phenotypes.

    Directory of Open Access Journals (Sweden)

    Qiaoli Li

    Full Text Available Pseudoxanthoma elasticum (PXE, a heritable ectopic mineralization disorder, is caused by mutations in the ABCC6 gene. Null mice (Abcc6(-/- recapitulate the genetic, histopathologic and ultrastructural features of PXE, and they demonstrate early and progressive mineralization of vibrissae dermal sheath, which serves as a biomarker of the overall mineralization process. Recently, as part of a mouse aging study at The Jackson Laboratory, 31 inbred mouse strains were necropsied, and two of them, KK/HlJ and 129S1/SvImJ, were noted to have vibrissae dermal mineralization similar to Abcc6(-/- mice. These two strains were shown to harbor a single nucleotide polymorphism (rs32756904 in the Abcc6 gene, which resulted in out-of-frame splicing and marked reduction in ABCC6 protein expression in the liver of these mice. The same polymorphism is present in two additional mouse strains, DBA/2J and C3H/HeJ, with similar reduction in Abcc6 protein levels, yet these mice did not demonstrate tissue mineralization when kept on standard rodent diet. However, all four mouse strains, when placed on experimental diet enriched in phosphate and low in magnesium, developed extensive ectopic mineralization. These results indicate that the genetic background of mice and the mineral composition of their diet can profoundly modulate the ectopic mineralization process predicated on mutations in the Abcc6 gene. These mice provide novel model systems to study the pathomechanisms and the reasons for strain background on phenotypic variability of PXE.

  2. Genetic Modeling of GIS-Based Cell Clusters and Its Application in Mineral Resources Prediction

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    This paper presents a synthetic analysis method for multi-sourced geological data from geographic information system (GIS). In the previous practices of mineral resources prediction, a usually adopted methodology has been statistical analysis of cells delimitated based on thoughts of random sampiing. That might lead to insufficient utilization of local spatial information, for a cell is treated as a point without internal structure. We now take "cell clusters", i. e. , spatial associations of cells, as basic units of statistics, thus the spatial configuration information of geological variables is easier to be detected and utilized, and the accuracy and reliability of prediction are improved. We build a linear multi-discriminating model for the clusters via genetic algorithm. Both the right-judgment rates and the in-class vs. between-class distance ratios are considered to form the evolutional adaptive values of the population. An application of the method in gold mineral resources prediction in east Xinjiang, China is presented.

  3. Genetic Types of Diamond Mineralization

    Institute of Scientific and Technical Information of China (English)

    A.A.MARAKUSHEV; 桑隆康; 等

    1998-01-01

    The paper describes the proposed models of diamond formation both in meteorites and in kimberlite and lamproite bodies.metamorphic complexes and explosive-ring structures ("astroblemes"),The diamond distribution in meteorites(chondrites,iron meteorites and ureilites)is restricted to taente-kamasite phase.The diamond generation here is tied up with the first stage of evolution of the planets,This stage is characterized by high pressure of hydrogen. leading to the formation of the planet envelope,The second stage of planet evolution began with the progressive imopoverishment of their atmospheres in hydrogen due to its predominant emission into the space and to progressive development of oxidative conditions.The model appears to have proved the relict nature of diamond mineraolization in meteorites.Diamond and other high-pressure minerals(its"satellites") were crystallized without any exception in the early intratelluric stages of peridotite and eclogite-pyroxenite magma evolution just before the magma intrusion into the higher levels of the mantle and crust where diamond is not thermodynamically stable,The ultramafic intrusive bodies(bearing rich relict diamonds)in the dase of a platform paaear to be the substrata for the formation of kimberlite-lamproite magma chambers as a result of magmatic replacement.The model explains the polyfacial nature of diamondiferous eclotgites,pyroxenites and peridotites and discusses the process of inheritance of their diamond mineralization by kimberlites and lamproites.Dimond oproductivity of metamorthic complexes is originated by the inheritance of their diamonds from the above-mentioned primary diamondiferous rocks.Large diamondiferous explosive-ring structures were formed by high-energy endogenic explosion of fluid which came from the Earth's core.This high energy differs endogenic impactogenesis from explosive volcanism.It proceeds at very high temperature to create diaplectic galsses(monomineral pseudomorphs)-the product of

  4. Mathematical model for bone mineralization

    Directory of Open Access Journals (Sweden)

    Svetlana V Komarova

    2015-08-01

    Full Text Available Defective bone mineralization has serious clinical manifestations, including deformities and fractures, but the regulation of this extracellular process is not fully understood. We have developed a mathematical model consisting of ordinary differential equations that describe collagen maturation, production and degradation of inhibitors, and mineral nucleation and growth. We examined the roles of individual processes in generating normal and abnormal mineralization patterns characterized using two outcome measures: mineralization lag time and degree of mineralization. Model parameters describing the formation of hydroxyapatite mineral on the nucleating centers most potently affected the degree of mineralization, while the parameters describing inhibitor homeostasis most effectively changed the mineralization lag time. Of interest, a parameter describing the rate of matrix maturation emerged as being capable of counter-intuitively increasing both the mineralization lag time and the degree of mineralization. We validated the accuracy of model predictions using known diseases of bone mineralization such as osteogenesis imperfecta and X-linked hypophosphatemia. The model successfully describes the highly non-linear mineralization dynamics, which includes an initial lag phase when osteoid is present but no mineralization is evident, then fast primary mineralization, followed by secondary mineralization characterized by a continuous slow increase in bone mineral content. The developed model can potentially predict the function for a mutated protein based on the histology of pathologic bone samples from mineralization disorders of unknown etiology.

  5. Predicting complex mineral structures using genetic algorithms.

    Science.gov (United States)

    Mohn, Chris E; Kob, Walter

    2015-10-28

    We show that symmetry-adapted genetic algorithms are capable of finding the ground state of a range of complex crystalline phases including layered- and incommensurate super-structures. This opens the way for the atomistic prediction of complex crystal structures of functional materials and mineral phases.

  6. Evaluation of volcanic reservoirs with the "QAPM mineral model" using a genetic algorithm%基于QAPM矿物模型遗传算法评价火成岩储层

    Institute of Scientific and Technical Information of China (English)

    潘保芝; 薛林福; 黄布宙; 闫桂京; 张丽华

    2008-01-01

    Gas-bearing volcanic reservoirs have been found in the deep Songliao Basin, China. Choosing proper interpretation parameters for log evaluation is difficult due to complicated mineral compositions and variable mineral contents. Based on the QAPF classification scheme given by IUGS, we propose a method to determine the mineral contents of volcanic rocks using log data and a genetic algorithm. According to the QAPF scheme, minerals in volcanic rocks are divided into five groups: Q(quartz), A (Alkaline feldspar), P (plagioclase), M (mafic) and F (feldspathoid). We propose a model called QAPM including porosity for the volumetric analysis of reservoirs. The log response equations for density, apparent neutron porosity, transit time, gamma ray and volume photoelectrical cross section index were first established with the mineral parameters obtained from the Schlumberger handbook of log mineral parameters. Then the volumes of the four minerals in the matrix were calculated using the genetic algorithm (GA). The calculated porosity, based on the interpretation parameters, can be compared with core porosity, and the rock names given in the paper based on QAPF classification according to the four mineral contents are compatible with those from the chemical analysis of the core samples.

  7. Multiphase Sequestration Geochemistry: Model for Mineral Carbonation

    Energy Technology Data Exchange (ETDEWEB)

    White, Mark D.; McGrail, B. Peter; Schaef, Herbert T.; Hu, Jian Z.; Hoyt, David W.; Felmy, Andrew R.; Rosso, Kevin M.; Wurstner, Signe K.

    2011-04-01

    Carbonation of formation minerals converts low viscosity supercritical CO2 injected into deep saline reservoirs for geologic sequestration into an immobile form. Until recently the scientific focus of mineralization reactions with reservoir rocks has been those that follow an aqueous-mediated dissolution/precipitation mechanism, driven by the sharp reduction in pH that occurs with CO2 partitioning into the aqueous phase. For sedimentary basin formations the kinetics of aqueous-mediated dissolution/precipitation reactions are sufficiently slow to make the role of mineralization trapping insignificant over a century period. For basaltic saline formations aqueous-phase mineralization progresses at a substantially higher rate, making the role of mineralization trapping significant, if not dominant, over a century period. The overlooked mineralization reactions for both sedimentary and basaltic saline formations, however, are those that occur in liquid or supercritical CO2 phase; where, dissolved water appears to play a catalyst role in the formation of carbonate minerals. A model is proposed in this paper that describes mineral carbonation over sequestration reservoir conditions ranging from dissolved CO2 in aqueous brine to dissolved water in supercritical CO2. The model theory is based on a review of recent experiments directed at understanding the role of water in mineral carbonation reactions of interest in geologic sequestration systems occurring under low water contents.

  8. Characteristics of porosity and permeability layer of fossil Halimeda reef mineral rock of Miocene in the Xisha Islands and its genetic model

    Institute of Scientific and Technical Information of China (English)

    XU Hong; WEI Kai; CUI Ruyong; ZHU Yurui; EBERLI G P; LUO Wei; ZHAO Xinwei; CAI Ying; LIU Xinyu; YAN Guijing; ZHANG Bolin

    2015-01-01

    Halimeda is one of the major reef-building algas in the middle Miocene of Xisha, and one of the significant reef-building algas in the algal reef oil and gas field of the South China Sea. However, there have been few reports regarding the characteristics of mineral rocks, reservoir porosity and permeability layers, and sedimentation-diagenetic-evolution of fossil Halimeda systems. The present paper briefly introduces the relevant studies on chlorophyta Halimeda and the research status of oil and gas exploration. Through the 1 043 m core of the Xichen-1 well, we studied the characteristics of the mineral rocks and porosity and permeability of the middle Miocene Halimeda of the Yongle Atoll, identified and described the segments of fossil Halimeda, and pointed out that most of the segment slides are vertical sections in ovular, irregular or long strips. The overwhelming majority of these fossil Halimeda found and studied are vertical sections instead of cross sections. In this paper, knowledge regarding the cross sections of fossil Halimeda is reported and proven to be similar with the microscopic characteristics of modern living Halimeda;fossil Halimeda are buried in superposition;it is shown that there are different structures present, including typical bio-segment structure, and due to its feature of coexisting with red alga, tying structure, twining structure and encrusting structure are all present;and finally, it is suggested to classify the fossil Halimeda into segment algal reef dolomites. In addition, all of the studied intervals are moderately dolomitized. Secondary microcrystalline-dolosparite dominates the original aragonite raphide zones, and aphanitic-micrite dolomite plays the leading role in the cortexes and medullas;in the aragonite raphide zones between medulla and cysts, secondary dissolved pores and intercrystalline pores are formed inside the segments, and algal frame holes are formed between segments;therefore, a pore space network system

  9. Mathematical Model for the Mineralization of Bone

    Science.gov (United States)

    Martin, Bruce

    1994-01-01

    A mathematical model is presented for the transport and precipitation of mineral in refilling osteons. One goal of this model was to explain calcification 'halos,' in which the bone near the haversian canal is more highly mineralized than the more peripheral lamellae, which have been mineralizing longer. It was assumed that the precipitation rate of mineral is proportional to the difference between the local concentration of calcium ions and an equilibrium concentration and that the transport of ions is by either diffusion or some other concentration gradient-dependent process. Transport of ions was assumed to be slowed by the accumulation of mineral in the matrix along the transport path. ne model also mimics bone apposition, slowing of apposition during refilling, and mineralization lag time. It was found that simple diffusion cannot account for the transport of calcium ions into mineralizing bone, because the diffusion coefficient is two orders of magnitude too low. If a more rapid concentration gradient-driven means of transport exists, the model demonstrates that osteonal geometry and variable rate of refilling work together to produce calcification halos, as well as the primary and secondary calcification effect reported in the literature.

  10. Mineral potential mapping with mathematical geological models

    NARCIS (Netherlands)

    Porwal, A.K.

    2006-01-01

    Mathematical geological models are being increasingly used by natural resources delineation and planning agencies for mapping areas of mineral potential in order to optimize land use in accordance with socio-economic needs of the society. However, a key problem in spatial-mathematical-model-based mi

  11. Mineral potential mapping with mathematical geological models

    NARCIS (Netherlands)

    Porwal, A.K.

    2006-01-01

    Mathematical geological models are being increasingly used by natural resources delineation and planning agencies for mapping areas of mineral potential in order to optimize land use in accordance with socio-economic needs of the society. However, a key problem in spatial-mathematical-model-based

  12. Modeling optimal mineral nutrition for hazelnut micropropagation

    Science.gov (United States)

    Micropropagation of hazelnut (Corylus avellana L.) is typically difficult due to the wide variation in response among cultivars. This study was designed to overcome that difficulty by modeling the optimal mineral nutrients for micropropagation of C. avellana selections using a response surface desig...

  13. Genetic parameters for concentrations of minerals in longissimus muscle and their associations with palatability traits in Angus cattle.

    Science.gov (United States)

    Mateescu, R G; Garmyn, A J; Tait, R G; Duan, Q; Liu, Q; Mayes, M S; Garrick, D J; Van Eenennaam, A L; Vanoverbeke, D L; Hilton, G G; Beitz, D C; Reecy, J M

    2013-03-01

    The objective of this study was to estimate genetic parameters for concentrations of minerals in LM and to evaluate their associations with beef palatability traits. Samples of LM from 2,285 Angus cattle were obtained and fabricated into steaks for analysis of mineral concentrations and for trained sensory panel assessments. Nine minerals, including calcium, copper, iron, magnesium, manganese, phosphorus, potassium, sodium, and zinc, were quantified. Restricted maximum likelihood procedures were used to obtain estimates of variance and covariance components under a multiple-trait animal model. Estimates of heritability for mineral concentrations in LM varied from 0.01 to 0.54. Iron and sodium were highly and moderately heritable, respectively, whereas the other minerals were lowly heritable except for calcium, copper, and manganese, which exhibited no genetic variation. Strong positive genetic correlations existed between iron and zinc (0.49, P minerals (P > 0.05). Beefy flavor was positively associated with calcium, iron, and zinc and negatively associated with sodium concentration, whereas a painty or fishy flavor was positively associated with sodium and negatively associated with calcium and potassium concentrations (P < 0.05). Beef is a major contributor of iron and zinc in the human diet, and these results demonstrate sufficient genetic variation for these traits to be improved through marker-assisted selection programs without compromising beef palatability.

  14. Genetic susceptibility to progressive massive fibrosis in coal miners

    Energy Technology Data Exchange (ETDEWEB)

    Yucesoy, B.; Johnson, V.J.; Kissling, G.E.; Fluharty, K.; Kashon, M.L.; Slaven, J.; Germolec, D.; Vallyathan, V.; Luster, M.I. [NIOSH, Morgantown, WV (United States)

    2008-06-15

    Progressive massive fibrosis (PMF) is a chronic interstitial lung disease with a complex aetiology that can occur after cumulative dust exposure. A case-control study was conducted to test the hypothesis that single nucleotide polymorphisms (SNPs) within genes involved in inflammatory and fibrotic processes modulate the risk of PMF development. The study population consisted of 648 underground coal miners participating in the National Coal Workers Autopsy Study, of which 304 were diagnosed with PMF SNPs that influence the regulation of interleukin (IL)-1, IL-6, tumour necrosis factor-alpha, transforming growth factor-beta 1, vascular endothelial growth factor (VEGF), epidermal growth factor intercellular cell adhesion molecule (ICAM)-1 and matrix metalloproteinase-2 genes were determined using a 5'-nuclease real-time PCR assay. There were no significant differences in the distribution of any individual SNP or haplotype between the PMF and control groups. However, the polygenotype of VEGF +405/ICAM-1 +241/IL-6 -174 (C-A-G) conferred an increased risk for PMF (odds ratio 3.4, 95% confidence interval 1.3-8.8). The present study suggests that the examined genetic variations that help regulate inflammatory and fibrotic processes are unlikely to strongly influence susceptibility to this interstitial lung disease, although the role of vascular endothelial growth factor, intercellular cell adhesion molecule-1 and interleukin-6 polymorphisms in the development of progressive massive fibrosis may require further investigation.

  15. Mineral resources estimation based on block modeling

    Science.gov (United States)

    Bargawa, Waterman Sulistyana; Amri, Nur Ali

    2016-02-01

    The estimation in this paper uses three kinds of block models of nearest neighbor polygon, inverse distance squared and ordinary kriging. The techniques are weighting scheme which is based on the principle that block content is a linear combination of the grade data or the sample around the block being estimated. The case study in Pongkor area, here is gold-silver resource modeling that allegedly shaped of quartz vein as a hydrothermal process of epithermal type. Resources modeling includes of data entry, statistical and variography analysis of topography and geological model, the block model construction, estimation parameter, presentation model and tabulation of mineral resources. Skewed distribution, here isolated by robust semivariogram. The mineral resources classification generated in this model based on an analysis of the kriging standard deviation and number of samples which are used in the estimation of each block. Research results are used to evaluate the performance of OK and IDS estimator. Based on the visual and statistical analysis, concluded that the model of OK gives the estimation closer to the data used for modeling.

  16. The structural and genetic position uranium-thorium mineralization of Azov megablock

    Directory of Open Access Journals (Sweden)

    Katalenets A.I.

    2014-12-01

    Full Text Available The genetic characteristics of development and placement uranium-thorium mineralization and distribution of their concentrations in Azov megablock areas are examined. The main structures of Azov megablock areas controlling of distribution of metasomatic types and ore occurrence related with them are set. Preliminary basis for the allocation of boundaries and areas of ore districts is created. Considered theoretical and practical problem associated with the establishment of regional characteristics, genetic types of mineralization, its structural and temporary accommodation, the development of search criteria and characteristics of mineralization, the release of potentially mineralized areas and study areas of prospecting for Azov megablock of Ukrainian shield. The research is based on data on the geological structure of the PM, and the structural control of the placement lithochemical uranium and thorium anomalies occurrences and deposits, typomorphic properties of minerals, the phase distribution of uranium, thorium. Distribution of uranium and thorium mineralization in areas considered structure is: own minerals, isomorphic impurity in minerals associated with them, or turn on the first to the last. Uranium and thorium PM mineralization is characterized by a genetic (paragenetic involving mineral associations exogenous and metasomatic rocks.

  17. Measurement and Modelling of Scaling Minerals

    DEFF Research Database (Denmark)

    Villafafila Garcia, Ada

    2005-01-01

    of scale formation found in many industrial processes, and especially in oilfield and geothermal operations. We want to contribute to the study of this problem by releasing a simple and accurate thermodynamic model capable of calculating the behaviour of scaling minerals, covering a wide range......-liquid equilibrium of sulphate scaling minerals (SrSO4, BaSO4, CaSO4 and CaSO4•2H2O) at temperatures up to 300ºC and pressures up to 1000 bar is described in chapter 4. Results for the binary systems (M2+, )-H2O; the ternary systems (Na+, M2+, )-H2O, and (Na+, M2+, Cl-)-H2O; and the quaternary systems (Na+, M2+)(Cl...

  18. Measurement and Modelling of Scaling Minerals

    DEFF Research Database (Denmark)

    Villafafila Garcia, Ada

    2005-01-01

    of scale formation found in many industrial processes, and especially in oilfield and geothermal operations. We want to contribute to the study of this problem by releasing a simple and accurate thermodynamic model capable of calculating the behaviour of scaling minerals, covering a wide range...... of temperature and pressure. Reliable experimental solubility measurements under conditions similar to those found in reality will help the development of strong and consistent models. Chapter 1 is a short introduction to the problem of scale formation, the model chosen to study it, and the experiments performed...... the thermodynamic model used in this Ph.D. project. A review of alternative activity coefficient models an earlier work on scale formation is provided. A guideline to the parameter estimation procedure and the number of parameters estimated in the present work are also described. The prediction of solid...

  19. Hg and As Minerals in Fluid Inclusions from the Williams Mine, Hemlo, and Their Genetic Implications

    Institute of Scientific and Technical Information of China (English)

    LU HUANZHANG(卢焕章); JAYANTA. GUHA; DON. C. HARRIS

    2002-01-01

    The Hemlo mineralization is enigmatic compared to general Archean lode gold deposits based on the fact that it is characterized by an exotic mineralogy containing elements such as As, Hg, Sb, Ba, V and Mo. The genetic concepts range from syngenetic to epigenetic types of mineralization. This reconnaissance study was designed to examine the relationship of Hg-As minerals with respect to fluid inclusions in the Williams mine (formerly known as the Page Williams mine) covering the A and C ore zones.

  20. Genetic influence on bone mineral density in Korean twins and families: the healthy twin study.

    Science.gov (United States)

    Park, J-H; Song, Y-M; Sung, J; Lee, K; Kim, Y S; Park, Y S

    2012-04-01

    Bone mineral density (BMD), a representative marker of osteoporosis risk, is found to be highly heritable in this Korean study, which is very consistent with the findings in Western populations. This finding strongly supports that genetic factors are significant determinants of osteoporosis risk along with individual biological and behavioral factors. Although genetic factors are known to contribute significantly to variations in BMD in Western populations, such an association has not been fully evaluated in an Asian population. This study was conducted to determine the role of genetic factors on BMD in Korean population. The study participants were 2,728 men and women consisting of 497 monozygotic (MZ) twin pairs, 119 dizygotic (DZ) twin pairs, and 1,496 first-degree relatives from the Healthy Twin Study. BMD was measured using dual-energy X-ray absorptiometry. Quantitative genetic analysis based on a variance decomposition model was performed. Age and the measured covariates accounted for 17~61% of the variation in BMD, depending on the sites of measurement. After accounting for the covariate effects, the heritability of BMD at the whole body, thoracic and lumbar spine, whole ribs, whole pelvis, whole arms, and whole legs were 0.76, 0.72, 0.73, 0.71, 0.51, and 0.75, respectively. The pair-wise correlation of BMD was the highest within MZ twin pairs, followed by DZ twin pairs, sibling pairs, and parents-child pairs. Cross-trait correlation analysis revealed a positive genetic correlation between BMDs at different sites, ranging from 0.80 (arm and leg BMD) to 0.50 (pelvis and arm BMD). The high heritability of BMD in this Korean population similar to those found in Western populations and the significant common genetic basis between BMDs at different sites strongly supports a significant role of genetic determinants on the risk of osteoporosis.

  1. Graphical models for genetic analyses

    DEFF Research Database (Denmark)

    Lauritzen, Steffen Lilholt; Sheehan, Nuala A.

    2003-01-01

    This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas...... of graphical models and genetics. The potential of graphical models is explored and illustrated through a number of example applications where the genetic element is substantial or dominating....

  2. Characterization and modelling of the mechanical properties of mineral wool

    DEFF Research Database (Denmark)

    Chapelle, Lucie

    2016-01-01

    the comparison of individual characteristics of different mineral wool materials and provide simple descriptors of the 3D structure. All the methods described here are applied to glass wool and stone wool. By developing a FEM model including the real characteristic of the mineral wool fibre structure, the effect......Mineral wool designates a highly porous network of fibres drawn by spinning molten minerals. Traditionally, mineral wool products have found application as thermal and acoustic insulation of buildings. Recent concepts where mineral wool products are subjected to higher structural loads have emerged...... properties of mineral wool relate closely to the arrangement and characteristics of the fibres inside the material. Because of the complex architecture of mineral wool, the characterization and the understanding of the mechanism of deformations require a new methodology. In this PhD thesis, a methodology...

  3. [Genetic aspects of the relationship between isoquinoline alkaloids and mineral elements in greater celandine (Chelidonium majus L.)].

    Science.gov (United States)

    Buzuk, G N; Lovkova, M Ia; Sokolova, S M; Tiutekin, Iu V

    2003-01-01

    Interrelations between the total content of isoquinoline alkaloids, concentrations of quaternary protoberberines and benzophenanthridines, and the amount of K, Cu, Co, Al, Ba, and Zn in aerial parts of individual celandine plants were revealed, within a single cenopopulation, using correlation analysis and regression analysis. Mathematical models describing the regulation of isoquinoline metabolism by some of the mineral elements were obtained in the analytical form. The results suggest that this process is genetically determined.

  4. Mineral vein dynamics modelling (FRACS II)

    Energy Technology Data Exchange (ETDEWEB)

    Urai, J.; Virgo, S.; Arndt, M. [RWTH Aachen (Germany); and others

    2016-08-15

    The Mineral Vein Dynamics Modeling group ''FRACS'' started out as a team of 7 research groups in its first phase and continued with a team of 5 research groups at the Universities of Aachen, Tuebingen, Karlsruhe, Mainz and Glasgow during its second phase ''FRACS 11''. The aim of the group was to develop an advanced understanding of the interplay between fracturing, fluid flow and fracture healing with a special emphasis on the comparison of field data and numerical models. Field areas comprised the Oman mountains in Oman (which where already studied in detail in the first phase), a siliciclastic sequence in the Internal Ligurian Units in Italy (closed to Sestri Levante) and cores of Zechstein carbonates from a Lean Gas reservoir in Northern Germany. Numerical models of fracturing, sealing and interaction with fluid that were developed in phase I where expanded in phase 11. They were used to model small scale fracture healing by crystal growth and the resulting influence on flow, medium scale fracture healing and its influence on successive fracturing and healing, as well as large scale dynamic fluid flow through opening and closing fractures and channels as a function of fluid overpressure. The numerical models were compared with structures in the field and we were able to identify first proxies for mechanical vein-hostrock properties and fluid overpressures versus tectonic stresses. Finally we propose a new classification of stylolites based on numerical models and observations in the Zechstein cores and continued to develop a new stress inversion tool to use stylolites to estimate depth of their formation.

  5. Engineering Genetically-Encoded Mineralization and Magnetism via Directed Evolution.

    Science.gov (United States)

    Liu, Xueliang; Lopez, Paola A; Giessen, Tobias W; Giles, Michael; Way, Jeffrey C; Silver, Pamela A

    2016-11-29

    Genetically encoding the synthesis of functional nanomaterials such as magnetic nanoparticles enables sensitive and non-invasive biological sensing and control. Via directed evolution of the natural iron-sequestering ferritin protein, we discovered key mutations that lead to significantly enhanced cellular magnetism, resulting in increased physical attraction of ferritin-expressing cells to magnets and increased contrast for cellular magnetic resonance imaging (MRI). The magnetic mutants further demonstrate increased iron biomineralization measured by a novel fluorescent genetic sensor for intracellular free iron. In addition, we engineered Escherichia coli cells with multiple genomic knockouts to increase cellular accumulation of various metals. Lastly to explore further protein candidates for biomagnetism, we characterized members of the DUF892 family using the iron sensor and magnetic columns, confirming their intracellular iron sequestration that results in increased cellular magnetization.

  6. Dynamic Model of Mineralization Enrichment and Its Applications

    Institute of Scientific and Technical Information of China (English)

    2000-01-01

    This paper studies the chaos dynamic mechanism of the migration, enrichment and mineralization of elements in the crust. The research shows that the interaction of the nonlinear process in the geological environment is an essential factor for the uneven distribution of elements and the mineralization in the crust, determining the element contents and the fractal structure of the distribution of the large- and small-sized mineral deposits. The logistic map is a better mathematical model describing the behavior of the chaos dynamic. The parameter μ, i.e. , the mineralizing potential, is employed to divide the region into non-mineralization region or mineralization region.The value of the parameterμ in model (3) with true data (in Xinjiang Au tomatio region, China) is obtained with the statistical method. The forecasting results are generally in accordance with those obtained with other methods, for example, with the characteristic analysis.

  7. Genetic analysis identifies quantitative trait loci controlling rosette mineral concentrations in Arabidopsis thaliana under drought

    NARCIS (Netherlands)

    Ghandilyan, A.; Barboza, L.; Tisne, S.; Granier, C.; Reymond, M.; Koornneef, M.; Schat, H.; Aarts, M.G.M.

    2009-01-01

    • Rosettes of 25 Arabidopsis thaliana accessions and an Antwerp-1 (An-1) × Landsberg erecta (Ler) population of recombinant inbred lines (RILs) grown in optimal watering conditions (OWC) and water deficit conditions (WDC) were analysed for mineral concentrations to identify genetic loci involved in

  8. Genetic sharing with cardiovascular disease risk factors and diabetes reveals novel bone mineral density loci

    NARCIS (Netherlands)

    S. Reppe (Sjur); Y. Wang (Yunpeng); W.K. Thompson (Wesley K.); L.K. McEvoy (Linda K.); N.J. Schork (Nicholas); V. Zuber (Verena); M. Leblanc (Marissa); F. Bettella (Francesco); I.G. Mills (Ian G.); R.S. Desikan (Rahul S.); S. Djurovic (Srdjan); K.M. Gautvik (Kaare); A.M. Dale (Anders); O.A. Andreassen (Ole A.); K. Estrada Gil (Karol); U. Styrkarsdottir (Unnur); E. Evangelou (Evangelos); Y.-H. Hsu (Yi-Hsiang); E.L. Duncan (Emma); E.E. Ntzani (Evangelia); L. Oei (Ling); O.M.E. Albagha (Omar M.); N. Amin (Najaf); J.P. Kemp (John); D.L. Koller (Daniel); G. Li (Guo); C.-T. Liu (Ching-Ti); R.L. Minster (Ryan); A. Moayyeri (Alireza); L. Vandenput (Liesbeth); D. Willner (Dana); S.-M. Xiao (Su-Mei); L.M. Yerges-Armstrong (Laura); H.-F. Zheng (Hou-Feng); N. Alonso (Nerea); J. Eriksson (Joel); C.M. Kammerer (Candace); S. Kaptoge (Stephen); P.J. Leo (Paul); G. Thorleifsson (Gudmar); S.G. Wilson (Scott); J.F. Wilson (James F); V. Aalto (Ville); M. Alen (Markku); A.K. Aragaki (Aaron); T. Aspelund (Thor); J.R. Center (Jacqueline); Z. Dailiana (Zoe); C. Duggan; M. Garcia (Melissa); N. Garcia-Giralt (Natàlia); S. Giroux (Sylvie); G. Hallmans (Göran); L.J. Hocking (Lynne); L.B. Husted (Lise Bjerre); K. Jameson (Karen); R. Khusainova (Rita); G.S. Kim (Ghi Su); C. Kooperberg (Charles); T. Koromila (Theodora); M. Kruk (Marcin); M. Laaksonen (Marika); A.Z. Lacroix (Andrea Z.); S.H. Lee (Seung Hun); P.C. Leung (Ping C.); J.R. Lewis (Joshua); L. Masi (Laura); S. Mencej-Bedrac (Simona); T.V. Nguyen (Tuan); X. Nogues (Xavier); M.S. Patel (Millan); J. Prezelj (Janez); L.M. Rose (Lynda); S. Scollen (Serena); K. Siggeirsdottir (Kristin); G.D. Smith; O. Svensson (Olle); S. Trompet (Stella); O. Trummer (Olivia); N.M. van Schoor (Natasja); J. Woo (Jean); K. Zhu (Kun); S. Balcells (Susana); M.L. Brandi; B.M. Buckley (Brendan M.); S. Cheng (Sulin); C. Christiansen; C. Cooper (Charles); G.V. Dedoussis (George); I. Ford (Ian); M. Frost (Morten); D. Goltzman (David); J. González-Macías (Jesús); M. Kähönen (Mika); M. Karlsson (Magnus); E.K. Khusnutdinova (Elza); J.-M. Koh (Jung-Min); P. Kollia (Panagoula); B.L. Langdahl (Bente); W.D. Leslie (William D.); P. Lips (Paul); O. Ljunggren (Östen); R. Lorenc (Roman); J. Marc (Janja); D. Mellström (Dan); B. Obermayer-Pietsch (Barbara); D. Olmos (David); U. Pettersson-Kymmer (Ulrika); D.M. Reid (David); J.A. Riancho (José); P.M. Ridker (Paul); M.F. Rousseau (Francois); P.E. Slagboom (Eline); N.L.S. Tang (Nelson L.S.); R. Urreizti (Roser); W. Van Hul (Wim); J. Viikari (Jorma); M.T. Zarrabeitia (María); Y.S. Aulchenko (Yurii); M.C. Castaño Betancourt (Martha); E. Grundberg (Elin); L. Herrera (Lizbeth); T. Ingvarsson (Torvaldur); H. Johannsdottir (Hrefna); T. Kwan (Tony); R. Li (Rui); R.N. Luben (Robert); M.C. Medina-Gomez (Carolina); S.T. Palsson (Stefan Th); J.I. Rotter (Jerome I.); G. Sigurdsson (Gunnar); J.B.J. van Meurs (Joyce); D.J. Verlaan (Dominique); F.M. Williams (Frances); A.R. Wood (Andrew); Y. Zhou (Yanhua); T. Pastinen (Tomi); S. Raychaudhuri (Soumya); J.A. Cauley (Jane); D.I. Chasman (Daniel); G.R. Clark (Graeme); S.R. Cummings (Steven R.); P. Danoy (Patrick); E.M. Dennison (Elaine); R. Eastell (Richard); J.A. Eisman (John); V. Gudnason (Vilmundur); A. Hofman (Albert); R.D. Jackson (Rebecca); G. Jones (Graeme); J.W. Jukema (Jan Wouter); K.T. Khaw; T. Lehtimäki (Terho); Y. Liu (Yongmei); M. Lorentzon (Mattias); E. McCloskey (Eugene); B.D. Mitchell (Braxton); K. Nandakumar (Kannabiran); G.C. Nicholson (Geoffrey); B.A. Oostra (Ben); M. Peacock (Munro); H.A.P. Pols (Huibert A. P.); R.L. Prince (Richard); O. Raitakari (Olli); I.R. Reid (Ian); J. Robbins (John); P.N. Sambrook (Philip); P.C. Sham (Pak Chung); A.R. Shuldiner (Alan); F.A. Tylavsky (Frances); C.M. van Duijn (Cock); N.J. Wareham (Nicholas J.); L.A. Cupples (Adrienne); M.J. Econs (Michael); D.M. Evans (David); T.B. Harris (Tamara B.); A.W.C. Kung (Annie Wai Chee); B.M. Psaty (Bruce); J. Reeve (Jonathan); T.D. Spector (Timothy); E.A. Streeten (Elizabeth); M.C. Zillikens (Carola); U. Thorsteinsdottir (Unnur); C. Ohlsson (Claes); D. Karasik (David); J.B. Richards (J. Brent); M.A. Brown (Matthew); J-A. Zwart (John-Anker); A.G. Uitterlinden (André); S.H. Ralston (Stuart); J.P.A. Ioannidis (John P.A.); D.P. Kiel (Douglas P.); F. Rivadeneira Ramirez (Fernando)

    2015-01-01

    textabstractBone Mineral Density (BMD) is a highly heritable trait, but genome-wide association studies have identified few genetic risk factors. Epidemiological studies suggest associations between BMD and several traits and diseases, but the nature of the suggestive comorbidity is still unknown. W

  9. Use of stable isotopes and mathematical modelling to investigate human mineral metabolism.

    Science.gov (United States)

    Dainty, J R

    2001-12-01

    Individuals have varying needs for minerals that are dependent, amongst other things, on their lifestyle, age and genetic makeup. Knowledge of exact individual nutritional requirements should lead to better health, increased quality of life and reduced need for expensive medical care. Bioavailability, nutrient-gene interactions and whole-body metabolism all need to be investigated further if we are to progress towards the goal of defining optimal health and nutritional status. The discussion which follows will critically review the latest developments in the area of metabolism for several of the minerals that are essential for human health: Ca, Zn, Cu and Se. Stable-isotope tracers and mathematical modelling are some of the tools being used to facilitate the greater understanding in uptake, utilisation and excretion of these minerals. Stable isotopes, administered in physiological doses, present little or no risk to volunteers and allow metabolic studies to be carried out in vulnerable population groups such as children and pregnant women. Intrinsic labelling of foodstuffs ensures that the tracer and the native mineral will behave similarly once inside the body. Advances in computing power and software dedicated to solving nutritional problems have made it possible for investigators to use mathematical modelling in their experimental work. Mineral metabolism is ideally suited to a form of modelling known as compartmental analysis, which allows rates of mineral transferand sizes of mineral stores to be calculated accurately without the need for invasive sampling of body tissues.

  10. Relationships between protein and mineral during enamel development in normal and genetically altered mice

    Science.gov (United States)

    Smith, Charles E.; Hu, Yuanyuan; Richardson, Amelia S.; Bartlett, John D.; Hu, Jan C-C.; Simmer, James P.

    2012-01-01

    The purpose of this study was to quantify and compare the amounts of volatiles (mostly protein) and mineral present in developing incisor enamel in normal mice and in those genetically engineered for absence of intact enamelin, ameloblastin, matrix metalloproteinase 20 (MMP20) or kallikrein-related peptidase 4 (KLK4). Data indicated that all mice showed peaks in the gross weight of volatiles and a similar weight of mineral at locations on incisors normally associated with early maturation. Thereafter, the content of volatiles on normal incisors declined rapidly by as much as 62%, but not by 100%, over 2 mm, accompanied by increases of ~threefold in mineral weights. Enamelin heterozygous mice (lower incisors) showed a decrease in volatile content across the maturation stage, yet mineral failed to increase significantly. Mmp20 null mice showed no significant loss of volatiles from maturing enamel, yet the amount of mineral increased. Klk4 null mice showed normal mineral acquisition up to early maturation, but the input of new volatiles in mid to late maturation caused the final mineralization to slow below normal levels. These results suggest that it is not only the amount of protein but also the nature or type of protein or fragments present in the local crystallite environment that affects their volumetric expansion as they mature. PMID:22243238

  11. Mineral Bionization - Surface Chemical Modeling of the Emergence of Life

    Science.gov (United States)

    Arrhenius, G.

    2001-12-01

    The earliest stages in entering an RNA-world require natural mechanisms that are capable of selective concentration of simple aldehydes from dilute solution in the environment (4), furthermore phosphorylation of the sequestered aldehydes (2) and their catalytic condensation to form, selectively, tetrose- (threose) or pentose- (ribose) phosphate (3); the latter representing the R in RNA. A variety of common positively charged sheet structure minerals (mixed valence double layer metal hydroxide minerals such as hydrotalcite and green rust) have proven to be remarkably capable of performing these crucial tasks under simplified natural conditions (1). These prebiotic model reactions have demonstrated plausible closure of the gap, previously thought to preclude the natural formation of nucleoside phosphates, the backbone components of the information carrying genetic material. Pioneering research by other workers (5) has demonstrated the feasibility of necessary further steps in the chain toward functional RNA; mineral (montmorillonite) catalyzed oligomerization of nucleotides, the formation of complementary RNA strands (6) and the enzymatic activity of RNA (ribozymes). These contributions have placed the initially conjectural concept of an initial RNA-world on an experimental footing. Remaining problems include the initial transfer of information to spontaneously forming RNA, sufficient to convey biofunctionallity (7). Also in this central problem mineral surface interactions may be speculated to play a natural role; a question that is open to experimental verification. References. 1. Pitsch, S.; Eschenmoser, A.; Gedulin, B.; Hui, S. and Arrhenius, G. Origins Life Evol. Biosphere, 1994, 24 (5), 389. 2. Kolb, V.; Zhang, S.; Xu, Y.; Arrhenius, G. Origins Life Evol. Biosphere, 1997, 27, 485. 3. Krishnamurthy, R.; Pitsch, S.; Arrhenius, G. Origins Life Evol. Biosphere, Origins Life Evol. Biosphere 1999, 29, 139 4. Pitsch, S.; Krishnamurthy, R.; Arrhenius, G. Helv. Chim

  12. Deposit model for heavy-mineral sands in coastal environments: Chapter L in Mineral deposit models for resource assessment

    Science.gov (United States)

    Van Gosen, Bradley S.; Fey, David L.; Shah, Anjana K.; Verplanck, Philip L.; Hoefen, Todd M.

    2014-01-01

    This report provides a descriptive model of heavy-mineral sands, which are sedimentary deposits of dense minerals that accumulate with sand, silt, and clay in coastal environments, locally forming economic concentrations of the heavy minerals. This deposit type is the main source of titanium feedstock for the titanium dioxide (TiO2) pigments industry, through recovery of the minerals ilmenite (Fe2+TiO3), rutile (TiO2), and leucoxene (an alteration product of ilmenite). Heavy-mineral sands are also the principal source of zircon (ZrSiO4) and its zirconium oxide; zircon is often recovered as a coproduct. Other heavy minerals produced as coproducts from some deposits are sillimanite/kyanite, staurolite, monazite, and garnet. Monazite [(Ce,La,Nd,Th)PO4] is a source of rare earth elements as well as thorium, which is used in thorium-based nuclear power under development in India and elsewhere.

  13. A DYNAMIC EVALUATION MODEL OF MINERAL RESOURCE PROPERTY

    Institute of Scientific and Technical Information of China (English)

    芮建伟; 冯志亮

    2000-01-01

    Based on the value theory of mineral resource, a dynamic evaluation model of mineral resource property is erected, which not only takes the factors of extractions into consideration but also those of explorations. The solution process of the model is described and the differential solution is presented. Then the paper comes to the conclusion that the differential solution is also the optimal depletion path of the resource.

  14. Graphical models for genetic analyses

    DEFF Research Database (Denmark)

    Lauritzen, Steffen Lilholt; Sheehan, Nuala A.

    2003-01-01

    This paper introduces graphical models as a natural environment in which to formulate and solve problems in genetics and related areas. Particular emphasis is given to the relationships among various local computation algorithms which have been developed within the hitherto mostly separate areas...

  15. In vitro evaluation of caseinophosphopeptides from different genetic variants on bone mineralization

    Directory of Open Access Journals (Sweden)

    Giovanni Tulipano

    2010-01-01

    Full Text Available Casein phosphopeptides (CPPs have been shown to enhance calcium solubility and to increase the calcification by in vitro analyses. The aim of our study was to investigate the effects of four selected casein peptides, which differ in the number of phosphorylated serines, on osteoblast mineralization in vitro. The chosen peptides, related to different casein genetic variants, were obtained by chemical synthesis and tested on murine osteoblast cell line (MC3T3-E1. Our results suggest that the distinct peptides in protein hydrolysates may differentially affect calcium deposition in the extracellular matrix and that the genetic variation within the considered peptides is involved in their differential effect.

  16. Genetic Mechanism of Mineral Inclusions in Zircons from the Khondalite Series, Southeastern Inner Mongolia

    Institute of Scientific and Technical Information of China (English)

    2003-01-01

    sillimanite garnet potash feldspar gneiss and garnet biotite plagioclase gneiss, have experienced granulite-facies metamorphism.Secondary electron microscopic images of zircons from the khondalite series display distinct zoning from core to rim, and are genetically related to the primary, prograde, and peak metamorphic mineral inclusion assemblages respectively. These images reveal irregular zoning patterns and varying thickness of cores and rims. The abundance of inclusions complicates the conventional U-Pb age dating. Therefore, the SHRIMP micro-spot U-Pb method is essential for the protolith and metamorphic age dating of the khondalite series, southeastern Inner Mongolia.

  17. REE Geochemical Characteristics of Tungsten Minerals as a Discriminant Indicator of Genetic Types of Ore Deposits

    Institute of Scientific and Technical Information of China (English)

    张玉学; 刘文茂; 等

    1990-01-01

    Tungsten minerals (scheelite and wolframite)from two genetic types of granitoids show significant dif-ferences in REE distribution,probably due to different material sources and origins.Tungsten miner-als in granite porphyry of the crust-mantle source are relatively high in ∑REE(1884ppm on average).∑ Ce is rich relative to ∑Y and ∑Ce/∑Y is relatively high(>1).The chondrite-normalized REE distribution patterns are characterized by a group of rightward-inclined curves.Tungsten minerals in quartz veins intruding the granites of crust origin have lower ∑REE (335 ppm on average).∑Y is rich relative to ∑Ce and ∑Ce/∑Y is relatively low(<1).The chondrite-normalized REE distribution patterns are characterized by a group of leftward-inclined curves.So the REE distribution patterns can be used to discriminate the sources of rock-and ore-forming materials and the genetic types of W deposits so as to provide clues to ore prospecting.

  18. Modeling Nitrogen Mineralization in Paddy Soils of Shanghai Region

    Institute of Scientific and Technical Information of China (English)

    LI Hui-Lin; HAN Yong; CAI Zu-Cong

    2003-01-01

    Six paddy soils of Shanghai, China, were studied after 120 days of anaerobic incubation at 25 ℃ and 35 ℃. Four models, the effective accumulated temperature model, the one-component first-order exponential model (the one-pool model), the two-component first-order exponential model (the two-pool model), and the two-component first-order plus zero-order exponential model including a constant term (the special model),were fitted to the data of observed mineral-N during incubation using non-linear regression procedures. The two-pool model and the special model gave the best fits amongst the four models, and parameters in the special model were more reasonable than those in the other three. Results showed that the special model gave a better prediction of nitrogen mineralization under flooded conditions than the other three models.

  19. Genetic types, mineralization styles, and geodynamic settings of Mesozoic tungsten deposits in South China

    Science.gov (United States)

    Zhao, Wen Winston; Zhou, Mei-Fu; Li, Yan Hei Martin; Zhao, Zheng; Gao, Jian-Feng

    2017-04-01

    South China hosts the most abundant and largest tungsten (W) deposits in the world, being a famous W metallogenic region. Located at the eastern part of the South China Block, which was formed by amalgamation of the Yangtze and Cathaysia Blocks during the Neoproterozoic, these W deposits were mainly formed during the Mesozoic. The W mineralization is dominanted by greisen, quartz-vein, skarn, and porphyry types, all of which are genetically related to the evolution of highly fractionated granitoids. Four episodes of W mineralization are recognized: (1) Late Triassic (230-210 Ma) in the central and western parts of South China; (2) Middle Jurassic (ca. 170 Ma) to Early Cretaceous (ca. 140 Ma) in the interior of South China, with the mineralization being concentrated in southern Jiangxi Province between 165 and 150 Ma; (3) Early Cretaceous (136-120 Ma) with deposits across South China; and (4) Late Cretaceous (100-80 Ma) mainly in the southwestern parts of South China. These four periods of mineralization are closely related to the closure of paleo-Tethys and subduction of the paleo-Pacific plate. In the Late Triassic, these two events caused local extensional environments, facilitating emplacement of the peraluminous granitoids, and formation of the W deposits. In the Middle Jurassic, break-off of the subducting oceanic plate resulted in emplacement of highly fractionated granites in the Nanling region. Later anticlockwise rotation of the paleo-Pacific plate created widespread S-type granitoids and associated Middle Jurassic to Early Cretaceous W mineralization in the interior of South China. Since 136 Ma, rollback of the subducting Pacific plate resulted in weak W mineralization across South China. Finally, a change of direction in the retreating plate from SE to ESE resulted in intensive mineralization of the southwestern part of South China.

  20. Genetic determinism of bone and mineral metabolism in meat-type chickens: A QTL mapping study.

    Science.gov (United States)

    Mignon-Grasteau, Sandrine; Chantry-Darmon, Céline; Boscher, Marie-Yvonne; Sellier, Nadine; Chabault-Dhuit, Marie; Le Bihan-Duval, Elisabeth; Narcy, Agnès

    2016-12-01

    Skeletal integrity in meat-type chickens is affected by many factors including rapid growth rate, nutrition and genetics. To investigate the genetic basis of bone and mineral metabolism, a QTL detection study was conducted in an intercross between two lines of meat-type chickens divergently selected for their high (D +) or low (D -) digestive efficiency. Tibia size (length, diameter, volume) and ash content were determined at 3 weeks of age as well as phosphorus (P) retention and plasma concentration. Heritability of these traits and their genetic correlations with digestive efficiency were estimated. A QTL mapping study was performed using 3379 SNP markers. Tibia size, weight, ash content and breaking strength were highly heritable (0.42 to 0.61). Relative tibia diameter and volume as well as P retention were strongly and positively genetically correlated with digestive efficiency (0.57 to 0.80). A total of 35 QTL were identified (9 for tibia weight, 13 for tibia size, 5 for bone strength, 5 for bone mineralization, 2 for plasma P concentration and 1 for P retention). Six QTL were genome-wide significant, and 3 QTL for tibia relative volume, weight and ash weight on chromosome 6 were fixed, the positive allele coming from the D-line. For two QTL for ash content on chromosome 18 and relative tibia length on chromosome 26, the confidence intervals were small enough to identify potential candidate genes. These findings support the evidence of multiple genetic loci controlling bone and mineral metabolism. The identification of candidate genes may provide new perspectives in the understanding of bone regulation, even beyond avian species.

  1. Minerals

    Directory of Open Access Journals (Sweden)

    Vaquero, M. P.

    1998-08-01

    Full Text Available The possible changes in the mineral composition of food during frying could be the consequence of losses by leaching, or changes in concentrations caused by exchanges between the food and culinary fat of other compounds. The net result depends on the type of food, the frying fat used and the frying process. Moreover, the modifications that frying produces in other nutrients could indirectly affect the availability of dietary minerals. The most outstanding ones are those that can take place in the fat or in the protein. With respect to the interactions between frying oils and minerals, we have recent knowledge concerning the effects of consuming vegetable oils used in repeated fryings of potatoes without turnover, on the nutritive utilization of dietary minerals. The experiments have been carried out in pregnant and growing rats, which consumed diets containing, as a sole source of fat, the testing frying oils or unused oils. It seems that the consumption of various frying oils, with a polar compound content lower or close to the maximum limit of 25% accepted for human consumption, does not alter the absorption and metabolism of calcium, phosphorous, iron or copper. Magnesium absorption from diets containing frying oils tends to increase but the urinary excretion of this element increases, resulting imperceptible the variations in the magnesium balance. The urinary excretion of Zn also increased although its balance remained unchanged. Different studies referring to the effects of consuming fried fatty fish on mineral bioavailability will also be presented. On one hand, frying can cause structural changes in fish protein, which are associated with an increase in iron absorption and a decrease in body zinc retention. The nutritive utilization of other elements such as magnesium, calcium and copper seems to be unaffected. On the other hand; it has been described that an excess of fish fatty acids in the diet produces iron depletion, but when fatty

  2. Estimation of genetic parameters and detection of quantitative trait loci for minerals in Danish Holstein and Danish Jersey milk

    DEFF Research Database (Denmark)

    Buitenhuis, Albert Johannes; Poulsen, Nina Aagaard; Sehested, Jakob

    2015-01-01

    Background Bovine milk provides important minerals, essential for human nutrition and dairy product quality. For changing the mineral composition of the milk to improve dietary needs in human nutrition and technological properties of milk, a thorough understanding of the genetics underlying milk...... mineral contents is important. Therefore the aim of this study was to 1) estimate the genetic parameters for individual minerals in Danish Holstein (DH) (n = 371) and Danish Jersey (DJ) (n = 321) milk, and 2) detect genomic regions associated with mineral content in the milk using a genome...... The results show that Ca, Zn, P and Mg show high heritabilities. In combination with the GWAS results this opens up possibilities to select for specific minerals in bovine milk....

  3. Surface Complexation Modelling in Metal-Mineral-Bacteria Systems

    Science.gov (United States)

    Johnson, K. J.; Fein, J. B.

    2002-12-01

    The reactive surfaces of bacteria and minerals can determine the fate, transport, and bioavailability of aqueous heavy metal cations. Geochemical models are instrumental in accurately accounting for the partitioning of the metals between mineral surfaces and bacteria cell walls. Previous research has shown that surface complexation modelling (SCM) is accurate in two-component systems (metal:mineral and metal:bacteria); however, the ability of SCMs to account for metal distribution in mixed metal-mineral-bacteria systems has not been tested. In this study, we measure aqueous Cd distributions in water-bacteria-mineral systems, and compare these observations with predicted distributions based on a surface complexation modelling approach. We measured Cd adsorption in 2- and 3-component batch adsorption experiments. In the 2-component experiments, we measured the extent of adsorption of 10 ppm aqueous Cd onto either a bacterial or hydrous ferric oxide sorbent. The metal:bacteria experiments contained 1 g/L (wet wt.) of B. subtilis, and were conducted as a function of pH; the metal:mineral experiments were conducted as a function of both pH and HFO content. Two types of 3-component Cd adsorption experiments were also conducted in which both mineral powder and bacteria were present as sorbents: 1) one in which the HFO was physically but not chemically isolated from the system using sealed dialysis tubing, and 2) others where the HFO, Cd and B. subtilis were all in physical contact. The dialysis tubing approach enabled the direct determination of the concentration of Cd on each sorbing surface, after separation and acidification of each sorbent. The experiments indicate that both bacteria and mineral surfaces can dominate adsorption in the system, depending on pH and bacteria:mineral ratio. The stability constants, determined using the data from the 2-component systems, along with those for other surface and aqueous species in the systems, were used with FITEQL to

  4. The influence of the genetic and non-genetic factors on bone mineral density and osteoporotic fractures in Chinese women.

    Science.gov (United States)

    Deng, Yan-Hua; Zhao, Lin; Zhang, Min-Jia; Pan, Chun-Ming; Zhao, Shuang-Xia; Zhao, Hong-Yan; Sun, Li-Hao; Tao, Bei; Song, Huai-Dong; Wang, Wei-Qing; Ning, Guang; Liu, Jian-Min

    2013-02-01

    To investigate the effects of genetic and non-genetic factors on bone mineral densities (BMDs) and osteoporotic fractures. This was a cross-sectional study to investigate the relationships between 18 SNPs and non-genetic factors with BMDs and osteoporotic fractures in 1012 Chinese Han women. Five SNPs in genes GPR177, CTNNB1, MEF2C, SOX6, and TNFRSF11B were associated with L1-4 or total hip BMDs. rs11898505 in SPTBN1 gene was associated with osteoporotic fractures. Subjects carrying the largest number of risk alleles (highest 10 %) not only had lower BMD values as compared to those carrying the least number of risk alleles (lowest 10 %), they also had a higher risk of fracture [P = 0.002, OR = 2.252, 95 %CI (1.136, 4.463)]. Results from multivariate stepwise regression analysis revealed that age [P < 0.001, OR = 1.038, 95 % CI (1.018, 1.058)], number of falls in a year [P < 0.001, OR = 2.347, 95 % CI (1.459, 3.774)], the G risk allele in rs11898505 [P = 0.023, OR = 1.559, 95 % CI (1.062, 2.290)], and the L1-4 BMD [P = 0.017, OR = 0.286, 95 % CI (0.102, 0.798)] were associated with the occurrence of osteoporotic fractures. Genetic (rs11898505) and non-genetic factors (age, number of falls in a year and L1-4 BMD) could work in concert to contribute to the risk of osteoporotic fractures.

  5. Progress on geoenvironmental models for selected mineral deposit types, edited by R. R. Seal, II and N. K. Foley

    Science.gov (United States)

    Seal, Robert R., II; Foley, Nora K.

    2002-01-01

    Since the beginning of economic geology as a subdiscipline of the geological sciences, economic geologists have tended to classify mineral deposits on the basis of geological, mineralogical, and geochemical criteria, in efforts to systematize our understanding of mineral deposits as an aid to exploration. These efforts have led to classifications based on commodity, geologic setting (Cox and Singer, 1986), inferred temperatures and pressures of ore formation (Lindgren, 1933), and genetic setting (Park and MacDiarmid, 1975; Jensen and Bateman, 1979). None of these classification schemes is mutually exclusive; instead, there is considerable overlap among all of these classifications. A natural outcome of efforts to classify mineral deposits is the development of “mineral deposit models.” A mineral deposit model is a systematically arranged body of information that describes some or all of the essential characteristics of a selected group of mineral deposits; it presents a concept within which essential attributes may be distinguished and from which extraneous, coincidental features may be recognized and excluded (Barton, 1993). Barton (1993) noted that the grouping of deposits on the basis of common characteristics forms the basis for a classification, but the specification of the characteristics required for belonging to the group is the basis for a model. Models range from purely descriptive to genetic. A genetic model is superior to a descriptive model because it provides a basis to distinguish essential from extraneous attributes, and it has flexibility to accommodate variability in sources, processes, and local controls. In general, a descriptive model is a necessary prerequisite to a genetic model.

  6. Modelling of mineral matter transformation and deposition in furnaces

    Energy Technology Data Exchange (ETDEWEB)

    Magda, Adrian

    2012-07-01

    In this work, a CFD (Computational Fluid Dynamics) tool was developed to simulate the ash deposition on the heat transfer surfaces of furnaces. The effects of such slagging and fouling deposits on boiler operation and pollutants formation was investigated. Major particles physical transformations are reviewed in Chapter 2, while Chapter 3, encompasses an intensive literature review on the main mineral components in coals. Differentiating between mineral species is of great importance as minerals with low softening /melting temperature or eutectic points formed between different mineral inclusions facilitate deposition. For each individual mineral specie the known chemical and physical processes and effects with regard to deposition are presented in detail. The complexity and variability of the coal mineralogy points towards the use of chemical mechanisms that account for as many as possible chemical compounds and interactions. Reliable and accurate thermochemical data are therefore needed. For this purpose a mineral matter, coal and biomass and chemical activity databases were generated. Each mineral description is compiled into several subset databases. One subset refers to the polynomial format to calculate the mineral thermodynamic properties, e.g. enthalpy, entropy and specific heat capacity. The mineral database contains detailed descriptions for 200 individual mineral species, while the coal and biomass database contains 110 biomass and coal chemical analyses. The chemical reactions and their kinetic details sum up 70 entries, Chapter 4. Florean is a three-dimensional simulation program developed at the Institute for Fuel and Heat Technology. Besides conservation equations for mass, momentum and energy, FLOREAN has the capability to calculate chemical reactions and pollutants formation. The main conservation equations and program modelling capabilities are presented in Chapter 5. The EnSight Gold format and the ParaView post-processor are implemented for data

  7. Genetic determinants of trabecular and cortical volumetric bone mineral densities and bone microstructure.

    Directory of Open Access Journals (Sweden)

    Lavinia Paternoster

    Full Text Available Most previous genetic epidemiology studies within the field of osteoporosis have focused on the genetics of the complex trait areal bone mineral density (aBMD, not being able to differentiate genetic determinants of cortical volumetric BMD (vBMD, trabecular vBMD, and bone microstructural traits. The objective of this study was to separately identify genetic determinants of these bone traits as analysed by peripheral quantitative computed tomography (pQCT. Separate GWA meta-analyses for cortical and trabecular vBMDs were performed. The cortical vBMD GWA meta-analysis (n = 5,878 followed by replication (n = 1,052 identified genetic variants in four separate loci reaching genome-wide significance (RANKL, rs1021188, p = 3.6×10⁻¹⁴; LOC285735, rs271170, p = 2.7×10⁻¹²; OPG, rs7839059, p = 1.2×10⁻¹⁰; and ESR1/C6orf97, rs6909279, p = 1.1×10⁻⁹. The trabecular vBMD GWA meta-analysis (n = 2,500 followed by replication (n = 1,022 identified one locus reaching genome-wide significance (FMN2/GREM2, rs9287237, p = 1.9×10⁻⁹. High-resolution pQCT analyses, giving information about bone microstructure, were available in a subset of the GOOD cohort (n = 729. rs1021188 was significantly associated with cortical porosity while rs9287237 was significantly associated with trabecular bone fraction. The genetic variant in the FMN2/GREM2 locus was associated with fracture risk in the MrOS Sweden cohort (HR per extra T allele 0.75, 95% confidence interval 0.60-0.93 and GREM2 expression in human osteoblasts. In conclusion, five genetic loci associated with trabecular or cortical vBMD were identified. Two of these (FMN2/GREM2 and LOC285735 are novel bone-related loci, while the other three have previously been reported to be associated with aBMD. The genetic variants associated with cortical and trabecular bone parameters differed, underscoring the complexity of the genetics of bone parameters. We propose

  8. Behavior genetic modeling of human fertility

    DEFF Research Database (Denmark)

    Rodgers, J L; Kohler, H P; Kyvik, K O;

    2001-01-01

    Try) and number of children (NumCh). Behavior genetic models were fitted using structural equation modeling and DF analysis. A consistent medium-level additive genetic influence was found for NumCh, equal across genders; a stronger genetic influence was identified for FirstTry, greater for females than for males...

  9. Arc-related porphyry molybdenum deposit model: Chapter D in Mineral deposit models for resource assessment

    Science.gov (United States)

    Taylor, Ryan D.; Hammarstrom, Jane M.; Piatak, Nadine M.; Seal, Robert R., II

    2012-01-01

    This report provides a descriptive model for arc-related porphyry molybdenum deposits. Presented within are geological, geochemical, and mineralogical characteristics that differentiate this deposit type from porphyry copper and alkali-feldspar rhyolite-granite porphyry molybdenum deposits. The U.S. Geological Survey's effort to update existing mineral deposit models spurred this research, which is intended to supplement previously published models for this deposit type that help guide mineral-resource and mineral-environmental assessments.

  10. Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene

    Science.gov (United States)

    Bælum, Jacob; Prestat, Emmanuel; David, Maude M.; Strobel, Bjarne W.

    2012-01-01

    Mineralization potentials, rates, and kinetics of the three phenoxy acid (PA) herbicides, 2,4-dichlorophenoxyacetic acid (2,4-D), 4-chloro-2-methylphenoxyacetic acid (MCPA), and 2-(4-chloro-2-methylphenoxy)propanoic acid (MCPP), were investigated and compared in 15 soils collected from five continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate the genetic potential for degrading PA in the soils. In 25 of the 45 mineralization scenarios, ∼60% mineralization was observed within 118 days. Elevated concentrations of tfdA in the range 1 × 105 to 5 × 107 gene copies g−1 of soil were observed in soils where mineralization could be described by using growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization patterns which were best fitted by the exponential model yielded a higher tfdA gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model. PMID:22635998

  11. A Complex Systems Model Approach to Quantified Mineral Resource Appraisal

    Science.gov (United States)

    Gettings, M.E.; Bultman, M.W.; Fisher, F.S.

    2004-01-01

    For federal and state land management agencies, mineral resource appraisal has evolved from value-based to outcome-based procedures wherein the consequences of resource development are compared with those of other management options. Complex systems modeling is proposed as a general framework in which to build models that can evaluate outcomes. Three frequently used methods of mineral resource appraisal (subjective probabilistic estimates, weights of evidence modeling, and fuzzy logic modeling) are discussed to obtain insight into methods of incorporating complexity into mineral resource appraisal models. Fuzzy logic and weights of evidence are most easily utilized in complex systems models. A fundamental product of new appraisals is the production of reusable, accessible databases and methodologies so that appraisals can easily be repeated with new or refined data. The data are representations of complex systems and must be so regarded if all of their information content is to be utilized. The proposed generalized model framework is applicable to mineral assessment and other geoscience problems. We begin with a (fuzzy) cognitive map using (+1,0,-1) values for the links and evaluate the map for various scenarios to obtain a ranking of the importance of various links. Fieldwork and modeling studies identify important links and help identify unanticipated links. Next, the links are given membership functions in accordance with the data. Finally, processes are associated with the links; ideally, the controlling physical and chemical events and equations are found for each link. After calibration and testing, this complex systems model is used for predictions under various scenarios.

  12. Routine Discovery of Complex Genetic Models using Genetic Algorithms.

    Science.gov (United States)

    Moore, Jason H; Hahn, Lance W; Ritchie, Marylyn D; Thornton, Tricia A; White, Bill C

    2004-02-01

    Simulation studies are useful in various disciplines for a number of reasons including the development and evaluation of new computational and statistical methods. This is particularly true in human genetics and genetic epidemiology where new analytical methods are needed for the detection and characterization of disease susceptibility genes whose effects are complex, nonlinear, and partially or solely dependent on the effects of other genes (i.e. epistasis or gene-gene interaction). Despite this need, the development of complex genetic models that can be used to simulate data is not always intuitive. In fact, only a few such models have been published. We have previously developed a genetic algorithm approach to discovering complex genetic models in which two single nucleotide polymorphisms (SNPs) influence disease risk solely through nonlinear interactions. In this paper, we extend this approach for the discovery of high-order epistasis models involving three to five SNPs. We demonstrate that the genetic algorithm is capable of routinely discovering interesting high-order epistasis models in which each SNP influences risk of disease only through interactions with the other SNPs in the model. This study opens the door for routine simulation of complex gene-gene interactions among SNPs for the development and evaluation of new statistical and computational approaches for identifying common, complex multifactorial disease susceptibility genes.

  13. Mineral dust transport in the Arctic modelled with FLEXPART

    Science.gov (United States)

    Groot Zwaaftink, Christine; Grythe, Henrik; Stohl, Andreas

    2016-04-01

    Aeolian transport of mineral dust is suggested to play an important role in many processes. For instance, mineral aerosols affect the radiation balance of the atmosphere, and mineral deposits influence ice sheet mass balances and terrestrial and ocean ecosystems. While many efforts have been done to model global dust transport, relatively little attention has been given to mineral dust in the Arctic. Even though this region is more remote from the world's major dust sources and dust concentrations may be lower than elsewhere, effects of mineral dust on for instance the radiation balance can be highly relevant. Furthermore, there are substantial local sources of dust in or close to the Arctic (e.g., in Iceland), whose impact on Arctic dust concentrations has not been studied in detail. We therefore aim to estimate contributions of different source regions to mineral dust in the Arctic. We have developed a dust mobilization routine in combination with the Lagrangian dispersion model FLEXPART to make such estimates. The lack of details on soil properties in many areas requires a simple routine for global simulations. However, we have paid special attention to the dust sources on Iceland. The mobilization routine does account for topography, snow cover and soil moisture effects, in addition to meteorological parameters. FLEXPART, driven with operational meteorological data from European Centre for Medium-Range Weather Forecasts, was used to do a three-year global dust simulation for the years 2010 to 2012. We assess the model performance in terms of surface concentration and deposition at several locations spread over the globe. We will discuss how deposition and dust load patterns in the Arctic change throughout seasons based on the source of the dust. Important source regions for mineral dust found in the Arctic are not only the major desert areas, such as the Sahara, but also local bare-soil regions. From our model results, it appears that total dust load in the

  14. Behavior genetic modeling of human fertility

    DEFF Research Database (Denmark)

    Rodgers, J L; Kohler, H P; Kyvik, K O

    2001-01-01

    Try) and number of children (NumCh). Behavior genetic models were fitted using structural equation modeling and DF analysis. A consistent medium-level additive genetic influence was found for NumCh, equal across genders; a stronger genetic influence was identified for FirstTry, greater for females than for males......Behavior genetic designs and analysis can be used to address issues of central importance to demography. We use this methodology to document genetic influence on human fertility. Our data come from Danish twin pairs born from 1953 to 1959, measured on age at first attempt to get pregnant (First...

  15. Numerical modelling of structural controls on fluid flow and mineralization

    Directory of Open Access Journals (Sweden)

    Yanhua Zhang

    2011-07-01

    Full Text Available This paper presents the results of a set of numerical models focussing on structural controls on hydrothermal mineralization. We first give an overview of natural phenomena of structurally-controlled ore formation and the background theory and mechanisms for such controls. We then provide the results of a group of simple 2D numerical models validated through comparison with Cu-vein structure observed near the Shilu Copper deposit (Yangchun, Guangdong Province, China and finally a case study of 3D numerical modelling applied to the Hodgkinson Province in North Queensland (Australia. Two modelling approaches, discrete deformation modelling and continuum coupled deformation and fluid flow modelling, are involved. The 2D model-derived patterns are remarkably consistent with the Cu-vein structure from the Shilu Copper deposit, and show that both modelling approaches can realistically simulate the mechanical behaviours of shear and dilatant fractures. The continuum coupled deformation and fluid flow model indicates that pattern of the Cu-veins near the Shilu deposit is the result of shear strain localization, development of dilation and fluid focussing into the dilatant fracture segments. The 3D case-study models (with deformation and fluid flow coupling on the Hodgkinson Province generated a number of potential gold mineralization targets.

  16. Hg and As Minerals in Fluid Inclusions from the Williams Mine,Hemlo,and Their Genetic Implications

    Institute of Scientific and Technical Information of China (English)

    卢焕章; ANDDON.C.HARRIS

    2002-01-01

    The Hemlo mineralization is enigmatic compared to general Archean lode gold deposits based on the fact that is characterized by an exotic mineralogy containing elements such as As,Hg,Sb,Ba,V and Mo.The genetic concepts range from syngenetc to epigenetic types of mineralization.This reconnaissance study was designed to examine the relationshp of Hg-As minerals with respect of fluid inclusions in the Williams mine(formerly known as the Page Williams mine)covering the A and C ore zones.

  17. A synthesis of mineralization styles with an integrated genetic model of carbonatite-syenite-hosted REE deposits in the Cenozoic Mianning-Dechang REE metallogenic belt, the eastern Tibetan Plateau, southwestern China

    Science.gov (United States)

    Liu, Yan; Hou, Zengqian

    2017-04-01

    The Cenozoic Mianning-Dechang (MD) rare earth element (REE) belt in eastern Tibet is an important source of light REE in southwest China. The belt is 270 km long and 15 km wide. The total REE resources are >3 Mt of light rare earth oxides (REO), including 3.17 Mt of REO at Maoniuping (average grade = 2.95 wt.%), 81,556 t at Dalucao (average grade = 5.21 wt.%), 0.1 Mt at Muluozhai (average grade = 3.97 wt.%), and 5764 t of REO at Lizhuang (average grade = 2.38 wt.%). Recent results from detailed geological surveys, and studies of petrographic features, ore-forming ages, ore forming conditions, and wallrock alteration are synthesized in this paper. REE mineralization within this belt is associated with carbonatite-syenite complexes, with syenites occurring as stocks intruded by carbonatitic sills or dikes. The mineralization is present as complex vein systems that contain veinlet, stringer, stockwork, and brecciated pipe type mineralization. Carbonatites in these carbonatite-related REE deposits (CARDs) are extremely rich in light REEs, Sr (>5000 ppm), and Ba (>1000 ppm), and have low Sr/Ba and high Ba/Th ratios, and radiogenic Sr-Nd isotopic compositions. These fertile magmas, which may lead to the formation of REE deposits, were generated by the partial melting of sub-continental lithospheric mantle (SCLM) that was metasomatized by REE- and CO2-rich fluids derived from subducted marine sediments. We suggest that this refertilization occurred along cratonic margins and, in particular, at a convergent margin where small-volume carbonatitic melts ascended along trans-lithospheric faults and transported REEs into the overlying crust, leading to the formation of the CARDs. The formation of fertile carbonatites requires a thick lithosphere and/or high pressures (>25 kbar), a metasomatized and enriched mantle source, and favorable pathways for magma to ascend into the overlying crust where REE-rich fluids exsolve from cooling magma. The optimal combination of these three

  18. Economic modelling under conditions of exploitation of cohesive construction minerals

    Directory of Open Access Journals (Sweden)

    Milan Mikoláš

    2011-01-01

    Full Text Available Managers of mining companies use for decision-making on optimization of manufacturing processes advanced modelling methods and simulations on computers. The article proposes and analyses the model of a mining company production cycle consisting of a three-dimensional quarry model, technology model and economic-mathematical model. Based on the latter model an economic simulation model of a quarry has been created in the MS Excel program currently available on all personal computers, which measures outputs in the form of changes in total and unit costs according to the generic classification of costs in response to changes in inputs in the form of parameters of technology equipment and other operating parameters. Managers use the economic simulation model of quarry as decision support to increase profitability or improve competitiveness of their product from the sector of construction minerals.

  19. GENETIC MARKERS OF LOW BONE MINERAL DENSITY IN PATIENTS WITH CYSTIC FIBROSIS.

    Directory of Open Access Journals (Sweden)

    Tatjana Jakovska

    2015-03-01

    Full Text Available Introduction: failure to maintain bone mass density is a major problem in patients with cystic fibrosis (CF. CF is due to mutations in the CFTR gene and other genes may contribute to modifying the disease. Genetic and environmental factors may play a role in determining the variability of bone mass. Aim of the study: to analyse the association between polymorphic variants of genes considered to be risk factors of bone metabolism disturbances and decreased bone mineral density (BMD in children and adults with CF in R. Macedonia. Materials and methods: the study included 80 clinically stable CF patients (age range 5-36y, who regularly attended the CF center at the Pediatric Clinic in Skopje, Macedonia. Three candidate genes likely associated with BMD variability were studied: the vitamin D receptor (VDR gene, the estrogen receptor alpha (ESR1 and the type I alpha I collagen (COLIA1 gene. A complete bone and CF evaluation was obtained for all patients: 55 had normal BMD (group 1, 17 were osteopenic (group 2 and 8 were osteoporotic (group 3. Results: Low bone mineral density (Z score < -1SD was found in 31.25% patients and in 10% of them BMD was below -2SD. Patients with low BMD had worse BMI, FEV1 and more severe symptoms of CF. No significant correlation was found between COLIA1 and VDR polymorphisms and BMD. Conclusion: There was no evidence that the genes under study may modulate bone phenotype in CF.

  20. Genetics of Bone Mineralization and Morphology in Inbred Mice: Analysis of the HcB/Dem Recombinant Congenic Strains

    Science.gov (United States)

    2005-04-01

    data for parameters with skewed distil- 3- PONT BEND MODULUS butions. Results of this analysis are summarized in Table 2. Ir TT . We used these data to...the pathogenesis of osteoporosis. I Bone Miner Res 9:739- [be murine strength is achieved. 743. 1002 YERSHOV ET AL. 16. Demant P, Hart AA 1986...Recombinant congenic strains--a 37. Linder E, Schork N 1994 Genetic dissection of complex traits. new tool for analyzing genetic traits determined by more than

  1. Modeling of miner track system during steering motion

    Institute of Scientific and Technical Information of China (English)

    刘少军; 韩庆珏

    2015-01-01

    Equipment for deep sea mining has risen from a position of virtual non-existence to a major industrial significance and in deep sea bed mining, the miner is the key equipment of the whole system that charges with the most complex and dangerous task. Evaluation of trafficability for tracked vehicles for deep sea mining is essential. Rare earth elements (REEs) are used in a wide range of modern applications. These applications are highly specific and substitutes are inferior or unknown. One possible source of the REE could be the poly-metallic nodule, at present explored in the tropical part of the Pacific Ocean. In developing miners of high performance, dynamic behaviour should be investigated under various traveling conditions. The mechanics of tracked vehicles is of continuing interest to organizations and agencies that specify design and operate tracked vehicles. Most works done are on the complete track vehicle system but in this work the research activity is aimed only at the track system with the basic aim of optimizing the track system design so that it can be manufactured by using the minimum resources. Equations and models are developed for the track system of a miner during steering motion. These equations and models could further be used for design optimization of the track system.

  2. Geological modelling of mineral deposits for prediction in mining

    Science.gov (United States)

    Sides, E. J.

    Accurate prediction of the shape, location, size and properties of the solid rock materials to be extracted during mining is essential for reliable technical and financial planning. This is achieved through geological modelling of the three-dimensional (3D) shape and properties of the materials present in mineral deposits, and the presentation of results in a form which is accessible to mine planning engineers. In recent years the application of interactive graphics software, offering 3D database handling, modelling and visualisation, has greatly enhanced the options available for predicting the subsurface limits and characteristics of mineral deposits. A review of conventional 3D geological interpretation methods, and the model struc- tures and modelling methods used in reserve estimation and mine planning software packages, illustrates the importance of such approaches in the modern mining industry. Despite the widespread introduction and acceptance of computer hardware and software in mining applications, in recent years, there has been little fundamental change in the way in which geology is used in orebody modelling for predictive purposes. Selected areas of current research, aimed at tackling issues such as the use of orientation data, quantification of morphological differences, incorporation of geological age relationships, multi-resolution models and the application of virtual reality hardware and software, are discussed.

  3. Effective Rule Based Classifier using Multivariate Filter and Genetic Miner for Mammographic Image Classification

    Directory of Open Access Journals (Sweden)

    Nirase Fathima Abubacker

    2015-06-01

    Full Text Available Mammography is an important examination in the early detection of breast abnormalities. Automatic classifications of mammogram images into normal, benign or malignant would help the radiologists in diagnosis of breast cancer cases. This study investigates the effectiveness of using rule-based classifiers with multivariate filter and genetic miner to classify mammogram images. The method discovers association rules with the classes as the consequence and classifies the images based on the Highest Average Confidence of the association rules (HAvC matched for the classes. In the association rules mining stage, Correlation based Feature Selection (CFS plays an enormous significance to reduce the complexity of image mining process is used in this study as a feature selection method and a modified genetic association rule mining technique, the GARM, is used to discover the rules. The method is evaluated on mammogram image dataset with 240 images taken from DDSM. The performance of the method is compared against other classifiers such as SMO; Naïve Bayes and J48. The performance of the proposed method is promising with 88% accuracy and outperforms other classifiers in the context of mammogram image classification.

  4. Genetic network models: a comparative study

    Science.gov (United States)

    van Someren, Eugene P.; Wessels, Lodewyk F. A.; Reinders, Marcel J. T.

    2001-06-01

    Currently, the need arises for tools capable of unraveling the functionality of genes based on the analysis of microarray measurements. Modeling genetic interactions by means of genetic network models provides a methodology to infer functional relationships between genes. Although a wide variety of different models have been introduced so far, it remains, in general, unclear what the strengths and weaknesses of each of these approaches are and where these models overlap and differ. This paper compares different genetic modeling approaches that attempt to extract the gene regulation matrix from expression data. A taxonomy of continuous genetic network models is proposed and the following important characteristics are suggested and employed to compare the models: inferential power; predictive power; robustness; consistency; stability and computational cost. Where possible, synthetic time series data are employed to investigate some of these properties. The comparison shows that although genetic network modeling might provide valuable information regarding genetic interactions, current models show disappointing results on simple artificial problems. For now, the simplest models are favored because they generalize better, but more complex models will probably prevail once their bias is more thoroughly understood and their variance is better controlled.

  5. Quantum chemical modeling of uranyl adsorption on mineral surfaces

    Energy Technology Data Exchange (ETDEWEB)

    Kremleva, A.; Krueger, S.; Roesch, N. [Dept. Chemie and Catalysis Research Center, Technische Univ. Muenchen, Garching (Germany)

    2010-07-01

    We overview quantum mechanical simulations that model the adsorption of actinide ions at solvated mineral surfaces. Pertinent examples illustrate the status of this emerging field of computational chemistry. In particular, we describe our own studies on uranyl adsorption on kaolinite. Already the few available results, from applications of density functional methods to cluster models or periodic slab models, show that such calculations are a useful complement to experimental investigations. Detailed information at the atomic level from accurate electronic structure calculations on well defined model systems helps to refine current interpretations of the chemical nature of uranyl adsorption species and to discover new features of these interface systems. Results from quantum mechanical simulations also provide a valuable reference for future experimental investigations. (orig.)

  6. Genetic Algorithm Calibration of Probabilistic Cellular Automata for Modeling Mining Permit Activity

    Science.gov (United States)

    Louis, S.J.; Raines, G.L.

    2003-01-01

    We use a genetic algorithm to calibrate a spatially and temporally resolved cellular automata to model mining activity on public land in Idaho and western Montana. The genetic algorithm searches through a space of transition rule parameters of a two dimensional cellular automata model to find rule parameters that fit observed mining activity data. Previous work by one of the authors in calibrating the cellular automaton took weeks - the genetic algorithm takes a day and produces rules leading to about the same (or better) fit to observed data. These preliminary results indicate that genetic algorithms are a viable tool in calibrating cellular automata for this application. Experience gained during the calibration of this cellular automata suggests that mineral resource information is a critical factor in the quality of the results. With automated calibration, further refinements of how the mineral-resource information is provided to the cellular automaton will probably improve our model.

  7. A systematic study of multiple minerals precipitation modelling in wastewater treatment

    DEFF Research Database (Denmark)

    Kazadi Mbamba, Christian; Tait, Stephan; Flores-Alsina, Xavier

    2015-01-01

    Mineral solids precipitation is important in wastewater treatment. However approaches to minerals precipitation modelling are varied, often empirical, and mostly focused on single precipitate classes. A common approach, applicable to multi-species precipitates, is needed to integrate into existin...

  8. Ectopic mineralization disorders of the extracellular matrix of connective tissue: molecular genetics and pathomechanisms of aberrant calcification.

    Science.gov (United States)

    Li, Qiaoli; Jiang, Qiujie; Uitto, Jouni

    2014-01-01

    Ectopic mineralization of connective tissues is a complex process leading to deposition of calcium phosphate complexes in the extracellular matrix, particularly affecting the skin and the arterial blood vessels and common in age-associated disorders. A number of initiating and contributing metabolic and environmental factors are linked to aberrant mineralization in these diseases, making the identification of precise pathomechanistic pathways exceedingly difficult. However, there has been significant recent progress in understanding the ectopic mineralization processes through study of heritable single-gene disorders, which have allowed identification of discrete pathways and contributing factors leading to aberrant connective tissue mineralization. These studies have provided support for the concept of an intricate mineralization/anti-mineralization network present in peripheral connective tissues, providing a perspective to development of pharmacologic approaches to limit the phenotypic consequences of ectopic mineralization. This overview summarizes the current knowledge of ectopic heritable mineralization disorders, with accompanying animal models, focusing on pseudoxanthoma elasticum and generalized arterial calcification of infancy, two autosomal recessive diseases manifesting with extensive connective tissue mineralization in the skin and the cardiovascular system.

  9. Genetically Modified Pig Models for Human Diseases

    Institute of Scientific and Technical Information of China (English)

    Nana Fan; Liangxue Lai

    2013-01-01

    Genetically modified animal models are important for understanding the pathogenesis of human disease and developing therapeutic strategies.Although genetically modified mice have been widely used to model human diseases,some of these mouse models do not replicate important disease symptoms or pathology.Pigs are more similar to humans than mice in anatomy,physiology,and genome.Thus,pigs are considered to be better animal models to mimic some human diseases.This review describes genetically modified pigs that have been used to model various diseases including neurological,cardiovascular,and diabetic disorders.We also discuss the development in gene modification technology that can facilitate the generation of transgenic pig models for human diseases.

  10. Development of a global model of mineral dust aerosol microphysics

    Directory of Open Access Journals (Sweden)

    Y. H. Lee

    2008-10-01

    Full Text Available A mineral dust module is developed and implemented into the global aerosol microphysics model, GISS-TOMAS. The model is evaluated against long-term measurements of dust surface mass concentrations and deposition fluxes. Predicted mass concentrations and deposition fluxes are in error on average by a factor of 3 and 5, respectively. The comparison shows that the model performs better near the dust source regions but underestimates surface concentrations and deposition fluxes in more remote regions. For example, including only sites with measured dust concentrations of at least 0.5 μg m−3, the model prediction agrees with observations to within a factor of 2. It was hypothesized that the lifetime of dust, 2.6 days in our base case, is too short and causes the underestimation in remote areas. However, a sensitivity simulation with smaller dust particles and increased lifetime, 3.7 days, does not significantly improve the comparison. We conclude that the underestimation of mineral dust in remote areas results from local factors and sources not well described by the dust source function and/or the GCM meteorology. The effect of dust aerosols on CCN(0.2% concentrations is negligible in most regions of the globe; however, CCN(0.2% concentrations decrease by 10–20% in dusty regions as a result of coagulational scavenging of CCN particles by dust and a decrease in H2SO4 condensation to CCN particles due to the additional surface area of dust.

  11. Stratiform chromite deposit model: Chapter E in Mineral deposit models for resource assessment

    Science.gov (United States)

    Schulte, Ruth F.; Taylor, Ryan D.; Piatak, Nadine M.; Seal, Robert R., II

    2012-01-01

    A new descriptive stratiform chromite deposit model was prepared which will provide a framework for understanding the characteristics of stratiform chromite deposits worldwide. Previous stratiform chromite deposit models developed by the U.S. Geological Survey (USGS) have been referred to as Bushveld chromium, because the Bushveld Complex in South Africa is the only stratified, mafic-ultramafic intrusion presently mined for chromite and is the most intensely researched. As part of the on-going effort by the USGS Mineral Resources Program to update existing deposit models for the upcoming national mineral resource assessment, this revised stratiform chromite deposit model includes new data on the geological, mineralogical, geophysical, and geochemical attributes of stratiform chromite deposits worldwide. This model will be a valuable tool in future chromite resource and environmental assessments and supplement previously published models used for mineral resource evaluation.

  12. Genetic labelling and application of the isoproturon-mineralizing Sphingomonas sp. strain SRS2 in soil and rhizosphere

    DEFF Research Database (Denmark)

    Kristensen, K.E.; Jacobsen, C.S.; Hansen, L.H.

    2006-01-01

    AIMS: To construct a luxAB-labelled Sphingomonas sp. strain SRS2 maintaining the ability to mineralize the herbicide isoproturon and usable for monitoring the survival and distribution of strain SRS2 on plant roots in laboratory systems. METHODS AND RESULTS: We inserted the mini-Tn5-luxAB marker...... into strain SRS2 using conjugational mating. In the transconjugant mutants luciferase was produced in varying levels. The mutants showed significant differences in their ability to degrade isoproturon. One luxAB-labelled mutant maintained the ability to mineralize isoproturon and was therefore selected...... for monitoring colonization of barley roots. CONCLUSIONS: We successfully constructed a genetically labelled isoproturon-mineralizing-strain SRS2 and demonstrated its ability to survive in soil and its colonization of rhizosphere. SIGNIFICANCE AND IMPACT OF THE STUDY: The construction of a luxAB-labelled strain...

  13. Genetic models of homosexuality: generating testable predictions

    OpenAIRE

    Gavrilets, Sergey; Rice, William R.

    2006-01-01

    Homosexuality is a common occurrence in humans and other species, yet its genetic and evolutionary basis is poorly understood. Here, we formulate and study a series of simple mathematical models for the purpose of predicting empirical patterns that can be used to determine the form of selection that leads to polymorphism of genes influencing homosexuality. Specifically, we develop theory to make contrasting predictions about the genetic characteristics of genes influencing homosexuality inclu...

  14. Genetic search feature selection for affective modeling

    DEFF Research Database (Denmark)

    Martínez, Héctor P.; Yannakakis, Georgios N.

    2010-01-01

    Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built...

  15. Genetic models of homosexuality: generating testable predictions.

    Science.gov (United States)

    Gavrilets, Sergey; Rice, William R

    2006-12-22

    Homosexuality is a common occurrence in humans and other species, yet its genetic and evolutionary basis is poorly understood. Here, we formulate and study a series of simple mathematical models for the purpose of predicting empirical patterns that can be used to determine the form of selection that leads to polymorphism of genes influencing homosexuality. Specifically, we develop theory to make contrasting predictions about the genetic characteristics of genes influencing homosexuality including: (i) chromosomal location, (ii) dominance among segregating alleles and (iii) effect sizes that distinguish between the two major models for their polymorphism: the overdominance and sexual antagonism models. We conclude that the measurement of the genetic characteristics of quantitative trait loci (QTLs) found in genomic screens for genes influencing homosexuality can be highly informative in resolving the form of natural selection maintaining their polymorphism.

  16. Development of a global model of mineral dust aerosol microphysics

    Directory of Open Access Journals (Sweden)

    Y. H. Lee

    2009-04-01

    Full Text Available A mineral dust module is developed and implemented into the global aerosol microphysics model, GISS-TOMAS. The model is evaluated against long-term measurements of dust surface mass concentrations and deposition fluxes. Predicted mass concentrations and deposition fluxes are in error on average by a factor of 3 and 5, respectively. The comparison shows that the model performs better near the dust source regions but underestimates surface concentrations and deposition fluxes in more remote regions. Including only sites with measured dust concentrations of at least 0.5 μg m−3, the model prediction agrees with observations to within a factor of 2. It was hypothesized that the lifetime of dust, 2.6 days in our base case, is too short and causes the underestimation in remote areas. However, a sensitivity simulation with smaller dust particles and increased lifetime, 3.7 days, does not significantly improve the comparison. These results suggest that the underestimation of mineral dust in remote areas may result from local factors/sources not well described by the global dust source function used here or the GCM meteorology. The effect of dust aerosols on CCN(0.2% concentrations is negligible in most regions of the globe; however, CCN(0.2% concentrations change decrease by 10–20% in dusty regions the impact of dust on CCN(0.2% concentrations in dusty regions is very sensitive to the assumed size distribution of emissions. If emissions are predominantly in the coarse mode, CCN(0.2% decreases in dusty regions up to 10–20% because dust competes for condensable H2SO4, reducing the condensational growth of ultrafine mode particles to CCN sizes. With significant fine mode emissions, however, CCN(0.2% doubles in Saharan source regions because the direct emission of dust particles outweighs any microphysical feedbacks. The impact of dust on CCN concentrations active at various water supersaturations is also investigated

  17. Exploration criteria for mineral target mapping based on 3D geological modeling in the Taebaek mineralized belt in Korea

    Science.gov (United States)

    Oh, H. J.; Kihm, Y. H.; Cho, S. J.

    2015-12-01

    We constructed a three-dimensional (3D) geological model based on a 1:50,000-scaled geologic map and determined the exploration criteria for skarn deposit target mapping in the Taebaek mineralized belt. All available geological and geophysical data were compiled in a 3D computing environment using GOCAD software. Twenty-four stratigraphic horizons and more than 100 fault surfaces are defined in the 3D geological model. The primary geological criteria for skarn mineralization in the Taebaek mineralized belt included the presence of an NE-oriented strike-slip fault, key stratigraphic horizons, and a high magnetic susceptibility anomaly based on 3D inversion of magnetic data. The 3D geological criteria were extracted from the 3D geological model for skarn deposit target mapping in the belt. The distance values of the three criteria (NE strike-slip fault, limestone horizon, and area of high magnetic susceptibility) were divided into four classes based on cutoff values determined by experts. The weight values for all of the geological criteria and the score value for each class of the distance criteria were also estimated based on expert knowledge. The weights and scores of geological criteria derived from expert knowledge serve as useful guides for target mapping in the Taebaek mineralized belt.

  18. Prediction of Mineral Scale Formation in Geothermal and Oilfield Operations using the Extended UNIQUAC Model. Part I: Sulphate Scaling Minerals

    DEFF Research Database (Denmark)

    Garcia, Ada V.; Thomsen, Kaj; Stenby, Erling Halfdan

    2005-01-01

    Pressure parameters are added to the Extended UNIQUAC model presented by Thomsen and Rasmussen (1999). The improved model has been used for correlation and prediction of solid-liquid equilibrium (SLE) of scaling minerals (CaSO4, CaSO4·2H2O, BaSO4 and SrSO4) at temperatures up to 300°C and pressures...

  19. Genetic models for CNS inflammation

    DEFF Research Database (Denmark)

    Owens, T; Wekerle, H; Antel, J

    2001-01-01

    The use of transgenic technology to over-express or prevent expression of genes encoding molecules related to inflammation has allowed direct examination of their role in experimental disease. This article reviews transgenic and knockout models of CNS demyelinating disease, focusing primarily on ...

  20. Genetically engineered mouse models of prostate cancer

    NARCIS (Netherlands)

    Nawijn, Martijn C.; Bergman, Andreas M.; van der Poel, Henk G.

    2008-01-01

    Objectives: Mouse models of prostate cancer are used to test the contribution of individual genes to the transformation process, evaluate the collaboration between multiple genetic lesions observed in a single tumour, and perform preclinical intervention studies in prostate cancer research. Methods:

  1. Adaptive Genetic Algorithm Model for Intrusion Detection

    Directory of Open Access Journals (Sweden)

    K. S. Anil Kumar

    2012-09-01

    Full Text Available Intrusion detection systems are intelligent systems designed to identify and prevent the misuse of computer networks and systems. Various approaches to Intrusion Detection are currently being used, but they are relatively ineffective. Thus the emerging network security systems need be part of the life system and this ispossible only by embedding knowledge into the network. The Adaptive Genetic Algorithm Model - IDS comprising of K-Means clustering Algorithm, Genetic Algorithm and Neural Network techniques. Thetechnique is tested using multitude of background knowledge sets in DARPA network traffic datasets.

  2. Identification of genetic loci associated with crude protein and mineral concentrations in alfalfa (Medicago sativa) using association mapping.

    Science.gov (United States)

    Jia, Congjun; Wu, Xinming; Chen, Min; Wang, Yunqi; Liu, Xiqiang; Gong, Pan; Xu, Qingfang; Wang, Xuemin; Gao, Hongwen; Wang, Zan

    2017-06-06

    Alfalfa (Medicago sativa) is one of the most important legume forage species in China and many other countries of the world. It provides a quality source of proteins and minerals to animals. Genetic underpinnings for these important traits, however, are elusive. An alfalfa (M. sativa) association mapping study for six traits, namely crude protein (CP), rumen undegraded protein (RUP), and four mineral elements (Ca, K, Mg and P), was conducted in three consecutive years using a large collection encompassing 336 genotypes genotyped with 85 simple sequence repeat (SSR) markers. All the traits were significantly influenced by genotype, environment, and genotype × environment interaction. Eight-five significant associations (P alfalfa quality. The markers could be used in assisting selection for the individual traits in breeding populations for developing new alfalfa cultivars.

  3. Animal Models of Parkinson's Disease: Vertebrate Genetics

    Science.gov (United States)

    Lee, Yunjong; Dawson, Valina L.; Dawson, Ted M.

    2012-01-01

    Parkinson's disease (PD) is a complex genetic disorder that is associated with environmental risk factors and aging. Vertebrate genetic models, especially mice, have aided the study of autosomal-dominant and autosomal-recessive PD. Mice are capable of showing a broad range of phenotypes and, coupled with their conserved genetic and anatomical structures, provide unparalleled molecular and pathological tools to model human disease. These models used in combination with aging and PD-associated toxins have expanded our understanding of PD pathogenesis. Attempts to refine PD animal models using conditional approaches have yielded in vivo nigrostriatal degeneration that is instructive in ordering pathogenic signaling and in developing therapeutic strategies to cure or halt the disease. Here, we provide an overview of the generation and characterization of transgenic and knockout mice used to study PD followed by a review of the molecular insights that have been gleaned from current PD mouse models. Finally, potential approaches to refine and improve current models are discussed. PMID:22960626

  4. Zebra fish: an uncharted behavior genetic model.

    Science.gov (United States)

    Gerlai, Robert

    2003-09-01

    The zebra fish has been a preferred subject of genetic analysis. It produces a large number of offspring that can be kept in small aquaria, it can be easily mutagenized using chemical mutagens (e.g., ethyl nitrosourea [ENU]), and high-resolution genetic maps exist that aid identification of novel genes. Libraries containing large numbers of mutant fish have been generated, and the genetic mechanisms of the development of zebra fish, whose embryo is transparent, have been extensively studied. Given the extensive homology of its genome with that of other vertebrate species including our own and given the available genetic tools, zebra fish has become a popular model organism. Despite this popularity, however, surprisingly little is known about its behavior. It is argued that behavioral analysis is a powerful tool with which the function of the brain may be studied, and the zebra fish will represent an excellent subject of such analysis. The present paper is a proof of concept study that uses pharmacological manipulation (exposure to alcohol) to show that the zebra fish is amenable to the behavioral genetic analysis of aggression and thus may allow us to reveal molecular mechanisms of this behavioral phenomenon relevant to vertebrates.

  5. Multi-scale interactions of geological processes during mineralization: cascade dynamics model and multifractal simulation

    Directory of Open Access Journals (Sweden)

    L. Yao

    2011-03-01

    Full Text Available Relations between mineralization and certain geological processes are established mostly by geologist's knowledge of field observations. However, these relations are descriptive and a quantitative model of how certain geological processes strengthen or hinder mineralization is not clear, that is to say, the mechanism of the interactions between mineralization and the geological framework has not been thoroughly studied. The dynamics behind these interactions are key in the understanding of fractal or multifractal formations caused by mineralization, among which singularities arise due to anomalous concentration of metals in narrow space. From a statistical point of view, we think that cascade dynamics play an important role in mineralization and studying them can reveal the nature of the various interactions throughout the process. We have constructed a multiplicative cascade model to simulate these dynamics. The probabilities of mineral deposit occurrences are used to represent direct results of mineralization. Multifractal simulation of probabilities of mineral potential based on our model is exemplified by a case study dealing with hydrothermal gold deposits in southern Nova Scotia, Canada. The extent of the impacts of certain geological processes on gold mineralization is related to the scale of the cascade process, especially to the maximum cascade division number nmax. Our research helps to understand how the singularity occurs during mineralization, which remains unanswered up to now, and the simulation may provide a more accurate distribution of mineral deposit occurrences that can be used to improve the results of the weights of evidence model in mapping mineral potential.

  6. Genetic Algorithm Based Microscale Vehicle Emissions Modelling

    Directory of Open Access Journals (Sweden)

    Sicong Zhu

    2015-01-01

    Full Text Available There is a need to match emission estimations accuracy with the outputs of transport models. The overall error rate in long-term traffic forecasts resulting from strategic transport models is likely to be significant. Microsimulation models, whilst high-resolution in nature, may have similar measurement errors if they use the outputs of strategic models to obtain traffic demand predictions. At the microlevel, this paper discusses the limitations of existing emissions estimation approaches. Emission models for predicting emission pollutants other than CO2 are proposed. A genetic algorithm approach is adopted to select the predicting variables for the black box model. The approach is capable of solving combinatorial optimization problems. Overall, the emission prediction results reveal that the proposed new models outperform conventional equations in terms of accuracy and robustness.

  7. The station of modeling the mine resources in economical geology investigations and determination of mineral deposits genes & reserves

    Directory of Open Access Journals (Sweden)

    Sharif, J.A.

    2015-05-01

    Full Text Available In recent days, computer is becoming one of the most essential instruments in advanced countries for the researchers and the domain of its application is going to be increased every day. Using the 3D modeling of the earth, its mine resources and the brilliant details which are given by the models, the researching and exploring groups will find out the inconspicuous and attractive aspects of the genetic structure and the geological history of these resources. In this paper which is a result of the researches done as the case study on a group of aragonite deposits in West Azarbaijan province, modeling of under study mineral deposits and the genetic approaches obtained from the models lead into explore and discover some other resources of the same minerals which is widely accepted recently in the market of decorative rocks in Iran. In modeling procedure of these resources which is a product of the geysers, the profile of these lime generating springs and their directional order on some specific hidden fracture is determined and approximate location of the new resources for the next explorations is assigned. At the moment, these assigned locations as new resources are being explored and even exploited.

  8. Genetic variability for mineral concentration of Eruca sativa L. and Diplotaxis tenuifolia L. accessions

    Directory of Open Access Journals (Sweden)

    Mehmet Kadri Bozokalfa

    2009-01-01

    Full Text Available Eruca sativa L. (rocket or arugula and Diplotaxis tenuifolia L. (perennial wall-rocket, are important leafyvegetables and are significant sources of minerals for human nutrition and commonly found in the Mediterranean basin,southern Europe, and Central Asia. The objectives of this study were to determine genotypic variability among and within E.sativa and D. tenuifolia genotypes for NO3, NO2, N, P, K, Ca, Mg, Na, Fe, Cu, Zn, and Mn concentrations; to estimate genotypex environment interaction; and to assess relationships among leaf mineral concentration during two consecutive springseasons. E. sativa and D. tenuifolia leaves contained significant amounts of nutritionally important minerals. In general,genotypic variation was lower than phenotypic variation for all mineral concentrations considered, indicating the influence ofenvironment on the expression of analyzed traits. The variance between genotypes and relative importance within genotypevariation indicates that NO3, NO2, K, Mn, Zn, and Cu concentrations may be improved by selecting among cultivars, if theheritability is adequate.

  9. Genetic analysis of the effect of zinc deficiency on Arabidopsis growth and mineral concentrations

    NARCIS (Netherlands)

    Ghandilyan, A.; Kutman, U.B.; Kutman, B.Y.; Cakmak, I.; Aarts, M.G.M.

    2012-01-01

    Aims Zinc deficiency is a common micronutrient deficiency in plants growing in many different regions of the world and is associated with disturbances in uptake and accumulation of mineral nutrients. Despite many published data on physiological factors affecting ion accumulation in Zn deficient plan

  10. The Influence of Vitamin D Receptor Genetic Variants on Bone Mineral Density and Osteoporosis in Chinese Postmenopausal Women

    Directory of Open Access Journals (Sweden)

    Wei He

    2015-01-01

    Full Text Available Growing evidence indicates that the vitamin D receptor (VDR gene is an important candidate gene for influencing the development of osteoporosis. The aim of the study was to evaluate the potential association between genetic variants of VDR gene and bone mineral density (BMD and osteoporosis in Chinese postmenopausal women. The study included 970 Chinese postmenopausal women at the postmenopausal osteoporosis (482 and healthy controls (488. The BMD of lumbar spine (L2–4 anterior-posterior view, femoral neck hip, and total hip was evaluated using the Norland XR-46 dual energy X-ray absorptiometry (DEXA. The genotypes of VDR genetic variants were determined by the created restriction site-PCR (CRS-PCR and confirmed by DNA sequencing methods. Our data indicated that the VDR p.Glicine (Gly14 alanine (Ala and p.histidine (His 305 glutanine (Gln genetic variants were statistically associated with adjusted femoral neck hip BMD, adjusted lumbar spine BMD, and adjusted total hip BMD (P values < 0.05. Results from this study suggest that the VDR p.Gly14Ala and p.His305Gln genetic variants are significantly associated with BMD decrease in Chinese postmenopausal women and might be used as molecular markers for assessing the risk of BMD and osteoporosis.

  11. Modeling resistance to genetic control of insects.

    Science.gov (United States)

    Alphey, Nina; Bonsall, Michael B; Alphey, Luke

    2011-02-07

    The sterile insect technique is an area-wide pest control method that reduces pest populations by releasing mass-reared sterile insects which compete for mates with wild insects. Modern molecular tools have created possibilities for improving and extending the sterile insect technique. As with any new insect control method, questions arise about potential resistance. Genetic RIDL(®)(1) (Release of Insects carrying a Dominant Lethal) technology is a proposed modification of the technique, releasing insects that are homozygous for a repressible dominant lethal genetic construct rather than being sterilized by irradiation. Hypothetical resistance to the lethal mechanism is a potential threat to RIDL strategies' effectiveness. Using population genetic and population dynamic models, we assess the circumstances under which monogenic biochemically based resistance could have a significant impact on the effectiveness of releases for population control. We assume that released insects would be homozygous susceptible to the lethal genetic construct and therefore releases would have a built-in element of resistance dilution. We find that this effect could prevent or limit the spread of resistance to RIDL constructs; the outcomes are subject to competing selective forces deriving from the fitness properties of resistance and the release ratio. Resistance that is spreading and capable of having a significant detrimental impact on population reduction is identifiable, signaling in advance a need for mitigating action.

  12. Evolutionary algorithms in genetic regulatory networks model

    CERN Document Server

    Raza, Khalid

    2012-01-01

    Genetic Regulatory Networks (GRNs) plays a vital role in the understanding of complex biological processes. Modeling GRNs is significantly important in order to reveal fundamental cellular processes, examine gene functions and understanding their complex relationships. Understanding the interactions between genes gives rise to develop better method for drug discovery and diagnosis of the disease since many diseases are characterized by abnormal behaviour of the genes. In this paper we have reviewed various evolutionary algorithms-based approach for modeling GRNs and discussed various opportunities and challenges.

  13. Genetic search feature selection for affective modeling

    DEFF Research Database (Denmark)

    Martínez, Héctor P.; Yannakakis, Georgios N.

    2010-01-01

    Automatic feature selection is a critical step towards the generation of successful computational models of affect. This paper presents a genetic search-based feature selection method which is developed as a global-search algorithm for improving the accuracy of the affective models built....... The method is tested and compared against sequential forward feature selection and random search in a dataset derived from a game survey experiment which contains bimodal input features (physiological and gameplay) and expressed pairwise preferences of affect. Results suggest that the proposed method...

  14. Parametrization of organic nitrogen mineralization models in soil treated with swine raising wastewater

    Directory of Open Access Journals (Sweden)

    Demétrius David da Silva

    2010-08-01

    Full Text Available Little is known about the mineralization dynamic of organic nitrogen contained in swine manure, so models need to be adjusted for its prediction. The objective of the present study was to parameterize and assess models of organic nitrogen mineralization in soil treated with swine raising wastewater (SRW at different temperatures and water contents. Samples of 57.3 cm3 of dystrophic Red-Yellow Latosol were mixed with SRW at the application dose of 400 kg ha-1 nitrogen, placed in plastic cups and incubated at four different temperatures (15, 20, 25 and 35°C and water contents corresponding to tensions of 10, 30, 200 and 1500 kPa. Samples were removed from the incubated soil after 3, 6, 12, 24, 48 and 96 days to quantify the ammonium and nitrate concentrations. The parameters of the soil organic nitrogen mineralization models were determined from the organic nitrogen mineralization values obtained over the different incubation periods. The value of the potentially mineralizable nitrogen (N0 in soil with application of SRW was superior that of the soil without application of SRW. The mineralization constant (k in soil with application of SRW was always superior that of the soil without application of SRW. There was a tendency for the simple exponential model to underestimate the values of the mineralized nitrogen concentration. In most of the situations the potential model was more efficient than the simple exponential model to predict the mineralization of the organic nitrogen.

  15. Modeling mineral phase change chemistry of groundwater in a rural-urban fringe.

    Science.gov (United States)

    Singh, S K; Srivastava, Prashant K; Gupta, M; Mukherjee, S

    2012-01-01

    This research paper aims to determine the genetic origin of the chemical elements in groundwater. It deals with the results of physicochemical parameters, to evaluate the hydro-geochemistry of groundwater in rural-urban fringe of district Bareilly, India. Pre- and post-monsoon sampling has been carried out, which reveals inter-seasonal variability effect on the hydro-geochemical processes. Geochemical modeling especially computation of saturation index was undertaken using the WATEQ4F model. Majority of samples fall in the category of undersaturation, which further suggests that groundwater still has potential to dissolve more minerals. Chemical categorizations of groundwater samples were performed with the help of the Aquachem model. Grouping of groundwater on the Piper diagram reveals a common composition and origin. In most of the area, water facies is of Ca(2+)-HCO(3)(-) type in both the seasons. It also indicates that in pre-monsoon, ion exchange is the dominant process, whereas in post-monsoon, both ion exchanges as well as reverse ion exchanges are reported in the groundwater of the study area.

  16. Homogeneized modeling of mineral dust emissions over Europe and Africa using the CHIMERE model

    Directory of Open Access Journals (Sweden)

    R. Briant

    2014-05-01

    Full Text Available In the region including Africa and Europe, the main part of mineral dust emissions is observed in Africa. The particles are thus transported towards Europe and constitute a non-negligible part of the surface aerosols measured and controlled in the framework of the European air quality legislation. The modelling of these African dust emissions fluxes and transport is widely studied and complex parameterizations are already used in regional to global model for this Sahara-Sahel region. In a lesser extent, mineral dust emissions occur locally in Europe, mainly over agricultural areas. Their modelling is generally poorly done or just ignored. But in some cases, this contribution may be important and may impact the European air quality budget. In this study, we propose an homogeneized calculations of mineral dust fluxes for Europe and Africa. For that, we extended the CHIMERE dust production model (DPM by using new soil and surface datasets, and the global aeolian roughness length dataset provided by GARLAP from microwave and visible satellite observations. This DPM is detailed along with academic tests case results and simulation on a real case results.

  17. A model for continuous improvement at a South African minerals benefication plant

    Directory of Open Access Journals (Sweden)

    Ras, Eugene Ras

    2015-05-01

    Full Text Available South Africa has a variety of mineral resources, and several minerals beneficiation plants are currently in operation. These plants must be operated effectively to ensure that the end-users of its products remain internationally competitive. To achieve this objective, plants need a sustainable continuous improvement programme. Several frameworks for continuous improvement are used, with variable success rates, in beneficiation plants around the world. However, none of these models specifically addresses continuous improvement from a minerals-processing point of view. The objective of this research study was to determine which factors are important for a continuous improvement model at a minerals beneficiation plant, and to propose a new model using lean manufacturing, six sigma, and the theory of constraints. A survey indicated that managers in the industry prefer a model that combines various continuous improvement models.

  18. Genetic Identification of Quantitative Trait Loci for Contents of Mineral Nutrients in Rice Grain

    Institute of Scientific and Technical Information of China (English)

    Ana Luisa Garcia-Oliveira; Lubin Tan; Yongcai Fu; Chuanqing Sun

    2009-01-01

    In present study, Fe, Zn, Mn, Cu, Ca, Mg, P and K contents of 85 Introgression linee (ILs) derived from a cross between an elite indica cultivar Teqing and the wild rice (Oryza rufipogon) were measured by inductively coupled argon plasma (ICAP) spectrometry. Substantial variation was observed for all traits and most of the mineral elements were significantly positive correlated or independent except for Fe with Cu. A total of 31 putative quantitative trait loci (QTLs) were detected for these eight mineral elements by single point analysis. Wild rice (O. rufipogon) contributed favorable alleles for most of the QTLs (26 QTLs), and chromosomes 1, 9 and 12 exhibited 14 QTLs (45%) for these traits. One major effect of QTL for zinc content accounted for the largest proportion of phenotypic variation (11%-19%) was detected near the simple sequence repeats marker RM152 on chromosome 8. The co-locations of QTLs for some mineral elements observed in this mapping population suggested the relationship was at a molecular level among these traits and could be helpful for simultaneous improvement of these traits in rice grain by marker assisted selection.

  19. Direct Visualization of Aggregate Morphology and Dynamics in a Model Soil Organic–Mineral System

    Energy Technology Data Exchange (ETDEWEB)

    Hufschmid, Ryan D.; Newcomb, Christina J.; Grate, Jay W.; De Yoreo, James J.; Browning, Nigel D.; Qafoku, Nikolla

    2017-04-03

    Interactions between mineral surfaces and organic matter are ubiquitous in soils and the environment. Through both physical and chemical mechanisms, organic-mineral assemblages prevent decomposition of soil organic matter by limiting accessibility or reducing efficacy of enzymes and microbes. To understand the mechanisms underlying organic-mineral interactions, researchers have begun to interrogate these systems at smaller length scales. Current techniques that maintain a hydrated state and allow researchers to characterize nanometer length scales are limited. Here we chose a model organic-mineral system and performed complementary imaging techniques that enable direct nanoscale observations in environmentally relevant conditions: cryogenic TEM and in-situ liquid cell TEM. We observed a three-fold increase in aggregate size of goethite nanoparticles upon addition of a model organic phosphate ligand and quantification of nanoparticle orientation reveals a preference for side-to-side interactions independent of the addition of an organic ligand. Additionally, in-situ liquid cell TEM experiments provides a dynamic view of the interactions allowing us to report velocities of mineral assemblages during aggregation and disaggregation, which could potentially provide binding energetics and kinetic parameters about organic-mineral and mineral-mineral systems.

  20. Latent spatial models and sampling design for landscape genetics

    Science.gov (United States)

    Hanks, Ephraim M.; Hooten, Mevin B.; Knick, Steven T.; Oyler-McCance, Sara J.; Fike, Jennifer A.; Cross, Todd B.; Schwartz, Michael K.

    2016-01-01

    We propose a spatially-explicit approach for modeling genetic variation across space and illustrate how this approach can be used to optimize spatial prediction and sampling design for landscape genetic data. We propose a multinomial data model for categorical microsatellite allele data commonly used in landscape genetic studies, and introduce a latent spatial random effect to allow for spatial correlation between genetic observations. We illustrate how modern dimension reduction approaches to spatial statistics can allow for efficient computation in landscape genetic statistical models covering large spatial domains. We apply our approach to propose a retrospective spatial sampling design for greater sage-grouse (Centrocercus urophasianus) population genetics in the western United States.

  1. Large genetic animal models of Huntington's Disease.

    Science.gov (United States)

    Morton, A Jennifer; Howland, David S

    2013-01-01

    The dominant nature of the Huntington's disease gene mutation has allowed genetic models to be developed in multiple species, with the mutation causing an abnormal neurological phenotype in all animals in which it is expressed. Many different rodent models have been generated. The most widely used of these, the transgenic R6/2 mouse, carries the mutation in a fragment of the human huntingtin gene and has a rapidly progressive and fatal neurological phenotype with many relevant pathological changes. Nevertheless, their rapid decline has been frequently questioned in the context of a disease that takes years to manifest in humans, and strenuous efforts have been made to make rodent models that are genetically more 'relevant' to the human condition, including full length huntingtin gene transgenic and knock-in mice. While there is no doubt that we have learned, and continue to learn much from rodent models, their usefulness is limited by two species constraints. First, the brains of rodents differ significantly from humans in both their small size and their neuroanatomical organization. Second, rodents have much shorter lifespans than humans. Here, we review new approaches taken to these challenges in the development of models of Huntington's disease in large brained, long-lived animals. We discuss the need for such models, and how they might be used to fill specific niches in preclinical Huntington's disease research, particularly in testing gene-based therapeutics. We discuss the advantages and disadvantages of animals in which the prodromal period of disease extends over a long time span. We suggest that there is considerable 'value added' for large animal models in preclinical Huntington's disease research.

  2. Genetic mouse models for otitis media

    Institute of Scientific and Technical Information of China (English)

    Qingyin Zheng; Ken R Johnson

    2003-01-01

    @@ Genetics of Otitis Media (OM): OM is affected by multiple factors including eustachian tube (ET) structure and function, immune status, innate mucosal defense, genetic susceptibility, and pathogens.

  3. GENETIC-BASED NUTRITION RECOMMENDATION MODEL

    Directory of Open Access Journals (Sweden)

    S. A.A. Fayoumi

    2014-01-01

    Full Text Available Evolutionary computing is the collective name for a range of problem-solving techniques based on principles of biological evolution, such as natural selection and genetic inheritance. These techniques are being widely applied to a variety of problems in many vital fields. Also, Evolutionary Algorithms (EA which applied the principles of Evolutionary computations, such as genetic algorithm, particle swarm, ant colony and bees algorithm and so on play an important role in decision making process. EAs serve a lot of fields which can affect our life directly, such as medicine, engineering, transportations, communications. One of these vital fields is Nutrition which can be viewed from several points of view as medical, physical, social, environmental and psychological point of view. This study, presents a proposed model that shows how evolutionary computing generally and genetic algorithm specifically-as a powerful algorithm of evolutionary algorithms-can be used to recommend an appropriate nutrition style in a medical and physical sides only to each person according to his/her personal and medical measurements.

  4. Correlation between Cu mineralization and major faults using multifractal modelling in the Tarom area (NW Iran)

    Science.gov (United States)

    Nouri, Reza; Jafari, Mohammad Reza; Arian, Mehran; Feizi, Faranak; Afzal, Peyman

    2013-10-01

    The Tarom 1: 100,000 sheet is located within the Cenozoic Tarom-Hashtjin volcano-plutonic belt, NW Iran. Reconstruction of the tectonic and structural setting of the hydrothermal deposits is fundamental to predictive models of different ore deposits. Since fractal/multifractal modelling is an effective instrument for separation of geological and mineralized zones from background, therefore Concentration-Distance to Major Fault (C-DMF) fractal model and distribution of Cu anomalies were used to classify Cu mineralizations according to their distance to major faults. Application of the C-DMF model for the classification of Cu mineralization in the Tarom 1: 100,000 sheet reveals that the main copper mineralizations have a strong correlation with their distance to major faults in the area. The distances of known copper mineralizations having Cu values higher than 2.2 % to major faults are less than 10 km showing a positive correlation between Cu mineralization and tectonic events. Moreover, extreme and high Cu anomalies based on stream sediments and lithogeochemical data were identified by the Number-Size (N-S) fractal model. These anomalies have distances to major faults less than 10 km and validate the results derived via the C-DMF fractal model. The C-DMF fractal modelling can be utilized for the reconnaissance and prospecting of magmatic and hydrothermal deposits.

  5. Proceedings for a Workshop on Deposit Modeling, Mineral Resource Assessment, and Their Role in Sustainable Development

    Science.gov (United States)

    Briskey, Joseph A.; Schulz, Klaus J.

    2007-01-01

    Preface The world's use of nonfuel mineral resources continues to increase to support a growing population and increasing standards of living. The ability to meet this increasing demand is affected especially by concerns about possible environmental degradation associated with minerals production and by competing land uses. What information does the world need to support global minerals development in a sustainable way? Informed planning and decisions concerning sustainability and future mineral resource supply require a long-term perspective and an integrated approach to resource, land use, economic, and environmental management worldwide. Such perspective and approach require unbiased information on the global distribution of identified and especially undiscovered resources, the economic and political factors influencing their development, and the potential environmental consequences of their exploitation. The U.S. Geological Survey and the former Deposit Modeling Program of the International Union of Geological Sciences (IUGS) of the United Nations Educational, Scientific and Cultural Organization (UNESCO) sponsored a workshop on 'Deposit Modeling, Mineral Resource Assessment, and Their Role in Sustainable Development' at the 31st International Geological Congress (IGC) in Rio de Janeiro, Brazil, on August 18-19, 2000. The purpose of the workshop was to review the state-of-the-art in mineral deposit modeling and resource assessment and to examine the role of global assessments of nonfuel mineral resources in sustainable development. The workshop addressed questions such as the following: Which of the available mineral deposit models and assessment methods are best suited for predicting the locations, deposit types, and amounts of undiscovered nonfuel mineral resources remaining in the world? What is the availability of global geologic, mineral deposit, and mineral exploration information? How can mineral resource assessments be used to address economic and

  6. Medulloblastoma: Molecular Genetics and Animal Models

    Directory of Open Access Journals (Sweden)

    Corey Raffel

    2004-07-01

    Full Text Available Medulloblastoma is a primary brain tumor found in the cerebellum of children. The tumor occurs in association with two inherited cancer syndromes: Turcot syndrome and Gorlin syndrome. Insights into the molecular biology of the tumor have come from looking at alterations in the genes altered in these syndromes, PTC and APC, respectively. Murine models of medulloblastoma have been constructed based on these alterations. Additional murine models that, while mimicking the appearance of the human tumor, seem unrelated to the human tumor's molecular alterations have been made. In this review, the clinical picture, origin, molecular biology, murine models of medulloblastoma are discussed. Although a great deal has been discovered about this tumor, the genetic alterations responsible for tumor development in a majority of patients have yet to be described.

  7. Genetically engineered mouse models and human osteosarcoma

    Directory of Open Access Journals (Sweden)

    Ng Alvin JM

    2012-10-01

    Full Text Available Abstract Osteosarcoma is the most common form of bone cancer. Pivotal insight into the genes involved in human osteosarcoma has been provided by the study of rare familial cancer predisposition syndromes. Three kindreds stand out as predisposing to the development of osteosarcoma: Li-Fraumeni syndrome, familial retinoblastoma and RecQ helicase disorders, which include Rothmund-Thomson Syndrome in particular. These disorders have highlighted the important roles of P53 and RB respectively, in the development of osteosarcoma. The association of OS with RECQL4 mutations is apparent but the relevance of this to OS is uncertain as mutations in RECQL4 are not found in sporadic OS. Application of the knowledge or mutations of P53 and RB in familial and sporadic OS has enabled the development of tractable, highly penetrant murine models of OS. These models share many of the cardinal features associated with human osteosarcoma including, importantly, a high incidence of spontaneous metastasis. The recent development of these models has been a significant advance for efforts to improve our understanding of the genetics of human OS and, more critically, to provide a high-throughput genetically modifiable platform for preclinical evaluation of new therapeutics.

  8. Genetic Algorithms Principles Towards Hidden Markov Model

    Directory of Open Access Journals (Sweden)

    Nabil M. Hewahi

    2011-10-01

    Full Text Available In this paper we propose a general approach based on Genetic Algorithms (GAs to evolve Hidden Markov Models (HMM. The problem appears when experts assign probability values for HMM, they use only some limited inputs. The assigned probability values might not be accurate to serve in other cases related to the same domain. We introduce an approach based on GAs to find
    out the suitable probability values for the HMM to be mostly correct in more cases than what have been used to assign the probability values.

  9. Genetic Programming for Automatic Hydrological Modelling

    Science.gov (United States)

    Chadalawada, Jayashree; Babovic, Vladan

    2017-04-01

    One of the recent challenges for the hydrologic research community is the need for the development of coupled systems that involves the integration of hydrologic, atmospheric and socio-economic relationships. This poses a requirement for novel modelling frameworks that can accurately represent complex systems, given, the limited understanding of underlying processes, increasing volume of data and high levels of uncertainity. Each of the existing hydrological models vary in terms of conceptualization and process representation and is the best suited to capture the environmental dynamics of a particular hydrological system. Data driven approaches can be used in the integration of alternative process hypotheses in order to achieve a unified theory at catchment scale. The key steps in the implementation of integrated modelling framework that is influenced by prior understanding and data, include, choice of the technique for the induction of knowledge from data, identification of alternative structural hypotheses, definition of rules, constraints for meaningful, intelligent combination of model component hypotheses and definition of evaluation metrics. This study aims at defining a Genetic Programming based modelling framework that test different conceptual model constructs based on wide range of objective functions and evolves accurate and parsimonious models that capture dominant hydrological processes at catchment scale. In this paper, GP initializes the evolutionary process using the modelling decisions inspired from the Superflex framework [Fenicia et al., 2011] and automatically combines them into model structures that are scrutinized against observed data using statistical, hydrological and flow duration curve based performance metrics. The collaboration between data driven and physical, conceptual modelling paradigms improves the ability to model and manage hydrologic systems. Fenicia, F., D. Kavetski, and H. H. Savenije (2011), Elements of a flexible approach

  10. Genetically biodiverse potato cultivars grown on a suitable agricultural soil under compost amendment or mineral fertilization: yield, quality, genetic and epigenetic variations, soil properties.

    Science.gov (United States)

    Cicatelli, Angela; Baldantoni, Daniela; Iovieno, Paola; Carotenuto, Maurizio; Alfani, Anna; De Feis, Italia; Castiglione, Stefano

    2014-09-15

    The use of compost for soil amendment is a promising agricultural practice environmentally and economically viable. In the framework of a wide research project designed to evaluate the effects of soil amendment with municipal solid waste compost in comparison with traditional mineral fertilization practices, 54 different cultivars (Cvs) of potatoes were AFLP (amplified fragment length polymorphism) molecularly fingerprinted. The seven most genetically biodiverse potato Cvs were used to establish an experimental field in southern Italy. The field area was divided into two portions fertilized with compost (20 Mg ha(-1)) or with ammonium sulphate (200 kg ha(-1)). No significant differences in productivity, organoleptic characteristics and element concentrations were observed between the potato tubers obtained with both kinds of soil fertilization, while the tubers grown on compost amended soil showed, on average, higher K concentrations with respect to those grown on mineral fertilised soil. cDNA-AFLP (complementary DNA-AFLP) and MSAP (methylation sensitive amplified polymorphism) analyses were carried out on both leaves and tubers of one selected Cv to estimate if any transcriptome alterations or epigenetic modifications were induced by the two kinds of fertilization, however no variations were detected. Chemical and biological soil qualities (i.e., microbial respiration, FDA hydrolysis, alkaline and acid phosphatase) were assessed on soil samples at the start of the experiment and at the end of potato crop cycle. No significant differences in soil pH and limited ones, in the available fraction of some trace elements, were observed; while conductivity was much higher for the compost amended portion of the experimental field. Microbial respiration, FDA hydrolysis and acid phosphatase activities were significantly increased by compost amendment, in comparison with mineral fertilization. Finally, a sensory panel of potato Cvs detected no significant differences among

  11. Simultaneous quantification of depolymerization and mineralization rates by a novel 15N tracing model

    Science.gov (United States)

    Andresen, Louise C.; Björsne, Anna-Karin; Bodé, Samuel; Klemedtsson, Leif; Boeckx, Pascal; Rütting, Tobias

    2016-09-01

    The depolymerization of soil organic matter, such as proteins and (oligo-)peptides, into monomers (e.g. amino acids) is currently considered to be the rate-limiting step for nitrogen (N) availability in terrestrial ecosystems. The mineralization of free amino acids (FAAs), liberated by the depolymerization of peptides, is an important fraction of the total mineralization of organic N. Hence, the accurate assessment of peptide depolymerization and FAA mineralization rates is important in order to gain a better process-based understanding of the soil N cycle. In this paper, we present an extended numerical 15N tracing model Ntrace, which incorporates the FAA pool and related N processes in order to provide a more robust and simultaneous quantification of depolymerization and gross mineralization rates of FAAs and soil organic N. We discuss analytical and numerical approaches for two forest soils, suggest improvements of the experimental work for future studies, and conclude that (i) when about half of all depolymerized peptide N is directly mineralized, FAA mineralization can be as important a rate-limiting step for total gross N mineralization as peptide depolymerization rate; (ii) gross FAA mineralization and FAA immobilization rates can be used to develop FAA use efficiency (NUEFAA), which can reveal microbial N or carbon (C) limitation.

  12. Models of genetic counseling and their effects on multicultural genetic counseling.

    Science.gov (United States)

    Lewis, Linwood J

    2002-06-01

    This theoretical paper examines challenges to multicultural genetic counseling, counseling between culturally different clients and counselors, in the context of Kessler's typology of models of genetic counseling (Kessler S (1997) J Genet Counsel 6:287-295). It is suggested that challenges such as resistance to multicultural genetic counseling education may be due to conceptions about genetic counseling as a biomedical field that transcends questions of culture as well as lack of multicultural training or prejudice. Directions for future research and recommendations for multicultural genetic counseling education are briefly explored.

  13. Laboratory tools to quantify biogenic dissolution of rocks and minerals: a model rock biofilm growing in percolation columns

    Directory of Open Access Journals (Sweden)

    Franz eSeiffert

    2016-04-01

    Full Text Available Sub-aerial biofilms (SAB are ubiquitous, self-sufficient microbial ecosystems found on mineral surfaces at all altitudes and latitudes. SABs, which are the principal causes of weathering on exposed terrestrial surfaces, are characterised by patchy growth dominated by associations of algae, cyanobacteria, fungi and heterotrophic bacteria. A recently developed in vitro system to study colonisation of rocks exposed to air included two key SAB participants - the rock-inhabiting ascomycete Knufia petricola (CBS 123872 and the phototrophic cyanobacterium Nostoc punctiforme ATCC29133. Both partners are genetically tractable and we used them here to study weathering of granite, K-feldspar and plagioclase. Small fragments of the various rocks or minerals (1 to 6 mm were packed into flow-through columns and incubated with 0.1% glucose and 10 µM thiamine-hydrochloride (90 µL.min-1 to compare weathering with and without biofilms. Dissolution of the minerals was followed by: analysing (i the degradation products in the effluent from the columns via Inductively Coupled Plasma Spectroscopy and (ii by studying polished sections of the incubated mineral fragment/grains using scanning electron microscopy, transmission electron microscopy and energy dispersive X-ray analyses. K. petricola/N. punctiforme stimulated release of Ca, Na, Mg and Mn. Analyses of the polished sections confirmed depletion of Ca, Na and K near the surface of the fragments. The abrupt decrease in Ca concentration observed in peripheral areas of plagioclase fragments favoured a dissolution-reprecipitation mechanism. Percolation columns in combination with a model biofilm can thus be used to study weathering in closed systems. Columns can easily be filled with different minerals and biofilms, the effluent as well as grains can be collected after long-term exposure under axenic conditions and easily analysed.

  14. Laboratory tools to quantify biogenic dissolution of rocks and minerals: a model rock biofilm growing in percolation columns

    Science.gov (United States)

    Seiffert, Franz; Bandow, Nicole; Kalbe, Ute; Milke, Ralf; Gorbushina, Anna

    2016-04-01

    Sub-aerial biofilms (SAB) are ubiquitous, self-sufficient microbial ecosystems found on mineral surfaces at all altitudes and latitudes. SABs, which are the principal causes of weathering on exposed terrestrial surfaces, are characterised by patchy growth dominated by associations of algae, cyanobacteria, fungi and heterotrophic bacteria. A recently developed in vitro system to study colonisation of rocks exposed to air included two key SAB participants - the rock-inhabiting ascomycete Knufia petricola (CBS 123872) and the phototrophic cyanobacterium Nostoc punctiforme ATCC29133. Both partners are genetically tractable and we used them here to study weathering of granite, K-feldspar and plagioclase. Small fragments of the various rocks or minerals (1 to 6 mm) were packed into flow-through columns and incubated with 0.1% glucose and 10 µM thiamine-hydrochloride (90 µL.min-1) to compare weathering with and without biofilms. Dissolution of the minerals was followed by: analysing (i) the degradation products in the effluent from the columns via Inductively Coupled Plasma Spectroscopy and (ii) by studying polished sections of the incubated mineral fragment/grains using scanning electron microscopy, transmission electron microscopy and energy dispersive X-ray analyses. K. petricola/N. punctiforme stimulated release of Ca, Na, Mg and Mn. Analyses of the polished sections confirmed depletion of Ca, Na and K near the surface of the fragments. The abrupt decrease in Ca concentration observed in peripheral areas of plagioclase fragments favoured a dissolution-reprecipitation mechanism. Percolation columns in combination with a model biofilm can thus be used to study weathering in closed systems. Columns can easily be filled with different minerals and biofilms, the effluent as well as grains can be collected after long-term exposure under axenic conditions and easily analysed.

  15. Large animal models of rare genetic disorders: sheep as phenotypically relevant models of human genetic disease.

    Science.gov (United States)

    Pinnapureddy, Ashish R; Stayner, Cherie; McEwan, John; Baddeley, Olivia; Forman, John; Eccles, Michael R

    2015-09-02

    Animals that accurately model human disease are invaluable in medical research, allowing a critical understanding of disease mechanisms, and the opportunity to evaluate the effect of therapeutic compounds in pre-clinical studies. Many types of animal models are used world-wide, with the most common being small laboratory animals, such as mice. However, rodents often do not faithfully replicate human disease, despite their predominant use in research. This discordancy is due in part to physiological differences, such as body size and longevity. In contrast, large animal models, including sheep, provide an alternative to mice for biomedical research due to their greater physiological parallels with humans. Completion of the full genome sequences of many species, and the advent of Next Generation Sequencing (NGS) technologies, means it is now feasible to screen large populations of domesticated animals for genetic variants that resemble human genetic diseases, and generate models that more accurately model rare human pathologies. In this review, we discuss the notion of using sheep as large animal models, and their advantages in modelling human genetic disease. We exemplify several existing naturally occurring ovine variants in genes that are orthologous to human disease genes, such as the Cln6 sheep model for Batten disease. These, and other sheep models, have contributed significantly to our understanding of the relevant human disease process, in addition to providing opportunities to trial new therapies in animals with similar body and organ size to humans. Therefore sheep are a significant species with respect to the modelling of rare genetic human disease, which we summarize in this review.

  16. Warehouse Optimization Model Based on Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Guofeng Qin

    2013-01-01

    Full Text Available This paper takes Bao Steel logistics automated warehouse system as an example. The premise is to maintain the focus of the shelf below half of the height of the shelf. As a result, the cost time of getting or putting goods on the shelf is reduced, and the distance of the same kind of goods is also reduced. Construct a multiobjective optimization model, using genetic algorithm to optimize problem. At last, we get a local optimal solution. Before optimization, the average cost time of getting or putting goods is 4.52996 s, and the average distance of the same kinds of goods is 2.35318 m. After optimization, the average cost time is 4.28859 s, and the average distance is 1.97366 m. After analysis, we can draw the conclusion that this model can improve the efficiency of cargo storage.

  17. 3D visualization and quantification of bone and teeth mineralization for the study of osteo/dentinogenesis in mice models

    Science.gov (United States)

    Marchadier, A.; Vidal, C.; Ordureau, S.; Lédée, R.; Léger, C.; Young, M.; Goldberg, M.

    2011-03-01

    Research on bone and teeth mineralization in animal models is critical for understanding human pathologies. Genetically modified mice represent highly valuable models for the study of osteo/dentinogenesis defects and osteoporosis. Current investigations on mice dental and skeletal phenotype use destructive and time consuming methods such as histology and scanning microscopy. Micro-CT imaging is quicker and provides high resolution qualitative phenotypic description. However reliable quantification of mineralization processes in mouse bone and teeth are still lacking. We have established novel CT imaging-based software for accurate qualitative and quantitative analysis of mouse mandibular bone and molars. Data were obtained from mandibles of mice lacking the Fibromodulin gene which is involved in mineralization processes. Mandibles were imaged with a micro-CT originally devoted to industrial applications (Viscom, X8060 NDT). 3D advanced visualization was performed using the VoxBox software (UsefulProgress) with ray casting algorithms. Comparison between control and defective mice mandibles was made by applying the same transfer function for each 3D data, thus allowing to detect shape, colour and density discrepencies. The 2D images of transverse slices of mandible and teeth were similar and even more accurate than those obtained with scanning electron microscopy. Image processing of the molars allowed the 3D reconstruction of the pulp chamber, providing a unique tool for the quantitative evaluation of dentinogenesis. This new method is highly powerful for the study of oro-facial mineralizations defects in mice models, complementary and even competitive to current histological and scanning microscopy appoaches.

  18. A novel 3-D mineralized tumor model to study breast cancer bone metastasis.

    Directory of Open Access Journals (Sweden)

    Siddharth P Pathi

    Full Text Available BACKGROUND: Metastatic bone disease is a frequent cause of morbidity in patients with advanced breast cancer, but the role of the bone mineral hydroxyapatite (HA in this process remains unclear. We have developed a novel mineralized 3-D tumor model and have employed this culture system to systematically investigate the pro-metastatic role of HA under physiologically relevant conditions in vitro. METHODOLOGY/PRINCIPAL FINDINGS: MDA-MB231 breast cancer cells were cultured within non-mineralized or mineralized polymeric scaffolds fabricated by a gas foaming-particulate leaching technique. Tumor cell adhesion, proliferation, and secretion of pro-osteoclastic interleukin-8 (IL-8 was increased in mineralized tumor models as compared to non-mineralized tumor models, and IL-8 secretion was more pronounced for bone-specific MDA-MB231 subpopulations relative to lung-specific breast cancer cells. These differences were pathologically significant as conditioned media collected from mineralized tumor models promoted osteoclastogenesis in an IL-8 dependent manner. Finally, drug testing and signaling studies with transforming growth factor beta (TGFbeta confirmed the clinical relevance of our culture system and revealed that breast cancer cell behavior is broadly affected by HA. CONCLUSIONS/SIGNIFICANCE: Our results indicate that HA promotes features associated with the neoplastic and metastatic growth of breast carcinoma cells in bone and that IL-8 may play an important role in this process. The developed mineralized tumor models may help to reveal the underlying cellular and molecular mechanisms that may ultimately enable more efficacious therapy of patients with advanced breast cancer.

  19. Genetic relationship between silver-lead-zinc mineralization in the Wutong deposit, Guangxi Province and Mesozoic granitic magmatism in the Nanling belt, southeast China

    Science.gov (United States)

    Lecumberri-Sanchez, Pilar; Romer, Rolf L.; Lüders, Volker; Bodnar, Robert J.

    2014-03-01

    More than 50 % of the world's total reserves of tungsten are in China and most tungsten deposits are located in the Nanling range in southeast China. This study explores the potential genetic relationship between tungsten-tin (W-Sn) mineralization and shallower Ag-Pb-Zn deposits in the Nanling range based on data from the Wutong deposit, Guangxi Province. The lead, oxygen, carbon, sulfur, and strontium isotopic compositions of minerals at Wutong indicate that a single crustal-derived fluid was responsible for mineralization. Wutong likely formed at relatively low temperatures (˜200-300 °C) and low pressures, as indicated by the similarity between homogenization temperatures of fluid inclusions and those estimated from S isotopic compositions of minerals. The hübnerite age (92.3-104.4 Ma) indicates that the Wutong mineralization is likely related to nearby Late Yanshanian (Cretaceous) S-type granites derived from Proterozoic crust. This mineralization event coincides with the last W-Sn mineralization event and the Cretaceous peak of mineralization in the Nanling range.

  20. Research and application of mineral resources assessment by weights of evidence model based on SIG

    Institute of Scientific and Technical Information of China (English)

    Yuanyuan Chuai; Keyan Xiao; Yihua Xuan; Shaobin Zhan

    2006-01-01

    Geological data are usually of the characteristics of multi-source, large amount and multi-scale. The construction of Spatial Information Grid overcomes the shortages of personal computers when dealing with geological data. The authors introduce the definition, architecture and flow of mineral resources assessment by weights of evidence model based on Spatial Information Grid (SIG). Meanwhile, a case study on the prediction of copper mineral occurrence in the Middle-Lower Yangtze metallogenic belt is given. The results show that mineral resources assessement based on SIG is an effective new method which provides a way of sharing and integrating distributed geospatial information and improves the efficiency greatly.

  1. Molecular statics calculations for iron oxide and oxyhydroxide minerals: Toward a flexible model of the reactive mineral-water interface

    Science.gov (United States)

    Rustad, James R.; Felmy, Andrew R.; Hay, Benjamin P.

    1996-05-01

    Molecular statics calculations are used to model the major FeOOH polymorphs and hematite. The potentials were taken from a previous investigation of Fe(III) in aqueous solutions which involved the extrapolation of the gas-phase Fe(III)-OH 2 potential energy surface to the solvated hexaaqua complex. Using this model for the solid phases, lattice parameters for goethite, akaganeite, lepidocrocite, and hematite are generally within 4% of experiment. Internal energies (at 0 K) were computed for each structure; lepidocrocite is energetically the most stable polymorph, followed by akaganeite, with goethite being the least stable. While the model exhibits some variances with experiment, it performs remarkably well, despite the challenging constraint of being consistent with a dissociating molecular dynamics model for water in its gas, aqueous, and solid phases. Because of this consistency, the model allows qualitative theoretical treatment of previously unapproachable problems in mineral-water interface geochemistry. We apply the model to identify surface species on the solvated (110) surface of goethite.

  2. Genetic spectrum assignment model with constraints in cognitive radio networks

    Directory of Open Access Journals (Sweden)

    Fang Ye

    2011-06-01

    Full Text Available The interference constraints of genetic spectrum assignment model in cognitive radio networks are analyzed in this paper. An improved genetic spectrum assignment model is proposed. The population of genetic algorithm is divided into two sets, the feasible spectrum assignment strategies and the randomly updated spectrum assignment strategies. The penalty function is added to the utility function to achieve the spectrum assignment strategy that satisfies the interference constraints and has better fitness. The proposed method is applicable in both the genetic spectrum assignment model and the quantum genetic spectrum assignment mode. It can ensure the randomness of partial chromosomes in the population to some extent, and reduce the computational complexity caused by the constraints-free procedure after the update of population. Simulation results show that the proposed method can achieve better performance than the conventional genetic spectrum assignment model and quantum genetic spectrum assignment model

  3. Mineral-deposit model for lithium-cesium-tantalum pegmatites

    Science.gov (United States)

    Bradley, Dwight C.; McCauley, Andrew D.; Stillings, Lisa M.

    2017-06-20

    Lithium-cesium-tantalum (LCT) pegmatites comprise a compositionally defined subset of granitic pegmatites. The major minerals are quartz, potassium feldspar, albite, and muscovite; typical accessory minerals include biotite, garnet, tourmaline, and apatite. The principal lithium ore minerals are spodumene, petalite, and lepidolite; cesium mostly comes from pollucite; and tantalum mostly comes from columbite-tantalite. Tin ore as cassiterite and beryllium ore as beryl also occur in LCT pegmatites, as do a number of gemstones and high-value museum specimens of rare minerals. Individual crystals in LCT pegmatites can be enormous: the largest spodumene was 14 meters long, the largest beryl was 18 meters long, and the largest potassium feldspar was 49 meters long.Lithium-cesium-tantalum pegmatites account for about one-fourth of the world’s lithium production, most of the tantalum production, and all of the cesium production. Giant deposits include Tanco in Canada, Greenbushes in Australia, and Bikita in Zimbabwe. The largest lithium pegmatite in the United States, at King’s Mountain, North Carolina, is no longer being mined although large reserves of lithium remain. Depending on size and attitude of the pegmatite, a variety of mining techniques are used, including artisanal surface mining, open-pit surface mining, small underground workings, and large underground operations using room-and-pillar design. In favorable circumstances, what would otherwise be gangue minerals (quartz, potassium feldspar, albite, and muscovite) can be mined along with lithium and (or) tantalum as coproducts.Most LCT pegmatites are hosted in metamorphosed supracrustal rocks in the upper greenschist to lower amphibolite facies. Lithium-cesium-tantalum pegmatite intrusions generally are emplaced late during orogeny, with emplacement being controlled by pre-existing structures. Typically, they crop out near evolved, peraluminous granites and leucogranites from which they are inferred to be

  4. Predictive GIS Model for Potential Mapping of Cu, Pb, Zn Mineralization

    Institute of Scientific and Technical Information of China (English)

    Tarik. B. Benomar; BIAN Fuling

    2006-01-01

    The geologic features indicative of Cu, Pb, Zn mineral deposits in a area are fractures (structure), and host rock sediments. Datasets used include Cu, Pb, Zn deposit points record, geological data, remote sensing imagery (Landsat TM5). The mineral potential of the study area is assessed by means of GIS based geodata integration techniques for generating predictive maps. GIS predictive model for Cu, Pb, Zn potential was carried out in this study area (Weixi) using weight of evidence. The weights of evidence modeling techniques is the data driven method in which the spatial associations of the indicative geologic features with the known mineral occurrences in the area are quantified, and weights statistically assigned to the geologic features. The best predictive map generated by this method defines 24% the area having potential for Cu, Pb, Zn mineralization further exploration work.

  5. Finite element 3D modeling of mechanical behavior of mineralized collagen microfibrils

    CERN Document Server

    Barkaoui, Abdelwahed

    2011-01-01

    The aim of this work is to develop a 3D finite elements model to study the nanomechanical behaviour of mineralized collagen microfibrils, which consists of three phases, (i) collagen phase formed by five tropocollagen (TC) molecules linked together with cross links, (ii) a mineral phase (Hydroxyapatite) and (iii) impure mineral phase, and to investigate the important role of individual properties of every constituent. The mechanical and the geometrical properties (TC molecule diameter) of both tropocollagen and mineral were taken into consideration as well as cross-links, which was represented by spring elements with adjusted properties based on experimental data. In the present paper an equivalent homogenised model was developed to assess the whole microfibril mechanical properties (Young's modulus and Poisson's ratio) under varying mechanical properties of each phase. In this study both equivalent Young's modulus and Poisson's ratio which were expressed as functions of Young's modulus of each phase were obt...

  6. Development of models for predicting carbon mineralization and associated phytotoxicity in compost-amended soil.

    Science.gov (United States)

    Aslam, Danielle N; Vandergheynst, Jean S; Rumsey, Thomas R

    2008-12-01

    Phytotoxicity of compost-amended soil is related to carbon mineralization associated with compost decomposition. The objective of this research was to determine if compost carbon mineralization potential, estimated using compost respiration rate measurements, could be combined with carbon mineralization kinetic models to predict phytotoxicity of compost-amended soil. First-order, second-order, and Monod kinetic models that include compost carbon mineralization potential, compost amendment rate, incubation time, and temperature were developed and compared for their ability to predict carbon mineralization kinetics. Experiments utilized two soil types amended with 0%, 5%, and 50% (v/v) food waste and green waste composts, incubated at 20 degrees C, 25 degrees C, 30 degrees C, 35 degrees C, and 45 degrees C for model development and under a diurnal temperature cycle from 20 degrees C to 30 degrees C for model validation. For most cases, a first-order model had an equivalent or better fit to the data than the other models. Mineralizable carbon estimated using the first-order model was significantly correlated to the probability of phytotoxicity in compost-amended soil.

  7. Implications of carbon saturation model structure for simulated nitrogen mineralization dynamics

    Directory of Open Access Journals (Sweden)

    C. M. White

    2014-06-01

    Full Text Available Carbon (C saturation theory suggests that soils have a~limited capacity to stabilize organic C and that this capacity may be regulated by intrinsic soil properties such as clay content and mineralogy. While C saturation theory has advanced our ability to predict soil C stabilization, we only have a weak understanding of how C saturation affects N cycling. In biogeochemical models, C and N cycling are tightly coupled, with C decomposition and respiration driving N mineralization. Thus, changing model structures from non-saturation to C saturation dynamics can change simulated N dynamics. Carbon saturation models proposed in the literature calculate a theoretical maximum C storage capacity of saturating pools based on intrinsic soil properties, such as clay content. The extent to which current C stocks fill the storage capacity of the pool is termed the C saturation ratio, and this ratio is used to regulate either the efficiency or the rate of C transfer from donor to receiving pools. In this study, we evaluated how the method of implementing C saturation and the number of pools in a model affected net N mineralization from decomposing plant residues. In models that use the C saturation ratio to regulate transfer efficiency, C saturation affected N mineralization, while in those in which the C saturation ratio regulates transfer rates, N mineralization was independent of C saturation. When C saturation ratio regulates transfer efficiency, as the saturation ratio increases, the threshold C : N ratio at which positive net N mineralization occurs also increases because more of the C in the residue is respired. In a single-pool model where C saturation ratio regulated the transfer efficiency, predictions of N mineralization from residue inputs were unrealistically high, missing the cycle of N immobilization and mineralization typically seen after the addition of high C : N inputs to soils. A more realistic simulation of N mineralization was achieved

  8. Fuzzy model of the computer integrated decision support and management system in mineral processing

    OpenAIRE

    Miljanović Igor; Vujić Slobodan

    2008-01-01

    During the research on the subject of computer integrated systems for decision making and management support in mineral processing based on fuzzy logic, realized at the Department of Applied Computing and System Engineering of the Faculty of Mining and Geology, University of Belgrade, for the needs of doctoral thesis of the first author, and wider demands of the mineral industry, the incompleteness of the developed and contemporary computer integrated systems fuzzy models was noticed. The pap...

  9. Genetic parameters for milk mineral content and acidity predicted by mid-infrared spectroscopy in Holstein-Friesian cows.

    Science.gov (United States)

    Toffanin, V; Penasa, M; McParland, S; Berry, D P; Cassandro, M; De Marchi, M

    2015-05-01

    The aim of the present study was to estimate genetic parameters for calcium (Ca), phosphorus (P) and titratable acidity (TA) in bovine milk predicted by mid-IR spectroscopy (MIRS). Data consisted of 2458 Italian Holstein-Friesian cows sampled once in 220 farms. Information per sample on protein and fat percentage, pH and somatic cell count, as well as test-day milk yield, was also available. (Co)variance components were estimated using univariate and bivariate animal linear mixed models. Fixed effects considered in the analyses were herd of sampling, parity, lactation stage and a two-way interaction between parity and lactation stage; an additive genetic and residual term were included in the models as random effects. Estimates of heritability for Ca, P and TA were 0.10, 0.12 and 0.26, respectively. Positive moderate to strong phenotypic correlations (0.33 to 0.82) existed between Ca, P and TA, whereas phenotypic weak to moderate correlations (0.00 to 0.45) existed between these traits with both milk quality and yield. Moderate to strong genetic correlations (0.28 to 0.92) existed between Ca, P and TA, and between these predicted traits with both fat and protein percentage (0.35 to 0.91). The existence of heritable genetic variation for Ca, P and TA, coupled with the potential to predict these components for routine cow milk testing, imply that genetic gain in these traits is indeed possible.

  10. Model comparisons and genetic and environmental parameter ...

    African Journals Online (AJOL)

    arc

    South African Journal of Animal Science 2005, 35 (1) ... Genetic and environmental parameters were estimated for pre- and post-weaning average daily gain ..... and BWT (and medium maternal genetic correlations) indicates that these traits ...

  11. Modelling the mechanics of partially mineralized collagen fibrils, fibres and tissue.

    Science.gov (United States)

    Liu, Yanxin; Thomopoulos, Stavros; Chen, Changqing; Birman, Victor; Buehler, Markus J; Genin, Guy M

    2014-03-01

    Progressive stiffening of collagen tissue by bioapatite mineral is important physiologically, but the details of this stiffening are uncertain. Unresolved questions about the details of the accommodation of bioapatite within and upon collagen's hierarchical structure have posed a central hurdle, but recent microscopy data resolve several major questions. These data suggest how collagen accommodates bioapatite at the lowest relevant hierarchical level (collagen fibrils), and suggest several possibilities for the progressive accommodation of bioapatite at higher hierarchical length scales (fibres and tissue). We developed approximations for the stiffening of collagen across spatial hierarchies based upon these data, and connected models across hierarchies levels to estimate mineralization-dependent tissue-level mechanics. In the five possible sequences of mineralization studied, percolation of the bioapatite phase proved to be an important determinant of the degree of stiffening by bioapatite. The models were applied to study one important instance of partially mineralized tissue, which occurs at the attachment of tendon to bone. All sequences of mineralization considered reproduced experimental observations of a region of tissue between tendon and bone that is more compliant than either tendon or bone, but the size and nature of this region depended strongly upon the sequence of mineralization. These models and observations have implications for engineered tissue scaffolds at the attachment of tendon to bone, bone development and graded biomimetic attachment of dissimilar hierarchical materials in general.

  12. Genetic Algorithm Approaches to Prebiobiotic Chemistry Modeling

    Science.gov (United States)

    Lohn, Jason; Colombano, Silvano

    1997-01-01

    We model an artificial chemistry comprised of interacting polymers by specifying two initial conditions: a distribution of polymers and a fixed set of reversible catalytic reactions. A genetic algorithm is used to find a set of reactions that exhibit a desired dynamical behavior. Such a technique is useful because it allows an investigator to determine whether a specific pattern of dynamics can be produced, and if it can, the reaction network found can be then analyzed. We present our results in the context of studying simplified chemical dynamics in theorized protocells - hypothesized precursors of the first living organisms. Our results show that given a small sample of plausible protocell reaction dynamics, catalytic reaction sets can be found. We present cases where this is not possible and also analyze the evolved reaction sets.

  13. Bio-mineralization and potential biogeochemical processes in bauxite deposits: genetic and ore quality significance

    Science.gov (United States)

    Laskou, Magdalini; Economou-Eliopoulos, Maria

    2013-08-01

    The Parnassos-Ghiona bauxite deposit in Greece of karst type is the 11th largest bauxite producer in the world. The mineralogical, major and trace-element contents and δ18O, δ12C, δ34S isotopic compositions of bauxite ores from this deposit and associated limestone provide valuable evidence for their origin and biogeochemical processes resulting in the beneficiation of low grade bauxite ores. The organic matter as thin coal layers, overlying the bauxite deposits, within limestone itself (negative δ12C isotopic values) and the negative δ34S values in sulfides within bauxite ores point to the existence of the appropriate circumstances for Fe bio-leaching and bio-mineralization. Furthermore, a consortium of microorganisms of varying morphological forms (filament-like and spherical to lenticular at an average size of 2 μm), either as fossils or presently living and producing enzymes, is a powerful factor to catalyze the redox reactions, expedite the rates of metal extraction and provide alternative pathways for metal leaching processes resulting in the beneficiation of bauxite ore.

  14. Genetic models of poljes in Sicily

    Science.gov (United States)

    Di Maggio, Cipriano; Madonia, Giuliana; Vattano, Marco; De Waele, Jo

    2016-04-01

    Geomorphological and geological studies have been carried out to contribute to the recognition of controlling causes and to the definition of genetic models for poljes of Sicily. A polje is a kilometric closed depression developed mainly on karst rocks, with a conspicuously flat and alluviated bottom affected by intermittent flooding. A polje is usually characterised by relatively steep slopes enclosing an almost perfectly horizontal floor, caused by lateral solution planation related to flooding events. The origin of a polje is due to dissolution of the land surface, although geological structure generally influences its genesis. These large depressions are often elongated according to the direction of main faults, in consequence of a control due to tectonics or to differential erosion. The performed researches have shown the existence of at least seven poljes located along the north-western (chain zone) and the southern (deformed foredeep zone) areas of Sicily. These large karst depressions are developed on Mesozoic limestone/dolomitic rocks within the chain zone and on Messinian gypsum rocks within the deformed foredeep zone. They are up to 4 km in length, can reach surfaces of 3-8 km2 and are around hundred metres deep, with steep slopes and a flat bottom. Generally, they are open, occasionally active depressions and their genesis seems to be strongly controlled by structure. In particular, the studied poljes occur in two different geological/geomorphological settings: a) in graben-like tectonic depressions, where important fault slopes/scarps border the flat bottom; b) in complex depressions controlled by structure, where wide fault line slopes/scarps or large inclined degraded structural surfaces mark the poljes. Finally, landscape analysis leads to the proposition of two main genetic models in which the development of poljes is primarily due to tectonics or differential erosion followed by dissolution.

  15. Genetic screens in Caenorhabditis elegans models for neurodegenerative diseases

    NARCIS (Netherlands)

    Alvarenga Fernandes Sin, Olga; Michels, Helen; Nollen, Ellen A. A.

    2014-01-01

    Caenorhabditis elegans comprises unique features that make it an attractive model organism in diverse fields of biology. Genetic screens are powerful to identify genes and C. elegans can be customized to forward or reverse genetic screens and to establish gene function. These genetic screens can be

  16. Genetic screens in Caenorhabditis elegans models for neurodegenerative diseases

    NARCIS (Netherlands)

    Alvarenga Fernandes Sin, Olga; Michels, Helen; Nollen, Ellen A. A.

    2014-01-01

    Caenorhabditis elegans comprises unique features that make it an attractive model organism in diverse fields of biology. Genetic screens are powerful to identify genes and C. elegans can be customized to forward or reverse genetic screens and to establish gene function. These genetic screens can be

  17. Research on Modeling of Genetic Networks Based on Information Measurement

    Institute of Scientific and Technical Information of China (English)

    ZHANG Guo-wei; SHAO Shi-huang; ZHANG Ying; LI Hai-ying

    2006-01-01

    As the basis of network of biology organism, the genetic network is concerned by many researchers.Current modeling methods to genetic network, especially the Boolean networks modeling method are analyzed. For modeling the genetic network, the information theory is proposed to mining the relations between elements in network. Through calculating the values of information entropy and mutual entropy in a case, the effectiveness of the method is verified.

  18. Mineral distribution in rat skeletons after exposure to a microgravity model

    Science.gov (United States)

    Arnaud, Sara B.; Harper, Jennifer S.; Navidi, Meena

    1995-01-01

    Exposure to space flight models induces changes in the distribution of bone mineral in the human skeleton that has the features of a gravitational gradient. Regional bone mineral measurements with dual energy x-ray absorptiometry (DEXA) in male adults exposed to head-down tilt bed rest for 30 days shown non-significant decrements in the pelvis and legs with 10% increases in the head region. Horizontal bed rest for 17 weeks reveals losses of bone mineral ranging from 2.2 to 10.4% from the lumbar spine to the calcaneus and an increase of 3.4% in the skull. Investigation of this phenomena would be most definitively carried out in an animal model. One candidate is the flight simulation model in the rat which removes body weight from the hind limbs and induces a cephalad fluid shift by suspending the animal by the tail. Weanling rats exposed to this model showed bone mineral to be lower in the hind limbs and higher in the skull after 3 weeks. These finds are similar in older 200 g animals after 2 weeks tail suspension. The purpose of this study was to determine the effect of age on the distribution of skeletal mineral in this model.

  19. Selected Geochemical Data for Modeling Near-Surface Processes in Mineral Systems

    Science.gov (United States)

    Giles, Stuart A.; Granitto, Matthew; Eppinger, Robert G.

    2009-01-01

    The database herein was initiated, designed, and populated to collect and integrate geochemical, geologic, and mineral deposit data in an organized manner to facilitate geoenvironmental mineral deposit modeling. The Microsoft Access database contains data on a variety of mineral deposit types that have variable environmental effects when exposed at the ground surface by mining or natural processes. The data tables describe quantitative and qualitative geochemical analyses determined by 134 analytical laboratory and field methods for over 11,000 heavy-mineral concentrate, rock, sediment, soil, vegetation, and water samples. The database also provides geographic information on geology, climate, ecoregion, and site contamination levels for over 3,000 field sites in North America.

  20. Fuzzy model of the computer integrated decision support and management system in mineral processing

    Directory of Open Access Journals (Sweden)

    Miljanović Igor

    2008-01-01

    Full Text Available During the research on the subject of computer integrated systems for decision making and management support in mineral processing based on fuzzy logic, realized at the Department of Applied Computing and System Engineering of the Faculty of Mining and Geology, University of Belgrade, for the needs of doctoral thesis of the first author, and wider demands of the mineral industry, the incompleteness of the developed and contemporary computer integrated systems fuzzy models was noticed. The paper presents an original model with the seven staged hierarchical monitoring-management structure, in which the shortcomings of the models utilized today were eliminated.

  1. Modeling gas formation and mineral precipitation in a granular iron column.

    Science.gov (United States)

    Jeen, Sung-Wook; Amos, Richard T; Blowes, David W

    2012-06-19

    In granular iron permeable reactive barriers (PRBs), hydrogen gas formation, entrapment and release of gas bubbles, and secondary mineral precipitation have been known to affect the permeability and reactivity. The multicomponent reactive transport model MIN3P was enhanced to couple gas formation and release, secondary mineral precipitation, and the effects of these processes on hydraulic properties and iron reactivity. The enhanced model was applied to a granular iron column, which was studied for the treatment of trichloroethene (TCE) in the presence of dissolved CaCO(3). The simulation reasonably reproduced trends in gas formation, secondary mineral precipitation, permeability changes, and reactivity changes observed over time. The simulation showed that the accumulation of secondary minerals reduced the reactivity of the granular iron over time, which in turn decreased the rate of mineral accumulation, and also resulted in a gradual decrease in gas formation over time. This study provides a quantitative assessment of the evolving nature of geochemistry and permeability, resulting from coupled processes of gas formation and mineral precipitation, which leads to a better understanding of the processes controlling the granular iron reactivity, and represents an improved method for incorporating these factors into the design of granular iron PRBs.

  2. Chromite Composition and Accessory Minerals in Chromitites from Sulawesi, Indonesia: Their Genetic Significance

    Directory of Open Access Journals (Sweden)

    Federica Zaccarini

    2016-05-01

    Full Text Available Several chromite deposits located in the in the South and Southeast Arms of Sulawesi, Indonesia, have been investigated by electron microprobe. According to the variation of the Cr# = Cr/(Cr + Fe3+, the chromite composition varies from Cr-rich to Al-rich. Small platinum-group minerals (PGM, 1–10 μm in size, occur in the chromitites. The most abundant PGM is laurite, which has been found included in fresh chromite or in contact with chlorite along cracks in the chromite. Laurite forms polygonal crystals, and it occurs as a single phase or in association with amphibole, chlorite, Co-pentlandite and apatite. Small blebs of irarsite (less than 2 μm across have been found associated with grains of awaruite and Co-pentlandite in the chlorite gangue of the chromitites. Grains of olivine, occurring in the silicate matrix or included in fresh chromite, have been analyzed. They show a composition typical of mantle-hosted olivine. The bimodal composition and the slight enrichment in TiO2 observed in some chromitites suggest a vertical zonation due to the fractionation of a single batch magma with an initial boninitic composition during its ascent, in a supra-subduction zone. This observation implies the accumulation of Cr-rich chromitites at deep mantle levels and the formation of the Al-rich chromitites close or above the Moho-transition zone. All of the laurites are considered to be magmatic in origin, i.e., entrapped as solid phases during the crystallization of chromite at temperature of around 1200 °C and a sulfur fugacity below the sulfur saturation. Irarsite possibly represents a low temperature, less than 400 °C, exsolution product.

  3. Relationship between obesity phenotypes and genetic determinants in a mouse model for juvenile obesity.

    Science.gov (United States)

    Brockmann, Gudrun A; Schäfer, Nadine; Hesse, Claudia; Heise, Sebastian; Neuschl, Christina; Wagener, Asja; Churchill, Gary A; Li, Renhua

    2013-09-16

    Obesity, a state of imbalance between lean mass and fat mass, is important for the etiology of diseases affected by the interplay of multiple genetic and environmental factors. Although genome-wide association studies have repeatedly associated genes with obesity and body weight, the mechanisms underlying the interaction between the muscle and adipose tissues remain unknown. Using 351 mice (at 10 wk of age) of an intercross population between Berlin Fat Mouse Inbred (BFMI) and C57BL/6NCrl (B6N) mice, we examined the causal relationships between genetic variations and multiple traits: body lean mass and fat mass, adipokines, and bone mineral density. Furthermore, evidence from structural equation modeling suggests causality among these traits. In the BFMI model, juvenile obesity affects lean mass and impairs bone mineral density via adipokines secreted from the white adipose tissues. While previous studies have indicated that lean mass has a causative effect on adiposity, in the Berlin Fat Mouse model that has been selected for juvenile obesity (at 9 wk of age) for >90 generations, however, the causality is switched from fat mass to lean mass. In addition, linkage studies and statistical modeling have indicated that quantitative trait loci on chromosomes 5 and 6 affect both lean mass and fat mass. These lines of evidence indicate that the muscle and adipose tissues interact with one another and the interaction is modulated by genetic variations that are shaped by selections. Experimental examinations are necessary to verify the biological role of the inferred causalities.

  4. Quantitative models of hydrothermal fluid-mineral reaction: The Ischia case

    Science.gov (United States)

    Di Napoli, Rossella; Federico, Cinzia; Aiuppa, Alessandro; D'Antonio, Massimo; Valenza, Mariano

    2013-03-01

    The intricate pathways of fluid-mineral reactions occurring underneath active hydrothermal systems are explored in this study by applying reaction path modelling to the Ischia case study. Ischia Island, in Southern Italy, hosts a well-developed and structurally complex hydrothermal system which, because of its heterogeneity in chemical and physical properties, is an ideal test sites for evaluating potentialities/limitations of quantitative geochemical models of hydrothermal reactions. We used the EQ3/6 software package, version 7.2b, to model reaction of infiltrating waters (mixtures of meteoric water and seawater in variable proportions) with Ischia's reservoir rocks (the Mount Epomeo Green Tuff units; MEGT). The mineral assemblage and composition of such MEGT units were initially characterised by ad hoc designed optical microscopy and electron microprobe analysis, showing that phenocrysts (dominantly alkali-feldspars and plagioclase) are set in a pervasively altered (with abundant clay minerals and zeolites) groundmass. Reaction of infiltrating waters with MEGT minerals was simulated over a range of realistic (for Ischia) temperatures (95-260 °C) and CO2 fugacities (10-0.2 to 100.5) bar. During the model runs, a set of secondary minerals (selected based on independent information from alteration minerals' studies) was allowed to precipitate from model solutions, when saturation was achieved. The compositional evolution of model solutions obtained in the 95-260 °C runs were finally compared with compositions of Ischia's thermal groundwaters, demonstrating an overall agreement. Our simulations, in particular, well reproduce the Mg-depleting maturation path of hydrothermal solutions, and have end-of-run model solutions whose Na-K-Mg compositions well reflect attainment of full-equilibrium conditions at run temperature. High-temperature (180-260 °C) model runs are those best matching the Na-K-Mg compositions of Ischia's most chemically mature water samples

  5. Response Of Mineralizing And Non-Mineralizing Bone Cells To Fluid Flow: An In Vitro Model For Mechanotransruction

    Science.gov (United States)

    Makuch, Lauren A.

    2004-01-01

    Humans reach peak bone mass at age 30. After this point, we lose 1 to 2 percent of bone mass each decade. In the microgravity environment of space, astronauts lose bone mass at an accelerated rate of 1 to 2 percent each month. When astronauts travel to Mars, they may be in space for as long as 3 years. During this time, they may lose about half of their bone mass from weight-bearing bones. This loss may be irreversible. The drastic loss in bone that astronauts experience in space makes them much more vulnerable to fractures. In addition, the corresponding removal of calcium from bone results in higher levels of calcium in the blood, which increases the risk of developing kidney stones. Currently, studies are being conducted which investigate factors governing bone adaptation and mechanotransduction. Bone is constantly adapting in response to mechanical stimuli. Increased mechanical loading stimulates bone formation and suppresses bone resorption. Reduction in mechanical loading caused by bedrest, disuse, or microgravity results in decreased bone formation and possibly increased bone resorption. Osteoblasts and osteoclasts are the two main cell types that participate in bone remodeling. Osteoblasts are anabolic (bone-forming) cells and osteoclasts are catabolic (bone-resorbing) cells. In microgravity, the activity of osteoblasts slows down and the activity of osteoclasts may speed up, causing a loss of bone density. Mechanotransduction, the molecular mechanism by which mechanical stimuli are converted to biochemical signals, is not yet understood. Exposure of cells to fluid flow imposes a shear stress on the cells. Several studies have shown that the shear stress that results from fluid flow induces a cellular response similar to that induced by mechanical loading. Thus, fluid flow can be used as an in vitro model to simulate the mechanical stress that bone cells experience in vivo. Previous in vitro studies have shown that fluid flow induces several responses in

  6. 3D geological modeling for mineral resource assessment of the Tongshan Cu deposit, Heilongjiang Province, China

    Directory of Open Access Journals (Sweden)

    Gongwen Wang

    2012-07-01

    Full Text Available Three-dimensional geological modeling (3DGM assists geologists to quantitatively study in three-dimensional (3D space structures that define temporal and spatial relationships between geological objects. The 3D property model can also be used to infer or deduce causes of geological objects. 3DGM technology provides technical support for extraction of diverse geoscience information, 3D modeling, and quantitative calculation of mineral resources. Based on metallogenic concepts and an ore deposit model, 3DGM technology is applied to analyze geological characteristics of the Tongshan Cu deposit in order to define a metallogenic model and develop a virtual borehole technology; a BP neural network and a 3D interpolation technique were combined to integrate multiple geoscience information in a 3D environment. The results indicate: (1 on basis of the concept of magmatic-hydrothermal Cu polymetallic mineralization and a porphyry Cu deposit model, a spatial relational database of multiple geoscience information for mineralization in the study area (geology, geophysics, geochemistry, borehole, and cross-section data was established, and 3D metallogenic geological objects including mineralization stratum, granodiorite, alteration rock, and magnetic anomaly were constructed; (2 on basis of the 3D ore deposit model, 23,800 effective surveys from 94 boreholes and 21 sections were applied to establish 3D orebody models with a kriging interpolation method; (3 combined 23,800 surveys involving 21 sections, using VC++ and OpenGL platform, virtual borehole and virtual section with BP network, and an improved inverse distance interpolation (IDW method were used to predict and delineate mineralization potential targets (Cu-grade of cell not less than 0.1%; (4 comparison of 3D ore bodies, metallogenic geological objects of mineralization, and potential targets of mineralization models in the study area, delineated the 3D spatial and temporal relationship and causal

  7. Adsorption mechanisms of microcystin variant conformations at water-mineral interfaces: A molecular modeling investigation.

    Science.gov (United States)

    Pochodylo, Amy L; Aoki, Thalia G; Aristilde, Ludmilla

    2016-10-15

    Microcystins (MCs) are potent toxins released during cyanobacterial blooms. Clay minerals are implicated in trapping MCs within soil particles in surface waters and sediments. In the absence of molecular characterization, the relevance of previously proposed adsorption mechanisms is lacking. Towards obtaining this characterization, we conducted Monte Carlo simulations combined with molecular dynamics relaxation of two MC variants, MC-leucine-arginine (MC-LR) and MC-leucine-alanine (MC-LA), adsorbed on hydrated montmorillonite with different electrolytes. The resulting adsorbate structures revealed how MC conformations and aqueous conditions dictate binding interactions at the mineral surface. Electrostatic coupling between the arginine residue and a carboxylate in MC-LR excluded the participation of arginine in mediating adsorption on montmorillonite in a NaCl solution. However, in a CaCl2 solution, the complexation of Ca by two carboxylate moieties in MC-LR changed the MC conformation, which allowed arginine to mediate electrostatic interaction with the mineral. By contrast, due to the lack of arginine in MC-LA, complexation of Ca by only one carboxylate in MC-LA was required to favor Ca-bridging interaction with the mineral. Multiple water-bridged H-bonding interactions were also important in anchoring MCs at the mineral surface. Our modeling results offer molecular insights into the structural and chemical factors that can control the fate of MCs at water-mineral interfaces.

  8. Modeling of the mineral transformation during the combustion of coal; Modellierung der Mineralumwandlung bei der Kohleverbrennung

    Energy Technology Data Exchange (ETDEWEB)

    Strelow, M.; Magda, S.; Magda, A.; Mueller, H. [Technische Universitaet Braunschweig (Germany). Institut fuer Waerme- und Brennstofftechnik

    2009-07-01

    The employment of new materials in the construction of steam generators in order to increase the steam parameters requires a detailed knowledge of the processes of transformation of the coal minerals in the steam generator with respect to forecast the slagging and contamination of the materials. Analyses of the materials in the raw coal and their integration are the basis for the modelling of the transformation processes in CFD programs. The chemical and physical processes are the release and integration of alkaline compounds which have a strong influence on the formation of first contamination layers on the heating surfaces as well as the transformation of the minerals of ash particles on their flight paths by the steam generator. For fast reactions, the modelling of the mineral transformation is carried out by acceptance of a chemical equilibrium, otherwise by kinetic reaction approaches.

  9. An overview of mineral dust modeling over East Asia

    Science.gov (United States)

    Chen, Siyu; Huang, Jianping; Qian, Yun; Zhao, Chun; Kang, Litai; Yang, Ben; Wang, Yong; Liu, Yuzhi; Yuan, Tiangang; Wang, Tianhe; Ma, Xiaojun; Zhang, Guolong

    2017-08-01

    East Asian dust (EAD) exerts considerable impacts on the energy balance and climate/climate change of the earth system through its influence on solar and terrestrial radiation, cloud properties, and precipitation efficiency. Providing an accurate description of the life cycle and climate effects of EAD is therefore critical to better understanding of climate change and socioeconomic development in East Asia and even worldwide. Dust modeling has undergone substantial development since the late 1990s, associated with improved understanding of the role of EAD in the earth system. Here, we review the achievements and progress made in recent decades in terms of dust modeling research, including dust emissions, long-range transport, radiative forcing (RF), and climate effects of dust particles over East Asia. Numerous efforts in dust/EAD modeling have been directed towards furnishing more sophisticated physical and chemical processes into the models on higher spatial resolutions. Meanwhile, more systematic observations and more advanced retrieval methods for instruments that address EAD related science issues have made it possible to evaluate model results and quantify the role of EAD in the earth system, and to further reduce the uncertainties in EAD simulations. Though much progress has been made, large discrepancies and knowledge gaps still exist among EAD simulations. The deficiencies and limitations that pertain to the performance of the EAD simulations referred to in the present study are also discussed.

  10. Genetically modified mouse models addressing gonadotropin function.

    Science.gov (United States)

    Ratner, Laura D; Rulli, Susana B; Huhtaniemi, Ilpo T

    2014-03-01

    The development of genetically modified animals has been useful to understand the mechanisms involved in the regulation of the gonadotropin function. It is well known that alterations in the secretion of a single hormone is capable of producing profound reproductive abnormalities. Human chorionic gonadotropin (hCG) is a glycoprotein hormone normally secreted by the human placenta, and structurally and functionally it is related to pituitary LH. LH and hCG bind to the same LH/hCG receptor, and hCG is often used as an analog of LH to boost gonadotropin action. There are many physiological and pathological conditions where LH/hCG levels and actions are elevated. In order to understand how elevated LH/hCG levels may impact on the hypothalamic-pituitary-gonadal axis we have developed a transgenic mouse model with chronic hCG hypersecretion. Female mice develop many gonadal and extragonadal phenotypes including obesity, infertility, hyperprolactinemia, and pituitary and mammary gland tumors. This article summarizes recent findings on the mechanisms involved in pituitary gland tumorigenesis and hyperprolactinemia in the female mice hypersecreting hCG, in particular the relationship of progesterone with the hyperprolactinemic condition of the model. In addition, we describe the role of hyperprolactinemia as the main cause of infertility and the phenotypic abnormalities in these mice, and the use of dopamine agonists bromocriptine and cabergoline to normalize these conditions. Copyright © 2014 Society for Biology of Reproduction & the Institute of Animal Reproduction and Food Research of Polish Academy of Sciences in Olsztyn. Published by Elsevier Urban & Partner Sp. z o.o. All rights reserved.

  11. Genetic analysis identifies DDR2 as a novel gene affecting bone mineral density and osteoporotic fractures in Chinese population.

    Directory of Open Access Journals (Sweden)

    Yan Guo

    Full Text Available DDR2 gene, playing an essential role in regulating osteoblast differentiation and chondrocyte maturation, may influence bone mineral density (BMD and osteoporosis, but the genetic variations actually leading to the association remain to be elucidated. Therefore, the aim of this study was to investigate whether the genetic variants in DDR2 are associated with BMD and fracture risk. This study was performed in three samples from two ethnicities, including 1,300 Chinese Han subjects, 700 Chinese Han subjects (350 with osteoporotic hip fractures and 350 healthy controls and 2,286 US white subjects. Twenty-eight SNPs in DDR2 were genotyped and tested for associations with hip BMD and fractures. We identified 3 SNPs in DDR2 significantly associated with hip BMD in the Chinese population after multiple testing adjustments, which were rs7521233 (P = 1.06×10-4, β: -0.018 for allele C, rs7553831 (P = 1.30×10-4, β: -0.018 for allele T, and rs6697469 (P = 1.59×10-3, β: -0.015 for allele C, separately. These three SNPs were in high linkage disequilibrium. Haplotype analyses detected two significantly associated haplotypes, including one haplotype in block 2 (P = 9.54×10-4, β: -0.016 where these three SNPs located. SNP rs6697469 was also associated with hip fractures (P = 0.043, OR: 1.42 in the Chinese population. The effect on fracture risk was consistent with its association with lower BMD. However, in the white population, we didn't observe significant associations with hip BMD. eQTL analyses revealed that SNPs associated with BMD also affected DDR2 mRNA expression levels in Chinese. Our findings, together with the prior biological evidence, suggest that DDR2 could be a new candidate for osteoporosis in Chinese population. Our results also reveal an ethnic difference, which highlights the need for further genetic studies in each ethnic group.

  12. Genetic analysis identifies DDR2 as a novel gene affecting bone mineral density and osteoporotic fractures in Chinese population.

    Science.gov (United States)

    Guo, Yan; Yang, Tie-Lin; Dong, Shan-Shan; Yan, Han; Hao, Ruo-Han; Chen, Xiao-Feng; Chen, Jia-Bin; Tian, Qing; Li, Jian; Shen, Hui; Deng, Hong-Wen

    2015-01-01

    DDR2 gene, playing an essential role in regulating osteoblast differentiation and chondrocyte maturation, may influence bone mineral density (BMD) and osteoporosis, but the genetic variations actually leading to the association remain to be elucidated. Therefore, the aim of this study was to investigate whether the genetic variants in DDR2 are associated with BMD and fracture risk. This study was performed in three samples from two ethnicities, including 1,300 Chinese Han subjects, 700 Chinese Han subjects (350 with osteoporotic hip fractures and 350 healthy controls) and 2,286 US white subjects. Twenty-eight SNPs in DDR2 were genotyped and tested for associations with hip BMD and fractures. We identified 3 SNPs in DDR2 significantly associated with hip BMD in the Chinese population after multiple testing adjustments, which were rs7521233 (P = 1.06×10-4, β: -0.018 for allele C), rs7553831 (P = 1.30×10-4, β: -0.018 for allele T), and rs6697469 (P = 1.59×10-3, β: -0.015 for allele C), separately. These three SNPs were in high linkage disequilibrium. Haplotype analyses detected two significantly associated haplotypes, including one haplotype in block 2 (P = 9.54×10-4, β: -0.016) where these three SNPs located. SNP rs6697469 was also associated with hip fractures (P = 0.043, OR: 1.42) in the Chinese population. The effect on fracture risk was consistent with its association with lower BMD. However, in the white population, we didn't observe significant associations with hip BMD. eQTL analyses revealed that SNPs associated with BMD also affected DDR2 mRNA expression levels in Chinese. Our findings, together with the prior biological evidence, suggest that DDR2 could be a new candidate for osteoporosis in Chinese population. Our results also reveal an ethnic difference, which highlights the need for further genetic studies in each ethnic group.

  13. Genetic and Environmental Bases of Reading and Spelling: A Unified Genetic Dual Route Model

    Science.gov (United States)

    Bates, Timothy C.; Castles, Anne; Luciano, Michelle; Wright, Margaret J.; Coltheart, Max; Martin, Nicholas G.

    2007-01-01

    We develop and test a dual-route model of genetic effects on reading aloud and spelling, based on irregular and non-word reading and spelling performance assessed in 1382 monozygotic and dizygotic twins. As in earlier research, most of the variance in reading was due to genetic effects. However, there were three more specific conclusions: the…

  14. Functional-mixed effects models for candidate genetic mapping in imaging genetic studies.

    Science.gov (United States)

    Lin, Ja-An; Zhu, Hongtu; Mihye, Ahn; Sun, Wei; Ibrahim, Joseph G

    2014-12-01

    The aim of this paper is to develop a functional-mixed effects modeling (FMEM) framework for the joint analysis of high-dimensional imaging data in a large number of locations (called voxels) of a three-dimensional volume with a set of genetic markers and clinical covariates. Our FMEM is extremely useful for efficiently carrying out the candidate gene approaches in imaging genetic studies. FMEM consists of two novel components including a mixed effects model for modeling nonlinear genetic effects on imaging phenotypes by introducing the genetic random effects at each voxel and a jumping surface model for modeling the variance components of the genetic random effects and fixed effects as piecewise smooth functions of the voxels. Moreover, FMEM naturally accommodates the correlation structure of the genetic markers at each voxel, while the jumping surface model explicitly incorporates the intrinsically spatial smoothness of the imaging data. We propose a novel two-stage adaptive smoothing procedure to spatially estimate the piecewise smooth functions, particularly the irregular functional genetic variance components, while preserving their edges among different piecewise-smooth regions. We develop weighted likelihood ratio tests and derive their exact approximations to test the effect of the genetic markers across voxels. Simulation studies show that FMEM significantly outperforms voxel-wise approaches in terms of higher sensitivity and specificity to identify regions of interest for carrying out candidate genetic mapping in imaging genetic studies. Finally, FMEM is used to identify brain regions affected by three candidate genes including CR1, CD2AP, and PICALM, thereby hoping to shed light on the pathological interactions between these candidate genes and brain structure and function.

  15. Spatial distribution of mineral dust single scattering albedo based on DREAM model

    Science.gov (United States)

    Kuzmanoski, Maja; Ničković, Slobodan; Ilić, Luka

    2016-04-01

    Mineral dust comprises a significant part of global aerosol burden. There is a large uncertainty in estimating role of dust in Earth's climate system, partly due to poor characterization of its optical properties. Single scattering albedo is one of key optical properties determining radiative effects of dust particles. While it depends on dust particle sizes, it is also strongly influenced by dust mineral composition, particularly the content of light-absorbing iron oxides and the mixing state (external or internal). However, an assumption of uniform dust composition is typically used in models. To better represent single scattering albedo in dust atmospheric models, required to increase accuracy of dust radiative effect estimates, it is necessary to include information on particle mineral content. In this study, we present the spatial distribution of dust single scattering albedo based on the Dust Regional Atmospheric Model (DREAM) with incorporated particle mineral composition. The domain of the model covers Northern Africa, Middle East and the European continent, with horizontal resolution set to 1/5°. It uses eight particle size bins within the 0.1-10 μm radius range. Focusing on dust episode of June 2010, we analyze dust single scattering albedo spatial distribution over the model domain, based on particle sizes and mineral composition from model output; we discuss changes in this optical property after long-range transport. Furthermore, we examine how the AERONET-derived aerosol properties respond to dust mineralogy. Finally we use AERONET data to evaluate model-based single scattering albedo. Acknowledgement We would like to thank the AERONET network and the principal investigators, as well as their staff, for establishing and maintaining the AERONET sites used in this work.

  16. An Overview of Mineral Dust Modeling over East Asia

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Siyu; Huang, Jianping; Qian, Yun; Zhao, Chun; Kang, Litai; Yang, Ben; Wang, Yong; Liu, Yuzhi; Yuan, Tiangang; Wang, Tianhe; Ma, Xiaojun; Zhang, Guolong

    2017-08-27

    Dust aerosol, one of the most abundant aerosol species in the atmosphere, has significant impacts on the energy balance and climatic feedback of the Earth system through its influence on solar and terrestrial radiation as well as clouds. East Asia is the one of prominent regions of dust generation. The East Asia dust life cycle and associated radiative and climatic effects are the outstanding science issues in understanding climate change at regional and even global scale. In the past decades, numerous dust models have been developed and applied to comprehend a series of dust-related processes studies, including emission, transport, and deposition, and to understand the effects of dust aerosol on the radiation and climate over East Asian. In this paper, we review the recent achievements and progresses in East Asian dust modeling research and discuss the potential challenges in future studies.

  17. ENHANCING THE ATOMIC-LEVEL UNDERSTANDING OF CO2 MINERAL SEQUESTRATION MECHANISMS VIA ADVANCED COMPUTATIONAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    A.V.G. Chizmeshya; M.J. McKelvy; G.H. Wolf; R.W. Carpenter; D.A. Gormley; J.R. Diefenbacher; R. Marzke

    2006-03-01

    have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO2 mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH)2. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO2 mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach has provided a deeper understanding of the key reaction mechanisms than either individual approach can alone. We used ab initio techniques to significantly advance our understanding of atomic-level processes at the solid

  18. ENHANCING THE ATOMIC-LEVEL UNDERSTANDING OF CO2 MINERAL SEQUESTRATION MECHANISMS VIA ADVANCED COMPUTATIONAL MODELING

    Energy Technology Data Exchange (ETDEWEB)

    A.V.G. Chizmeshya

    2003-12-19

    DOE/NETL managed National Mineral Sequestration Working Group we have already significantly improved our understanding of mineral carbonation. Group members at the Albany Research Center have recently shown that carbonation of olivine and serpentine, which naturally occurs over geological time (i.e., 100,000s of years), can be accelerated to near completion in hours. Further process refinement will require a synergetic science/engineering approach that emphasizes simultaneous investigation of both thermodynamic processes and the detailed microscopic, atomic-level mechanisms that govern carbonation kinetics. Our previously funded Phase I Innovative Concepts project demonstrated the value of advanced quantum-mechanical modeling as a complementary tool in bridging important gaps in our understanding of the atomic/molecular structure and reaction mechanisms that govern CO{sub 2} mineral sequestration reaction processes for the model Mg-rich lamellar hydroxide feedstock material Mg(OH){sub 2}. In the present simulation project, improved techniques and more efficient computational schemes have allowed us to expand and augment these capabilities and explore more complex Mg-rich, lamellar hydroxide-based feedstock materials, including the serpentine-based minerals. These feedstock materials are being actively investigated due to their wide availability, and low-cost CO{sub 2} mineral sequestration potential. Cutting-edge first principles quantum chemical, computational solid-state and materials simulation methodology studies proposed herein, have been strategically integrated with our new DOE supported (ASU-Argonne National Laboratory) project to investigate the mechanisms that govern mineral feedstock heat-treatment and aqueous/fluid-phase serpentine mineral carbonation in situ. This unified, synergetic theoretical and experimental approach will provide a deeper understanding of the key reaction mechanisms than either individual approach can alone. Ab initio techniques will

  19. Smoothed Particle Hydrodynamics Model for Reactive Transport and Mineral Precipitation

    Energy Technology Data Exchange (ETDEWEB)

    Tartakovsky, Alexandre M.; Scheibe, Timothy D.; Redden, George; Meakin, Paul; Fang, Yilin

    2006-06-30

    A new Lagrangian particle model based on smoothed particle hydrodynamics was used to simulate pore scale precipitation reactions. The side-by-side injection of reacting solutions into two halves of a two-dimensional granular porous medium was simulated. Precipitation on grain surfaces occurred along a narrow zone in the middle of the domain, where the reacting solutes mixed to generate a supersaturated reaction product. The numerical simulations qualitatively reproduced the behavior observed in related laboratory experiments.

  20. Sensitivity of mineral dissolution rates to physical weathering : A modeling approach

    Science.gov (United States)

    Opolot, Emmanuel; Finke, Peter

    2015-04-01

    There is continued interest on accurate estimation of natural weathering rates owing to their importance in soil formation, nutrient cycling, estimation of acidification in soils, rivers and lakes, and in understanding the role of silicate weathering in carbon sequestration. At the same time a challenge does exist to reconcile discrepancies between laboratory-determined weathering rates and natural weathering rates. Studies have consistently reported laboratory rates to be in orders of magnitude faster than the natural weathering rates (White, 2009). These discrepancies have mainly been attributed to (i) changes in fluid composition (ii) changes in primary mineral surfaces (reactive sites) and (iii) the formation of secondary phases; that could slow natural weathering rates. It is indeed difficult to measure the interactive effect of the intrinsic factors (e.g. mineral composition, surface area) and extrinsic factors (e.g. solution composition, climate, bioturbation) occurring at the natural setting, in the laboratory experiments. A modeling approach could be useful in this case. A number of geochemical models (e.g. PHREEQC, EQ3/EQ6) already exist and are capable of estimating mineral dissolution / precipitation rates as a function of time and mineral mass. However most of these approaches assume a constant surface area in a given volume of water (White, 2009). This assumption may become invalid especially at long time scales. One of the widely used weathering models is the PROFILE model (Sverdrup and Warfvinge, 1993). The PROFILE model takes into account the mineral composition, solution composition and surface area in determining dissolution / precipitation rates. However there is less coupling with other processes (e.g. physical weathering, clay migration, bioturbation) which could directly or indirectly influence dissolution / precipitation rates. We propose in this study a coupling between chemical weathering mechanism (defined as a function of reactive area

  1. Animal models for human genetic diseases

    African Journals Online (AJOL)

    Sharif Sons

    organisms are extensively used in applied research in agriculture, industry, and also in medicine, where they are ... in genetic disorder that is critical for embryonic .... by practical limitations and ethical concerns. ..... American journal of medical.

  2. Theoretical analysis of an iron mineral-based magnetoreceptor model in birds

    DEFF Research Database (Denmark)

    Solov'yov, Ilia; Greiner, Walter

    2007-01-01

    involves two types of iron minerals (magnetite and maghemite) that were found in subcellular compartments within sensory dendrites of the upper beak of several bird species. But so far a quantitative evaluation of the proposed receptor is missing. In this article, we develop a theoretical model...

  3. Modelling soil organic carbon concentration of mineral soils in arable lands using legacy soil data

    DEFF Research Database (Denmark)

    Suuster, E; Ritz, Christian; Roostalu, H

    2012-01-01

    as to the advantages and shortcomings of the different commonly used prediction methods. Therefore, we compared and evaluated the merits of the median approach, analysis of covariance, mixed models and random forests in the context of prediction of SOC concentrations of mineral soils under arable management in the A...

  4. Surface evolution of dissolving minerals investigated with a kinetic Ising model

    Science.gov (United States)

    Bandstra, Joel Z.; Brantley, Susan L.

    2008-06-01

    In natural weathering systems, both the chemistry and the topography of mineral surfaces change as rocks and minerals equilibrate to surface conditions. Most geochemical research has focused on changes in solution chemistry over time; however, temporal changes in surface topography may also yield information about rates and mechanisms of dissolution. We use stochastic dissolution simulations of a regular 2-D lattice with reaction mechanisms defined in terms of nearest neighbor interactions to elucidate how the surface area and reactivity of a crystal evolve during dissolution. Despite the simplicity of the model, it reproduces key features observed or inferred for mineral dissolution. Our model results indicate that: (i) dissolving surfaces reach a steady-state conformation after sufficient dissolution time, (ii) linear defects cause surface area and dissolution rate to vary in concert with one another, (iii) sigmoidal and non-sigmoidal rate vs. free-energy of reaction (Δ Grxn) behavior can be rationalized in terms of the multiple steps occurring during dissolution, and (iv) surface roughness as a function of Δ Grxn is highly sensitive to the reaction mechanism. When simulated times to reach steady-state are compared to published time series rate data using suitable scaling, good agreement is found for silicate minerals while the model significantly over-predicts the duration of the transient for Fe and Al oxides. The implication of our simple model is that many aspects of mineral dissolution behavior, including approach to steady-state, sigmoidal vs. non-sigmoidal rate vs. Δ Grxn behavior, and development of rougher surfaces in conditions further from equilibrium can be explained by nearest neighbor interactions and simple Kossel-type models where reactivity of a surface is defined in terms of perfect surface, step, and kink sites.

  5. A Mutation Model from First Principles of the Genetic Code.

    Science.gov (United States)

    Thorvaldsen, Steinar

    2016-01-01

    The paper presents a neutral Codons Probability Mutations (CPM) model of molecular evolution and genetic decay of an organism. The CPM model uses a Markov process with a 20-dimensional state space of probability distributions over amino acids. The transition matrix of the Markov process includes the mutation rate and those single point mutations compatible with the genetic code. This is an alternative to the standard Point Accepted Mutation (PAM) and BLOcks of amino acid SUbstitution Matrix (BLOSUM). Genetic decay is quantified as a similarity between the amino acid distribution of proteins from a (group of) species on one hand, and the equilibrium distribution of the Markov chain on the other. Amino acid data for the eukaryote, bacterium, and archaea families are used to illustrate how both the CPM and PAM models predict their genetic decay towards the equilibrium value of 1. A family of bacteria is studied in more detail. It is found that warm environment organisms on average have a higher degree of genetic decay compared to those species that live in cold environments. The paper addresses a new codon-based approach to quantify genetic decay due to single point mutations compatible with the genetic code. The present work may be seen as a first approach to use codon-based Markov models to study how genetic entropy increases with time in an effectively neutral biological regime. Various extensions of the model are also discussed.

  6. Association of genetic variations of genes encoding thrombospondin, type 1, domain-containing 4 and 7A with low bone mineral density in Japanese women with osteoporosis.

    Science.gov (United States)

    Mori, Seijiro; Kou, Ikuyo; Sato, Hidenori; Emi, Mitsuru; Ito, Hideki; Hosoi, Takayuki; Ikegawa, Shiro

    2008-01-01

    Twins and family studies have shown that genetic factors are important determinants of bone mass. Important aspects of bone mineral density (BMD) regulation are endocrine systems, notably hormonal regulation of adrenal corticoids, as indicated by clinical knowledge of glucocorticoid-induced osteoporosis. Glucocorticoid is known to negatively regulate bone mass in vivo, and glucocorticoid increases thrombospondin messenger ribonucleic acid (mRNA) levels. We studied single nucleotide polymorphisms (SNPs) in genes encoding thrombospondin, type 1, domain-containing 4 and 7A (THSD4 and THSD7A) for possible association with lumbar and femoral BMD among 337 Japanese women with osteoporosis who participated in the BioBank Japan project. Genetic variations of THSD4 and THSD7A loci displayed significant association with lumbar and femoral BMD. Most significant correlation was observed for THSD7A SNP rs12673692 with lumbar BMD (P = 0.00017). Homozygous carriers of the major (G) allele had the highest BMD [0.886 +/- 0.011 g/cm2, mean +/- standard deviation (SD)], whereas heterozygous carriers were intermediate (0.872 +/- 0.013 g/cm2) and homozygous A-allele carriers had the lowest (0.753 +/- 0.023 g/cm2). THSD4 SNP rs10851839 also displayed strong association with lumbar BMD (P = 0.0092). In addition, both THSD7A and THSD4 displayed significant association with femoral BMD in a recessive model (P = 0.036 and P = 0.0046, respectively). Results suggest that variations of THSD7A and THSD4 loci may be important determinants of osteoporosis in Japanese women.

  7. Risk Management Model in Surface Exploitation of Mineral Deposits

    Science.gov (United States)

    Stojanović, Cvjetko

    2016-06-01

    Risk management is an integrative part of all types of project management. One of the main tasks of pre-investment studies and other project documentation is the tendency to protect investment projects as much as possible against investment risks. Therefore, the provision and regulation of risk information ensure the identification of the probability of the emergence of adverse events, their forms, causes and consequences, and provides a timely measures of protection against risks. This means that risk management involves a set of management methods and techniques used to reduce the possibility of realizing the adverse events and consequences and thus increase the possibilities of achieving the planned results with minimal losses. Investment in mining projects are of capital importance because they are very complex projects, therefore being very risky, because of the influence of internal and external factors and limitations arising from the socio-economic environment. Due to the lack of a risk management system, numerous organizations worldwide have suffered significant financial losses. Therefore, it is necessary for any organization to establish a risk management system as a structural element of system management system as a whole. This paper presents an approach to a Risk management model in the project of opening a surface coal mine, developed based on studies of extensive scientific literature and personal experiences of the author, and which, with certain modifications, may find use for any investment project, both in the mining industry as well as in investment projects in other areas.

  8. Porphyry copper deposit model: Chapter B in Mineral deposit models for resource assessment

    Science.gov (United States)

    Ayuso, Robert A.; Barton, Mark D.; Blakely, Richard J.; Bodnar, Robert J.; Dilles, John H.; Gray, Floyd; Graybeal, Fred T.; Mars, John L.; McPhee, Darcy K.; Seal, Robert R., II; Taylor, Ryan D.; Vikre, Peter G.; John, David A.

    2010-01-01

    This report contains a revised descriptive model of porphyry copper deposits (PCDs), the world's largest source (about 60 percent) and resource (about 65 percent) of copper and a major source of molybdenum, gold and silver. Despite relatively low grades (average 0.44 percent copper in 2008), PCDs have significant economic and societal impacts due to their large size (commonly hundreds of millions to billions of metric tons), long mine lives (decades), and high production rates (billions of kilograms of copper per year). The revised model describes the geotectonic setting of PCDs, and provides extensive regional- to deposit-scale descriptions and illustrations of geological, geochemical, geophysical, and geoenvironmental characteristics. Current genetic theories are reviewed and evaluated, knowledge gaps are identified, and a variety of exploration and assessment guides are presented. A summary is included for users seeking overviews of specific topics.

  9. Statistical Inference of Biometrical Genetic Model With Cultural Transmission.

    Science.gov (United States)

    Guo, Xiaobo; Ji, Tian; Wang, Xueqin; Zhang, Heping; Zhong, Shouqiang

    2013-01-01

    Twin and family studies establish the foundation for studying the genetic, environmental and cultural transmission effects for phenotypes. In this work, we make use of the well established statistical methods and theory for mixed models to assess cultural transmission in twin and family studies. Specifically, we address two critical yet poorly understood issues: the model identifiability in assessing cultural transmission for twin and family data and the biases in the estimates when sub-models are used. We apply our models and theory to two real data sets. A simulation is conducted to verify the bias in the estimates of genetic effects when the working model is a sub-model.

  10. An In Vitro Murine Model of Vascular Smooth Muscle Cell Mineralization.

    Science.gov (United States)

    Kelynack, Kristen J; Holt, Stephen G

    2016-01-01

    Vascular calcification (VC) is seen ubiquitously in aging blood vessels and prematurely in disease states like renal failure. It is thought to be driven by a number of systemic and local factors that lead to extra-osseous deposition of mineral in the vascular wall and valves as a common endpoint. The response of resident vascular smooth muscle cell to these dystrophic signals appears to be important in this process. Whilst in vivo models allow the observation of global changes in a pro-calcific environment, identifying the specific cells and mechanisms involved has been largely garnered from in vitro experiments, which provide added benefits in terms of reproducibility, cost, and convenience. Here we describe a 7-21 day cell culture model of calcification developed using immortalized murine vascular smooth muscle cells (MOVAS-1). This model provides a method by which vascular smooth muscle cell involvement and manipulation within a mineralizing domain can be studied.

  11. Numeral eddy current sensor modelling based on genetic neural network

    Institute of Scientific and Technical Information of China (English)

    Yu A-Long

    2008-01-01

    This paper presents a method used to the numeral eddy current sensor modelling based on the genetic neural network to settle its nonlinear problem. The principle and algorithms of genetic neural network are introduced. In this method, the nonlinear model parameters of the numeral eddy current sensor are optimized by genetic neural network (GNN) according to measurement data. So the method remains both the global searching ability of genetic algorithm and the good local searching ability of neural network. The nonlinear model has the advantages of strong robustness,on-line modelling and high precision.The maximum nonlinearity error can be reduced to 0.037% by using GNN.However, the maximum nonlinearity error is 0.075% using the least square method.

  12. Genetic fuzzy system modeling and simulation of vascular behaviour

    DEFF Research Database (Denmark)

    Tang, Jiaowei; Boonen, Harrie C.M.

    in cardiovascular disease and ultimately improve pharmacotherapy. For this purpose, novel computational approaches incorporating adaptive properties, auto-regulatory control and rule sets will be assessed, properties that are commonly lacking in deterministic models based on differential equations. We hypothesize...... in principle for any physiological system that is characterized by auto-regulatory control and adaptation. Methods: Currently, one modeling approach is being investigated, Genetic Fuzzy System (GFS). In Genetic Fuzzy Systems, the model algorithm mimics the biologic genetic evolutionary process to learn...... chromosome or individual to define the fuzzy system. The model is implemented by combining the Matlab Genetic algorithm and Fuzzy system toolboxes, respectively. To test the performance of this method, experimental data sets about calculated pressure change in different blood vessels after several chemical...

  13. Artificial Neural Network Genetic Algorithm As Powerful Tool to Predict and Optimize In vitro Proliferation Mineral Medium for G × N15 Rootstock

    Science.gov (United States)

    Arab, Mohammad M.; Yadollahi, Abbas; Shojaeiyan, Abdolali; Ahmadi, Hamed

    2016-01-01

    One of the major obstacles to the micropropagation of Prunus rootstocks has, up until now, been the lack of a suitable tissue culture medium. Therefore, reformulation of culture media or modification of the mineral content might be a breakthrough to improve in vitro multiplication of G × N15 (garnem). We found artificial neural network in combination of genetic algorithm (ANN-GA) as a very precise and powerful modeling system for optimizing the culture medium, So that modeling the effects of MS mineral salts (NH4+, NO3-, PO42-, Ca2+, K+, SO42-, Mg2+, and Cl−) on in vitro multiplication parameters (the number of microshoots per explant, average length of microshoots, weight of calluses derived from the base of stem explants, and quality index of plantlets) of G × N15. Showed high R2 correlation values of 87, 91, 87, and 74 between observed and predicted values were found for these four growth parameters, respectively. According to the ANN-GA results, among the input variables, NH4+ and NO3- had the highest values of VSR in data set for the parameters studied. The ANN-GA showed that the best proliferation rate was obtained from medium containing (mM) 27.5 NO3-, 14 NH4+, 5 Ca2+, 25.9 K+, 0.7 Mg2+, 1.1 PO42-, 4.7 SO42-, and 0.96 Cl−. The performance of the medium optimized by ANN-GA, denoted as YAS (Yadollahi, Arab and Shojaeiyan), was compared to that of standard growth media for all Prunus rootstock, including the Murashige and Skoog (MS) medium, (specific media) EM, Quoirin and Lepoivre (QL) medium, and woody plant medium (WPM) Prunus. With respect to shoot length, shoot number per cultured explant and productivity (number of microshoots × length of microshoots), YAS was found to be superior to other media for in vitro multiplication of G × N15 rootstocks. In addition, our results indicated that by using ANN-GA, we were able to determine a suitable culture medium formulation to achieve the best in vitro productivity. PMID:27807436

  14. Artificial Neural Network Genetic Algorithm As Powerful Tool to Predict and Optimize In vitro Proliferation Mineral Medium for G × N15 Rootstock.

    Science.gov (United States)

    Arab, Mohammad M; Yadollahi, Abbas; Shojaeiyan, Abdolali; Ahmadi, Hamed

    2016-01-01

    One of the major obstacles to the micropropagation of Prunus rootstocks has, up until now, been the lack of a suitable tissue culture medium. Therefore, reformulation of culture media or modification of the mineral content might be a breakthrough to improve in vitro multiplication of G × N15 (garnem). We found artificial neural network in combination of genetic algorithm (ANN-GA) as a very precise and powerful modeling system for optimizing the culture medium, So that modeling the effects of MS mineral salts ([Formula: see text], [Formula: see text], [Formula: see text], Ca(2+), K(+), [Formula: see text], Mg(2+), and Cl(-)) on in vitro multiplication parameters (the number of microshoots per explant, average length of microshoots, weight of calluses derived from the base of stem explants, and quality index of plantlets) of G × N15. Showed high R(2) correlation values of 87, 91, 87, and 74 between observed and predicted values were found for these four growth parameters, respectively. According to the ANN-GA results, among the input variables, [Formula: see text] and [Formula: see text] had the highest values of VSR in data set for the parameters studied. The ANN-GA showed that the best proliferation rate was obtained from medium containing (mM) 27.5 [Formula: see text], 14 [Formula: see text], 5 Ca(2+), 25.9 K(+), 0.7 Mg(2+), 1.1 [Formula: see text], 4.7 [Formula: see text], and 0.96 Cl(-). The performance of the medium optimized by ANN-GA, denoted as YAS (Yadollahi, Arab and Shojaeiyan), was compared to that of standard growth media for all Prunus rootstock, including the Murashige and Skoog (MS) medium, (specific media) EM, Quoirin and Lepoivre (QL) medium, and woody plant medium (WPM) Prunus. With respect to shoot length, shoot number per cultured explant and productivity (number of microshoots × length of microshoots), YAS was found to be superior to other media for in vitro multiplication of G × N15 rootstocks. In addition, our results indicated that by

  15. The development of the asparagus miner (Ophiomyia simplex Loew; Diptera: Agromyzidae) in temperate zones: a degree-day model.

    Science.gov (United States)

    Morrison, William R; Andresen, Jeffrey; Szendrei, Zsofia

    2014-07-01

    The asparagus miner is a putative vector of Fusarium spp., which have been implicated in globally declining asparagus production. Growers currently apply broad-spectrum insecticides for the asparagus miner, but lack management guidelines for adequately controlling the pest. Our aims were (1) to determine the lower developmental threshold of the asparagus miner, (2) develop and validate a degree-day model describing its phenology, and (3) create a developmental time budget for the asparagus miner to help guide growers' management decisions. We found that the lower developmental threshold for the asparagus miner was 12.1 °C, and that the phenology of the asparagus miner could be reliably predicted over the course of a two-year study. Predictions from the model match well with previously published information on the bionomics of the asparagus miner, but fit better for sampling data collected from the midwestern and eastern United States than for the United Kingdom. The life cycle of the asparagus miner likely requires between 1500 and 2000 degree-days to complete; the longest developmental time requirement was for the pupal stagen This study provides tools for the targeted management of the asparagus miner by offering a degree-day model that may be used to predict its life stages in the north-eastern United States. © 2013 Society of Chemical Industry.

  16. Multiple comparisons in genetic association studies: a hierarchical modeling approach.

    Science.gov (United States)

    Yi, Nengjun; Xu, Shizhong; Lou, Xiang-Yang; Mallick, Himel

    2014-02-01

    Multiple comparisons or multiple testing has been viewed as a thorny issue in genetic association studies aiming to detect disease-associated genetic variants from a large number of genotyped variants. We alleviate the problem of multiple comparisons by proposing a hierarchical modeling approach that is fundamentally different from the existing methods. The proposed hierarchical models simultaneously fit as many variables as possible and shrink unimportant effects towards zero. Thus, the hierarchical models yield more efficient estimates of parameters than the traditional methods that analyze genetic variants separately, and also coherently address the multiple comparisons problem due to largely reducing the effective number of genetic effects and the number of statistically "significant" effects. We develop a method for computing the effective number of genetic effects in hierarchical generalized linear models, and propose a new adjustment for multiple comparisons, the hierarchical Bonferroni correction, based on the effective number of genetic effects. Our approach not only increases the power to detect disease-associated variants but also controls the Type I error. We illustrate and evaluate our method with real and simulated data sets from genetic association studies. The method has been implemented in our freely available R package BhGLM (http://www.ssg.uab.edu/bhglm/).

  17. Enterprise Projects Set Risk Element Transmission Chaotic Genetic Model

    Directory of Open Access Journals (Sweden)

    Cunbin Li

    2012-08-01

    Full Text Available In order to research projects set risk transfer process and improve risk management efficiency in projects management, combining chaos theory and genetic algorithm, put forward enterprise projects set risk element transmission chaos genetic model. Using logistic chaos mapping and chebyshev chaos mapping mixture, constructed a hybrid chaotic mapping system. The steps of adopting hybrid chaos mapping for genetic operation include projects set initialization, calculation of fitness, selection, crossover and mutation operators, fitness adjustment and condition judgment. The results showed that the model can simulate enterprise projects set risk transmission process very well and it also provides the basis for the enterprise managers to make decisions.

  18. The Neolithic transition in Europe: archaeological models and genetic evidence

    Directory of Open Access Journals (Sweden)

    Martin Richards

    2003-01-01

    Full Text Available The major pattern in the European gene pool is a southeast-northwest frequency gradient of classic genetic markers such as blood groups, which population geneticists initially attributed to the demographic impact of Neolithic farmers dispersing from the Near East. Molecular genetics has enriched this picture, with analyses of mitochondrial DNA and the Y chromosome allowing a more detailed exploration of alternative models for the spread of the Neolithic into Europe. This paper considers a range of possible models in the light of the detailed information now emerging from genetic studies.

  19. Yarn Strength Modelling Using Genetic Fuzzy Expert System

    Science.gov (United States)

    Banerjee, Debamalya; Ghosh, Anindya; Das, Subhasis

    2013-05-01

    This paper deals with the modelling of cotton yarn strength using genetic fuzzy expert system. Primarily a fuzzy expert system has been developed to model the cotton yarn strength from the constituent fibre parameters such as fibre strength, upper half mean length, fibre fineness and short fibre content. A binary coded genetic algorithm has been used to improve the prediction performance of the fuzzy expert system. The experimental validation confirms that the genetic fuzzy expert system has significantly better prediction accuracy and consistency than that of the fuzzy expert system.

  20. Application of a Lagrangian transport model to organo-mineral aggregates within the Nazaré canyon

    OpenAIRE

    S. Pando; Juliano, M.; Garcia, R.; P. A. de Jesus Mendes; Thomsen, L.

    2013-01-01

    In this study, a hydrodynamic model was applied to the Nazaré submarine canyon with boundary forcing provided by an operational forecast model for the West Iberian coast. After validation, a Lagrangian transport model was coupled to the hydrodynamic model to study the transport patterns of the organo-mineral aggregates along the Nazaré canyon comparing three different classes of organo-mineral aggregates. The results showed that the transport in the canyon is neither constant, nor unid...

  1. Application of a Lagrangian transport model to organo-mineral aggregates within the Nazaré canyon

    OpenAIRE

    Pando, S.; Juliano, M.; Garcia, R.; P. A. de Jesus Mendes; Thomsen, L.

    2013-01-01

    In this study, a hydrodynamic model was applied to the Nazaré submarine canyon with boundary forcing provided by an operational forecast model for the West Iberian coast. After validation, a Lagrangian transport model was coupled to the hydrodynamic model to study the transport patterns of the organo-mineral aggregates along the Nazaré canyon comparing three different classes of organo-mineral aggregates. The results showed that the transport in the canyon is neither constant, nor unid...

  2. A deposit model for Mississippi Valley-Type lead-zinc ores: Chapter A in Mineral deposit models for resource assessment

    Science.gov (United States)

    Leach, David L.; Taylor, Ryan D.; Fey, David L.; Diehl, Sharon F.; Saltus, Richard W.

    2010-01-01

    This report is a descriptive model of Mississippi Valley-Type (MVT) lead-zinc deposits that presents their geological, mineralogical and geochemical attributes and is part of an effort by the U.S. Geological Survey Mineral Resources Program to update existing models and develop new models that will be used for an upcoming national mineral resource assessment. This deposit modeling effort by the USGS is intended to supplement previously published models for use in mineral-resource and mineral-environmental assessments. Included in this report are geological, geophysical and geochemical assessment guides to assist in mineral resource estimation. The deposit attributes, including grade and tonnage of the deposits described in this report are based on a new mineral deposits data set of all known MVT deposits in the world.

  3. Modeling of Cation Binding in Hydrated 2:1 Clay Minerals - Final Report

    Energy Technology Data Exchange (ETDEWEB)

    Smith, David E.

    2000-09-14

    Hydrated 2:1 clay minerals are high surface area, layered silicates that play a unique role in determining the fate of radionuclides in the environment. This project consisted of developing and implementing computer simulation methods for molecular characterization of the swelling and ion exchange properties of Hydrated 2:1 clay minerals, and the subsequent analysis and theoretical modeling with a view toward improving contaminant transport modeling as well as soil remediation and radionuclide containment strategies. Project results included the (a) development of simulation methods to treat clays under environmentally relevant conditions of variable water vapor pressure; (b) calculation of clay swelling thermodynamics as a function of interlayer ion size and charge (calculated quantities include immersion energies, free energies, and entropies of swelling); and (c) calculation of ion exchange free energies, including contributions from changing interlayer water contents and layer spacing.

  4. Transmission function models of finite population genetic algorithms

    NARCIS (Netherlands)

    Kemenade, C.H.M. van; Kok, J.N.; La Poutré, J.A.; Thierens, D.

    1998-01-01

    Infinite population models show a deterministic behaviour. Genetic algorithms with finite populations behave non-deterministicly. For small population sizes, the results obtained with these models differ strongly from the results predicted by the infinite population model. When the population size i

  5. Modeling the Influence of Transport on Chemical Reactivity in Microbial Membranes: Mineral Precipitation/Dissolution Reactions.

    Science.gov (United States)

    Felmy, A. R.; Liu, C.; Clark, S.; Straatsma, T.; Rustad, J.

    2003-12-01

    It has long been known that microorganisms can alter the chemical composition of their immediate surroundings and influence such processes as ion uptake or adsorption and mineral precipitation dissolution. However, only recently have molecular imaging and molecular modeling capabilities been developed that begin to shed light on the nature of these processes at the nm to um scale at the surface of bacterial membranes. In this presentation we will show the results of recent molecular simulations of microbial surface reactions and describe our efforts to develop accurate non-equilibrium thermodynamic models for the microbial surface that can describe ion uptake and surface induced mineral precipitation. The thermodynamic models include the influence of the bacterial electrical double layer on the uptake of ions from solution and the removal, or exclusion, of ions from the surface of the cell, non-equilibrium diffusion and chemical reaction within the membrane, as well as a new thermodynamic approach to representing ion activities within the microbial membrane. In the latter case, the variability in the water content within the microbial membrane has a significant influence on the calculated mineral saturation indices. In such cases, we will propose the use of recently developed mixed solvent-electrolyte formalisms. Recent experimental data for mixed-solvent electrolyte systems will also be presented to demonstrate the potential impact of the variable water content on calculated ion activities within the membrane.

  6. Offline modeling for product quality prediction of mineral processing using modeling error PDF shaping and entropy minimization.

    Science.gov (United States)

    Ding, Jinliang; Chai, Tianyou; Wang, Hong

    2011-03-01

    This paper presents a novel offline modeling for product quality prediction of mineral processing which consists of a number of unit processes in series. The prediction of the product quality of the whole mineral process (i.e., the mixed concentrate grade) plays an important role and the establishment of its predictive model is a key issue for the plantwide optimization. For this purpose, a hybrid modeling approach of the mixed concentrate grade prediction is proposed, which consists of a linear model and a nonlinear model. The least-squares support vector machine is adopted to establish the nonlinear model. The inputs of the predictive model are the performance indices of each unit process, while the output is the mixed concentrate grade. In this paper, the model parameter selection is transformed into the shape control of the probability density function (PDF) of the modeling error. In this context, both the PDF-control-based and minimum-entropy-based model parameter selection approaches are proposed. Indeed, this is the first time that the PDF shape control idea is used to deal with system modeling, where the key idea is to turn model parameters so that either the modeling error PDF is controlled to follow a target PDF or the modeling error entropy is minimized. The experimental results using the real plant data and the comparison of the two approaches are discussed. The results show the effectiveness of the proposed approaches.

  7. Genetic programming-based chaotic time series modeling

    Institute of Scientific and Technical Information of China (English)

    张伟; 吴智铭; 杨根科

    2004-01-01

    This paper proposes a Genetic Programming-Based Modeling (GPM) algorithm on chaotic time series. GP is used here to search for appropriate model structures in function space, and the Particle Swarm Optimization (PSO) algorithm is used for Nonlinear Parameter Estimation (NPE) of dynamic model structures. In addition, GPM integrates the results of Nonlinear Time Series Analysis (NTSA) to adjust the parameters and takes them as the criteria of established models. Experiments showed the effectiveness of such improvements on chaotic time series modeling.

  8. Modeling the global emission, transport and deposition of trace elements associated with mineral dust

    Directory of Open Access Journals (Sweden)

    Y. Zhang

    2014-12-01

    Full Text Available Trace element deposition from desert dust has important impacts on ocean primary productivity. In this study, emission inventories for 8 elements, which are primarily of soil origin, Mg, P, Ca, Mn, Fe, K, Al, and Si were determined based on a global mineral dataset and a soils dataset. Datasets of elemental fractions were used to drive the desert dust model in the Community Earth System Model (CESM in order to simulate the elemental concentrations of atmospheric dust. Spatial variability of mineral dust elemental fractions was evident on a global scale, particularly for Ca. Simulations of global variations in the Ca / Al ratio, which typically ranged from around 0.1 to 5.0 in soil sources, were consistent with observations, suggesting this ratio to be a good signature for dust source regions. The simulated variable fractions of chemical elements are sufficiently different that estimates of deposition should include elemental variations, especially for Ca, Al and Fe. The model results have been evaluated with observational elemental aerosol concentration data from desert regions and dust events in non-dust regions, providing insights into uncertainties in the modeling approach. The ratios between modeled and observed elemental fractions ranged from 0.7 to 1.6 except for 3.4 and 3.5 for Mg and Mn, respectivly. Using the soil data base improved the correspondence of the spatial hetereogeneity in the modeling of several elements (Ca, Al and Fe compared to observations. Total and soluble dust associated element fluxes into different ocean basins and ice sheets regions have been estimated, based on the model results. Annual inputs of soluble Mg, P, Ca, Mn, Fe and K associated with dust using mineral dataset were 0.28 Tg, 16.89 Gg, 1.32 Tg, 22.84 Gg, 0.068 Tg, and 0.15 Tg to global oceans and ice sheets.

  9. Predicting the Mineral Composition of Dust Aerosols. Part 2; Model Evaluation and Identification of Key Processes with Observations

    Science.gov (United States)

    Perlwitz, J. P.; Garcia-Pando, C. Perez; Miller, R. L.

    2015-01-01

    A global compilation of nearly sixty measurement studies is used to evaluate two methods of simulating the mineral composition of dust aerosols in an Earth system model. Both methods are based upon a Mean Mineralogical Table (MMT) that relates the soil mineral fractions to a global atlas of arid soil type. The Soil Mineral Fraction (SMF) method assumes that the aerosol mineral fractions match the fractions of the soil. The MMT is based upon soil measurements after wet sieving, a process that destroys aggregates of soil particles that would have been emitted from the original, undisturbed soil. The second method approximately reconstructs the emitted aggregates. This model is referred to as the Aerosol Mineral Fraction (AMF) method because the mineral fractions of the aerosols differ from those of the wet-sieved parent soil, partly due to reaggregation. The AMF method remedies some of the deficiencies of the SMF method in comparison to observations. Only the AMF method exhibits phyllosilicate mass at silt sizes, where they are abundant according to observations. In addition, the AMF quartz fraction of silt particles is in better agreement with measured values, in contrast to the overestimated SMF fraction. Measurements at distinct clay and silt particle sizes are shown to be more useful for evaluation of the models, in contrast to the sum over all particles sizes that is susceptible to compensating errors, as illustrated by the SMF experiment. Model errors suggest that allocation of the emitted silt fraction of each mineral into the corresponding transported size categories is an important remaining source of uncertainty. Evaluation of both models and the MMT is hindered by the limited number of size-resolved measurements of mineral content that sparsely sample aerosols from the major dust sources. The importance of climate processes dependent upon aerosol mineral composition shows the need for global and routine mineral measurements.

  10. Genetic and non-genetic animal models for autism spectrum disorders (ASD).

    Science.gov (United States)

    Ergaz, Zivanit; Weinstein-Fudim, Liza; Ornoy, Asher

    2016-09-01

    Autism spectrum disorder (ASD) is associated, in addition to complex genetic factors, with a variety of prenatal, perinatal and postnatal etiologies. We discuss the known animal models, mostly in mice and rats, of ASD that helps us to understand the etiology, pathogenesis and treatment of human ASD. We describe only models where behavioral testing has shown autistic like behaviors. Some genetic models mimic known human syndromes like fragile X where ASD is part of the clinical picture, and others are without defined human syndromes. Among the environmentally induced ASD models in rodents, the most common model is the one induced by valproic acid (VPA) either prenatally or early postnatally. VPA induces autism-like behaviors following single exposure during different phases of brain development, implying that the mechanism of action is via a general biological mechanism like epigenetic changes. Maternal infection and inflammation are also associated with ASD in man and animal models. Copyright © 2016 Elsevier Inc. All rights reserved.

  11. The Ising model in physics and statistical genetics.

    Science.gov (United States)

    Majewski, J; Li, H; Ott, J

    2001-10-01

    Interdisciplinary communication is becoming a crucial component of the present scientific environment. Theoretical models developed in diverse disciplines often may be successfully employed in solving seemingly unrelated problems that can be reduced to similar mathematical formulation. The Ising model has been proposed in statistical physics as a simplified model for analysis of magnetic interactions and structures of ferromagnetic substances. Here, we present an application of the one-dimensional, linear Ising model to affected-sib-pair (ASP) analysis in genetics. By analyzing simulated genetics data, we show that the simplified Ising model with only nearest-neighbor interactions between genetic markers has statistical properties comparable to much more complex algorithms from genetics analysis, such as those implemented in the Allegro and Mapmaker-Sibs programs. We also adapt the model to include epistatic interactions and to demonstrate its usefulness in detecting modifier loci with weak individual genetic contributions. A reanalysis of data on type 1 diabetes detects several susceptibility loci not previously found by other methods of analysis.

  12. A NEW GENETIC SIMULATED ANNEALING ALGORITHM FOR FLOOD ROUTING MODEL

    Institute of Scientific and Technical Information of China (English)

    KANG Ling; WANG Cheng; JIANG Tie-bing

    2004-01-01

    In this paper, a new approach, the Genetic Simulated Annealing (GSA), was proposed for optimizing the parameters in the Muskingum routing model. By integrating the simulated annealing method into the genetic algorithm, the hybrid method could avoid some troubles of traditional methods, such as arduous trial-and-error procedure, premature convergence in genetic algorithm and search blindness in simulated annealing. The principle and implementing procedure of this algorithm were described. Numerical experiments show that the GSA can adjust the optimization population, prevent premature convergence and seek the global optimal result.Applications to the Nanyunhe River and Qingjiang River show that the proposed approach is of higher forecast accuracy and practicability.

  13. Geochemical inputs for hydrological models of deep-lying sedimentary units: Loss of mineral hydration water

    Science.gov (United States)

    Graf, D. L.; Anderson, D. E.

    1981-12-01

    Hydrological models that treat phenomena occurring deep in sedimentary piles, such as petroleum maturation and retention of chemical and radioactive waste, may require time spans of at least several million years. Many input quantities classically treated as constants will be variables on this time scale. Models sophisticated enough to include transport contributions from such processes as chemical diffusion, mineral dehydration and shale membrane behavior require considerable knowledge about regional geological history as well as the pertinent mineralogical and geochemical relationships. Simple dehydrations such as those of gypsum and halloysite occur at sharply-defined temperatures but, as with all mineral dehydration reactions, the equilibrium temperature is strongly dependent on the pore-fluid salinity and degree of overpressuring encountered in the subsurface. The dehydrations of analcime and smectite proceed by reactions involving other sedimentary minerals. The smectite reaction is crystallographically complex, yielding a succession of mixed-layered illite/smectites, and on the U.S.A. Gulf of Mexico coast continues over several million years at a particular stratigraphic interval.

  14. Urban net-zero water treatment and mineralization: experiments, modeling and design.

    Science.gov (United States)

    Englehardt, James D; Wu, Tingting; Tchobanoglous, George

    2013-09-01

    Water and wastewater treatment and conveyance account for approximately 4% of US electric consumption, with 80% used for conveyance. Net zero water (NZW) buildings would alleviate demands for a portion of this energy, for water, and for the treatment of drinking water for pesticides and toxic chemical releases in source water. However, domestic wastewater contains nitrogen loads much greater than urban/suburban ecosystems can typically absorb. The purpose of this work was to identify a first design of a denitrifying urban NZW treatment process, operating at ambient temperature and pressure and circum-neutral pH, and providing mineralization of pharmaceuticals (not easily regulated in terms of environmental half-life), based on laboratory tests and mass balance and kinetic modeling. The proposed treatment process is comprised of membrane bioreactor, iron-mediated aeration (IMA, reported previously), vacuum ultrafiltration, and peroxone advanced oxidation, with minor rainwater make-up and H2O2 disinfection residual. Similar to biological systems, minerals accumulate subject to precipitative removal by IMA, salt-free treatment, and minor dilution. Based on laboratory and modeling results, the system can produce potable water with moderate mineral content from commingled domestic wastewater and 10-20% rainwater make-up, under ambient conditions at individual buildings, while denitrifying and reducing chemical oxygen demand to below detection (<3 mg/L). While economics appear competitive, further development and study of steady-state concentrations and sludge management options are needed.

  15. CFD modeling of methane distribution at a continuous miner face with various curtain setback distances

    Institute of Scientific and Technical Information of China (English)

    Zhou Lihong; Pritchard Christopher; Zheng Yi

    2015-01-01

    Knowledge of the airflow patterns and methane distributions at a continuous miner face under different ventilation conditions can minimize the risks of explosion and injury to miners by accurately forecasting potentially hazardous face methane levels. This study focused on validating a series of computational fluid dynamics (CFD) models using full-scale ventilation gallery data that assessed how curtain setback distance impacted airflow patterns and methane distributions at an empty mining face (no continuous miner present). Three CFD models of face ventilation with 4.6, 7.6 and 10.7 m (15, 25, and 35 ft) blowing curtain setback distances were constructed and validated with experimental data collected in a full-scale ventilation test facility. Good agreement was obtained between the CFD simulation results and this data. Detailed airflow and methane distribution information are provided. Elevated methane zones at the working faces were identified with the three curtain setback distances. Visualization of the setback dis-tance impact on the face methane distribution was performed by utilizing the post-processing capability of the CFD software.

  16. Modeling of Possible Conditions for Origin of First Organic Forms in hot Mineral Water

    Directory of Open Access Journals (Sweden)

    Ignat Ignatov

    2014-12-01

    Full Text Available The composition of water, its temperature and pH value was analyzed in experiments with modelling of primary hydrosphere and possible conditions for origin of first organic forms in hot mineral water. For this aim the authors performed experiments with hot mineral and seawater from Bulgaria by IR-spectrometry (DNES-method. As model systems were used cactus juice of Echinopsis pachanoi and Mediterranean jellyfish Cotylorhiza tuberculata. It was considered the reactions of condensation and dehydration in alkaline aqueous solutions with рН = 9–10, resulting in synthesis from separate molecules larger organic molecules as polymers and short polipeptides. It was shown that hot alkaline mineral water with temperature from +65 0C to +95 0C and pH value from 9 to 11 is more suitable for the origination of life and living matter than other analyzed water samples. The pH value of seawater on contrary is limited to the range of 7,5 to 8,4 units. Two common local maximums were observed in the IR-spectra of jellyfish and seawater, which were more pronouncedly expressed in IR-spectra of jellyfish.

  17. Underground water quality model inversion of genetic algorithm

    Institute of Scientific and Technical Information of China (English)

    MA Ruijie; LI Xin

    2009-01-01

    The underground water quality model with non-linear inversion problem is ill-posed, and boils down to solving the minimum of nonlinear function. Genetic algorithms are adopted in a number of individuals of groups by iterative search to find the optimal solution of the problem, the encoding strings as its operational objective, and achieving the iterative calculations by the genetic operators. It is an effective method of inverse problems of groundwater, with incomparable advantages and practical significances.

  18. Modeling evolution of insect resistance to genetically modified crops

    OpenAIRE

    2015-01-01

    Genetically modified crops producing insecticidal proteins from Bacillus thuringiensis (Bt) for insect control have been planted on more than 200 million ha worldwide since 1996 [1]. Evolution of resistance by insect pests threatens the continued success of Bt crops [2, 3]. To delay pest resistance, refuges of non-Bt crops are planted near Bt crops to allow survival of susceptible pests [4, 5]. We used computer simulations of a population genetic model to determine if predictions from the the...

  19. A mechanistic model of spent fuel dissolution, secondary mineral precipitation, and Np release

    Energy Technology Data Exchange (ETDEWEB)

    Chen, Y.; Siegmann, E.; Mattie, P.; McNeish, J.; Sevougian, S.D.; Andrews, R.

    1999-07-01

    A mechanistic spent fuel dissolution model has been developed, based on the general reaction-transport code of AREST-CT. It considers the dissolution of spent fuel under flow conditions. The kinetic reactions of spent fuel dissolution and precipitation of schoepite, uranophane, soddyite, and Na-boltwoodite are included in the model. The results of model prediction are compared against the results of drip-tests that simulate the conditions that may occur in the Yucca Mountain Repository. Comparison shows that the modeling results match the laboratory observations very well and no contradiction has been found. It indicates that the model is a reasonably good representation of the real system. After validation, the model was used to investigate the release rate of Np from the dissolution of secondary uranyl minerals by examining various degrees of Np incorporation into secondary uranyl minerals. The predicted Np concentration in the aqueous phase is 3 orders of magnitude lower than the upper-bound of the Np solubility range currently used in DOE performance assessment analysis. It suggests that the Np solubility range currently used is too conservative and could be replaced with more realistic values.

  20. QSPR modeling mineral crystal lattice energy by optimal descriptors of the graph of atomic orbitals

    Science.gov (United States)

    Toropova, A. P.; Toropov, A. A.; Maksudov, S. Kh.

    2006-09-01

    Models of the crystal lattice of minerals of general formula of A mC n: m, n = 1,2: A = Li, K, Na, Mg, Ca, Mn, Cu, Zn, Sr, Cd, Ba, Hg, Pb, Cs, and Rb ; C = Be, O, F, S, Cl, Br, and I; as a mathematical function of their structure have been constructed. Two elucidations of molecular structure have been used: molecular graph (vertexes are atoms, i.e., Li, Na, K, etc.) and graph of atomic orbitals, GAO (vertexes are atomic orbitals, i.e., 1s 2, 2p 5, 3d 10, etc). Statistical characteristics of the GAO-based models are better.

  1. A Model of Genetic Variation in Human Social Networks

    CERN Document Server

    Fowler, James H; Christakis, Nicholas A

    2008-01-01

    Social networks influence the evolution of cooperation and they exhibit strikingly systematic patterns across a wide range of human contexts. Both of these facts suggest that variation in the topological attributes of human social networks might have a genetic basis. While genetic variation accounts for a significant portion of the variation in many complex social behaviors, the heritability of egocentric social network attributes is unknown. Here we show that three of these attributes (in-degree, transitivity, and centrality) are heritable. We then develop a "mirror network" method to test extant network models and show that none accounts for observed genetic variation in human social networks. We propose an alternative "attract and introduce" model that generates significant heritability as well as other important network features, and we show that this model with two simple forms of heterogeneity is well suited to the modeling of real social networks in humans. These results suggest that natural selection ...

  2. Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

    DEFF Research Database (Denmark)

    Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

    2013-01-01

    A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant....... The discrete time models used are multivariate variants of the discrete relative risk models. These models allow for regular parametric likelihood-based inference by exploring a coincidence of their likelihood functions and the likelihood functions of suitably defined multivariate generalized linear mixed...

  3. Multivariate Survival Mixed Models for Genetic Analysis of Longevity Traits

    DEFF Research Database (Denmark)

    Pimentel Maia, Rafael; Madsen, Per; Labouriau, Rodrigo

    2014-01-01

    A class of multivariate mixed survival models for continuous and discrete time with a complex covariance structure is introduced in a context of quantitative genetic applications. The methods introduced can be used in many applications in quantitative genetics although the discussion presented...... concentrates on longevity studies. The framework presented allows to combine models based on continuous time with models based on discrete time in a joint analysis. The continuous time models are approximations of the frailty model in which the hazard function will be assumed to be piece-wise constant....... The discrete time models used are multivariate variants of the discrete relative risk models. These models allow for regular parametric likelihood-based inference by exploring a coincidence of their likelihood functions and the likelihood functions of suitably defined multivariate generalized linear mixed...

  4. Genetic Model of an Aborted Porphyry-copper System

    Science.gov (United States)

    Papp, D. C.; Nitoi, E.; Szakacs, A.

    2009-05-01

    The Neogene Sturzii shallow intrusion from the East Carpathians (Bargau Mts., Romania), hosted by Paleogene-Miocene sediments of the Transcarpatian Flysch, developed as an immature porphyry copper structure. It consists of small volumes of dacites, andesites and related contact breccias, having a surface exposure of a few km2. Hydrothermal alteration occurred in the inner part of the intrusive body. The related mineralization consists of pyrite and chalcopyrite either as small veins or disseminated within the rock. A genetic model of the intrusive structure has been developed based on an integrated petrographic, geochemical, isotopic, fluid inclusion and geophysical study. The rapidly ascending calc-alkaline magmas that generated the intrusion are mantle-derived and contaminated with lower-crustal material. Pressure estimations for amphibole reveal significant differences between values corresponding to the crystal cores and rims, suggesting that decompression occurred during its crystallization. The occurrence of exploded fluid inclusions, as well as of primary igneous garnet, also indicate decompression regime during magma uplift and/or storage. All fluid inclusions identified in dacites are aqueous; C-N-S species were not detected. The general evolution of the fluids is toward decreasing salinity with decreasing temperature. Early high-T, high salinity fluids, most likely of magmatic origin, were subjected to a boiling event, related to a change of fluid pressure from litho- to hydrostatic, and followed by dilution with meteoric fluids as indicated by low salinities. These characteristics of the fluids suggest the tendency of the intrusion to evolve towards a porphyry copper system. We estimate that the evolution stopped due to decompression that allowed cold and dilute external fluids to enter the system and because of the small size of the intrusion that cooled down rapidly and could not induce extensive and long-lasting fluid circulation. Since there is no

  5. Genetics of traffic assignment models for strategic transport planning

    NARCIS (Netherlands)

    Bliemer, M.C.J.; Raadsen, M.P.H.; Brederode, L.J.N.; Bell, M.G.H.; Wismans, Luc Johannes Josephus; Smith, M.J.

    2016-01-01

    This paper presents a review and classification of traffic assignment models for strategic transport planning purposes by using concepts analogous to genetics in biology. Traffic assignment models share the same theoretical framework (DNA), but differ in capability (genes). We argue that all traffic

  6. Genetics of traffic assignment models for strategic transport planning

    NARCIS (Netherlands)

    Bliemer, M.C.J.; Raadsen, M.; Brederode, L.; Bell, M.; Wismans, L.J.J.; Smith, M.

    2016-01-01

    This paper presents a review and classification of traffic assignment models for strategic transport planning purposes by using concepts analogous to genetics in biology. Traffic assignment models share the same theoretical framework (DNA), but differ in capability (genes). We argue that all traffic

  7. Genetic models of absence epilepsy: New concepts and insights

    NARCIS (Netherlands)

    Luijtelaar, E.L.J.M. van; Coenen, A.M.L.

    2009-01-01

    The discovery, development, and use of genetic rodent models of absence epilepsy have led to a new theory about the origin of absence seizures. A focal zone has been identified in the peri-oral region of the somatosensory cortex in WAG/Rij and GAERS – the two most commonly used models – from which

  8. Genetic association in multivariate phenotypic data: power in five models

    NARCIS (Netherlands)

    Minica, C.C.; Boomsma, D.I.; van der Sluis, S.; Dolan, C.V.

    2010-01-01

    This article concerns the power of various data analytic strategies to detect the effect of a single genetic variant (GV) in multivariate data. We simulated exactly fitting monozygotic and dizygotic phenotypic data according to single and two common factor models, and simplex models. We calculated t

  9. Chromate adsorption on selected soil minerals: Surface complexation modeling coupled with spectroscopic investigation

    Energy Technology Data Exchange (ETDEWEB)

    Veselská, Veronika, E-mail: veselskav@fzp.czu.cz [Department of Environmental Geosciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcka 129, CZ-16521, Prague (Czech Republic); Fajgar, Radek [Department of Analytical and Material Chemistry, Institute of Chemical Process Fundamentals of the CAS, v.v.i., Rozvojová 135/1, CZ-16502, Prague (Czech Republic); Číhalová, Sylva [Department of Environmental Geosciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcka 129, CZ-16521, Prague (Czech Republic); Bolanz, Ralph M. [Institute of Geosciences, Friedrich-Schiller-University Jena, Carl-Zeiss-Promenade 10, DE-07745, Jena (Germany); Göttlicher, Jörg; Steininger, Ralph [ANKA Synchrotron Radiation Facility, Karlsruhe Institute of Technology, Hermann-von-Helmholtz-Platz 1, DE-76344, Eggenstein-Leopoldshafen (Germany); Siddique, Jamal A.; Komárek, Michael [Department of Environmental Geosciences, Faculty of Environmental Sciences, Czech University of Life Sciences Prague, Kamýcka 129, CZ-16521, Prague (Czech Republic)

    2016-11-15

    Highlights: • Study of Cr(VI) adsorption on soil minerals over a large range of conditions. • Combined surface complexation modeling and spectroscopic techniques. • Diffuse-layer and triple-layer models used to obtain fits to experimental data. • Speciation of Cr(VI) and Cr(III) was assessed. - Abstract: This study investigates the mechanisms of Cr(VI) adsorption on natural clay (illite and kaolinite) and synthetic (birnessite and ferrihydrite) minerals, including its speciation changes, and combining quantitative thermodynamically based mechanistic surface complexation models (SCMs) with spectroscopic measurements. Series of adsorption experiments have been performed at different pH values (3–10), ionic strengths (0.001–0.1 M KNO{sub 3}), sorbate concentrations (10{sup −4}, 10{sup −5}, and 10{sup −6} M Cr(VI)), and sorbate/sorbent ratios (50–500). Fourier transform infrared spectroscopy, X-ray photoelectron spectroscopy, and X-ray absorption spectroscopy were used to determine the surface complexes, including surface reactions. Adsorption of Cr(VI) is strongly ionic strength dependent. For ferrihydrite at pH <7, a simple diffuse-layer model provides a reasonable prediction of adsorption. For birnessite, bidentate inner-sphere complexes of chromate and dichromate resulted in a better diffuse-layer model fit. For kaolinite, outer-sphere complexation prevails mainly at lower Cr(VI) loadings. Dissolution of solid phases needs to be considered for better SCMs fits. The coupled SCM and spectroscopic approach is thus useful for investigating individual minerals responsible for Cr(VI) retention in soils, and improving the handling and remediation processes.

  10. Immune System Model Calibration by Genetic Algorithm

    NARCIS (Netherlands)

    Presbitero, A.; Krzhizhanovskaya, V.; Mancini, E.; Brands, R.; Sloot, P.

    2016-01-01

    We aim to develop a mathematical model of the human immune system for advanced individualized healthcare where medication plan is fine-tuned to fit a patient's conditions through monitored biochemical processes. One of the challenges is calibrating model parameters to satisfy existing experimental

  11. Application of a Lagrangian transport model to organo-mineral aggregates within the Nazaré canyon

    Directory of Open Access Journals (Sweden)

    S. Pando

    2013-01-01

    Full Text Available In this study, a hydrodynamic model was applied to the Nazaré submarine canyon with boundary forcing provided by an operational forecast model for the West Iberian coast. After validation, a Lagrangian transport model was coupled to the hydrodynamic model to study the transport patterns of the organo-mineral aggregates along the Nazaré canyon comparing three different classes of organo-mineral aggregates. The results showed that the transport in the canyon is neither constant, nor unidirectional and that there are preferential areas where suspended matter is resuspended, transported and deposited. The results showed that the transport of the larger size classes of organo-mineral aggregates is less pronounced, and that there is a decrease in the phytodetrital carbon flux along the canyon. The Nazaré canyon acts as depocenter of sedimentary organic matter and the canyon is not a conduit of organo-mineral aggregates to the deep sea.

  12. Modeling selenite adsorption envelopes on oxides, clay minerals, and soils using the triple layer model

    Science.gov (United States)

    Selenite adsorption behavior was investigated on amorphous aluminum and iron oxides, clay minerals: kaolinite, montmorillonite, and illite, and 45 surface and subsurface soil samples from the Southwestern and Midwestern regions of the USA as a function of solution pH. Selenite adsorption decreased ...

  13. Modeling selenate adsorption behavior on oxides, clay minerals, and soils using the triple layer model

    Science.gov (United States)

    Selenate adsorption behavior was investigated on amorphous aluminum oxide, amorphous iron oxide, goethite, clay minerals: kaolinites, montmorillonites, illite, and 18 soil samples from Hawaii, and the Southwestern and the Midwestern regions of the US as a function of solution pH. Selenate adsorpti...

  14. The quantitative genetics of indirect genetic effects: a selective review of modelling issues : Review

    NARCIS (Netherlands)

    Bijma, P.

    2014-01-01

    Indirect genetic effects (IGE) occur when the genotype of an individual affects the phenotypic trait value of another conspecific individual. IGEs can have profound effects on both the magnitude and the direction of response to selection. Models of inheritance and response to selection in traits sub

  15. [Improvement of genetics teaching using literature-based learning model].

    Science.gov (United States)

    Liang, Liang; Shiqian, Liang; Hongyan, Qin; Yong, Ji; Hua, Han

    2015-06-01

    Genetics is one of the most important courses for undergraduate students majoring in life science. In recent years, new knowledge and technologies are continually updated with deeper understanding of life science. However, the teaching model of genetics is still based on theoretical instruction, which makes the abstract principles hard to understand by students and directly affects the teaching effect. Thus, exploring a new teaching model is necessary. We have carried out a new teaching model, literature-based learning, in the course on Microbial Genetics for undergraduate students majoring in biotechnology since 2010. Here we comprehensively analyzed the implementation and application value of this model including pre-course knowledge, how to choose professional literature, how to organize teaching process and the significance of developing this new teaching model for students and teachers. Our literature-based learning model reflects the combination of "cutting-edge" and "classic" and makes book knowledge easy to understand, which improves students' learning effect, stimulates their interests, expands their perspectives and develops their ability. This practice provides novel insight into exploring new teaching model of genetics and cultivating medical talents capable of doing both basic and clinical research in the "precision medicine" era.

  16. Genetic variance of tolerance and the toxicant threshold model.

    Science.gov (United States)

    Tanaka, Yoshinari; Mano, Hiroyuki; Tatsuta, Haruki

    2012-04-01

    A statistical genetics method is presented for estimating the genetic variance (heritability) of tolerance to pollutants on the basis of a standard acute toxicity test conducted on several isofemale lines of cladoceran species. To analyze the genetic variance of tolerance in the case when the response is measured as a few discrete states (quantal endpoints), the authors attempted to apply the threshold character model in quantitative genetics to the threshold model separately developed in ecotoxicology. The integrated threshold model (toxicant threshold model) assumes that the response of a particular individual occurs at a threshold toxicant concentration and that the individual tolerance characterized by the individual's threshold value is determined by genetic and environmental factors. As a case study, the heritability of tolerance to p-nonylphenol in the cladoceran species Daphnia galeata was estimated by using the maximum likelihood method and nested analysis of variance (ANOVA). Broad-sense heritability was estimated to be 0.199 ± 0.112 by the maximum likelihood method and 0.184 ± 0.089 by ANOVA; both results implied that the species examined had the potential to acquire tolerance to this substance by evolutionary change.

  17. Modeling the MagnetoencephaloGram (MEG) Of Epileptic Patients Using Genetic Programming and Minimizing the Derived Models Using Genetic Algorithms

    Science.gov (United States)

    Theofilatos, Konstantinos; Georgopoulos, Efstratios; Likothanassis, Spiridon

    2009-09-01

    In this paper, a variation of traditional Genetic Programming(GP) is used to model the MagnetoencephaloGram(MEG) of Epileptic Patients. This variation is Linear Genetic Programming(LGP). LGP is a particular subset of GP wherein computer programs in population are represented as a sequence of instructions from imperative programming language or machine language. The derived models from this method were simplified using genetic algorithms. The proposed method was used to model the MEG signal of epileptic patients using 6 different datasets. Each dataset uses different number of previous values of MEG to predict the next value. The models were tested in datasets different from the ones which were used to produce them and the results were very promising.

  18. Predicting diabetic nephropathy using a multifactorial genetic model.

    Directory of Open Access Journals (Sweden)

    Ilana Blech

    Full Text Available AIMS: The tendency to develop diabetic nephropathy is, in part, genetically determined, however this genetic risk is largely undefined. In this proof-of-concept study, we tested the hypothesis that combined analysis of multiple genetic variants can improve prediction. METHODS: Based on previous reports, we selected 27 SNPs in 15 genes from metabolic pathways involved in the pathogenesis of diabetic nephropathy and genotyped them in 1274 Ashkenazi or Sephardic Jewish patients with Type 1 or Type 2 diabetes of >10 years duration. A logistic regression model was built using a backward selection algorithm and SNPs nominally associated with nephropathy in our population. The model was validated by using random "training" (75% and "test" (25% subgroups of the original population and by applying the model to an independent dataset of 848 Ashkenazi patients. RESULTS: The logistic model based on 5 SNPs in 5 genes (HSPG2, NOS3, ADIPOR2, AGER, and CCL5 and 5 conventional variables (age, sex, ethnicity, diabetes type and duration, and allowing for all possible two-way interactions, predicted nephropathy in our initial population (C-statistic = 0.672 better than a model based on conventional variables only (C = 0.569. In the independent replication dataset, although the C-statistic of the genetic model decreased (0.576, it remained highly associated with diabetic nephropathy (χ(2 = 17.79, p<0.0001. In the replication dataset, the model based on conventional variables only was not associated with nephropathy (χ(2 = 3.2673, p = 0.07. CONCLUSION: In this proof-of-concept study, we developed and validated a genetic model in the Ashkenazi/Sephardic population predicting nephropathy more effectively than a similarly constructed non-genetic model. Further testing is required to determine if this modeling approach, using an optimally selected panel of genetic markers, can provide clinically useful prediction and if generic models can be

  19. Modeling of Phenoxy Acid Herbicide Mineralization and Growth of Microbial Degraders in 15 Soils Monitored by Quantitative Real-Time PCR of the Functional tfdA Gene

    DEFF Research Database (Denmark)

    Bælum, Jacob; Prestat, Emmanuel; David, Maude M.

    2012-01-01

    continents. The mineralization patterns were fitted by zero/linear or exponential growth forms of the three-half-order models and by logarithmic (log), first-order, or zero-order kinetic models. Prior and subsequent to the mineralization event, tfdA genes were quantified using real-time PCR to estimate...... growth-linked kinetic models. A clear trend was observed that the mineralization rates of the three PAs occurred in the order 2,4-D > MCPA > MCPP, and a correlation was observed between rapid mineralization and soils exposed to PA previously. Finally, for 2,4-D mineralization, all seven mineralization...... patterns which were best fitted by the exponential model yielded a higher tfdA gene potential after mineralization had occurred than the three mineralization patterns best fitted by the Lin model....

  20. Model-free Estimation of Recent Genetic Relatedness

    Science.gov (United States)

    Conomos, Matthew P.; Reiner, Alexander P.; Weir, Bruce S.; Thornton, Timothy A.

    2016-01-01

    Genealogical inference from genetic data is essential for a variety of applications in human genetics. In genome-wide and sequencing association studies, for example, accurate inference on both recent genetic relatedness, such as family structure, and more distant genetic relatedness, such as population structure, is necessary for protection against spurious associations. Distinguishing familial relatedness from population structure with genotype data, however, is difficult because both manifest as genetic similarity through the sharing of alleles. Existing approaches for inference on recent genetic relatedness have limitations in the presence of population structure, where they either (1) make strong and simplifying assumptions about population structure, which are often untenable, or (2) require correct specification of and appropriate reference population panels for the ancestries in the sample, which might be unknown or not well defined. Here, we propose PC-Relate, a model-free approach for estimating commonly used measures of recent genetic relatedness, such as kinship coefficients and IBD sharing probabilities, in the presence of unspecified structure. PC-Relate uses principal components calculated from genome-screen data to partition genetic correlations among sampled individuals due to the sharing of recent ancestors and more distant common ancestry into two separate components, without requiring specification of the ancestral populations or reference population panels. In simulation studies with population structure, including admixture, we demonstrate that PC-Relate provides accurate estimates of genetic relatedness and improved relationship classification over widely used approaches. We further demonstrate the utility of PC-Relate in applications to three ancestrally diverse samples that vary in both size and genealogical complexity. PMID:26748516

  1. Genetic Algorithm Modeling with GPU Parallel Computing Technology

    CERN Document Server

    Cavuoti, Stefano; Brescia, Massimo; Pescapé, Antonio; Longo, Giuseppe; Ventre, Giorgio

    2012-01-01

    We present a multi-purpose genetic algorithm, designed and implemented with GPGPU / CUDA parallel computing technology. The model was derived from a multi-core CPU serial implementation, named GAME, already scientifically successfully tested and validated on astrophysical massive data classification problems, through a web application resource (DAMEWARE), specialized in data mining based on Machine Learning paradigms. Since genetic algorithms are inherently parallel, the GPGPU computing paradigm has provided an exploit of the internal training features of the model, permitting a strong optimization in terms of processing performances and scalability.

  2. Genetics

    Science.gov (United States)

    ... Inheritance; Heterozygous; Inheritance patterns; Heredity and disease; Heritable; Genetic markers ... The chromosomes are made up of strands of genetic information called DNA. Each chromosome contains sections of ...

  3. Calibration and validation of models for short-term decomposition and N mineralization of plant residues in the tropics

    Directory of Open Access Journals (Sweden)

    Alexandre Ferreira do Nascimento

    2012-12-01

    Full Text Available Insight of nutrient release patterns associated with the decomposition of plant residues is important for their effective use as a green manure in food production systems. Thus, this study aimed to evaluate the ability of the Century, APSIM and NDICEA simulation models for predicting the decomposition and N mineralization of crop residues in the tropical Atlantic forest biome, Brazil. The simulation models were calibrated based on actual decomposition and N mineralization rates of three types of crop residues with different chemical and biochemical composition. The models were also validated for different pedo-climatic conditions and crop residues conditions. In general, the accuracy of decomposition and N mineralization improved after calibration. Overall RMSE values for the decomposition and N mineralization of the crop materials varied from 7.4 to 64.6% before models calibration compared to 3.7 to 16.3 % after calibration. Therefore, adequate calibration of the models is indispensable for use them under humid tropical conditions. The NDICEA model generally outperformed the other models. However, the decomposition and N mineralization was not very accurate during the first 30 days of incubation, especially for easily decomposable crop residues. An additional model variable may be required to capture initial microbiological growth as affected by the moisture dynamics of the residues, as is the case in surface residues decomposition models.

  4. Modeling Lung Carcinogenesis in Radon-Exposed Miner Cohorts: Accounting for Missing Information on Smoking.

    Science.gov (United States)

    van Dillen, Teun; Dekkers, Fieke; Bijwaard, Harmen; Brüske, Irene; Wichmann, H-Erich; Kreuzer, Michaela; Grosche, Bernd

    2016-05-01

    Epidemiological miner cohort data used to estimate lung cancer risks related to occupational radon exposure often lack cohort-wide information on exposure to tobacco smoke, a potential confounder and important effect modifier. We have developed a method to project data on smoking habits from a case-control study onto an entire cohort by means of a Monte Carlo resampling technique. As a proof of principle, this method is tested on a subcohort of 35,084 former uranium miners employed at the WISMUT company (Germany), with 461 lung cancer deaths in the follow-up period 1955-1998. After applying the proposed imputation technique, a biologically-based carcinogenesis model is employed to analyze the cohort's lung cancer mortality data. A sensitivity analysis based on a set of 200 independent projections with subsequent model analyses yields narrow distributions of the free model parameters, indicating that parameter values are relatively stable and independent of individual projections. This technique thus offers a possibility to account for unknown smoking habits, enabling us to unravel risks related to radon, to smoking, and to the combination of both.

  5. Numerical Modeling of Arsenic Mobility during Reductive Iron-Mineral Transformations.

    Science.gov (United States)

    Rawson, Joey; Prommer, Henning; Siade, Adam; Carr, Jackson; Berg, Michael; Davis, James A; Fendorf, Scott

    2016-03-01

    Millions of individuals worldwide are chronically exposed to hazardous concentrations of arsenic from contaminated drinking water. Despite massive efforts toward understanding the extent and underlying geochemical processes of the problem, numerical modeling and reliable predictions of future arsenic behavior remain a significant challenge. One of the key knowledge gaps concerns a refined understanding of the mechanisms that underlie arsenic mobilization, particularly under the onset of anaerobic conditions, and the quantification of the factors that affect this process. In this study, we focus on the development and testing of appropriate conceptual and numerical model approaches to represent and quantify the reductive dissolution of iron oxides, the concomitant release of sorbed arsenic, and the role of iron-mineral transformations. The initial model development in this study was guided by data and hypothesized processes from a previously reported,1 well-controlled column experiment in which arsenic desorption from ferrihydrite coated sands by variable loads of organic carbon was investigated. Using the measured data as constraints, we provide a quantitative interpretation of the processes controlling arsenic mobility during the microbial reductive transformation of iron oxides. Our analysis suggests that the observed arsenic behavior is primarily controlled by a combination of reductive dissolution of ferrihydrite, arsenic incorporation into or co-precipitation with freshly transformed iron minerals, and partial arsenic redox transformations.

  6. Dissecting genetic and environmental mutation signatures with model organisms.

    Science.gov (United States)

    Segovia, Romulo; Tam, Annie S; Stirling, Peter C

    2015-08-01

    Deep sequencing has impacted on cancer research by enabling routine sequencing of genomes and exomes to identify genetic changes associated with carcinogenesis. Researchers can now use the frequency, type, and context of all mutations in tumor genomes to extract mutation signatures that reflect the driving mutational processes. Identifying mutation signatures, however, may not immediately suggest a mechanism. Consequently, several recent studies have employed deep sequencing of model organisms exposed to discrete genetic or environmental perturbations. These studies exploit the simpler genomes and availability of powerful genetic tools in model organisms to analyze mutation signatures under controlled conditions, forging mechanistic links between mutational processes and signatures. We discuss the power of this approach and suggest that many such studies may be on the horizon.

  7. Developmental genetics in emerging rodent models: case studies and perspectives.

    Science.gov (United States)

    Mallarino, Ricardo; Hoekstra, Hopi E; Manceau, Marie

    2016-08-01

    For decades, mammalian developmental genetic studies have focused almost entirely on two laboratory models: Mus and Rattus, species that breed readily in the laboratory and for which a wealth of molecular and genetic resources exist. These species alone, however, do not capture the remarkable diversity of morphological, behavioural and physiological traits seen across rodents, a group that represents >40% of all mammal species. Due to new advances in molecular tools and genomic technologies, studying the developmental events underlying natural variation in a wide range of species for a wide range of traits has become increasingly feasible. Here we review several recent studies and discuss how they not only provided technical resources for newly emerging rodent models in developmental genetics but also are instrumental in further encouraging scientists, from a wide range of research fields, to capitalize on the great diversity in development that has evolved among rodents.

  8. Nonlinear Modelling of Orthopyroxene and Amphibole Mineral Modes in Orbicules from Fisher Lake CA

    Science.gov (United States)

    Durant, D. G.; Fowler, A. D.

    2004-05-01

    Geochemical self-organization or spontaneous patterning, caused by positive feedback between reaction and transport, which creates amplification of any fluctuations in the system, can occur when a system is pushed into a far-from-equilibrium (FFE) state. The patterning is thus a construct of the system that allows the dissipation of those energies that pushed it into the FFE state and not a template forced onto the system by boundary conditions. The Fisher Lake CA orbicules contain plagioclase and orthopyroxene that show characteristics of FFE cooling; for instance, reverse-zoned radiating crystals organized in a highly complex pattern. The decimetre-scale orbicules are surrounded by a homogeneous mosaic of crystals characteristic of near-to-equilibrium (NTE) plutonic cooling environments. Thus the orbicular comb texture is interpreted as the response of a FFE magma toward achieving equilibrium. The innermost shell of an orbicule, containing the largest, most spectacular reverse-zoned branching orthopyroxene crystals, represents the largest step towards NTE. Rapid precipitation of minerals quickly decreased the free energy of the system such that an overshooting occurred, resulting in a chemical oscillation about the equilibrium value, which gradually decreased as the system approached NTE. Evidence of this mechanism is seen in the shell mineral modes of orthopyroxene and amphibole. Initially the oscillations are large and antithetical, i.e. as the amount of one mineral increases the other decreases and vice versa. The amplitudes of the oscillations gradually decrease flattening out to a more constant value or stable state; thus looking much like a damped pendulum. An empirical nonlinear model based on the modified Volterra-Lotka equations models these curves. The modelling demonstrates that pattern formation can occur without a periodic external forcing of the intensive variables of the magmatic system as the magma cools and solidifies. Smooth changes in these

  9. [Research on the model of spectral unmixing for minerals based on derivative of ratio spectroscopy].

    Science.gov (United States)

    Zhao, Heng-Qian; Zhang, Li-Fu; Wu, Tai-Xia; Huang, Chang-Ping

    2013-01-01

    The precise analysis of mineral abundance is a key difficulty in hyperspectral remote sensing research. In the present paper, based on linear spectral mixture model, the derivative of ratio spectroscopy (DRS) was introduced for spectral unmixing of visible to short-wave infrared (Vis-SWIR; 0.4 - 2.5 microm) reflectance data. The mixtures of different proportions of plaster and allochite were analyzed to estimate the accuracy of the spectral unmixing model based on DRS. For the best 5 strong linear bands, the Pearson correlation coefficient (PCC) of the abundances and the actual abundances were higher than 99.9%, while the root mean square error (RMSE) is less than 2.2%. The result shows that the new spectral unmixing model based on DRS is simple, of rigorous mathematical proof, and highly precise. It has a great potential in high-precision quantitative analysis of spectral mixture with fixed endmembers.

  10. Genetic programming-based chaotic time series modeling

    Institute of Scientific and Technical Information of China (English)

    张伟; 吴智铭; 杨根科

    2004-01-01

    This paper proposes a Genetic Programming-Based Modeling(GPM)algorithm on chaotic time series. GP is used here to search for appropriate model structures in function space,and the Particle Swarm Optimization(PSO)algorithm is used for Nonlinear Parameter Estimation(NPE)of dynamic model structures. In addition,GPM integrates the results of Nonlinear Time Series Analysis(NTSA)to adjust the parameters and takes them as the criteria of established models.Experiments showed the effectiveness of such improvements on chaotic time series modeling.

  11. Genetic signatures of natural selection in a model invasive ascidian

    Science.gov (United States)

    Lin, Yaping; Chen, Yiyong; Yi, Changho; Fong, Jonathan J.; Kim, Won; Rius, Marc; Zhan, Aibin

    2017-01-01

    Invasive species represent promising models to study species’ responses to rapidly changing environments. Although local adaptation frequently occurs during contemporary range expansion, the associated genetic signatures at both population and genomic levels remain largely unknown. Here, we use genome-wide gene-associated microsatellites to investigate genetic signatures of natural selection in a model invasive ascidian, Ciona robusta. Population genetic analyses of 150 individuals sampled in Korea, New Zealand, South Africa and Spain showed significant genetic differentiation among populations. Based on outlier tests, we found high incidence of signatures of directional selection at 19 loci. Hitchhiking mapping analyses identified 12 directional selective sweep regions, and all selective sweep windows on chromosomes were narrow (~8.9 kb). Further analyses indentified 132 candidate genes under selection. When we compared our genetic data and six crucial environmental variables, 16 putatively selected loci showed significant correlation with these environmental variables. This suggests that the local environmental conditions have left significant signatures of selection at both population and genomic levels. Finally, we identified “plastic” genomic regions and genes that are promising regions to investigate evolutionary responses to rapid environmental change in C. robusta. PMID:28266616

  12. Unraveling the genetics of chronic kidney disease using animal models

    NARCIS (Netherlands)

    Korstanje, Ron; DiPetrillo, K.

    2004-01-01

    Identifying genes underlying common forms of kidney disease in humans has proven difficult, expensive, and time consuming. Quantitative trait loci (QTL) for several complex traits are concordant among mice, rats, and humans, suggesting that genetic findings from these animal models are relevant to

  13. Noninvasive transcranial direct current stimulation in a genetic absence model

    NARCIS (Netherlands)

    Zobeiri, M.; Luijtelaar, E.L.J.M. van

    2013-01-01

    The proposed area of onset for absence epilepsy characteristic of spontaneously occurring spike and slow-wave discharges (SWDs) in the genetic absence rat model is the subgranular layer of the somatosensory cortex. Modulation of the hyperexcitable cortical foci by bilateral transcranial direct curre

  14. Sparse time series chain graphical models for reconstructing genetic networks

    NARCIS (Netherlands)

    Abegaz, Fentaw; Wit, Ernst

    2013-01-01

    We propose a sparse high-dimensional time series chain graphical model for reconstructing genetic networks from gene expression data parametrized by a precision matrix and autoregressive coefficient matrix. We consider the time steps as blocks or chains. The proposed approach explores patterns of co

  15. Geochemical modeling of fluid-fluid and fluid-mineral interactions during geological CO2 storage

    Science.gov (United States)

    Zhu, C.; Ji, X.; Lu, P.

    2013-12-01

    The long time required for effective CO2 storage makes geochemical modeling an indispensable tool for CCUS. One area of geochemical modeling research that is in urgent need is impurities in CO2 streams. Permitting impurities, such as H2S, in CO2 streams can lead to potential capital and energy savings. However, predicting the consequences of co-injection of CO2 and impurities into geological formations requires the understanding of the phase equilibrium and fluid-fluid interactions. To meet this need, we developed a statistical associating fluid theory (SAFT)-based equation of state (EOS) for the H2S-CO2-H2O-NaCl system at 373.15 dew pressures decrease with increasing H2S content, while the mass density increases at low pressures and decreases at high pressures. Furthermore, the EoS can be incorporated into reservoir simulators so that the dynamic development of mixed fluid plumes in the reservoir can be simulated. Accurate modeling of fluid-mineral interactions must confront unresolved uncertainties of silicate dissolution - precipitation reaction kinetics. Most prominent among these uncertainties is the well-known lab-field apparent discrepancy in dissolution rates. Although reactive transport models that simulate the interactions between reservoir rocks and brine, and their attendant effects on porosity and permeability changes, have proliferated, whether these results have acceptable uncertainties are unknown. We have conducted a series of batch experiments at elevated temperatures and numerical simulations of coupled dissolution and precipitation reactions. The results show that taking into account of reaction coupling is able to reduce the gap between the field and lab rates by about two orders of magnitude at elevated temperatures of 200-300 oC. Currently, we are using Si isotopes as a new tool to unravel the coupled reactions in ambient temperature laboratory experiments. These new experimental data, together with coupled reactive mass transport modeling

  16. Experimental Investigation and Simplistic Geochemical Modeling of CO2 Mineral Carbonation Using the Mount Tawai Peridotite

    Directory of Open Access Journals (Sweden)

    Omeid Rahmani

    2016-03-01

    Full Text Available In this work, the potential of CO2 mineral carbonation of brucite (Mg(OH2 derived from the Mount Tawai peridotite (forsterite based (Mg2SiO4 to produce thermodynamically stable magnesium carbonate (MgCO3 was evaluated. The effect of three main factors (reaction temperature, particle size, and water vapor were investigated in a sequence of experiments consisting of aqueous acid leaching, evaporation to dryness of the slurry mass, and then gas-solid carbonation under pressurized CO2. The maximum amount of Mg converted to MgCO3 is ~99%, which occurred at temperatures between 150 and 175 °C. It was also found that the reduction of particle size range from >200 to <75 µm enhanced the leaching rate significantly. In addition, the results showed the essential role of water vapor in promoting effective carbonation. By increasing water vapor concentration from 5 to 10 vol %, the mineral carbonation rate increased by 30%. This work has also numerically modeled the process by which CO2 gas may be sequestered, by reaction with forsterite in the presence of moisture. In both experimental analysis and geochemical modeling, the results showed that the reaction is favored and of high yield; going almost to completion (within about one year with the bulk of the carbon partitioning into magnesite and that very little remains in solution.

  17. Cluster approach to forming innovative model of developing mineral resources base of Russia’s regions

    Directory of Open Access Journals (Sweden)

    Andrey Gennad'evich Shelomentsev

    2012-03-01

    Full Text Available In this paper, the necessity of applying innovative model of developing mineral resources base of Russia’s regions and relevance of cluster approach for forming this model are proved. Components of process of clustering in the case of innovative developing mineral raw complex are proposed and analyzed: consolidation of socioeconomic potential of region, consolidation of potential of different branches of people’s activities, consolidation of processes of primary (wining sector in the single chain. In particular, the first component implies concentration of population in certain centers of gravitation. The second component implies consolidation of education, fundamental as well as applying science and production. The creating of administrative nets is necessary for that. For the realization of the first and the second components, the availability of clustering organization is necessary. The third component of process of clustering implies in prospect the adding of increasing amount of stages of product manufacturing. Eventually, the multi-stage structure of innovative process is analyzed.

  18. Effect of distance and depth on soil microbial biomass, N mineralization and genetic diversity of Rhizobia under Acacia senegal Tree

    Energy Technology Data Exchange (ETDEWEB)

    Fall, D.; Faye, A.; Sall, S. N.; Diouf, D.

    2009-07-01

    The relations between plants and soil biota involve positive and negative feedbacks between soil organisms, their chemical environment, and plants. Then, the characterization of microbial community functioning and their diversity are important to understand these linkages. An experiment was conducted in a field system for two years (2005 and 2006) to investigate the effect of distance from tree stem on soil microbial biomass, N mineral content and the diversity of rhizobia associated to Acacia senegal. (Author)

  19. Experimentation and modelling of mineral aerosol dissolution as source of transition metals in cloud droplets

    Science.gov (United States)

    Desboeufs, K.; Sofikitis, A.; Velay, J.; Losno, R.; Dulac, F.; Colin, J.

    2004-12-01

    Even at nano-molar concentrations, transition metals (TMI) could play an important role in the radical chemistry of the atmospheric liquid phase. For instance, cloud chemistry model calculations suggest that depletion of HOx by reactions between TMI and HO2/O2- radicals significantly slows down O3 production in polluted clouds. TMI are transferred into the liquid phase from aerosol particles by dissolution processes which can be a slow reaction. The dissolution kinetic of the solid phase thus competes with chemical kinetics in the homogeneous aqueous phase. It is therefore of importance to consider the evolution of TMI concentrations into cloud droplets in order to quantify the atmospheric impact of aerosols on the aqueous chemistry. Mineral particles including soil-derived particles and fly-ash are important sources of TMI in the troposphere.In order to parameterize the dissolution kinetic and concentrations of TMI from mineral particles into cloud droplets, we have conducted experimental laboratory simulations which mimic particles/water interactions occurring into droplets. These simulations were carried out in an open-flow reactor for typical atmospheric conditions (pH, ionic strength.). Data on TMI dissolution kinetic are provided for two generic kinds of mineral matrices from anthropogenic and natural sources: alumino-silicated and carbonaceous particles (dust, fly-ash, or urban particles). The concentrations of TMI released depend on pH, matrix type and particle-water contact time. The metals coming from carbonaceous particles are adsorbed impurities or salts and are very soluble with dissolution hardly dependent on pH. On the opposite, the metals dissolved from alumino-silicated particles are less soluble, notably the ones constitutive of the matrix network (Fe, Mn), and their dissolution is highly influenced by the pH. However, at a given pH, the results on the kinetic of dissolution emphasize that whatever the matrix, the TMI dissolution rates decrease

  20. Alteration minerals, fluids, and gases on early Mars: Predictions from 1-D flow geochemical modeling of mineral assemblages in meteorite ALH 84001

    Science.gov (United States)

    Melwani Daswani, Mohit; Schwenzer, Susanne P.; Reed, Mark H.; Wright, Ian P.; Grady, Monica M.

    2016-11-01

    Clay minerals, although ubiquitous on the ancient terrains of Mars, have not been observed in Martian meteorite Allan Hills (ALH) 84001, which is an orthopyroxenite sample of the early Martian crust with a secondary carbonate assemblage. We used a low-temperature (20 °C) one-dimensional (1-D) transport thermochemical model to investigate the possible aqueous alteration processes that produced the carbonate assemblage of ALH 84001 while avoiding the coprecipitation of clay minerals. We found that the carbonate in ALH 84001 could have been produced in a process, whereby a low-temperature ( 20 °C) fluid, initially equilibrated with the early Martian atmosphere, moved through surficial clay mineral and silica-rich layers, percolated through the parent rock of the meteorite, and precipitated carbonates (thereby decreasing the partial pressure of CO2) as it evaporated. This finding requires that before encountering the unweathered orthopyroxenite host of ALH 84001, the fluid permeated rock that became weathered during the process. We were able to predict the composition of the clay minerals formed during weathering, which included the dioctahedral smectite nontronite, kaolinite, and chlorite, all of which have been previously detected on Mars. We also calculated host rock replacement in local equilibrium conditions by the hydrated silicate talc, which is typically considered to be a higher temperature hydrothermal phase on Earth, but may have been a common constituent in the formation of Martian soils through pervasive aqueous alteration. Finally, goethite and magnetite were also found to precipitate in the secondary alteration assemblage, the latter associated with the generation of H2. Apparently, despite the limited water-rock interaction that must have led to the formation of the carbonates 3.9 Ga ago, in the vicinity of the ALH 84001 source rocks, clay formation would have been widespread.

  1. Occurrence model for volcanogenic beryllium deposits: Chapter F in Mineral deposit models for resource assessment

    Science.gov (United States)

    Foley, Nora K.; Hofstra, Albert H.; Lindsey, David A.; Seal, Robert R., II; Jaskula, Brian W.; Piatak, Nadine M.

    2012-01-01

    Current global and domestic mineral resources of beryllium (Be) for industrial uses are dominated by ores produced from deposits of the volcanogenic Be type. Beryllium deposits of this type can form where hydrothermal fluids interact with fluorine and lithophile-element (uranium, thorium, rubidium, lithium, beryllium, cesium, tantalum, rare earth elements, and tin) enriched volcanic rocks that contain a highly reactive lithic component, such as carbonate clasts. Volcanic and hypabyssal high-silica biotite-bearing topaz rhyolite constitutes the most well-recognized igneous suite associated with such Be deposits. The exemplar setting is an extensional tectonic environment, such as that characterized by the Basin and Range Province, where younger topaz-bearing igneous rock sequences overlie older dolomite, quartzite, shale, and limestone sequences. Mined deposits and related mineralized rocks at Spor Mountain, Utah, make up a unique economic deposit of volcanogenic Be having extensive production and proven and probable reserves. Proven reserves in Utah, as reported by the U.S. Geological Survey National Mineral Information Center, total about 15,900 tons of Be that are present in the mineral bertrandite (Be4Si2O7(OH)2). At the type locality for volcanogenic Be, Spor Mountain, the tuffaceous breccias and stratified tuffs that host the Be ore formed as a result of explosive volcanism that brought carbonate and other lithic fragments to the surface through vent structures that cut the underlying dolomitic Paleozoic sedimentary rock sequences. The tuffaceous sediments and lithic clasts are thought to make up phreatomagmatic base surge deposits. Hydrothermal fluids leached Be from volcanic glass in the tuff and redeposited the Be as bertrandite upon reaction of the hydrothermal fluid with carbonate clasts in lithic-rich sections of tuff. The localization of the deposits in tuff above fluorite-mineralized faults in carbonate rocks, together with isotopic evidence for the

  2. Modification of the RothC model to simulate soil C mineralization of exogenous organic matter

    Science.gov (United States)

    Mondini, Claudio; Cayuela, Maria Luz; Sinicco, Tania; Fornasier, Flavio; Galvez, Antonia; Sánchez-Monedero, Miguel Angel

    2017-07-01

    The development of soil organic C (SOC) models capable of producing accurate predictions for the long-term decomposition of exogenous organic matter (EOM) in soils is important for the effective management of organic amendments. However, reliable C modeling in amended soils requires specific optimization of current C models to take into account the high variability in EOM origin and properties. The aim of this work was to improve the prediction of C mineralization rates in amended soils by modifying the RothC model to encompass a better description of EOM quality. The standard RothC model, involving C input to the soil only as decomposable (DPM) or resistant (RPM) organic material, was modified by introducing additional pools of decomposable (DEOM), resistant (REOM) and humified (HEOM) EOM. The partitioning factors and decomposition rates of the additional EOM pools were estimated by model fitting to the respiratory curves of amended soils. For this task, 30 EOMs from 8 contrasting groups (compost, anaerobic digestates, sewage sludge, agro-industrial waste, crop residues, bioenergy by-products, animal residues and meat and bone meals) were added to 10 soils and incubated under different conditions. The modified RothC model was fitted to C mineralization curves in amended soils with great accuracy (mean correlation coefficient 0.995). In contrast to the standard model, the EOM-optimized RothC was able to better accommodate the large variability in EOM source and composition, as indicated by the decrease in the root mean square error of the simulations for different EOMs (from 29.9 to 3.7 % and 20.0 to 2.5 % for soils amended with bioethanol residue and household waste compost, respectively). The average decomposition rates for DEOM and REOM pools were 89 and 0.4 yr-1, higher than the standard model coefficients for DPM (10 yr-1) and RPM (0.3 yr-1). The results indicate that the explicit treatment of EOM heterogeneity enhances the model ability to describe amendment

  3. A genetic algorithm for solving supply chain network design model

    Science.gov (United States)

    Firoozi, Z.; Ismail, N.; Ariafar, S. H.; Tang, S. H.; Ariffin, M. K. M. A.

    2013-09-01

    Network design is by nature costly and optimization models play significant role in reducing the unnecessary cost components of a distribution network. This study proposes a genetic algorithm to solve a distribution network design model. The structure of the chromosome in the proposed algorithm is defined in a novel way that in addition to producing feasible solutions, it also reduces the computational complexity of the algorithm. Computational results are presented to show the algorithm performance.

  4. From classical genetics to quantitative genetics to systems biology: modeling epistasis.

    Directory of Open Access Journals (Sweden)

    David L Aylor

    2008-03-01

    Full Text Available Gene expression data has been used in lieu of phenotype in both classical and quantitative genetic settings. These two disciplines have separate approaches to measuring and interpreting epistasis, which is the interaction between alleles at different loci. We propose a framework for estimating and interpreting epistasis from a classical experiment that combines the strengths of each approach. A regression analysis step accommodates the quantitative nature of expression measurements by estimating the effect of gene deletions plus any interaction. Effects are selected by significance such that a reduced model describes each expression trait. We show how the resulting models correspond to specific hierarchical relationships between two regulator genes and a target gene. These relationships are the basic units of genetic pathways and genomic system diagrams. Our approach can be extended to analyze data from a variety of experiments, multiple loci, and multiple environments.

  5. The significance of genetics in pathophysiologic models of premature birth.

    Science.gov (United States)

    Uberos, Jose

    2017-05-31

    Prematurity is a major health problem in all countries, especially in certain ethic groups and increasing recurrence imply the influence of genetic factors. Published genetic polymorphisms are identified in relation to the 4 pathophysiological models of prematurity described: Chorioamniotic-decidual inflammation, premature contraction pathway, decidual haemorrhage and susceptibility to environmental toxins. 240 articles are identified, 52 articles are excluded because they are not original, not written in English or duplicated. From them 125 articles were included in qualitative analysis This review aims to update recent knowledge about genes associated with premature birth.

  6. Canalization and symmetry in Boolean models for genetic regulatory networks

    Energy Technology Data Exchange (ETDEWEB)

    Reichhardt, C J Olson [Theoretical Division and Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Bassler, Kevin E [Department of Physics, University of Houston, Houston, TX 77204-5005 (United States)

    2007-04-20

    Canalization of genetic regulatory networks has been argued to be favoured by evolutionary processes due to the stability that it can confer to phenotype expression. We explore whether a significant amount of canalization and partial canalization can arise in purely random networks in the absence of evolutionary pressures. We use a mapping of the Boolean functions in the Kauffman N-K model for genetic regulatory networks onto a k-dimensional Ising hypercube (where k = K) to show that the functions can be divided into different classes strictly due to geometrical constraints. The classes can be counted and their properties determined using results from group theory and isomer chemistry. We demonstrate that partially canalizing functions completely dominate all possible Boolean functions, particularly for higher k. This indicates that partial canalization is extremely common, even in randomly chosen networks, and has implications for how much information can be obtained in experiments on native state genetic regulatory networks.

  7. Fuzzy Modelling of Knee Joint with Genetic Optimization

    Directory of Open Access Journals (Sweden)

    B. S. K. K. Ibrahim

    2011-01-01

    Full Text Available Modelling of joint properties of lower limbs in people with spinal cord injury is significantly challenging for researchers due to the complexity of the system. The objective of this study is to develop a knee joint model capable of relating electrical parameters to dynamic joint torque as well as knee angle for functional electrical stimulation application. The joint model consists of a segmental dynamic, time-invariant passive properties and uncertain time-variant active properties. The knee joint model structure comprising optimised equations of motion and fuzzy models to represent the passive viscoelasticity and active muscle properties is formulated. The model thus formulated is optimised using genetic optimization, and validated against experimental data. The developed model can be used for simulation of joint movements as well as for control development. The results show that the model developed gives an accurate dynamic characterisation of the knee joint.

  8. Learning with Admixture: Modeling, Optimization, and Applications in Population Genetics

    DEFF Research Database (Denmark)

    Cheng, Jade Yu

    2016-01-01

    Population genetics is a branch of applied mathematics. It is a translation of scientific observations into mathematical models and their manipulations in order to produce quantitative predictions about evolution. Combining knowledge from genetics, statistics, and computer science, population...... data. Ohana's admixture module is based on classical structure modeling but uses new optimization subroutines through quadratic programming, which outperform the current state-of-the-art software in both speed and accuracy. Ohana presents a new method for phylogenetic tree inference using Gaussian...... the foundation for both CoalHMM and Ohana. Optimization modeling has been the main theme throughout my PhD, and it will continue to shape my work for the years to come. The algorithms and software I developed to study historical admixture and population evolution fall into a larger family of machine learning...

  9. Phase and sedimentation behavior of oil (octane) dispersions in the presence of model mineral aggregates.

    Science.gov (United States)

    Gupta, Anju; Sender, Maximilian; Fields, Sarah; Bothun, Geoffrey D

    2014-10-15

    Adsorption of suspended particles to the interface of surfactant-dispersed oil droplets can alter emulsion phase and sedimentation behavior. This work examines the effects of model mineral aggregates (silica nanoparticle aggregates or SNAs) on the behavior of oil (octane)-water emulsions prepared using sodium bis(2-ethylhexyl) sulfosuccinate (DOSS). Experiments were conducted at different SNA hydrophobicities in deionized and synthetic seawater (SSW), and at 0.5mM and 2.5mM DOSS. SNAs were characterized by thermogravimetric analysis (TGA) and dynamic light scattering (DLS), and the emulsions were examined by optical and cryogenic scanning electron microscopy. In deionized water, oil-in-water emulsions were formed with DOSS and the SNAs did not adhere to the droplets or alter emulsion behavior. In SSW, water-in-oil emulsions were formed with DOSS and SNA-DOSS binding through cation bridging led to phase inversion to oil-in-water emulsions. Droplet oil-mineral aggregates (OMAs) were observed for hydrophilic SNAs, while hydrophobic SNAs yielded quickly sedimenting agglomerated OMAs.

  10. Modelling and Observation of Mineral Dust Optical Properties over Central Europe

    Science.gov (United States)

    Chilinski, Michał T.; Markowicz, Krzysztof M.; Zawadzka, Olga; Stachlewska, Iwona S.; Kumala, Wojciech; Petelski, Tomasz; Makuch, Przemysław; Westphal, Douglas L.; Zagajewski, Bogdan

    2016-12-01

    This paper is focused on Saharan dust transport to Central Europe/Poland; we compare properties of atmospheric Saharan dust using data from NAAPS, MACC, AERONET as well as observations obtained during HyMountEcos campaign in June 2012. Ten years of dust climatology shows that long-range transport of Saharan dust to Central Europe is mostly during spring and summer. HYSPLIT back-trajectories indicate airmass transport mainly in November, but it does not agree with modeled maxima of dust optical depth. NAAPS model shows maximum of dust optical depth ( 0.04-0.05, 550 nm) in April-May, but the MACC modeled peak is broader ( 0.04). During occurrence of mineral dust over Central-Europe for 14% (NAAPS) / 12% (MACC) of days dust optical depths are above 0.05 and during 4% (NAAPS) / 2.5% (MACC) of days dust optical depths exceed 0.1. The HyMountEcos campaign took place in June-July 2012 in the mountainous region of Karkonosze. The analysis includes remote sensing data from lidars, sun-photometers, and numerical simulations from NAAPS, MACC, DREAM8b models. Comparison of simulations with observations demonstrates the ability of models to reasonably reproduce aerosol vertical distributions and their temporal variability. However, significant differences between simulated and measured AODs were found. The best agreement was achieved for MACC model.

  11. Modelling and Observation of Mineral Dust Optical Properties over Central Europe

    Directory of Open Access Journals (Sweden)

    Chilinski Michał T.

    2016-12-01

    Full Text Available This paper is focused on Saharan dust transport to Central Europe/Poland; we compare properties of atmospheric Saharan dust using data from NAAPS, MACC, AERONET as well as observations obtained during HyMountEcos campaign in June 2012. Ten years of dust climatology shows that long-range transport of Saharan dust to Central Europe is mostly during spring and summer. HYSPLIT back-trajectories indicate airmass transport mainly in November, but it does not agree with modeled maxima of dust optical depth. NAAPS model shows maximum of dust optical depth (~0.04-0.05, 550 nm in April-May, but the MACC modeled peak is broader (~0.04. During occurrence of mineral dust over Central-Europe for 14% (NAAPS / 12% (MACC of days dust optical depths are above 0.05 and during 4% (NAAPS / 2.5% (MACC of days dust optical depths exceed 0.1. The HyMountEcos campaign took place in June-July 2012 in the mountainous region of Karkonosze. The analysis includes remote sensing data from lidars, sun-photometers, and numerical simulations from NAAPS, MACC, DREAM8b models. Comparison of simulations with observations demonstrates the ability of models to reasonably reproduce aerosol vertical distributions and their temporal variability. However, significant differences between simulated and measured AODs were found. The best agreement was achieved for MACC model.

  12. Investigation of a mineral melting cupola furnace. Part II. Mathematical modeling

    Energy Technology Data Exchange (ETDEWEB)

    Leth-Miller, R.; Jensen, A.D.; Glarborg, P.; Jensen, L.M.; Hansen, P.B.; Jorgensen, S.B. [Rockwool International AS, Hedehusene (Denmark)

    2003-12-24

    A mathematical model of a mineral melting cupola furnace for stone wool production has been developed for improving cupola operation. The 1-D, first-engineering-principles model includes mass and heat balances for the gas phase, five solid phases, and four liquid phases. The gas and solid/liquid phases flow countercurrently. Seven chemical reactions account for the conversions of coke, iron oxide, limestone, and gaseous species. The heterogeneous reactions of coke conversion are limited by both kinetics and mass transport. Heat transfer between phases is modeled including both convection and radiation. The model predicts gas concentrations; mass flow rates; and temperature profiles of the solid, melt, and gas in the cupola, as well as heat loss to the water-cooled walls. Inputs to the model include the coke, rock, and blast air properties, the blast air amount, and the coke percentage in the charge. The unknown model parameters are estimated on the basis of input/output measurements. A comparison of the predicted and measured concentration and temperature profiles inside the cupola shows good agreement.

  13. An animal model of differential genetic risk for methamphetamine intake

    Directory of Open Access Journals (Sweden)

    Tamara ePhillips

    2015-09-01

    Full Text Available The question of whether genetic factors contribute to risk for methamphetamine (MA use and dependence has not been intensively investigated. Compared to human populations, genetic animal models offer the advantages of control over genetic family history and drug exposure. Using selective breeding, we created lines of mice that differ in genetic risk for voluntary MA intake and identified the chromosomal addresses of contributory genes. A quantitative trait locus was identified on chromosome 10 that accounts for more than 50% of the genetic variance in MA intake in the selected mouse lines. In addition, behavioral and physiological screening identified differences corresponding with risk for MA intake that have generated hypotheses that are testable in humans. Heightened sensitivity to aversive and certain physiological effects of MA, such as MA-induced reduction in body temperature, are hallmarks of mice bred for low MA intake. Furthermore, unlike MA-avoiding mice, MA-preferring mice are sensitive to rewarding and reinforcing MA effects, and to MA-induced increases in brain extracellular dopamine levels. Gene expression analyses implicate the importance of a network enriched in transcription factor genes, some of which regulate the mu opioid receptor gene, Oprm1, in risk for MA use. Neuroimmune factors appear to play a role in differential response to MA between the mice bred for high and low intake. In addition, chromosome 10 candidate gene studies provide strong support for a trace amine associated receptor 1 gene, Taar1, polymorphism in risk for MA intake. MA is a trace amine-associated receptor 1 (TAAR1 agonist, and a non-functional Taar1 allele segregates with high MA consumption. Thus, reduced TAAR1 function has the potential to increase risk for MA use. Overall, existing findings support the MA drinking lines as a powerful model for identifying genetic factors involved in determining risk for harmful MA use. Future directions include the

  14. Using the extended parallel process model to prevent noise-induced hearing loss among coal miners in Appalachia

    Energy Technology Data Exchange (ETDEWEB)

    Murray-Johnson, L.; Witte, K.; Patel, D.; Orrego, V.; Zuckerman, C.; Maxfield, A.M.; Thimons, E.D. [Ohio State University, Columbus, OH (US)

    2004-12-15

    Occupational noise-induced hearing loss is the second most self-reported occupational illness or injury in the United States. Among coal miners, more than 90% of the population reports a hearing deficit by age 55. In this formative evaluation, focus groups were conducted with coal miners in Appalachia to ascertain whether miners perceive hearing loss as a major health risk and if so, what would motivate the consistent wearing of hearing protection devices (HPDs). The theoretical framework of the Extended Parallel Process Model was used to identify the miners' knowledge, attitudes, beliefs, and current behaviors regarding hearing protection. Focus group participants had strong perceived severity and varying levels of perceived susceptibility to hearing loss. Various barriers significantly reduced the self-efficacy and the response efficacy of using hearing protection.

  15. [The emphases and basic procedures of genetic counseling in psychotherapeutic model].

    Science.gov (United States)

    Zhang, Yuan-Zhi; Zhong, Nanbert

    2006-11-01

    The emphases and basic procedures of genetic counseling are all different with those in old models. In the psychotherapeutic model, genetic counseling will not only focus on counselees' genetic disorders and birth defects, but also their psychological problems. "Client-centered therapy" termed by Carl Rogers plays an important role in genetic counseling process. The basic procedures of psychotherapeutic model of genetic counseling include 7 steps: initial contact, introduction, agendas, inquiry of family history, presenting information, closing the session and follow-up.

  16. A unified model of the standard genetic code.

    Science.gov (United States)

    José, Marco V; Zamudio, Gabriel S; Morgado, Eberto R

    2017-03-01

    The Rodin-Ohno (RO) and the Delarue models divide the table of the genetic code into two classes of aminoacyl-tRNA synthetases (aaRSs I and II) with recognition from the minor or major groove sides of the tRNA acceptor stem, respectively. These models are asymmetric but they are biologically meaningful. On the other hand, the standard genetic code (SGC) can be derived from the primeval RNY code (R stands for purines, Y for pyrimidines and N any of them). In this work, the RO-model is derived by means of group actions, namely, symmetries represented by automorphisms, assuming that the SGC originated from a primeval RNY code. It turns out that the RO-model is symmetric in a six-dimensional (6D) hypercube. Conversely, using the same automorphisms, we show that the RO-model can lead to the SGC. In addition, the asymmetric Delarue model becomes symmetric by means of quotient group operations. We formulate isometric functions that convert the class aaRS I into the class aaRS II and vice versa. We show that the four polar requirement categories display a symmetrical arrangement in our 6D hypercube. Altogether these results cannot be attained, neither in two nor in three dimensions. We discuss the present unified 6D algebraic model, which is compatible with both the SGC (based upon the primeval RNY code) and the RO-model.

  17. Genetic variants associated with neurodegenerative Alzheimer disease in natural models.

    Science.gov (United States)

    Salazar, Claudia; Valdivia, Gonzalo; Ardiles, Álvaro O; Ewer, John; Palacios, Adrián G

    2016-02-26

    The use of transgenic models for the study of neurodegenerative diseases has made valuable contributions to the field. However, some important limitations, including protein overexpression and general systemic compensation for the missing genes, has caused researchers to seek natural models that show the main biomarkers of neurodegenerative diseases during aging. Here we review some of these models-most of them rodents, focusing especially on the genetic variations in biomarkers for Alzheimer diseases, in order to explain their relationships with variants associated with the occurrence of the disease in humans.

  18. A Tri-Part Model for Genetics Literacy: Exploring Undergraduate Student Reasoning about Authentic Genetics Dilemmas

    Science.gov (United States)

    Shea, Nicole A.; Duncan, Ravit Golan; Stephenson, Celeste

    2015-01-01

    Genetics literacy is becoming increasingly important as advancements in our application of genetic technologies such as stem cell research, cloning, and genetic screening become more prevalent. Very few studies examine how genetics literacy is applied when reasoning about authentic genetic dilemmas. However, there is evidence that situational…

  19. A Tri-Part Model for Genetics Literacy: Exploring Undergraduate Student Reasoning about Authentic Genetics Dilemmas

    Science.gov (United States)

    Shea, Nicole A.; Duncan, Ravit Golan; Stephenson, Celeste

    2015-01-01

    Genetics literacy is becoming increasingly important as advancements in our application of genetic technologies such as stem cell research, cloning, and genetic screening become more prevalent. Very few studies examine how genetics literacy is applied when reasoning about authentic genetic dilemmas. However, there is evidence that situational…

  20. APPRAISAL OF THE SNAP MODEL FOR PREDICTING NITROGEN MINERALIZATION IN TROPICAL SOILS UNDER EUCALYPTUS

    Directory of Open Access Journals (Sweden)

    Philip James Smethurst

    2015-04-01

    Full Text Available The Soil Nitrogen Availability Predictor (SNAP model predicts daily and annual rates of net N mineralization (NNM based on daily weather measurements, daily predictions of soil water and soil temperature, and on temperature and moisture modifiers obtained during aerobic incubation (basal rate. The model was based on in situ measurements of NNM in Australian soils under temperate climate. The purpose of this study was to assess this model for use in tropical soils under eucalyptus plantations in São Paulo State, Brazil. Based on field incubations for one month in three, NNM rates were measured at 11 sites (0-20 cm layer for 21 months. The basal rate was determined in in situ incubations during moist and warm periods (January to March. Annual rates of 150-350 kg ha-1 yr-1 NNM predicted by the SNAP model were reasonably accurate (R2 = 0.84. In other periods, at lower moisture and temperature, NNM rates were overestimated. Therefore, if used carefully, the model can provide adequate predictions of annual NNM and may be useful in practical applications. For NNM predictions for shorter periods than a year or under suboptimal incubation conditions, the temperature and moisture modifiers need to be recalibrated for tropical conditions.

  1. Using ICP and micro-PIXE to investigate possible differences in the mineral composition of genetically modified versus wild-type sorghum grain

    Science.gov (United States)

    Ndimba, R.; Cloete, K.; Mehlo, L.; Kossmann, J.; Mtshali, C.; Pineda-Vargas, C.

    2017-08-01

    In the present study, possible differences in the mineral composition of transgenic versus non-transgenic sorghum grains were investigated using inductively coupled atomic emission spectroscopy (ICP-AES); and, in-tissue elemental mapping by micro Proton-Induced X-ray Emission (micro-PIXE) analysis. ICP AES was used to analyse the bulk mineral content of the wholegrain flour derived from each genotype; whilst micro-PIXE was used to interrogate localised differences in mineral composition specific to certain areas of the grain, such as the bran layer and the central endosperm tissue. According to the results obtained, no significant difference in the average Fe, Zn or Ca content was found to differentiate the transgenic from the wild-type grain using ICP-AES. However, using micro-PIXE, a significant reduction in zinc could be detected in the bran layer of the transgenic grains relative to wild-type. Although it is difficult to draw firm conclusions, as a result of the small sample size used in this study, micro-PIXE has nonetheless proven itself as a useful technique for highlighting the possibility that there may be reduced levels of zinc accumulation in the bran layer of the transgenic grains. Given that the genetic modification targets proteins that are highly concentrated in certain parts of the bran tissue, it seems plausible that the reduced levels of zinc may be an unintended consequence of the silencing of kafirin proteins. Although no immediate health or nutritional concerns emerge from this preliminary finding, it is noted that zinc plays an important biological role within this part of the grain as a structural stabiliser and antioxidant factor. Further study is therefore needed to assess more definitively the extent of the apparent localised reduction in zinc in the transgenic grains and how this may affect other important grain quality characteristics.

  2. 3D Geologic Modeling. The example of the Farim-Saliquinhé Phosphates Mineralization.

    Science.gov (United States)

    Ferreira, António; Charifo, Gilberto; Almeida, José

    2010-05-01

    The construction of three-dimensional geologic models representing both the structure and properties inherent to each geological unit is nowadays possible due to the computational development of the last decades. The 3D Geologic Modeling (3DGM) is very efficient for storage, display and transfer of geoscience information, and is a key tool in the oil industry in particular for the reservoir characterization and modeling; its use in other geosciences areas has been growing in recent years but is still scarce. In the present work we show a 3D geologic model of the phosphates mineralization of Farim-Saliquinhé (Guinea-Bissau) as a first example of the work being developed in the research center CICEGe (FCT-UNL) by its novel research group on 3DGM, and to demonstrate the usefulness of this kind of geologic models, built with appropriate software, in order to better represent, study, characterize and visualize a geologic case study. The phosphates mineralization of Farim-Saliquinhé (Guinea-Bissau) is a sedimentary deposit located near Saliquinhé, Farim and the Rio Cachéu. The deposit is composed by two members: 1) FPB, an early Middle to Upper Lutetian calcareous-phosphate member; 2) FPA, an upper member of descarbonatized phosphate. Micritic limestones are underlying the mineralized layers, while dolomitic limestones, the FPO phosphate interval, and a younger sandy clayey cover are overlying the phosphatic members (BRGM, 1983; Prian et al., 1987). This work is based on geologic and geochemical data from 69 vertical boreholes carried out by BRGM in the 80s (completed with topographic data). This survey covered an area of about 10x5 km and was aimed to determine the geometry and the reserves of the FPA and FPB phosphate mineralization. The 3D geologic model was developed in gOcad software, which uses a distinctive interpolation method to build the geometry of objects, the DSI - discrete smooth interpolation. The 3D geologic model was built on the BRGM's study area

  3. Genetic Mouse Models of Huntington's Disease: Focus on Electrophysiological Mechanisms

    Directory of Open Access Journals (Sweden)

    Carlos Cepeda

    2010-03-01

    Full Text Available The discovery of the HD (Huntington's disease gene in 1993 led to the creation of genetic mouse models of the disease and opened the doors for mechanistic studies. In particular, the early changes and progression of the disease could be followed and examined systematically. The present review focuses on the contribution of these genetic mouse models to the understanding of functional changes in neurons as the HD phenotype progresses, and concentrates on two brain areas: the striatum, the site of most conspicuous pathology in HD, and the cortex, a site that is becoming increasingly important in understanding the widespread behavioural abnormalities. Mounting evidence points to synaptic abnormalities in communication between the cortex and striatum and cell-cell interactions as major determinants of HD symptoms, even in the absence of severe neuronal degeneration and death.

  4. Exchange Rate Prediction using Neural – Genetic Model

    Directory of Open Access Journals (Sweden)

    MECHGOUG Raihane

    2012-10-01

    Full Text Available Neural network have successfully used for exchange rate forecasting. However, due to a large number of parameters to be estimated empirically, it is not a simple task to select the appropriate neural network architecture for exchange rate forecasting problem.Researchers often overlook the effect of neural network parameters on the performance of neural network forecasting. The performance of neural network is critically dependant on the learning algorithms, thenetwork architecture and the choice of the control parameters. Even when a suitable setting of parameters (weight can be found, the ability of the resulting network to generalize the data not seen during learning may be far from optimal. For these reasons it seemslogical and attractive to apply genetic algorithms. Genetic algorithms may provide a useful tool for automating the design of neural network. The empirical results on foreign exchange rate prediction indicate that the proposed hybrid model exhibits effectively improved accuracy, when is compared with some other time series forecasting models.

  5. Non-electrostatic surface complexation models for protons and lead(II) sorption onto single minerals and their mixture.

    Science.gov (United States)

    Pagnanelli, Francesca; Bornoroni, Lorena; Moscardini, Emanuela; Toro, Luigi

    2006-05-01

    Potentiometric titrations and lead sorption tests were conducted using muscovite, clinochlore, hematite, goethite, quartz, and a mixture of these same minerals. Mechanistic models were developed to represent and interpret these data. The aim was isolating the specific contribution of each mineral in proton and lead binding. Acid-base properties of each single mineral as well as their mixture were represented by discrete models, which consider the dissociation of n monoprotic sites (n-site/n-K(H) models). A one-site/one-K(H) model (logK(H1) = 10.69) was chosen for quartz (dissociation of SiOH edge hydroxyl groups). Goethite and hematite (FeOH groups) were represented by the same one-site/one-K(H) model (logK(H1) = 10.35). Three-site/three-K(H) models were used for muscovite (logK(H1) = 4.18; logK(H2) = 6.65; logK(H3) = 9.67) and clinochlore (logK(H1) = 3.84; logK(H2) = 6.57; logK(H3) = 9.71) assuming that SiOH and AlOH of the aluminosilicate matrix dissociate in the acid-neutral pH range while SiOH groups of quartz inclusions dissociate in the basic range. Similarly, the mixture of these minerals was represented by a three-site/three-K(H) model (logK(H1) = 3.39; logK(H2) = 6.72; logK(H3) = 10.82). According to crossed comparisons with single minerals, the first two sites of the mixture were associated with the aluminosilicate matrix (SiOH and AlOH respectively) and the third site with iron oxides (FeOH) and quartz groups. Additivity of proton binding in the mixture was demonstrated by simulating the mixture's titration curve. A unified model for the entire set of titration curves (single minerals and mixture) was also developed introducing a three-peak distribution function for proton affinity constants. Experimental data for lead sorption onto the mixture and individual minerals in 3-5 pH range denoted the competition between protons and metallic ions. The entire set of lead isotherms (individual mineral and mixture data) was represented adequately by a unified

  6. A Building Model Framework for a Genetic Algorithm Multi-objective Model Predictive Control

    DEFF Research Database (Denmark)

    Arendt, Krzysztof; Ionesi, Ana; Jradi, Muhyiddine

    2016-01-01

    implemented only in few buildings. The following difficulties hinder the widespread usage of MPC: (1) significant model development time, (2) limited portability of models, (3) model computational demand. In the present study a new model development framework for an MPC system based on a Genetic Algorithm (GA...

  7. Inferring modulators of genetic interactions with epistatic nested effects models.

    Science.gov (United States)

    Pirkl, Martin; Diekmann, Madeline; van der Wees, Marlies; Beerenwinkel, Niko; Fröhlich, Holger; Markowetz, Florian

    2017-04-01

    Maps of genetic interactions can dissect functional redundancies in cellular networks. Gene expression profiles as high-dimensional molecular readouts of combinatorial perturbations provide a detailed view of genetic interactions, but can be hard to interpret if different gene sets respond in different ways (called mixed epistasis). Here we test the hypothesis that mixed epistasis between a gene pair can be explained by the action of a third gene that modulates the interaction. We have extended the framework of Nested Effects Models (NEMs), a type of graphical model specifically tailored to analyze high-dimensional gene perturbation data, to incorporate logical functions that describe interactions between regulators on downstream genes and proteins. We benchmark our approach in the controlled setting of a simulation study and show high accuracy in inferring the correct model. In an application to data from deletion mutants of kinases and phosphatases in S. cerevisiae we show that epistatic NEMs can point to modulators of genetic interactions. Our approach is implemented in the R-package 'epiNEM' available from https://github.com/cbg-ethz/epiNEM and https://bioconductor.org/packages/epiNEM/.

  8. Modeling of atmospheric iron processing carried by mineral dust and its deposition to ocean

    Science.gov (United States)

    Nickovic, Slobodan; Vukovic, Ana; Vujadinovic, Mirjam

    2014-05-01

    Relatively insoluble iron in dust originating from desert soils increases its solubility after Fe carried by mineral dust is chemically processed by the atmosphere. After dust is deposited deposition to the ocean, soluble Fe as a nutrient could enhance the marine primary production. The atmospheric dust cycle is driven by the atmospheric processes often of smaller, meso-scales. The soil mineralogy of dust emitted from sources determines also how much Fe in the aerosol will be finding. Once Fe is exposed to the atmospheric processes, the atmospheric radiation, clouds and polluted air will chemically affect the iron in dust. Global dust-iron models, having typical horizontal resolutions of 100-300 km which are mostly used to numerically simulate the fate of iron in the atmosphere can provide rather global picture of the dust and iron transport, but not details. Such models often introduce simplistic approximation on the Fe content in dust-productive soils. To simulate the Fe processing we instead implemented a high resolution regional atmospheric dust-iron model with detailed 1km global map for the geographic distribution of Fe content in soil. We also introduced a parameterization of the Fe processing caused by dust mineralogy, cloud processes and solar radiation. We will present results from simulation experiments in order to explore the model capability to reproduce major observed patterns of deposited Fe into the Atlantic cruises.

  9. Numerical modelling of lawsonite thin film as radiative cooling minerals for dew harvesting

    Science.gov (United States)

    Benlattar, M.; Laatioui, S.; Oualim, E. M.; Mazroui, M.; Mouhsen, A.; Harmouchi, M.

    Harvesting dew can be used as a renewable complementary source of water both for drinking and agriculture in specific arid or semi-arid water-stressed areas. Condensation of water vapor by nighttime radiative cooling is the phenomenon that can be explained the dew formation on plants or surfaces. In this paper, we propose the lawsonite mineral, as a potential radiative cooling material, for exploiting this natural phenomenon. Furthermore, a computer model that includes meteorological parameters, obtained from the coastal region of Southern Morrocco (Mirleft-South of Agadir), is used to determine the thermal balance and fit to dew mass evolution. In order to form global estimates of dew formation potential via our dew formation model, we combined different meteorological data with radiative properties of natural lawsonite condenser (CaAl2Si2O7(OH)2·H2O) to enhance the modelled dew yield. The daily modelled yields show that significant amounts of dew water can be calculated as a function of the condenser temperature, the thickness condenser as well as the wind speed.

  10. Modelling genetic susceptibility to multiple sclerosis with family data.

    Science.gov (United States)

    O'Gorman, Cullen; Lin, Rui; Stankovich, James; Broadley, Simon A

    2013-01-01

    A genetic contribution to susceptibility is well established in multiple sclerosis (MS) and 57 associated genetic loci have been identified. We have undertaken a meta-analysis of familial risk studies with the aims of providing definitive figures for risks to relatives, performing a segregation analysis and estimating the proportion of the overall genetic risk that currently identified genes represent. We have used standard methods of meta-analysis combined with novel approaches to age adjustment to provide directly comparable estimates of lifetime risk. The overall recurrence risk for monozygotic twins was 18.2% and for siblings 2.7%. The recurrence risk for dizygotic twins was significantly higher than for siblings. The overall estimate of sibling relative risk (λ(S)) was 16.8. Risks for older relatives (parents, siblings, aunts, uncles and cousins) show a latitudinal gradient, in line with population risk. No latitudinal gradient for λ(S) was seen. Segregation analysis supports a multiplicative model of one locus of moderate effect with many loci of small effect. The estimated contribution of the 57 known MS loci is 18-24% of λ(S). This meta-analysis supports the notion of MS being in part the result of multiple genetic susceptibility factors and environmental factors.

  11. A numerical model of controlled bioinduced mineralization in a porous medium to prevent corrosion

    Science.gov (United States)

    Afanasyev, Michael; van Paassen, Leon; Heimovaara, Timo

    2013-04-01

    This paper presents a numerical model of controlled bioinduced mineralization in a porous medium as a possible corrosion protection mechanism. Corrosion is a significant economic problem - recent reports evaluate the annual cost of metal corrosion as 3-4% of the gross domestic product (GDP), in both developed and developing countries. Corrosion control methods currently used are costly and unsustainable as they require the use of larger volumes of materials, hazardous chemicals and regular inspections. As an alternative corrosion control method, bioinduced deposition of protective mineral layers has been proposed. Bioinduced precipitation of calcite has already been investigated for CO2 geological sequestration and soil improvement. To our knowledge, though, no numerical study of biomineralization for corrosion protection has been described yet. Our model includes three phases - solid, biofilm and mobile water. In the latter the reactive elements are dissolved, which are involved in the precipitation and the biofilm growth. The equations that describe the pore water flow, chemical reactions in the mobile water, consumption of substrate and expulsion of metabolic products by the biofilm are briefly presented. Also, the changes in porosity and permeability of the porous medium through biofilm growth and solids precipitation are included. Our main assumptions are that the biofilm is uniform, has a constant density and composition, that all chemical reactions except for substrate consumption occur in the mobile water, and that the precipitates are uniformly distributed on the surface of the solids. We validate the model with simple analytical solutions and against experimental data. The metabolism of the micro-organisms introduces changes in the physical and chemical characteristics of the environment, such as concentrations of chemicals and pH levels. As an extension to the model, we couple these changes to the rates of biofilm growth and precipitation rates. The

  12. Development and evaluation of a new sorption model for organic cations in soil: contributions from organic matter and clay minerals.

    Science.gov (United States)

    Droge, Steven T J; Goss, Kai-Uwe

    2013-12-17

    This study evaluates a newly proposed cation-exchange model that defines the sorption of organic cations to soil as a summed contribution of sorption to organic matter (OM) and sorption to phyllosilicate clay minerals. Sorption to OM is normalized to the fraction organic carbon (fOC), and sorption to clay is normalized to the estimated cation-exchange capacity attributed to clay minerals (CECCLAY). Sorption affinity is specified to a fixed medium composition, with correction factors for other electrolyte concentrations. The model applies measured sorption coefficients to one reference OM material and one clay mineral. If measured values are absent, then empirical relationships are available on the basis of molecular volume and amine type in combination with corrective increments for specific polar moieties. The model is tested using new sorption data generated at pH 6 for two Eurosoils, one enriched in clay and the other, OM, using 29 strong bases (pKa > 8). Using experimental data on reference materials for all tested compounds, model predictions for the two soils differed on average by only -0.1 ± 0.4 log units from measured sorption affinities. Within the chemical applicability domain, the model can also be applied successfully to various reported soil sorption data for organic cations. Particularly for clayish soils, the model shows that sorption of organic cations to clay minerals accounts for more than 90% of the overall affinity.

  13. A Software Pattern of the Genetic Algorithm -a Study on Reusable Object Model of Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    2001-01-01

    The Genetic Algorithm (GA) has been a pop research field, butthere is little concern on GA in view of Software Engineering and this result in a serie s of problems. In this paper, we extract a GA's software pattern, draw a model d iagram of the reusable objects, analyze the advantages and disadvantages of the pattern, and give a sample code at the end. We are then able to improve the reus ability and expansibility of GA. The results make it easier to program a new GA code by using some existing successful operators, thereby reducing the difficult ies and workload of programming a GA's code, and facilitate the GA application.

  14. Exploratory Bayesian model selection for serial genetics data.

    Science.gov (United States)

    Zhao, Jing X; Foulkes, Andrea S; George, Edward I

    2005-06-01

    Characterizing the process by which molecular and cellular level changes occur over time will have broad implications for clinical decision making and help further our knowledge of disease etiology across many complex diseases. However, this presents an analytic challenge due to the large number of potentially relevant biomarkers and the complex, uncharacterized relationships among them. We propose an exploratory Bayesian model selection procedure that searches for model simplicity through independence testing of multiple discrete biomarkers measured over time. Bayes factor calculations are used to identify and compare models that are best supported by the data. For large model spaces, i.e., a large number of multi-leveled biomarkers, we propose a Markov chain Monte Carlo (MCMC) stochastic search algorithm for finding promising models. We apply our procedure to explore the extent to which HIV-1 genetic changes occur independently over time.

  15. Hierarchical Stochastic Simulation Algorithm for SBML Models of Genetic Circuits

    Directory of Open Access Journals (Sweden)

    Leandro eWatanabe

    2014-11-01

    Full Text Available This paper describes a hierarchical stochastic simulation algorithm which has been implemented within iBioSim, a tool used to model, analyze, and visualize genetic circuits. Many biological analysis tools flatten out hierarchy before simulation, but there are many disadvantages associated with this approach. First, the memory required to represent the model can quickly expand in the process. Second, the flattening process is computationally expensive. Finally, when modeling a dynamic cellular population within iBioSim, inlining the hierarchy of the model is inefficient since models must grow dynamically over time. This paper discusses a new approach to handle hierarchy on the fly to make the tool faster and more memory-efficient. This approach yields significant performance improvements as compared to the former flat analysis method.

  16. Geochemical simulation of the formation of brine and salt minerals based on Pitzer model in Caka Salt Lake

    Institute of Scientific and Technical Information of China (English)

    LIU; Xingqi; CAI; Keqin; YU; Shengsong

    2004-01-01

    The geochemical simulation of the formation of brine and salt minerals based on Pitzer model was made in Caka Salt Lake. The evolution of the mixed surface-water and the mineral sequences were calculated and compared with the hydrochemical compositions of the brine and the salt minerals of the deposit in Caka Salt Lake. The results show that the formation temperature of the lake is between 0℃ and 5℃, which is well identical with other studies. The mixing of salt-karst water with the surface waters, neglected by the former researchers, is very important to the formation of the lake, indicating that the initial waters resulting in the formation of the lake are multi-source. It is the first time to use Pitzer model in China for making geochemical simulation of the formation and evolution of inland salt lake and satisfactory results have been achieved.

  17. Newly Developed Rat Model of Chronic Kidney Disease-Mineral Bone Disorder.

    Science.gov (United States)

    Watanabe, Kentaro; Fujii, Hideki; Goto, Shunsuke; Nakai, Kentaro; Kono, Keiji; Watanabe, Shuhei; Shinohara, Masami; Nishi, Shinichi

    2017-07-01

    Chronic kidney disease-mineral bone disorder (CKD-MBD) is associated with all-cause and cardiovascular morbidity and mortality in patients with CKD. Thus, elucidating its pathophysiological mechanisms is essential for improving the prognosis. We evaluated characteristics of CKD-MBD in a newly developed CKD rat model. We used male Sprague-Dawley (SD) rats and spontaneously diabetic Torii (SDT) rats, which are used as models for nonobese type 2 diabetes. CKD was induced by 5/6 nephrectomy (Nx). At 10 weeks, the rats were classified into six groups and administered with a vehicle or a low- or high-dose paricalcitol thrice a week. At 20 weeks, the rats were sacrificed; blood and urinary biochemical analyses and histological analysis of the aorta were performed. At 20 weeks, hemoglobin A1c (HbA1c) levels, blood pressure, and renal function were not significantly different among the six groups. Serum calcium and phosphate levels tended to be higher in SDT-Nx rats than in SD-Nx rats. The urinary excretion of calcium and phosphate was significantly greater in SDT-Nx rats than in SD-Nx rats. After administering paricalcitol, serum parathyroid hormone (PTH) and fibroblast growth factor 23 (FGF23) levels were significantly higher in SDT-Nx rats than in SD-Nx rats. The degree of aortic calcification was significantly more severe and the aortic calcium content was significantly greater in SDT-Nx rats than in SD-Nx rats. We suggest that our new CKD rat model using SDT rats represents a useful CKD-MBD model, and this model was greatly influenced by paricalcitol administration. Further studies are needed to clarify the detailed mechanisms underlying this model.

  18. Genetic Aspects of Autism Spectrum Disorders: Insights from Animal Models

    Directory of Open Access Journals (Sweden)

    Swati eBanerjee

    2014-02-01

    Full Text Available Autism spectrum disorders (ASD are a complex neurodevelopmental disorder that display a triad of core behavioral deficits including restricted interests, often accompanied by repetitive behavior, deficits in language and communication, and an inability to engage in reciprocal social interactions. ASD is among the most heritable disorders but is not a simple disorder with a singular pathology and has a rather complex etiology. It is interesting to note that perturbations in synaptic growth, development and stability underlie a variety of neuropsychiatric disorders, including ASD, schizophrenia, epilepsy and intellectual disability. Biological characterization of an increasing repertoire of synaptic mutants in various model organisms indicates synaptic dysfunction as causal in the pathophysiology of ASD. Our understanding of the genes and genetic pathways that contribute towards the formation, stabilization and maintenance of functional synapses coupled with an in-depth phenotypic analysis of the cellular and behavioral characteristics is therefore essential to unraveling the pathogenesis of these disorders. In this review, we discuss the genetic aspects of ASD emphasizing on the well conserved set of genes and genetic pathways implicated in this disorder, many of which contribute to synapse assembly and maintenance across species. We also review how fundamental research using animal models is providing key insights into the various facets of human ASD.

  19. Integrated Experimental and Modeling Studies of Mineral Carbonation as a Mechanism for Permanent Carbon Sequestration in Mafic/Ultramafic Rocks

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhengrong [Yale Univ., New Haven, CT (United States); Qiu, Lin [Yale Univ., New Haven, CT (United States); Zhang, Shuang [Yale Univ., New Haven, CT (United States); Bolton, Edward [Yale Univ., New Haven, CT (United States); Bercovici, David [Yale Univ., New Haven, CT (United States); Ague, Jay [Yale Univ., New Haven, CT (United States); Karato, Shun-Ichiro [Yale Univ., New Haven, CT (United States); Oristaglio, Michael [Yale Univ., New Haven, CT (United States); Zhu, Wen-Iu [Univ. of Maryland, College Park, MD (United States); Lisabeth, Harry [Univ. of Maryland, College Park, MD (United States); Johnson, Kevin [Univ. of Hawaii, Honolulu, HI (United States)

    2014-09-30

    A program of laboratory experiments, modeling and fieldwork was carried out at Yale University, University of Maryland, and University of Hawai‘i, under a DOE Award (DE-FE0004375) to study mineral carbonation as a practical method of geologic carbon sequestration. Mineral carbonation, also called carbon mineralization, is the conversion of (fluid) carbon dioxide into (solid) carbonate minerals in rocks, by way of naturally occurring chemical reactions. Mafic and ultramafic rocks, such as volcanic basalt, are natural candidates for carbonation, because the magnesium and iron silicate minerals in these rocks react with brines of dissolved carbon dioxide to form carbonate minerals. By trapping carbon dioxide (CO2) underground as a constituent of solid rock, carbonation of natural basalt formations would be a secure method of sequestering CO2 captured at power plants in efforts to mitigate climate change. Geochemical laboratory experiments at Yale, carried out in a batch reactor at 200°C and 150 bar (15 MPa), studied carbonation of the olivine mineral forsterite (Mg2SiO4) reacting with CO2 brines in the form of sodium bicarbonate (NaHCO3) solutions. The main carbonation product in these reactions is the carbonate mineral magnesite (MgCO3). A series of 32 runs varied the reaction time, the reactive surface area of olivine grains and powders, the concentration of the reacting fluid, and the starting ratio of fluid to olivine mass. These experiments were the first to study the rate of olivine carbonation under passive conditions approaching equilibrium. The results show that, in a simple batch reaction, olivine carbonation is fastest during the first 24 hours and then slows significantly and even reverses. A natural measure of the extent of carbonation is a quantity called the carbonation fraction, which compares the amount of carbon removed from solution, during a run, to the maximum amount

  20. Genetic Programming Modeling and Complexity Analysis of the Magnetoencephalogram of Epileptic Patients

    Science.gov (United States)

    Georgopoulos, Efstratios F.; Adamopoulos, Adam V.; Likothanassis, Spiridon D.

    In this work MagnetoEncephaloGram (MEG) recordings of epileptic patients are modeled using a genetic programming approach. This is the first time that genetic programming is used to model MEG signal. Numerous experiments were conducted giving highly successful results. It is demonstrated that genetic programming can produce very simple nonlinear models that fit with great accuracy the observed data of MEG.

  1. The substitution of mineral fertilizers by compost from household waste in Cameroon: economic analysis with a partial equilibrium model.

    Science.gov (United States)

    Jaza Folefack, Achille Jean

    2009-05-01

    This paper analyses the possibility of substitution between compost and mineral fertilizer in order to assess the impact on the foreign exchange savings in Cameroon of increasing the use of compost. In this regard, a partial equilibrium model was built up and used as a tool for policy simulations. The review of existing literature already suggests that, the compost commercial value i.e. value of substitution (33,740 FCFA tonne(-1)) is higher compared to the compost real price (30,000 FCFA tonne(-1)), proving that it could be profitable to substitute the mineral fertilizer by compost. Further results from the scenarios used in the modelling exercise show that, increasing the compost availability is the most favourable policy for the substitution of mineral fertilizer by compost. This policy helps to save about 18.55% of the annual imported mineral fertilizer quantity and thus to avoid approximately 8.47% of the yearly total import expenditure in Cameroon. The policy of decreasing the transport rate of compost in regions that are far from the city is also favourable to the substitution. Therefore, in order to encourage the substitution of mineral fertilizer by compost, programmes of popularization of compost should be highlighted and be among the top priorities in the agricultural policy of the Cameroon government.

  2. Modelling the genetic risk in age-related macular degeneration.

    Directory of Open Access Journals (Sweden)

    Felix Grassmann

    Full Text Available Late-stage age-related macular degeneration (AMD is a common sight-threatening disease of the central retina affecting approximately 1 in 30 Caucasians. Besides age and smoking, genetic variants from several gene loci have reproducibly been associated with this condition and likely explain a large proportion of disease. Here, we developed a genetic risk score (GRS for AMD based on 13 risk variants from eight gene loci. The model exhibited good discriminative accuracy, area-under-curve (AUC of the receiver-operating characteristic of 0.820, which was confirmed in a cross-validation approach. Noteworthy, younger AMD patients aged below 75 had a significantly higher mean GRS (1.87, 95% CI: 1.69-2.05 than patients aged 75 and above (1.45, 95% CI: 1.36-1.54. Based on five equally sized GRS intervals, we present a risk classification with a relative AMD risk of 64.0 (95% CI: 14.11-1131.96 for individuals in the highest category (GRS 3.44-5.18, 0.5% of the general population compared to subjects with the most common genetic background (GRS -0.05-1.70, 40.2% of general population. The highest GRS category identifies AMD patients with a sensitivity of 7.9% and a specificity of 99.9% when compared to the four lower categories. Modeling a general population around 85 years of age, 87.4% of individuals in the highest GRS category would be expected to develop AMD by that age. In contrast, only 2.2% of individuals in the two lowest GRS categories which represent almost 50% of the general population are expected to manifest AMD. Our findings underscore the large proportion of AMD cases explained by genetics particularly for younger AMD patients. The five-category risk classification could be useful for therapeutic stratification or for diagnostic testing purposes once preventive treatment is available.

  3. Genetic mouse models of brain ageing and Alzheimer's disease.

    Science.gov (United States)

    Bilkei-Gorzo, Andras

    2014-05-01

    Progression of brain ageing is influenced by a complex interaction of genetic and environmental factors. Analysis of genetically modified animals with uniform genetic backgrounds in a standardised, controlled environment enables the dissection of critical determinants of brain ageing on a molecular level. Human and animal studies suggest that increased load of damaged macromolecules, efficacy of DNA maintenance, mitochondrial activity, and cellular stress defences are critical determinants of brain ageing. Surprisingly, mouse lines with genetic impairment of anti-oxidative capacity generally did not show enhanced cognitive ageing but rather an increased sensitivity to oxidative challenge. Mouse lines with impaired mitochondrial activity had critically short life spans or severe and rapidly progressing neurodegeneration. Strains with impaired clearance in damaged macromolecules or defects in the regulation of cellular stress defences showed alterations in the onset and progression of cognitive decline. Importantly, reduced insulin/insulin-like growth factor signalling generally increased life span but impaired cognitive functions revealing a complex interaction between ageing of the brain and of the body. Brain ageing is accompanied by an increased risk of developing Alzheimer's disease. Transgenic mouse models expressing high levels of mutant human amyloid precursor protein showed a number of symptoms and pathophysiological processes typical for early phase of Alzheimer's disease. Generally, therapeutic strategies effective against Alzheimer's disease in humans were also active in the Tg2576, APP23, APP/PS1 and 5xFAD lines, but a large number of false positive findings were also reported. The 3xtg AD model likely has the highest face and construct validity but further studies are needed. Copyright © 2013 Elsevier Inc. All rights reserved.

  4. Evolution of the quaternary magmatic system, Mineral Mountains, Utah: Interpretations from chemical and experimental modeling

    Energy Technology Data Exchange (ETDEWEB)

    Nash, W.P.; Crecraft, H.R.

    1982-09-01

    The evolution of silicic magmas in the upper crust is characterized by the establishment of chemical and thermal gradients in the upper portion of magma chambers. The chemical changes observed in rhyolite magmas erupted over a period of 300,000 years in the Mineral Mountains are similar to those recorded at Twin Peaks, Utah, and in the spatially zoned Bishop Tuff from Long Valley, California. Chemical and fluid dynamic models indicate that cooling of a silicic magma body from the top and sides can result in the formation of a roof zone above a convecting region which is chemically and thermally stratified, as well as highly fractionated and water rich. Crystallization experiments have been performed with sodium carbonate solutions as an analog to crystallization in magmatic systems. Top and side cooling of a homogeneous sodium carbonate solution results in crystallization along the top and sides and upward convection of sodium carbonate-depleted fluid. A stably stratified roof zone, which is increasingly water rich and cooler upwards, develops over a thermally and chemically homogeneous convecting region. Crystallization at the top ultimately ceases, and continued upward convection of water-rich fluid causes a slight undersaturation adjacent to the roof despite cooler temperatures. By analogy, crystallization at the margins of a magma chamber and buoyant rise of the fractionated boundary layer into the roof zone can account for the chemical evolution of the magma system at the Mineral Mountains. To produce compositionally stratified silicic magmas requires thermal input to a silicic system via mafic magmas. The small volume, phenocryst-poor rhyolite magma which persisted for at least 300,000 years in the Mineral Mountains requires the presence of a continued thermal input from a mafic magma source. The presence of silicic lavas signifies that there is a substantial thermal anomaly both in the crust and upper mantle. The production of silicic lavas requires (1) the

  5. Model reduction using the genetic algorithm and routh approximations

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    A new method of model reduction combining the genetic algorithm(GA) with the Routh approximation method is presented. It is suggested that a high-order system can be approximated by a low-order model with a time delay. The denominator parameters of the reduced-order model are determined by the Routh approximation method, then the numerator parameters and time delay are identified by the GA. The reduced-order models obtained by the proposed method will always be stable if the original system is stable and produce a good approximation to the original system in both the frequency domain and time domain. Two numerical examples show that the method is computationally simple and efficient.

  6. Modelling of mineral dust for interglacial and glacial climate conditions with a focus on Antarctica

    Directory of Open Access Journals (Sweden)

    N. Sudarchikova

    2015-05-01

    Full Text Available The mineral dust cycle responds to climate variations and plays an important role in the climate system by affecting the radiative balance of the atmosphere and modifying biogeochemistry. Polar ice cores provide unique information about deposition of aeolian dust particles transported over long distances. These cores are a palaeoclimate proxy archive of climate variability thousands of years ago. The current study is a first attempt to simulate past interglacial dust cycles with a global aerosol–climate model ECHAM5-HAM. The results are used to explain the dust deposition changes in Antarctica in terms of quantitative contribution of different processes, such as emission, atmospheric transport and precipitation, which will help to interpret palaeodata from Antarctic ice cores. The investigated periods include four interglacial time slices: the pre-industrial control (CTRL, mid-Holocene (6000 yr BP; hereafter referred to as "6 kyr", last glacial inception (115 000 yr BP; hereafter "115 kyr" and Eemian (126 000 yr BP; hereafter "126 kyr". One glacial time interval, the Last Glacial Maximum (LGM (21 000 yr BP; hereafter "21 kyr", was simulated as well to be a reference test for the model. Results suggest an increase in mineral dust deposition globally, and in Antarctica, in the past interglacial periods relative to the pre-industrial CTRL simulation. Approximately two-thirds of the increase in the mid-Holocene and Eemian is attributed to enhanced Southern Hemisphere dust emissions. Slightly strengthened transport efficiency causes the remaining one-third of the increase in dust deposition. The moderate change in dust deposition in Antarctica in the last glacial inception period is caused by the slightly stronger poleward atmospheric transport efficiency compared to the pre-industrial. Maximum dust deposition in Antarctica was simulated for the glacial period. LGM dust deposition in Antarctica is substantially increased due to 2.6 times higher

  7. Genetic diversity in the SIR model of pathogen evolution.

    Science.gov (United States)

    Gordo, Isabel; Gomes, M Gabriela M; Reis, Daniel G; Campos, Paulo R A

    2009-01-01

    We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR). We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts), where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0)(1+s)) is higher than the fitness of the resident strain (R(0)). We show that this invasion probability is given by the relative increment in R(0) of the new pathogen (s). By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  8. Genetic diversity in the SIR model of pathogen evolution.

    Directory of Open Access Journals (Sweden)

    Isabel Gordo

    Full Text Available We introduce a model for assessing the levels and patterns of genetic diversity in pathogen populations, whose epidemiology follows a susceptible-infected-recovered model (SIR. We model the population of pathogens as a metapopulation composed of subpopulations (infected hosts, where pathogens replicate and mutate. Hosts transmit pathogens to uninfected hosts. We show that the level of pathogen variation is well predicted by analytical expressions, such that pathogen neutral molecular variation is bounded by the level of infection and increases with the duration of infection. We then introduce selection in the model and study the invasion probability of a new pathogenic strain whose fitness (R(0(1+s is higher than the fitness of the resident strain (R(0. We show that this invasion probability is given by the relative increment in R(0 of the new pathogen (s. By analyzing the patterns of genetic diversity in this framework, we identify the molecular signatures during the replacement and compare these with those observed in sequences of influenza A.

  9. Genetic evaluation of European quails by random regression models

    Directory of Open Access Journals (Sweden)

    Flaviana Miranda Gonçalves

    2012-09-01

    Full Text Available The objective of this study was to compare different random regression models, defined from different classes of heterogeneity of variance combined with different Legendre polynomial orders for the estimate of (covariance of quails. The data came from 28,076 observations of 4,507 female meat quails of the LF1 lineage. Quail body weights were determined at birth and 1, 14, 21, 28, 35 and 42 days of age. Six different classes of residual variance were fitted to Legendre polynomial functions (orders ranging from 2 to 6 to determine which model had the best fit to describe the (covariance structures as a function of time. According to the evaluated criteria (AIC, BIC and LRT, the model with six classes of residual variances and of sixth-order Legendre polynomial was the best fit. The estimated additive genetic variance increased from birth to 28 days of age, and dropped slightly from 35 to 42 days. The heritability estimates decreased along the growth curve and changed from 0.51 (1 day to 0.16 (42 days. Animal genetic and permanent environmental correlation estimates between weights and age classes were always high and positive, except for birth weight. The sixth order Legendre polynomial, along with the residual variance divided into six classes was the best fit for the growth rate curve of meat quails; therefore, they should be considered for breeding evaluation processes by random regression models.

  10. Nickel-cobalt laterites: a deposit model: Chapter H in Mineral deposit models for resource assessment

    Science.gov (United States)

    Marsh, Erin; Anderson, Eric J.; Gray, Floyd

    2013-01-01

    Nickel-cobalt (Ni-Co) laterite deposits are supergene enrichments of Ni±Co that form from intense chemical and mechanical weathering of ultramafic parent rocks. These regolith deposits typically form within 26 degrees of the equator, although there are a few exceptions. They form in active continental margins and stable cratonic settings. It takes as little as one million years for a laterite profile to develop. Three subtypes of Ni-Co laterite deposits are classified according to the dominant Ni-bearing mineralogy, which include hydrous magnesium (Mg)-silicate, smectite, and oxide. These minerals form in weathering horizons that begin with the unweathered protolith at the base, saprolite next, a smectite transition zone only in profiles where drainage is very poor, followed by limonite, and then capped with ferricrete at the top. The saprolite contains Ni-rich hydrous Mg-silicates, the Ni-rich clays occur in the transition horizon, and Ni-rich goethite occurs in the limonite. Although these subtypes of deposits are the more widely used terms for classification of Ni-Co laterite deposits, most deposits have economic concentrations of Ni in more than one horizon. Because of their complex mineralogy and heterogeneous concentrations, mining of these metallurgically complex deposits can be challenging. Deposits range in size from 2.5 to about 400 million tonnes, with Ni and Co grades of 0.66–2.4 percent (median 1.3) and 0.01–0.15 percent (median 0.08), respectively. Modern techniques of ore delineation and mineralogical identification are being developed to aid in streamlining the Ni-Co laterite mining process, and low-temperature and low-pressure ore processing techniques are being tested that will treat the entire weathered profile. There is evidence that the production of Ni and Co from laterites is more energy intensive than that of sulfide ores, reflecting the environmental impact of producing a Ni-Co laterite deposit. Tailings may include high levels of

  11. Impact of surface roughness and soil texture on mineral dust emission fluxes modeling

    Science.gov (United States)

    Menut, Laurent; PéRez, Carlos; Haustein, Karsten; Bessagnet, Bertrand; Prigent, Catherine; Alfaro, StéPhane

    2013-06-01

    Dust production models (DPM) used to estimate vertical fluxes of mineral dust aerosols over arid regions need accurate data on soil and surface properties. The Laboratoire Inter-Universitaire des Systemes Atmospheriques (LISA) data set was developed for Northern Africa, the Middle East, and East Asia. This regional data set was built through dedicated field campaigns and include, among others, the aerodynamic roughness length, the smooth roughness length of the erodible fraction of the surface, and the dry (undisturbed) soil size distribution. Recently, satellite-derived roughness length and high-resolution soil texture data sets at the global scale have emerged and provide the opportunity for the use of advanced schemes in global models. This paper analyzes the behavior of the ERS satellite-derived global roughness length and the State Soil Geographic data base-Food and Agriculture Organization of the United Nations (STATSGO-FAO) soil texture data set (based on wet techniques) using an advanced DPM in comparison to the LISA data set over Northern Africa and the Middle East. We explore the sensitivity of the drag partition scheme (a critical component of the DPM) and of the dust vertical fluxes (intensity and spatial patterns) to the roughness length and soil texture data sets. We also compare the use of the drag partition scheme to a widely used preferential source approach in global models. Idealized experiments with prescribed wind speeds show that the ERS and STATSGO-FAO data sets provide realistic spatial patterns of dust emission and friction velocity thresholds in the region. Finally, we evaluate a dust transport model for the period of March to July 2011 with observed aerosol optical depths from Aerosol Robotic Network sites. Results show that ERS and STATSGO-FAO provide realistic simulations in the region.

  12. Mineral dust aerosols over the Sahara: Meteorological controls on emission and transport and implications for modeling

    Science.gov (United States)

    Knippertz, Peter; Todd, Martin C.

    2012-02-01

    Atmospheric mineral dust has recently become an important research field in Earth system science because of its impacts on radiation, clouds, atmospheric dynamics and chemistry, air quality, and biogeochemical cycles. Studying and modeling dust emission and transport over the world's largest source region, the Sahara, is particularly challenging because of the complex meteorology and a very sparse observational network. Recent advances in satellite retrievals together with ground- and aircraft-based field campaigns have fostered our understanding of the spatiotemporal variability of the dust aerosol and its atmospheric drivers. We now have a more complete picture of the key processes in the atmosphere associated with dust emission. These cover a range of scales from (1) synoptic scale cyclones in the northern sector of the Sahara, harmattan surges and African easterly waves, through (2) low-level jets and cold pools of mesoscale convective systems (particularly over the Sahel), to (3) microscale dust devils and dusty plumes, each with its own pronounced diurnal and seasonal characteristics. This paper summarizes recent progress on monitoring and analyzing the dust distribution over the Sahara and discusses implications for numerical modeling. Among the key challenges for the future are a better quantification of the relative importance of single processes and a more realistic representation of the effects of the smaller-scale meteorological features in dust models. In particular, moist convection has been recognized as a major limitation to our understanding because of the inability of satellites to observe dust under clouds and the difficulties of numerical models to capture convective organization.

  13. Interferometric study of the dolomite dissolution: a new conceptual model for mineral dissolution

    Science.gov (United States)

    Lttge, A.; Winkler, U.; Lasaga, A. C.

    2003-03-01

    The dissolution rate and mechanism of three different cleavage faces of a dolomite crystal from Navarra (near Pamplona), Spain, were studied in detail by vertical scanning interferometry techniques. A total of 37 different regions (each about 124 × 156 μm in size) on the three sample surfaces were monitored as a function of time during dissolution at 25°C and pH 3. Dissolution produced shallow etch pits with widths reaching 20 μm during 8 h of dissolution. Depth development as a function of time was remarkably similar for all etch pits on a given dolomite surface. On the basis of etch pit distribution and volume as a function of time, the calculated dissolution rate increases from near zero to 4 × 10 -11 mol cm -2 s -1 over 5 h. The time variation is different for each of the three cleavage surfaces studied. In addition, the absolute dissolution rates of different parts of the dolomite crystal surface can be computed by using a reference surface. The different surfaces yield an "average" rate of 1.08 × 10 -11 mol cm -2 s -1 with a standard deviation of 0.3 × 10 -11 mol cm -2 s -1 based on about 60 analyses. The mean absolute rate of the dolomite surface is about 10 times slower than the rate calculated from etch pit dissolution alone. On the other hand, earlier batch rate data that used BET surface areas yield rates that are at least 30 to 60 times faster than our directly measured mean dissolution rate for the same pH and temperature. A conceptual model for mineral dissolution has been inferred from the surface topography obtained by the interferometry investigations. In this model, mineral dissolution is not dominated by etch pit formation itself but rather by extensive dissolution stepwaves that originate at the outskirts of the etch pits. These stepwaves control the overall dissolution as well as the dependence on temperature and saturation state.

  14. Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil.

    Science.gov (United States)

    Saavedra, Juan Matías; Acevedo, Francisca; González, Myriam; Seeger, Michael

    2010-07-01

    Polychlorobiphenyls (PCBs) are classified as "high-priority pollutants." Diverse microorganisms are able to degrade PCBs. However, bacterial degradation of PCBs is generally incomplete, leading to the accumulation of chlorobenzoates (CBAs) as dead-end metabolites. To obtain a microorganism able to mineralize PCB congeners, the bph locus of Burkholderia xenovorans LB400, which encodes one of the most effective PCB degradation pathways, was incorporated into the genome of the CBA-degrading bacterium Cupriavidus necator JMP134-X3. The bph genes were transferred into strain JMP134-X3, using the mini-Tn5 transposon system and biparental mating. The genetically modified derivative, C. necator strain JMS34, had only one chromosomal insertion of bph locus, which was stable under nonselective conditions. This modified bacterium was able to grow on biphenyl, 3-CBA and 4-CBA, and degraded 3,5-CBA in the presence of m-toluate. The strain JMS34 mineralized 3-CB, 4-CB, 2,4'-CB, and 3,5-CB, without accumulation of CBAs. Bioaugmentation of PCB-polluted soils with C. necator strain JMS34 and with the native B. xenovorans LB400 was monitored. It is noteworthy that strain JMS34 degraded, in 1 week, 99% of 3-CB and 4-CB and approximately 80% of 2,4'-CB in nonsterile soil, as well as in sterile soil. Additionally, the bacterial count of strain JMS34 increased by almost two orders of magnitude in PCB-polluted nonsterile soil. In contrast, the presence of native microflora reduced the degradation of these PCBs by strain LB400 from 73% (sterile soil) to approximately 50% (nonsterile soil). This study contributes to the development of improved biocatalysts for remediation of PCB-contaminated environments.

  15. Mineralization of PCBs by the genetically modified strain Cupriavidus necator JMS34 and its application for bioremediation of PCBs in soil

    Energy Technology Data Exchange (ETDEWEB)

    Saavedra, Juan Matias; Acevedo, Francisca; Gonzalez, Myriam; Seeger, Michael [Universidad Tecnica Federico Santa Maria, Valparaiso (Chile). Lab. de Microbiologia Molecular y Biotecnologia

    2010-07-15

    Polychlorobiphenyls (PCBs) are classified as ''high-priority pollutants''. Diverse microorganisms are able to degrade PCBs. However, bacterial degradation of PCBs is generally incomplete, leading to the accumulation of chlorobenzoates (CBAs) as dead-end metabolites. To obtain a microorganism able to mineralize PCB congeners, the bph locus of Burkholderia xenovorans LB400, which encodes one of the most effective PCB degradation pathways, was incorporated into the genome of the CBA-degrading bacterium Cupriavidus necator JMP134-X3. The bph genes were transferred into strain JMP134-X3, using the mini-Tn5 transposon system and biparental mating. The genetically modified derivative, C. necator strain JMS34, had only one chromosomal insertion of bph locus, which was stable under nonselective conditions. This modified bacterium was able to grow on biphenyl, 3-CBA and 4-CBA, and degraded 3,5-CBA in the presence of m-toluate. The strain JMS34 mineralized 3-CB, 4-CB, 2,4{sup '}-CB, and 3,5-CB, without accumulation of CBAs. Bioaugmentation of PCB-polluted soils with C. necator strain JMS34 and with the native B. xenovorans LB400 was monitored. It is noteworthy that strain JMS34 degraded, in 1 week, 99% of 3-CB and 4-CB and approximately 80% of 2,4{sup '}-CB in nonsterile soil, as well as in sterile soil. Additionally, the bacterial count of strain JMS34 increased by almost two orders of magnitude in PCB-polluted nonsterile soil. In contrast, the presence of native microflora reduced the degradation of these PCBs by strain LB400 from 73% (sterile soil) to approximately 50% (nonsterile soil). This study contributes to the development of improved biocatalysts for remediation of PCB-contaminated environments. (orig.)

  16. Gravitational Lens Modeling with Genetic Algorithms and Particle Swarm Optimizers

    CERN Document Server

    Rogers, Adam

    2011-01-01

    Strong gravitational lensing of an extended object is described by a mapping from source to image coordinates that is nonlinear and cannot generally be inverted analytically. Determining the structure of the source intensity distribution also requires a description of the blurring effect due to a point spread function. This initial study uses an iterative gravitational lens modeling scheme based on the semilinear method to determine the linear parameters (source intensity profile) of a strongly lensed system. Our 'matrix-free' approach avoids construction of the lens and blurring operators while retaining the least squares formulation of the problem. The parameters of an analytical lens model are found through nonlinear optimization by an advanced genetic algorithm (GA) and particle swarm optimizer (PSO). These global optimization routines are designed to explore the parameter space thoroughly, mapping model degeneracies in detail. We develop a novel method that determines the L-curve for each solution automa...

  17. In vivo Drosophilia genetic model for calcium oxalate nephrolithiasis.

    Science.gov (United States)

    Hirata, Taku; Cabrero, Pablo; Berkholz, Donald S; Bondeson, Daniel P; Ritman, Erik L; Thompson, James R; Dow, Julian A T; Romero, Michael F

    2012-12-01

    Nephrolithiasis is a major public health problem with a complex and varied etiology. Most stones are composed of calcium oxalate (CaOx), with dietary excess a risk factor. Because of complexity of mammalian system, the details of stone formation remain to be understood. Here we have developed a nephrolithiasis model using the genetic model Drosophila melanogaster, which has a simple, transparent kidney tubule. Drosophilia reliably develops CaOx stones upon dietary oxalate supplementation, and the nucleation and growth of microliths can be viewed in real time. The Slc26 anion transporter dPrestin (Slc26a5/6) is strongly expressed in Drosophilia kidney, and biophysical analysis shows that it is a potent oxalate transporter. When dPrestin is knocked down by RNAi in fly kidney, formation of microliths is reduced, identifying dPrestin as a key player in oxalate excretion. CaOx stone formation is an ancient conserved process across >400 My of divergent evolution (fly and human), and from this study we can conclude that the fly is a good genetic model of nephrolithiasis.

  18. The ontology of genetic susceptibility factors (OGSF) and its application in modeling genetic susceptibility to vaccine adverse events.

    Science.gov (United States)

    Lin, Yu; He, Yongqun

    2014-01-01

    Due to human variations in genetic susceptibility, vaccination often triggers adverse events in a small population of vaccinees. Based on our previous work on ontological modeling of genetic susceptibility to disease, we developed an Ontology of Genetic Susceptibility Factors (OGSF), a biomedical ontology in the domain of genetic susceptibility and genetic susceptibility factors. The OGSF framework was then applied in the area of vaccine adverse events (VAEs). OGSF aligns with the Basic Formal Ontology (BFO). OGSF defines 'genetic susceptibility' as a subclass of BFO:disposition and has a material basis 'genetic susceptibility factor'. The 'genetic susceptibility to pathological bodily process' is a subclasses of 'genetic susceptibility'. A VAE is a type of pathological bodily process. OGSF represents different types of genetic susceptibility factors including various susceptibility alleles (e.g., SNP and gene). A general OGSF design pattern was developed to represent genetic susceptibility to VAE and associated genetic susceptibility factors using experimental results in genetic association studies. To test and validate the design pattern, two case studies were populated in OGSF. In the first case study, human gene allele DBR*15:01 is susceptible to influenza vaccine Pandemrix-induced Multiple Sclerosis. The second case study reports genetic susceptibility polymorphisms associated with systemic smallpox VAEs. After the data of the Case Study 2 were represented using OGSF-based axioms, SPARQL was successfully developed to retrieve the susceptibility factors stored in the populated OGSF. A network of data from the Case Study 2 was constructed by using ontology terms and individuals as nodes and ontology relations as edges. Different social network analys is (SNA) methods were then applied to verify core OGSF terms. Interestingly, a SNA hub analysis verified all susceptibility alleles of SNPs and a SNA closeness analysis verified the susceptibility genes in Case

  19. Retrieving the hydrous minerals on Mars by sparse unmixing and the Hapke model using MRO/CRISM data

    Science.gov (United States)

    Lin, Honglei; Zhang, Xia

    2017-05-01

    The hydrous minerals on Mars preserve records of potential past aqueous activity. Quantitative information regarding mineralogical composition would enable a better understanding of the formation processes of these hydrous minerals, and provide unique insights into ancient habitable environments and the geological evolution of Mars. The Compact Reconnaissance Imaging Spectrometer for Mars (CRISM) has the advantage of both a high spatial and spectral resolution, which makes it suitable for the quantitative analysis of minerals on Mars. However, few studies have attempted to quantitatively retrieve the mineralogical composition of hydrous minerals on Mars using visible-infrared (VISIR) hyperspectral data due to their distribution characteristics (relatively low concentrations, located primarily in Noachian terrain, and unclear or unknown background minerals) and limitations of the spectral unmixing algorithms. In this study, we developed a modified sparse unmixing (MSU) method, combining the Hapke model with sparse unmixing. The MSU method considers the nonlinear mixed effects of minerals and avoids the difficulty of determining the spectra and number of endmembers from the image. The proposed method was tested successfully using laboratory mixture spectra and an Airborne Visible Infrared Imaging Spectrometer (AVIRIS) image of the Cuprite site (Nevada, USA). Then it was applied to CRISM hyperspectral images over Gale crater. Areas of hydrous mineral distribution were first identified by spectral features of water and hydroxyl absorption. The MSU method was performed on these areas, and the abundances were retrieved. The results indicated that the hydrous minerals consisted mostly of hydrous silicates, with abundances of up to 35%, as well as hydrous sulfates, with abundances ≤10%. Several main subclasses of hydrous minerals (e.g., Fe/Mg phyllosilicate, prehnite, and kieserite) were retrieved. Among these, Fe/Mg- phyllosilicate was the most abundant, with abundances

  20. Epidemic Modelling by Ripple-Spreading Network and Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Jian-Qin Liao

    2013-01-01

    Full Text Available Mathematical analysis and modelling is central to infectious disease epidemiology. This paper, inspired by the natural ripple-spreading phenomenon, proposes a novel ripple-spreading network model for the study of infectious disease transmission. The new epidemic model naturally has good potential for capturing many spatial and temporal features observed in the outbreak of plagues. In particular, using a stochastic ripple-spreading process simulates the effect of random contacts and movements of individuals on the probability of infection well, which is usually a challenging issue in epidemic modeling. Some ripple-spreading related parameters such as threshold and amplifying factor of nodes are ideal to describe the importance of individuals’ physical fitness and immunity. The new model is rich in parameters to incorporate many real factors such as public health service and policies, and it is highly flexible to modifications. A genetic algorithm is used to tune the parameters of the model by referring to historic data of an epidemic. The well-tuned model can then be used for analyzing and forecasting purposes. The effectiveness of the proposed method is illustrated by simulation results.

  1. Using biotic ligand models to predict metal toxicity in mineralized systems

    Science.gov (United States)

    Smith, Kathleen S.; Balistrieri, Laurie S.; Todd, Andrew S.

    2015-01-01

    The biotic ligand model (BLM) is a numerical approach that couples chemical speciation calculations with toxicological information to predict the toxicity of aquatic metals. This approach was proposed as an alternative to expensive toxicological testing, and the U.S. Environmental Protection Agency incorporated the BLM into the 2007 revised aquatic life ambient freshwater quality criteria for Cu. Research BLMs for Ag, Ni, Pb, and Zn are also available, and many other BLMs are under development. Current BLMs are limited to ‘one metal, one organism’ considerations. Although the BLM generally is an improvement over previous approaches to determining water quality criteria, there are several challenges in implementing the BLM, particularly at mined and mineralized sites. These challenges include: (1) historically incomplete datasets for BLM input parameters, especially dissolved organic carbon (DOC), (2) several concerns about DOC, such as DOC fractionation in Fe- and Al-rich systems and differences in DOC quality that result in variations in metal-binding affinities, (3) water-quality parameters and resulting metal-toxicity predictions that are temporally and spatially dependent, (4) additional influences on metal bioavailability, such as multiple metal toxicity, dietary metal toxicity, and competition among organisms or metals, (5) potential importance of metal interactions with solid or gas phases and/or kinetically controlled reactions, and (6) tolerance to metal toxicity observed for aquatic organisms living in areas with elevated metal concentrations.

  2. Lower mantle thermal structure deduced from seismic tomography, mineral physics and numerical modelling

    Science.gov (United States)

    Cadek, O.; Yuen, D. A.; Steinbach, V.; Chopelas, A.; Matyska, C.

    1994-01-01

    The long-wavelength thermal anomalies in the lower mantle have been mapped out using several seismic tomographic models in conjunction with thermodynamic parameters derived from high-pressure mineral physics experiments. These parameters are the depth variations of thermal expansivity and of the proportionality factor between changes in density and seismic velocity. The giant plume-like structures in the lower mantle under the Pacific Ocean and Africa have outer fringes with thermal anomalies around 300-400 K, but very high temperatures are found in the center of the plumes near the base of the core-mantle boundary. These extreme values can exceed +1500 K and may reflect large hot thermal anomalies in the lower mantle, which are supported by recent measurements of high melting temperatures of perovskite and iron. Extremely cold anomalies, around -1500 K, are found for anomalies in the deep mantle around the Pacific rim and under South America. Numerical simulations show that large negative thermal anomalies in the mid-lower mantle have modest magnitudes of around -500 K. correlation pattern exists between the present-day locations of cold masses in the lower mantle and the sites of past subduction since the Cretaceous. Results from correlation analysis show that the slab mass-flux in the lower mantle did not conform to a steady-state nature but exhibited time-dependent behavior.

  3. Mapping of the stochastic Lotka-Volterra model to models of population genetics and game theory

    Science.gov (United States)

    Constable, George W. A.; McKane, Alan J.

    2017-08-01

    The relationship between the M -species stochastic Lotka-Volterra competition (SLVC) model and the M -allele Moran model of population genetics is explored via timescale separation arguments. When selection for species is weak and the population size is large but finite, precise conditions are determined for the stochastic dynamics of the SLVC model to be mappable to the neutral Moran model, the Moran model with frequency-independent selection, and the Moran model with frequency-dependent selection (equivalently a game-theoretic formulation of the Moran model). We demonstrate how these mappings can be used to calculate extinction probabilities and the times until a species' extinction in the SLVC model.

  4. Genetic Diseases and Genetic Determinism Models in French Secondary School Biology Textbooks

    Science.gov (United States)

    Castera, Jeremy; Bruguiere, Catherine; Clement, Pierre

    2008-01-01

    The presentation of genetic diseases in French secondary school biology textbooks is analysed to determine the major conceptions taught in the field of human genetics. References to genetic diseases, and the processes by which they are explained (monogeny, polygeny, chromosomal anomaly and environmental influence) are studied in recent French…

  5. Genetic Diseases and Genetic Determinism Models in French Secondary School Biology Textbooks

    Science.gov (United States)

    Castera, Jeremy; Bruguiere, Catherine; Clement, Pierre

    2008-01-01

    The presentation of genetic diseases in French secondary school biology textbooks is analysed to determine the major conceptions taught in the field of human genetics. References to genetic diseases, and the processes by which they are explained (monogeny, polygeny, chromosomal anomaly and environmental influence) are studied in recent French…

  6. Calibration of Uncertainty Analysis of the SWAT Model Using Genetic Algorithms and Bayesian Model Averaging

    Science.gov (United States)

    In this paper, the Genetic Algorithms (GA) and Bayesian model averaging (BMA) were combined to simultaneously conduct calibration and uncertainty analysis for the Soil and Water Assessment Tool (SWAT). In this hybrid method, several SWAT models with different structures are first selected; next GA i...

  7. Constructing the barley model for genetic transformation in Triticeae

    Institute of Scientific and Technical Information of China (English)

    LÜ Bo; WU Jia-jie; FU Dao-lin

    2015-01-01

    Barley (Hordeum vulgare L.) is one of the oldest domesticated crops, showing dramatic adaptation to various climate and environmental conditions. As a major cereal crop, barley ranks the 4th after wheat, maize and rice in terms of planting area and production al over the world. Due to its diploid nature, the cultivated barley is considered as an ideal model to study the polyploid wheat and other Triticeae species. Here, we reviewed the development, optimization, and application of transgenic approaches in barley. The most efifcient and robust genetic transformation has been built on the Agrobacterium-mediated transfer in conjunction with the immature embryo-based regeneration. We then discussed future considerations of using more practical technologies in barley transformation, such as the T-DNA/transposon tagging and the genome editing. As a cereal crop amenable to genetic transformation, barley wil serve as the most valuable carrier for global functional genomics in Triticeae and is becoming the most practical model for generating value-added products.

  8. Mathematical Modeling of Intestinal Iron Absorption Using Genetic Programming

    Science.gov (United States)

    Colins, Andrea; Gerdtzen, Ziomara P.; Nuñez, Marco T.; Salgado, J. Cristian

    2017-01-01

    Iron is a trace metal, key for the development of living organisms. Its absorption process is complex and highly regulated at the transcriptional, translational and systemic levels. Recently, the internalization of the DMT1 transporter has been proposed as an additional regulatory mechanism at the intestinal level, associated to the mucosal block phenomenon. The short-term effect of iron exposure in apical uptake and initial absorption rates was studied in Caco-2 cells at different apical iron concentrations, using both an experimental approach and a mathematical modeling framework. This is the first report of short-term studies for this system. A non-linear behavior in the apical uptake dynamics was observed, which does not follow the classic saturation dynamics of traditional biochemical models. We propose a method for developing mathematical models for complex systems, based on a genetic programming algorithm. The algorithm is aimed at obtaining models with a high predictive capacity, and considers an additional parameter fitting stage and an additional Jackknife stage for estimating the generalization error. We developed a model for the iron uptake system with a higher predictive capacity than classic biochemical models. This was observed both with the apical uptake dataset used for generating the model and with an independent initial rates dataset used to test the predictive capacity of the model. The model obtained is a function of time and the initial apical iron concentration, with a linear component that captures the global tendency of the system, and a non-linear component that can be associated to the movement of DMT1 transporters. The model presented in this paper allows the detailed analysis, interpretation of experimental data, and identification of key relevant components for this complex biological process. This general method holds great potential for application to the elucidation of biological mechanisms and their key components in other complex

  9. P-V-T equations of state of lower mantle minerals: Constraints on mantle composition models

    Science.gov (United States)

    Fei, Y.; Zhang, L.; Frank, M.; Corgne, A.; Wheeler, K.; Meng, Y.

    2004-12-01

    Ferropericlase (Mg,Fe)O is likely a stable phase coexisting with silicate perovskite in the Earth's lower mantle. Determination of a reliable P-V-T equation-of-state of this phase is therefore crucial for developing compositional and mineralogical models of the Earth's interior. In this study, we report new compression data on ferropericlase up to 136 GPa, covering the entire pressure range of the lower mantle. The experiments were performed at the HPCAT 16-ID-B beamline (Advanced Photon Source), using monochromatic X-radiation and a CCD area detector. We used (Mg0.6Fe0.4)O as the starting material. The powdered sample was sandwiched between NaCl and a mixture of NaCl-Au in an externally heated high-temperature diamond anvil cell. The sample was annealed at each pressure increment by laser heating. High-quality diffraction data were collected up to 136 GPa. The same starting material was also studied up to 27 GPa and 2173 K in a multi-anvil apparatus by X-ray diffraction. A reliable P-V-T equation of state for (Mg0.6Fe0.4)O was developed by combining the two data sets. The new results, together with our recent P-V-T data for Al-bearing perovskite up to 105 GPa and 1000 K, provide solid density measurements for the two most important lower mantle minerals under simultaneous high pressure and temperature conditions. The new data are used to model the density profile of the lower mantle and provide tight constraints on its chemical composition.

  10. Modeling and experimental evaluation of the thermal insulation properties of mineral wool products at high temperature

    Energy Technology Data Exchange (ETDEWEB)

    Dianous, P. de [Isover Saint-Gobain, Rantigny (France). Thermal Lab.; Pincemin, F. [Saint-Gobain Recherche, Aubervilliers (France); Boulet, P.; Jeandel, G. [LEMTA, Vandoeuvre Les Nancy (France). Faculte des Sciences

    1997-11-01

    The authors have studied radiative transfer through insulating materials made of fibers and slugs (modeled respectively as infinite cylinders and spheres) at elevated temperatures. The same theoretical analysis is used for both fibers and spheres. Kerker-Mie theory is applied to determine the radiative coefficients of each type of particle, from the bulk glass complex refractive index and the fiber and slug diameter spectrum. Average radiative coefficients are determined for both fibers and slugs. The independent scattering hypothesis enables the authors to derive the total radiative coefficients of the whole material using a mass weighted average. The radiative transfer equation is solved for a one-dimensional problem, using the multiflux approximation. The conductive part is determined using a semi-empirical formula. The coupling between conduction and radiation is accounted for. This radiative model is applied to mineral wool products at room and elevated temperatures (400 C). Materials made of glass or rock fibers are considered. Special attention is given to fibrous materials with slugs. The authors show that radiative heat transfer reaches a minimum for given fiber and slug diameters. They study the respective contribution of fibers and slugs to radiative transfer as a function of the mean diameter and the amount of slugs present in the fibrous material. Calculated fluxes are compared to experimental ones measured on industrial rock and glass wool products for temperatures ranging from 24 to 400 C. The calculations are performed using the diameter spectra of fibers and slugs measured for these products. The influence of fiber orientation is also studied to better fit experimental data.

  11. Integer programming model for optimizing bus timetable using genetic algorithm

    Science.gov (United States)

    Wihartiko, F. D.; Buono, A.; Silalahi, B. P.

    2017-01-01

    Bus timetable gave an information for passengers to ensure the availability of bus services. Timetable optimal condition happened when bus trips frequency could adapt and suit with passenger demand. In the peak time, the number of bus trips would be larger than the off-peak time. If the number of bus trips were more frequent than the optimal condition, it would make a high operating cost for bus operator. Conversely, if the number of trip was less than optimal condition, it would make a bad quality service for passengers. In this paper, the bus timetabling problem would be solved by integer programming model with modified genetic algorithm. Modification was placed in the chromosomes design, initial population recovery technique, chromosomes reconstruction and chromosomes extermination on specific generation. The result of this model gave the optimal solution with accuracy 99.1%.

  12. An Intelligent Model for Pairs Trading Using Genetic Algorithms.

    Science.gov (United States)

    Huang, Chien-Feng; Hsu, Chi-Jen; Chen, Chi-Chung; Chang, Bao Rong; Li, Chen-An

    2015-01-01

    Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice.

  13. An Intelligent Model for Pairs Trading Using Genetic Algorithms

    Science.gov (United States)

    Hsu, Chi-Jen; Chen, Chi-Chung; Li, Chen-An

    2015-01-01

    Pairs trading is an important and challenging research area in computational finance, in which pairs of stocks are bought and sold in pair combinations for arbitrage opportunities. Traditional methods that solve this set of problems mostly rely on statistical methods such as regression. In contrast to the statistical approaches, recent advances in computational intelligence (CI) are leading to promising opportunities for solving problems in the financial applications more effectively. In this paper, we present a novel methodology for pairs trading using genetic algorithms (GA). Our results showed that the GA-based models are able to significantly outperform the benchmark and our proposed method is capable of generating robust models to tackle the dynamic characteristics in the financial application studied. Based upon the promising results obtained, we expect this GA-based method to advance the research in computational intelligence for finance and provide an effective solution to pairs trading for investment in practice. PMID:26339236

  14. Controversies about the genetic model of colorectal tumorigenesis.

    Science.gov (United States)

    Waliszewski, P

    1995-01-01

    According to the genetic model, intestinal tumorigenesis is a result of the ordered in time inactivation of tumor suppressor genes and the activation of oncogenes. A tacit assumption is that both genes involved in the regulation of proliferation and growth factor-inducible genes, although inactivated, would not be changed during that process. The model requires that cancer cell population is homogenous, exists in a deterministic environment, and develops in a teleological manner. Meanwhile, tumorigenesis is rather a combination of both deterministic and stochastic molecular phenomena. Therefore, a novel notion of bifurcating point genes is defined as a generalization of the idea of tumor suppressor genes and oncogenes. Alternative stochastic mechanisms of tumorigenesis are discussed such as a decreased expression of intestinal-specific genes in cancer cells, most likely reflecting adaptation to survival within a heterogeneous, and non-equilibrated cellular population.

  15. Adaptive Fixation in Two-Locus Models of Stabilizing Selection and Genetic Drift

    OpenAIRE

    Wollstein, Andreas; Stephan, Wolfgang

    2014-01-01

    The relationship between quantitative genetics and population genetics has been studied for nearly a century, almost since the existence of these two disciplines. Here we ask to what extent quantitative genetic models in which selection is assumed to operate on a polygenic trait predict adaptive fixations that may lead to footprints in the genome (selective sweeps). We study two-locus models of stabilizing selection (with and without genetic drift) by simulations and analytically. For symmetr...

  16. Tackling intraspecific genetic structure in distribution models better reflects species geographical range.

    Science.gov (United States)

    Marcer, Arnald; Méndez-Vigo, Belén; Alonso-Blanco, Carlos; Picó, F Xavier

    2016-04-01

    Genetic diversity provides insight into heterogeneous demographic and adaptive history across organisms' distribution ranges. For this reason, decomposing single species into genetic units may represent a powerful tool to better understand biogeographical patterns as well as improve predictions of the effects of GCC (global climate change) on biodiversity loss. Using 279 georeferenced Iberian accessions, we used classes of three intraspecific genetic units of the annual plant Arabidopsis thaliana obtained from the genetic analyses of nuclear SNPs (single nucleotide polymorphisms), chloroplast SNPs, and the vernalization requirement for flowering. We used SDM (species distribution models), including climate, vegetation, and soil data, at the whole-species and genetic-unit levels. We compared model outputs for present environmental conditions and with a particularly severe GCC scenario. SDM accuracy was high for genetic units with smaller distribution ranges. Kernel density plots identified the environmental variables underpinning potential distribution ranges of genetic units. Combinations of environmental variables accounted for potential distribution ranges of genetic units, which shrank dramatically with GCC at almost all levels. Only two genetic clusters increased their potential distribution ranges with GCC. The application of SDM to intraspecific genetic units provides a detailed picture on the biogeographical patterns of distinct genetic groups based on different genetic criteria. Our approach also allowed us to pinpoint the genetic changes, in terms of genetic background and physiological requirements for flowering, that Iberian A. thaliana may experience with a GCC scenario applying SDM to intraspecific genetic units.

  17. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon

    Directory of Open Access Journals (Sweden)

    S. Pando

    2013-06-01

    Full Text Available In this study, a hydrodynamic model was applied to the Nazaré submarine canyon with boundary forcing provided by an operational forecast model for the west Iberian coast for the spring of 2009. After validation, a lagrangian transport model was coupled to the hydrodynamic model to study and compare the transport patterns of three different classes of organo-mineral aggregates along the Nazaré canyon. The results show that the transport in the canyon is neither constant, nor unidirectional and that there are preferential areas where deposited matter is resuspended and redistributed. The transport of the larger class size of organo-mineral aggregates (2000 μm and 4000 μm is less pronounced, and a decrease in the phytodetrital carbon flux along the canyon is observed. During the modelled period, the Nazaré canyon acts as a depocentre of sedimentary organic matter rather than a conduit of organo-mineral aggregates to the deep sea, as has been reported by other authors. The results of this study are crucial for the understanding of the oceanic carbon sequestration at the continental margin, and therefore important for evaluating the role of submarine canyons within the global carbon cycle.

  18. Application of a lagrangian transport model to organo-mineral aggregates within the Nazaré canyon

    Science.gov (United States)

    Pando, S.; Juliano, M. F.; García, R.; Mendes, P. A. de Jesus; Thomsen, L.

    2013-06-01

    In this study, a hydrodynamic model was applied to the Nazaré submarine canyon with boundary forcing provided by an operational forecast model for the west Iberian coast for the spring of 2009. After validation, a lagrangian transport model was coupled to the hydrodynamic model to study and compare the transport patterns of three different classes of organo-mineral aggregates along the Nazaré canyon. The results show that the transport in the canyon is neither constant, nor unidirectional and that there are preferential areas where deposited matter is resuspended and redistributed. The transport of the larger class size of organo-mineral aggregates (2000 μm and 4000 μm) is less pronounced, and a decrease in the phytodetrital carbon flux along the canyon is observed. During the modelled period, the Nazaré canyon acts as a depocentre of sedimentary organic matter rather than a conduit of organo-mineral aggregates to the deep sea, as has been reported by other authors. The results of this study are crucial for the understanding of the oceanic carbon sequestration at the continental margin, and therefore important for evaluating the role of submarine canyons within the global carbon cycle.

  19. Kinetic analysis of mineral formation during in vitro modeling of matrix vesicle mineralization: effect of annexin A5, phosphatidylserine, and type II collagen.

    Science.gov (United States)

    Genge, Brian R; Wu, Licia N Y; Wuthier, Roy E

    2007-08-15

    Matrix vesicles (MVs) are involved in de novo mineral formation by nearly all vertebrate tissues. The driving force for MV mineralization is a nucleational core composed of three principal constituents: (i) amorphous calcium phosphate (ACP), complexed in part with phosphatidylserine (PS) to form (ii) calcium-phosphate-lipid complexes (CPLX), and (iii) annexin A5 (AnxA5), the principal lipid-dependent Ca(2+)-binding protein in MVs. We describe methods for reconstituting the nucleational core using a biomimetic approach and for analyzing the kinetics of its induction of mineral formation. The method is based on light scattering by the nascent crystallites at 340 nm and monitors mineral formation at regular intervals without disturbing the system using an automated plate reader. It yields precise replicate values that typically agree within less than 5%. As with MVs, mineral formation by the synthetic complex follows a sigmoidal pattern; following a quiescent induction period, rapid formation ensues for a limited time, followed by a distinct decline in rate that continues to slow, ultimately reaching a maximal asymptotic value. Key to quantization of mineral formation is the use of first-derivative analysis, which defines the induction time, the rate and the amount of initial mineral formation. Furthermore, using a five-parameter logistic curve-fitting algorithm, the maximal amount of mineral formation can be predicted accurately. Using these methods, we document the dramatic finding that AnxA5 synergistically activates PS-CPLX, transforming it from a very weak nucleator of mineral formation to a potent one. The methods presented should enable systematic study of the effects of numerous other factors thought to contribute to mineral formation.

  20. Exploring Middle School Students' Understanding of Three Conceptual Models in Genetics

    Science.gov (United States)

    Bresler Freidenreich, Hava; Golan Duncan, Ravit; Shea, Nicole

    2011-11-01

    Genetics is the cornerstone of modern biology and a critical aspect of scientific literacy. Research has shown, however, that many high school graduates lack fundamental understandings in genetics necessary to make informed decisions about issues and emerging technologies in this domain, such as genetic screening, genetically modified foods, etc. Genetic literacy entails understanding three interrelated models: a genetic model that describes patterns of genetic inheritance, a meiotic model that describes the process by which genes are segregated into sex cells, and a molecular model that describes the mechanisms that link genotypes to phenotypes within an individual. Currently, much of genetics instruction, especially in terms of the molecular model, occurs at the high school level, and we know little about the ways in which middle school students can reason about these models. Furthermore, we do not know the extent to which carefully designed instruction can help younger students develop coherent and interrelated understandings in genetics. In this paper, we discuss a research study aimed at elucidating middle school students' abilities to reason about the three genetic models. As part of our research, we designed an eight-week inquiry unit that was implemented in a combined sixth- to eighth-grade science classroom. We describe our instructional design and report results based on an analysis of written assessments, clinical interviews, and artifacts of the unit. Our findings suggest that middle school students are able to successfully reason about all three genetic models.

  1. Effect of Keishibukuryogan on Genetic and Dietary Obesity Models

    Directory of Open Access Journals (Sweden)

    Fengying Gao

    2015-01-01

    Full Text Available Obesity has been recognized as one of the most important risk factors for a variety of chronic diseases, such as diabetes, hypertension/cardiovascular diseases, steatosis/hepatitis, and cancer. Keishibukuryogan (KBG, Gui Zhi Fu Ling Wan in Chinese is a traditional Chinese/Japanese (Kampo medicine that has been known to improve blood circulation and is also known for its anti-inflammatory or scavenging effect. In this study, we evaluated the effect of KBG in two distinct rodent models of obesity driven by either a genetic (SHR/NDmcr-cp rat model or dietary (high-fat diet-induced mouse obesity model mechanism. Although there was no significant effect on the body composition in either the SHR rat or the DIO mouse models, KBG treatment significantly decreased the serum level of leptin and liver TG level in the DIO mouse, but not in the SHR rat model. Furthermore, a lower fat deposition in liver and a smaller size of adipocytes in white adipose tissue were observed in the DIO mice treated with KBG. Importantly, we further found downregulation of genes involved in lipid metabolism in the KBG-treated liver, along with decreased liver TG and cholesterol level. Our present data experimentally support in fact that KBG can be an attractive Kampo medicine to improve obese status through a regulation of systemic leptin level and/or lipid metabolism.

  2. A time study of cancer genetic counselors using a genetic counselor-only patient care model versus a traditional combined genetic counselor plus medical geneticist care model.

    Science.gov (United States)

    Heald, Brandie; Gustafson, Shanna; Mester, Jessica; Arscott, Patricia; Lynch, Katherine; Moline, Jessica; Eng, Charis

    2013-09-01

    Analyses of time-based effort have determined that clinical genetic services are labor-intensive, although these data derive primarily from studying geneticists' efforts in the pediatric model. No studies have investigated the time and patient care activities of cancer genetic counselors (GCs) in traditional clinics with a medical geneticist (GC/MD) compared with genetic counselor-only (GCO) appointments. In this study, 6 GCs prospectively tracked time spent in patient care activities in both clinical settings. The authors found that overall, GCs' time spent per patient was lower for GCO versus GC/MD visits. No differences were seen in time spent on results disclosure, but differences were noted in case preparation, face-to-face, and follow-up times. Furthermore, no differences were seen in number of case preparation activities or topics covered during a session. These data suggest that GCO visits result in better use of GCs' time, without a trade-off in number of patient-related activities.

  3. Obesity: from animal models to human genetics to practical applications.

    Science.gov (United States)

    Warden, Craig H; Fisler, Janis S

    2010-01-01

    Although many animal models are used in genetic studies, the mouse is most common. Analysis of single-gene mutations, linkage analysis in crossbred strains, and gene targeting are the primary techniques used to associate obesity phenotypes with specific genes or alleles. The orthologous human gene can then be tested, either in linkage studies in families or in genome-wide association studies (GWAS), for effect on the phenotype. Frequent lack of concordance between mouse and human obesity genes may be due to the difference in phenotypes measured in humans (body mass index) versus mouse (fat mass or % body fat), lack of intermediate phenotypes, and the fact that identified genes account for only a small percentage of the heritability of common obesity, suggesting that many genes remain unknown. New technology allows analysis of individual genomes at a reasonable cost, making large-scale obesity genome projects in humans feasible. Such projects could identify common allelic variants that contribute to obesity and to variable individual response to obesity therapy. Currently, family history may be more predictive than genetics for risk of obesity, but individual testing could ultimately guide therapy and, in the aggregate, guide public health policy. The primary limitation to development of genotype-based diets is that successful randomized diet trials of widely ranging macronutrient content, adequately powered for finding rare Mendelian mutations, have not been performed. Copyright © 2010 Elsevier Inc. All rights reserved.

  4. Molecular genetics of cancer and tumorigenesis: Drosophila models

    Institute of Scientific and Technical Information of China (English)

    Wu-Min Deng

    2011-01-01

    Why do some cells not respond to normal control of cell division and become tumorous? Which signals trigger some tumor cells to migrate and colonize other tissues? What genetic factors are responsible for tumorigenesis and cancer development? What environmental factors play a role in cancer formation and progression? In how many ways can our bodies prevent and restrict the growth of cancerous cells?How can we identify and deliver effective drugs to fight cancer? In the fight against cancer,which kills more people than any other disease,these and other questions have long interested researchers from a diverse range of fields.To answer these questions and to fight cancer more effectively,we must increase our understanding of basic cancer biology.Model organisms,including the fruit fly Drosophila melanogaster,have played instrumental roles in our understanding of this devastating disease and the search for effective cures.Drosophila and its highly effective,easy-touse,and ever-expanding genetic tools have contributed toand enriched our knowledge of cancer and tumor formation tremendously.

  5. Structure Refinement for Vulnerability Estimation Models using Genetic Algorithm Based Model Generators

    Directory of Open Access Journals (Sweden)

    2009-01-01

    Full Text Available In this paper, a method for model structure refinement is proposed and applied in estimation of cumulative number of vulnerabilities according to time. Security as a quality characteristic is presented and defined. Vulnerabilities are defined and their importance is assessed. Existing models used for number of vulnerabilities estimation are enumerated, inspecting their structure. The principles of genetic model generators are inspected. Model structure refinement is defined in comparison with model refinement and a method for model structure refinement is proposed. A case study shows how the method is applied and the obtained results.

  6. Accumulation of biomass and mineral elements with calendar time by corn: application of the expanded growth model.

    Directory of Open Access Journals (Sweden)

    Allen R Overman

    Full Text Available The expanded growth model is developed to describe accumulation of plant biomass (Mg ha(-1 and mineral elements (kg ha(-1 in with calendar time (wk. Accumulation of plant biomass with calendar time occurs as a result of photosynthesis for green land-based plants. A corresponding accumulation of mineral elements such as nitrogen, phosphorus, and potassium occurs from the soil through plant roots. In this analysis, the expanded growth model is tested against high quality, published data on corn (Zea mays L. growth. Data from a field study in South Carolina was used to evaluate the application of the model, where the planting time of April 2 in the field study maximized the capture of solar energy for biomass production. The growth model predicts a simple linear relationship between biomass yield and the growth quantifier, which is confirmed with the data. The growth quantifier incorporates the unit processes of distribution of solar energy which drives biomass accumulation by photosynthesis, partitioning of biomass between light-gathering and structural components of the plants, and an aging function. A hyperbolic relationship between plant nutrient uptake and biomass yield is assumed, and is confirmed for the mineral elements nitrogen (N, phosphorus (P, and potassium (K. It is concluded that the rate limiting process in the system is biomass accumulation by photosynthesis and that nutrient accumulation occurs in virtual equilibrium with biomass accumulation.

  7. Accumulation of biomass and mineral elements with calendar time by cotton: application of the expanded growth model.

    Directory of Open Access Journals (Sweden)

    Allen R Overman

    Full Text Available Accumulation of plant biomass (Mg ha(-1 with calendar time (wk occurs as a result of photosynthesis for green land-based plants. A corresponding accumulation of mineral elements (kg ha(-1 such as nitrogen, phosphorus, and potassium occurs from the soil through plant roots. Field data from literature for the warm-season annual cotton (Gossypium hirsutum L. are used in this analysis. The expanded growth model is used to describe accumulation of biomass and mineral elements with calendar time. The growth model predicts a simple linear relationship between biomass yield and the growth quantifier, which is confirmed with the data. The growth quantifier incorporates the unit processes of distribution of solar energy which drives biomass accumulation by photosynthesis, partitioning of biomass between light-gathering and structural components of the plants, and an aging function. A hyperbolic relationship between plant nutrient uptake and biomass yield is assumed, and is confirmed for the mineral elements nitrogen, phosphorus, and potassium. It is concluded that the rate limiting process in the system is biomass accumulation by photosynthesis and that nutrient accumulation occurs in virtual equilibrium with biomass accumulation. The expanded growth model describes field data from California and Alabama rather well. Furthermore, all model parameters were common for the two sites with the exception of the yield factor A which accounts for differences in soil types, environmental conditions, fertilizer levels, and plant population.

  8. Estimation of genetic parameters and genetic change for stillbirth in Iranian Holstein cows: a comparison between linear and threshold models

    OpenAIRE

    N.G. HOSSEIN-ZADEH

    2008-01-01

    Data on stillbirth from the Animal Breeding Center of Iran collected from January 1990 to December 2007 and comprising 668810 Holstein calving events from 2506 herds were analyzed. Linear and threshold animal and sire models were used to estimate genetic parameters and genetic trends for stillbirth in the first, second, and third parities. Mean incidence of stillbirth decreased from first to third parities: 23.7%, 22.1%, and 21.8%, respectively. Phenotypic rates of stillbirth decreased from 1...

  9. Chapter 9: Model Systems for Formation and Dissolution of Calcium Phosphate Minerals

    Energy Technology Data Exchange (ETDEWEB)

    Orme, C A; Giocondi, J L

    2006-07-29

    Calcium phosphates are the mineral component of bones and teeth. As such there is great interest in understanding the physical mechanisms that underlie their growth, dissolution, and phase stability. Control is often achieved at the cellular level by the manipulation of solution states and the use of crystal growth modulators such as peptides or other organic molecules. This chapter begins with a discussion of solution speciation in body fluids and relates this to important crystal growth parameters such as the supersaturation, pH, ionic strength and the ratio of calcium to phosphate activities. We then discuss the use of scanning probe microscopy as a tool to measure surface kinetics of mineral surfaces evolving in simplified solutions. The two primary themes that we will touch on are the use of microenvironments that temporally evolve the solution state to control growth and dissolution; and the use of various growth modifiers that interact with the solution species or with mineral surfaces to shift growth away from the lowest energy facetted forms. The study of synthetic minerals in simplified solution lays the foundation for understand mineralization process in more complex environments found in the body.

  10. Genetics

    DEFF Research Database (Denmark)

    Christensen, Kaare; McGue, Matt

    2016-01-01

    The sequenced genomes of individuals aged ≥80 years, who were highly educated, self-referred volunteers and with no self-reported chronic diseases were compared to young controls. In these data, healthy ageing is a distinct phenotype from exceptional longevity and genetic factors that protect...

  11. Local identification of piecewise deterministic models of genetic networks

    NARCIS (Netherlands)

    Cinquemani, Eugenio; Milias-Argeitis, Andreas; Summers, Sean; Lygeros, John

    2009-01-01

    We address the identification of genetic networks under stationary conditions. A stochastic hybrid description of the genetic interactions is considered and an approximation of it in stationary conditions is derived. Contrary to traditional structure identification methods based on fitting determini

  12. Behavioral phenotypes of genetic mouse models of autism.

    Science.gov (United States)

    Kazdoba, T M; Leach, P T; Crawley, J N

    2016-01-01

    More than a hundred de novo single gene mutations and copy-number variants have been implicated in autism, each occurring in a small subset of cases. Mutant mouse models with syntenic mutations offer research tools to gain an understanding of the role of each gene in modulating biological and behavioral phenotypes relevant to autism. Knockout, knockin and transgenic mice incorporating risk gene mutations detected in autism spectrum disorder and comorbid neurodevelopmental disorders are now widely available. At present, autism spectrum disorder is diagnosed solely by behavioral criteria. We developed a constellation of mouse behavioral assays designed to maximize face validity to the types of social deficits and repetitive behaviors that are central to an autism diagnosis. Mouse behavioral assays for associated symptoms of autism, which include cognitive inflexibility, anxiety, hyperactivity, and unusual reactivity to sensory stimuli, are frequently included in the phenotypic analyses. Over the past 10 years, we and many other laboratories around the world have employed these and additional behavioral tests to phenotype a large number of mutant mouse models of autism. In this review, we highlight mouse models with mutations in genes that have been identified as risk genes for autism, which work through synaptic mechanisms and through the mTOR signaling pathway. Robust, replicated autism-relevant behavioral outcomes in a genetic mouse model lend credence to a causal role for specific gene contributions and downstream biological mechanisms in the etiology of autism.

  13. Ripple-Spreading Network Model Optimization by Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Xiao-Bing Hu

    2013-01-01

    Full Text Available Small-world and scale-free properties are widely acknowledged in many real-world complex network systems, and many network models have been developed to capture these network properties. The ripple-spreading network model (RSNM is a newly reported complex network model, which is inspired by the natural ripple-spreading phenomenon on clam water surface. The RSNM exhibits good potential for describing both spatial and temporal features in the development of many real-world networks where the influence of a few local events spreads out through nodes and then largely determines the final network topology. However, the relationships between ripple-spreading related parameters (RSRPs of RSNM and small-world and scale-free topologies are not as obvious or straightforward as in many other network models. This paper attempts to apply genetic algorithm (GA to tune the values of RSRPs, so that the RSNM may generate these two most important network topologies. The study demonstrates that, once RSRPs are properly tuned by GA, the RSNM is capable of generating both network topologies and therefore has a great flexibility to study many real-world complex network systems.

  14. Toward Developing Genetic Algorithms to Aid in Critical Infrastructure Modeling

    Energy Technology Data Exchange (ETDEWEB)

    2007-05-01

    Today’s society relies upon an array of complex national and international infrastructure networks such as transportation, telecommunication, financial and energy. Understanding these interdependencies is necessary in order to protect our critical infrastructure. The Critical Infrastructure Modeling System, CIMS©, examines the interrelationships between infrastructure networks. CIMS© development is sponsored by the National Security Division at the Idaho National Laboratory (INL) in its ongoing mission for providing critical infrastructure protection and preparedness. A genetic algorithm (GA) is an optimization technique based on Darwin’s theory of evolution. A GA can be coupled with CIMS© to search for optimum ways to protect infrastructure assets. This includes identifying optimum assets to enforce or protect, testing the addition of or change to infrastructure before implementation, or finding the optimum response to an emergency for response planning. This paper describes the addition of a GA to infrastructure modeling for infrastructure planning. It first introduces the CIMS© infrastructure modeling software used as the modeling engine to support the GA. Next, the GA techniques and parameters are defined. Then a test scenario illustrates the integration with CIMS© and the preliminary results.

  15. Identification of Hammerstein Model Based on Quantum Genetic Algorithm

    OpenAIRE

    Zhang Hai Li

    2013-01-01

    Nonlinear system identification is a main topic of modern identification. A new method for nonlinear system identification is presented by using Quantum Genetic Algorithm(QGA).The problems of nonlinear system identification are cast as function optimization overprameter space,and the Quantum Genetic Algorithm is adopted to solve the optimization problem. Simulation experiments show that: compared with the genetic algorithm, quantum genetic algorithm is an effective swarm intelligence algorith...

  16. Integrated Experimental and Modeling Studies of Mineral Carbonation as a Mechanism for Permanent Carbon Sequestration in Mafic/Ultramafic Rocks

    Energy Technology Data Exchange (ETDEWEB)

    Wang, Zhengrong [Yale Univ., New Haven, CT (United States); Qiu, Lin [Yale Univ., New Haven, CT (United States); Zhang, Shuang [Yale Univ., New Haven, CT (United States); Bolton, Edward [Yale Univ., New Haven, CT (United States); Bercovici, David [Yale Univ., New Haven, CT (United States); Ague, Jay [Yale Univ., New Haven, CT (United States); Karato, Shun-Ichiro [Yale Univ., New Haven, CT (United States); Oristaglio, Michael [Yale Univ., New Haven, CT (United States); Zhu, Wen-Iu [Univ. of Maryland, College Park, MD (United States); Lisabeth, Harry [Univ. of Maryland, College Park, MD (United States); Johnson, Kevin [Univ. of Hawaii, Honolulu, HI (United States)

    2014-09-30

    A program of laboratory experiments, modeling and fieldwork was carried out at Yale University, University of Maryland, and University of Hawai‘i, under a DOE Award (DE-FE0004375) to study mineral carbonation as a practical method of geologic carbon sequestration. Mineral carbonation, also called carbon mineralization, is the conversion of (fluid) carbon dioxide into (solid) carbonate minerals in rocks, by way of naturally occurring chemical reactions. Mafic and ultramafic rocks, such as volcanic basalt, are natural candidates for carbonation, because the magnesium and iron silicate minerals in these rocks react with brines of dissolved carbon dioxide to form carbonate minerals. By trapping carbon dioxide (CO2) underground as a constituent of solid rock, carbonation of natural basalt formations would be a secure method of sequestering CO2 captured at power plants in efforts to mitigate climate change. Geochemical laboratory experiments at Yale, carried out in a batch reactor at 200°C and 150 bar (15 MPa), studied carbonation of the olivine mineral forsterite (Mg2SiO4) reacting with CO2 brines in the form of sodium bicarbonate (NaHCO3) solutions. The main carbonation product in these reactions is the carbonate mineral magnesite (MgCO3). A series of 32 runs varied the reaction time, the reactive surface area of olivine grains and powders, the concentration of the reacting fluid, and the starting ratio of fluid to olivine mass. These experiments were the first to study the rate of olivine carbonation under passive conditions approaching equilibrium. The results show that, in a simple batch reaction, olivine carbonation is fastest during the first 24 hours and then slows significantly and even reverses. A natural measure of the extent of carbonation is a quantity called the carbonation fraction, which compares the amount of carbon removed from solution, during a run, to the maximum amount

  17. Geology, Mineral Deposit Model and Potential of the Suwar Cu-Ni Sulphide Prospect, Northwest Yemen

    Institute of Scientific and Technical Information of China (English)

    Abdulkarim M.; Al-Nagashi; Li Xujun

    2002-01-01

    The Suwar Cu-Ni sulphide prospect is very highly regarded for its potential to host a major nickel-copper sulphide deposit in Republic of Yemen, a mineral resource lacking country. The ore-hosting intrusion is a lopolith about 6km long and lkm wide and more than 300m deep. There are two types of Cu-Ni mineralizations in the prospect: primary massive chalcopyrite+ pyrrhotite+ pentlandite controlled by gravitational and structural traps while the secondary Cu-Ni mineralization is coarse grained and occur as veins, veinlets, fracture fill, blebs or associated with coarse, re-crystallized carbonate in shear zones and faults. The deposit type of the prospect is believed to be the one associated with the ultramafic component of a large, broadly differentiated noritic, gabbroid intrusive. It is suggested that the prospect and adjacent area possibly contain a similar world class Ni-Cu deposits as that in Jinchuan, China.

  18. Predicting Mineral N Release during Decomposition of Organic Wastes in Soil by Use of the SOILN_NO Model

    Directory of Open Access Journals (Sweden)

    Trine A. Sogn

    2011-01-01

    Full Text Available In order to predict the mineral N release associated with the use of organic waste as fertilizer in agricultural plant production, the adequacy of the SOILN_NO model has been evaluated. The original thought was that the model calibrated to data from simple incubation experiments could predict the mineral N release from organic waste products used as N fertilizer on agricultural land. First, the model was calibrated to mineral N data achieved in a laboratory experiment where different organic wastes were added to soil and incubated at 15°C for 8 weeks. Secondly, the calibrated model was tested by use of NO3 − leaching data from soil columns with barley growing in 4 different soil types, added organic waste and exposed to natural climatic conditions during three growing seasons. The SOILN_NO model reproduced relatively well the NO3 − leaching from some of the soils included in the outdoor experiment, but failed to reproduce others. Use of the calibrated model often induced underestimation of the observed NO3 − leaching. To achieve a satisfactory simulation of the NO3 − leaching, recalibration of the model had to be carried out. Thus, SOILN_NO calibrated to data from simple incubation experiments in the laboratory could not directly be used as a tool to predict the N-leaching following organic waste application in more natural agronomic plant production systems. The results emphasised the need for site- and system-specific data for model calibration before using a model for predictive purposes related to fertilizer N value of organic wastes applied to agricultural land.

  19. Genetic fuzzy system modeling and simulation of vascular behaviour

    DEFF Research Database (Denmark)

    Tang, Jiaowei; Boonen, Harrie C.M.

    and find the optimal parameters in a Fuzzy Control set that can control the fluctuation of physical features in a blood vessel, based on experimental data (training data). Our solution is to create chromosomes or individuals composed of a sequence of parameters in the fuzzy system and find the best...... chromosome or individual to define the fuzzy system. The model is implemented by combining the Matlab Genetic algorithm and Fuzzy system toolboxes, respectively. To test the performance of this method, experimental data sets about calculated pressure change in different blood vessels after several chemical...... treatments are chosen as training and testing data sets. In the simulation, the fuzzy control system is trained by pressure data of one blood vessel and tested with pressure data of other blood vessels. Results: Right now, some rough results show that trained fuzzy control system can be used to predict...

  20. New Genetics

    Science.gov (United States)

    ... Home > Science Education > The New Genetics The New Genetics Living Laboratories Classroom Poster Order a Free Copy ... Piece to a Century-Old Evolutionary Puzzle Computing Genetics Model Organisms RNA Interference The New Genetics is ...

  1. Stress, glucocorticoids and absences in a genetic epilepsy model.

    Science.gov (United States)

    Tolmacheva, Elena A; Oitzl, Melly S; van Luijtelaar, Gilles

    2012-05-01

    Although stress can alter the susceptibility of patients and animal models to convulsive epilepsy, little is known about the role of stress and glucocorticoid hormones in absence epilepsy. We measured the basal and acute stress-induced (foot-shocks: FS) concentrations of corticosterone in WAG/Rij rats, non-epileptic inbred ACI rats and outbred Wistar rats. The WAG/Rij strain is a genetic model for absence epilepsy and comorbidity for depression, which originates from the population of Wistar rats and, therefore, shares their genetic background. In a separate experiment, WAG/Rij rats were exposed to FS on three consecutive days. Electroencephalograms (EEGs) were recorded before and after FS, and the number of absence seizures (spike-wave-discharges, SWDs) was quantified. Both WAG/Rij rats and ACI rats exhibited elevated basal levels of corticosterone and a rapid corticosterone increase in response to acute stress. The WAG/Rij rats also displayed the most rapid normalization of corticosterone during the recovery phase compared to that of ACI and Wistar rats. FS had a biphasic effect on SWDs; an initial suppression was followed by an aggravation of the SWDs. By the third day, this aggravation of seizures was present in the hour preceding FS. This increase in SWDs may arise from anticipatory stress about the upcoming FS. Together, these results suggest that the distinct secretion profile of corticosterone found in WAG/Rij rats may contribute to the severity of the epileptic phenotype. Although the acute stressor results in an initial suppression of SWDs followed by an increase in SWDs, stress prior to a predictable negative event aggravates absences.

  2. A Mathematical Model Accounting for the Organisation in Multiplets of the Genetic Code

    OpenAIRE

    Sciarrino, A.

    2001-01-01

    Requiring stability of genetic code against translation errors, modelised by suitable mathematical operators in the crystal basis model of the genetic code, the main features of the organisation in multiplets of the mitochondrial and of the standard genetic code are explained.

  3. Estimation of genetic parameters and genetic change for stillbirth in Iranian Holstein cows: a comparison between linear and threshold models

    Directory of Open Access Journals (Sweden)

    N.G. HOSSEIN-ZADEH

    2008-12-01

    Full Text Available Data on stillbirth from the Animal Breeding Center of Iran collected from January 1990 to December 2007 and comprising 668810 Holstein calving events from 2506 herds were analyzed. Linear and threshold animal and sire models were used to estimate genetic parameters and genetic trends for stillbirth in the first, second, and third parities. Mean incidence of stillbirth decreased from first to third parities: 23.7%, 22.1%, and 21.8%, respectively. Phenotypic rates of stillbirth decreased from 1993 to 1998, for first, second and third calvings, and then increased from 1998 to 2007 for the first three parities. Direct heritability estimates of stillbirth for parities 1, 2 and 3 ranged from 2.2 to 8.7%, 0.6 to 5.1% and 0.1 to 3.8%, respectively, and maternal heritability estimates of stillbirth for parities 1, 2 and 3 ranged from 1.4 to 6.3%, 0.5 to 4.2% and 0.08 to 2.0%, respectively, using linear and threshold animal models. The threshold sire model estimates of heritabilities for stillbirth in this study were 0.021 to 0.071, while the linear sire model estimates of heritabilities for stillbirth in the current study were from 0.003 to 0.021 over the parities. There was a slightly increasing genetic trend for stillbirth rate in parities 1 and 2 over time with the analysis of linear animal and linear sire models. There was a significant decreasing genetic trend for stillbirth rate in parity 1 and 3 over time with the analysis of threshold animal and threshold sire models, but the genetic trend for stillbirth rate in parity 2 with these models of analysis was significantly positive. The low estimates of heritability obtained in this study implied that much of the improvement in stillbirth could be attained by improvement of production environment rather than genetic selection.;

  4. Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

    Science.gov (United States)

    Johnson, Ronald; Kennon, Tillman

    2009-01-01

    Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

  5. Experimental Population Genetics in the Introductory Genetics Laboratory Using "Drosophila" as a Model Organism

    Science.gov (United States)

    Johnson, Ronald; Kennon, Tillman

    2009-01-01

    Hypotheses of population genetics are derived and tested by students in the introductory genetics laboratory classroom as they explore the effects of biotic variables (physical traits of fruit flies) and abiotic variables (island size and distance) on fruit fly populations. In addition to this hypothesis-driven experiment, the development of…

  6. Genetic models for the study of luteinizing hormone receptor function

    Directory of Open Access Journals (Sweden)

    Prema eNarayan

    2015-09-01

    Full Text Available The luteinizing hormone/chorionic gonadotropin receptor, LHCGR, is essential for fertility in men and women. LHCGR binds luteinizing hormone (LH as well as the highly homologous chorionic gonadotropin (CG. Signaling from LHCGR is required for steroidogenesis and gametogenesis in males and females and for sexual differentiation in the male. The importance of LHCGR in reproductive physiology is underscored by the large number of naturally occurring inactivating and activating mutations in the receptor that result in reproductive disorders. Consequently, several genetically modified mouse models have been developed for the study of LHCGR function. They include targeted deletion of LH and LHCGR that mimic inactivating mutations in hormone and receptor, expression of a constitutively active mutant in LHCGR that mimics activating mutations associated with familial male-limited precocious puberty and transgenic models of LH and hCG overexpression. This review summarizes the salient findings from these models and their utility in understanding the physiological and pathological consequences of loss and gain of function in LHCGR signaling.

  7. Process-based modeling of silicate mineral weathering responses to increasing atmospheric CO2 and climate change

    Science.gov (United States)

    Banwart, Steven A.; Berg, Astrid; Beerling, David J.

    2009-12-01

    A mathematical model describes silicate mineral weathering processes in modern soils located in the boreal coniferous region of northern Europe. The process model results demonstrate a stabilizing biological feedback mechanism between atmospheric CO2 levels and silicate weathering rates as is generally postulated for atmospheric evolution. The process model feedback response agrees within a factor of 2 of that calculated by a weathering feedback function of the type generally employed in global geochemical carbon cycle models of the Earth's Phanerozoic CO2 history. Sensitivity analysis of parameter values in the process model provides insight into the key mechanisms that influence the strength of the biological feedback to weathering. First, the process model accounts for the alkalinity released by weathering, whereby its acceleration stabilizes pH at values that are higher than expected. Although the process model yields faster weathering with increasing temperature, because of activation energy effects on mineral dissolution kinetics at warmer temperature, the mineral dissolution rate laws utilized in the process model also result in lower dissolution rates at higher pH values. Hence, as dissolution rates increase under warmer conditions, more alkalinity is released by the weathering reaction, helping maintain higher pH values thus stabilizing the weathering rate. Second, the process model yields a relatively low sensitivity of soil pH to increasing plant productivity. This is due to more rapid decomposition of dissolved organic carbon (DOC) under warmer conditions. Because DOC fluxes strongly influence the soil water proton balance and pH, this increased decomposition rate dampens the feedback between productivity and weathering. The process model is most sensitive to parameters reflecting soil structure; depth, porosity, and water content. This suggests that the role of biota to influence these characteristics of the weathering profile is as important, if not

  8. Detecting reduced bone mineral density from dental radiographs using statistical shape models

    NARCIS (Netherlands)

    Allen, P.D.; Graham, J.; Farnell, D.J.J.; Harrison, E.J.; Jacobs, R.; Nicopoulou-Karyianni, K.; Lindh, C.; van der Stelt, P.F.; Horner, K.; Devlin, H.

    2007-01-01

    We describe a novel method of estimating reduced bone mineral density (BMD) from dental panoramic tomograms (DPTs), which show the entire mandible. Careful expert width measurement of the inferior mandibular cortex has been shown to be predictive of BMD in hip and spine osteopenia and osteoporosis.

  9. A generic transport-reactive model for simulating microbially influenced mineral precipitation in porous medium

    NARCIS (Netherlands)

    Zhou, J.; Van Turnhout, A.G.; Heimovaara, T.J.; Afanasyev, M.

    2015-01-01

    The spatial and temporal distribution of precipitated minerals is one of the key factors governing various processes in the sub-surface environment, including microbially influenced corrosion (MIC) (Huang, 2002), bio-cementation (van Paassen et al., 2010) and sediment diagenesis (Paraska et al., 201

  10. A generic transport-reactive model for simulating microbially influenced mineral precipitation in porous medium

    NARCIS (Netherlands)

    Zhou, J.; Van Turnhout, A.G.; Heimovaara, T.J.; Afanasyev, M.

    2015-01-01

    The spatial and temporal distribution of precipitated minerals is one of the key factors governing various processes in the sub-surface environment, including microbially influenced corrosion (MIC) (Huang, 2002), bio-cementation (van Paassen et al., 2010) and sediment diagenesis (Paraska et al.,

  11. Polarization in Raman spectroscopy helps explain bone brittleness in genetic mouse models

    Science.gov (United States)

    Makowski, Alexander J.; Pence, Isaac J.; Uppuganti, Sasidhar; Zein-Sabatto, Ahbid; Huszagh, Meredith C.; Mahadevan-Jansen, Anita; Nyman, Jeffry S.

    2014-01-01

    Abstract. Raman spectroscopy (RS) has been extensively used to characterize bone composition. However, the link between bone biomechanics and RS measures is not well established. Here, we leveraged the sensitivity of RS polarization to organization, thereby assessing whether RS can explain differences in bone toughness in genetic mouse models for which traditional RS peak ratios are not informative. In the selected mutant mice—activating transcription factor 4 (ATF4) or matrix metalloproteinase 9 (MMP9) knock-outs—toughness is reduced but differences in bone strength do not exist between knock-out and corresponding wild-type controls. To incorporate differences in the RS of bone occurring at peak shoulders, a multivariate approach was used. Full spectrum principal components analysis of two paired, orthogonal bone orientations (relative to laser polarization) improved genotype classification and correlation to bone toughness when compared to traditional peak ratios. When applied to femurs from wild-type mice at 8 and 20 weeks of age, the principal components of orthogonal bone orientations improved age classification but not the explanation of the maturation-related increase in strength. Overall, increasing polarization information by collecting spectra from two bone orientations improves the ability of multivariate RS to explain variance in bone toughness, likely due to polarization sensitivity to organizational changes in both mineral and collagen. PMID:25402627

  12. Polarization in Raman spectroscopy helps explain bone brittleness in genetic mouse models

    Science.gov (United States)

    Makowski, Alexander J.; Pence, Isaac J.; Uppuganti, Sasidhar; Zein-Sabatto, Ahbid; Huszagh, Meredith C.; Mahadevan-Jansen, Anita; Nyman, Jeffry S.

    2014-11-01

    Raman spectroscopy (RS) has been extensively used to characterize bone composition. However, the link between bone biomechanics and RS measures is not well established. Here, we leveraged the sensitivity of RS polarization to organization, thereby assessing whether RS can explain differences in bone toughness in genetic mouse models for which traditional RS peak ratios are not informative. In the selected mutant mice-activating transcription factor 4 (ATF4) or matrix metalloproteinase 9 (MMP9) knock-outs-toughness is reduced but differences in bone strength do not exist between knock-out and corresponding wild-type controls. To incorporate differences in the RS of bone occurring at peak shoulders, a multivariate approach was used. Full spectrum principal components analysis of two paired, orthogonal bone orientations (relative to laser polarization) improved genotype classification and correlation to bone toughness when compared to traditional peak ratios. When applied to femurs from wild-type mice at 8 and 20 weeks of age, the principal components of orthogonal bone orientations improved age classification but not the explanation of the maturation-related increase in strength. Overall, increasing polarization information by collecting spectra from two bone orientations improves the ability of multivariate RS to explain variance in bone toughness, likely due to polarization sensitivity to organizational changes in both mineral and collagen.

  13. Mineral oils

    Science.gov (United States)

    Furby, N. W.

    1973-01-01

    The characteristics of lubricants made from mineral oils are discussed. Types and compositions of base stocks are reviewed and the product demands and compositions of typical products are outlined. Processes for commercial production of mineral oils are examined. Tables of data are included to show examples of product types and requirements. A chemical analysis of three types of mineral oils is reported.

  14. Evaluating sensitivity of silicate mineral dissolution rates to physical weathering using a soil evolution model (SoilGen2.25)

    Science.gov (United States)

    Opolot, E.; Finke, P. A.

    2015-11-01

    Silicate mineral dissolution rates depend on the interaction of a number of factors categorized either as intrinsic (e.g. mineral surface area, mineral composition) or extrinsic (e.g. climate, hydrology, biological factors, physical weathering). Estimating the integrated effect of these factors on the silicate mineral dissolution rates therefore necessitates the use of fully mechanistic soil evolution models. This study applies a mechanistic soil evolution model (SoilGen) to explore the sensitivity of silicate mineral dissolution rates to the integrated effect of other soil-forming processes and factors. The SoilGen soil evolution model is a 1-D model developed to simulate the time-depth evolution of soil properties as a function of various soil-forming processes (e.g. water, heat and solute transport, chemical and physical weathering, clay migration, nutrient cycling, and bioturbation) driven by soil-forming factors (i.e., climate, organisms, relief, parent material). Results from this study show that although soil solution chemistry (pH) plays a dominant role in determining the silicate mineral dissolution rates, all processes that directly or indirectly influence the soil solution composition play an equally important role in driving silicate mineral dissolution rates. Model results demonstrated a decrease of silicate mineral dissolution rates with time, an obvious effect of texture and an indirect but substantial effect of physical weathering on silicate mineral dissolution rates. Results further indicated that clay migration and plant nutrient recycling processes influence the pH and thus the silicate mineral dissolution rates. Our silicate mineral dissolution rates results fall between field and laboratory rates but were rather high and more close to the laboratory rates possibly due to the assumption of far from equilibrium reaction used in our dissolution rate mechanism. There is therefore a need to include secondary mineral precipitation mechanism in our

  15. Statistical analysis of results from the quantitative mapping of fracture minerals in Laxemar. Site descriptive modelling - complementary studies

    Energy Technology Data Exchange (ETDEWEB)

    Loefgren, Martin (Niressa AB, Norsborg (Sweden)); Sidborn, Magnus (Kemakta Konsult AB, Stockholm (Sweden))

    2010-12-15

    generally shown to be small and if comparing the cumulative distribution functions for the data subsets of the 17 rock volumes, more similarities than dissimilarities are found. No general trends can be observed in data with respect to elevation and location of the rock volumes. These conclusions are made from the perspective of radionuclide retention and groundwater composition modelling. Such modelling is not so sensitive to local deviations in fracture mineral abundances, as flow path averaging is of major importance. In other scientific fields, these deviations may be attributed greater importance. It is shown from parametric analyses that the normal distribution fairly well describes the logarithm of d{sub mean} data. Concerning the visible coverage, log{sub 10}(C{sub vis}) data are fairly well described by truncated normal distributions. The distributions fitted to data from the entire site fairly well represent the individual rock volumes. In fractures where the mineral amounts could be quantified, the following means and standard deviations for the normal distribution of log{sub 10}(d{sub mean} [mm]) are suggested: calcite mu = -1.21 and sigma = 0.76, chlorite mu = -0.83 and sigma = 0.48, clay minerals mu = -1.12 and sigma = 0.51, pyrite mu = -4.43 and sigma = 1.17. In fractures where the mineral visible coverage could be estimated, the following parameters for a truncated normal distribution of log{sub 10}(C{sub vis}) are suggested: calcite alpha = 0.96 and beta = 0.65, chlorite alpha = 1.43 and beta = 0.45, clay minerals alpha = 1.39 and beta = 0.41, pyrite alpha = -1.90 and beta = 1.08. For hematite, the data are so scarce that no well founded conclusion can be drawn. The potential correlation between the abundance of fracture minerals and the local transmissivity (which is related to the groundwater flow rate) has been evaluated, but no apparent correlation has been found. However, this evaluation is of preliminary character

  16. Smooth-Threshold Multivariate Genetic Prediction with Unbiased Model Selection.

    Science.gov (United States)

    Ueki, Masao; Tamiya, Gen

    2016-04-01

    We develop a new genetic prediction method, smooth-threshold multivariate genetic prediction, using single nucleotide polymorphisms (SNPs) data in genome-wide association studies (GWASs). Our method consists of two stages. At the first stage, unlike the usual discontinuous SNP screening as used in the gene score method, our method continuously screens SNPs based on the output from standard univariate analysis for marginal association of each SNP. At the second stage, the predictive model is built by a generalized ridge regression simultaneously using the screened SNPs with SNP weight determined by the strength of marginal association. Continuous SNP screening by the smooth thresholding not only makes prediction stable but also leads to a closed form expression of generalized degrees of freedom (GDF). The GDF leads to the Stein's unbiased risk estimation (SURE), which enables data-dependent choice of optimal SNP screening cutoff without using cross-validation. Our method is very rapid because computationally expensive genome-wide scan is required only once in contrast to the penalized regression methods including lasso and elastic net. Simulation studies that mimic real GWAS data with quantitative and binary traits demonstrate that the proposed method outperforms the gene score method and genomic best linear unbiased prediction (GBLUP), and also shows comparable or sometimes improved performance with the lasso and elastic net being known to have good predictive ability but with heavy computational cost. Application to whole-genome sequencing (WGS) data from the Alzheimer's Disease Neuroimaging Initiative (ADNI) exhibits that the proposed method shows higher predictive power than the gene score and GBLUP methods.

  17. Toward a genetically-informed model of borderline personality disorder.

    Science.gov (United States)

    Livesley, John

    2008-02-01

    This article describes a conceptual framework for describing borderline personality disorder (BPD) based on empirical studies of the phenotypic structure and genetic architecture of personality. The proposed phenotype has 2 components: (1) a description of core self and interpersonal pathology-the defining features of personality disorder-as these features are expressed in the disorder; and (2) a set of traits based on the anxious-dependent or emotional dysregulation factor of the four-factor model of PD. Four kinds of traits are described: emotional (anxiousness, emotional reactivity, emotional intensity, and pessimistic-anhedonia), interpersonal (submissiveness, insecure attachment, social apprehensiveness, and need for approval), cognitive (cognitive dysregulation), and self-harm (behaviors and ideas). Formulation of the phenotype was guided by the conceptualization of personality as a system of interrelated sub-systems. The psychopathology associated with BPD involves most components of the system. The trait structure of the disorder is assumed to reflect the genetic architecture of personality and individual traits are assumed to be based on adaptive mechanisms. It is suggested that borderline traits are organized around the trait of anxiousness and that an important feature of BPD is dysregulation of the threat management system leading to pervasive fearfulness and unstable emotions. The interpersonal traits are assumed to be heritable characteristics that evolved to deal with interpersonal threats that arose as a result of social living. The potential for unstable and conflicted interpersonal relationships that is inherent to the disorder is assumed to result from the interplay between the adaptive structure of personality and psychosocial adversity. The etiology of the disorder is discussed in terms of biological and environmental factors associated with each component of the phenotype.

  18. Influence of sterilization on the mineralization of titanium implants induced by incubation in various biological model fluids.

    Science.gov (United States)

    Serro, A P; Saramago, B

    2003-11-01

    The aim of this work was to investigate the effect of the sterilization processes on the mineralization of titanium implants induced by incubation in various biological model fluids. Titanium samples were submitted to the following sterilization processes used for implant materials: steam autoclaving, glow discharge Ar plasma treatment and gamma-irradiation. The modification of the treated surfaces was evaluated by contact angle determinations, X-ray photoelectron spectroscopy (XPS), laser profilometry and X-ray diffraction. The most significant modifications were detected on the wettability: while the samples treated with Ar plasma became highly hydrophilic (water contact angle approximately 0 degrees), gamma-irradiation and steam sterilization induced an increase in the hydrophobicity. After being sterilized, the samples were incubated for one week in three biological model fluids: Hanks' Balanced Salt Solution, Kokubo's simulated body fluid (SBF) and a fluid, designated by SBF0, with the same composition of SBF but without buffer TRIS. The level of mineralization of the incubated Ti samples, assessed by dynamic contact angle analysis, scanning electron microscopy, electron dispersive spectroscopy and XPS, indicated that the early stages of mineralization are essentially independent of the sterilization method. In contrast, the incubating fluid plays a determinant role, SBFO being the most efficient medium for biomineralization of titanium.

  19. Molecular genetics and animal models in autistic disorder.

    Science.gov (United States)

    Andres, Christian

    2002-01-01

    Autistic disorder is a behavioural syndrome beginning before the age of 3 years and lasting over the whole lifetime. It is characterised by impaired communication, impaired social interactions, and repetitive interests and behaviour. The prevalence is about 7/10,000 taking a restrictive definition and more than 1/500 with a broader definition, including all the pervasive developmental disorders. The importance of genetic factors has been highlighted by epidemiological studies showing that autistic disorder is one of the most genetic neuropsychiatric diseases. The relative risk of first relatives is about 100-fold higher than the risk in the normal population and the concordance in monozygotic twin is about 60%. Different strategies have been applied on the track of susceptibility genes. The systematic search of linked loci led to contradictory results, in part due to the heterogeneity of the clinical definitions, to the differences in the DNA markers, and to the different methods of analysis used. An oversimplification of the inferred model is probably also cause of our disappointment. More work is necessary to give a clearer picture. One region emerges more frequently: the long arm of chromosome 7. Several candidate genes have been studied and some gave indications of association: the Reelin gene and the Wnt2 gene. Cytogenetical abnormalities are frequent at 15q11-13, the region of the Angelman and Prader-Willi syndrome. Imprinting plays an important role in this region, no candidate gene has been identified in autism. Biochemical abnormalities have been found in the serotonin system. Association and linkage studies gave no consistent results with some serotonin receptors and in the transporter, although it seems interesting to go further in the biochemical characterisation of the serotonin transporter activity, particularly in platelets, easily accessible. Two monogenic diseases have been associated with autistic disorder: tuberous sclerosis and fragile X. A

  20. [Approach to depressogenic genes from genetic analyses of animal models].

    Science.gov (United States)

    Yoshikawa, Takeo

    2004-01-01

    Human depression or mood disorder is defined as a complex disease, making positional cloning of susceptibility genes a formidable task. We have undertaken genetic analyses of three different animal models for depression, comparing our results with advanced database resources. We first performed quantitative trait loci (QTL) analysis on two mouse models of "despair", namely, the forced swim test (FST) and tail suspension test (TST), and detected multiple chromosomal loci that control immobility time in these tests. Since one QTL detected on mouse chromosome 11 harbors the GABA A receptor subunit genes, we tested these genes for association in human mood disorder patients. We obtained significant associations of the alpha 1 and alpha 6 subunit genes with the disease, particularly in females. This result was striking, because we had previously detected an epistatic interaction between mouse chromosomes 11 and X that regulates immobility time in these animals. Next, we performed genome-wide expression analyses using a rat model of depression, learned helplessness (LH). We found that in the frontal cortex of LH rats, a disease implicated region, the LIM kinase 1 gene (Limk 1) showed greatest alteration, in this case down-regulation. By combining data from the QTL analysis of FST/TST and DNA microarray analysis of mouse frontal cortex, we identified adenylyl cyclase-associated CAP protein 1 (Cap 1) as another candidate gene for depression susceptibility. Both Limk 1 and Cap 1 are key players in the modulation of actin G-F conversion. In summary, our current study using animal models suggests disturbances of GABAergic neurotransmission and actin turnover as potential pathophysiologies for mood disorder.

  1. Control of groundwater pH during bioremediation: Improvement and validation of a geochemical model to assess the buffering potential of ground silicate minerals

    Science.gov (United States)

    Lacroix, Elsa; Brovelli, Alessandro; Holliger, Christof; Barry, D. A.

    2014-05-01

    Accurate control of groundwater pH is of critical importance for in situ biological treatment of chlorinated solvents. The use of ground silicate minerals mixed with groundwater is an appealing buffering strategy as silicate minerals may act as long-term sources of alkalinity. In a previous study, we developed a geochemical model for evaluation of the pH buffering capacity of such minerals. The model included the main microbial processes driving groundwater acidification as well as mineral dissolution. In the present study, abiotic mineral dissolution experiments were conducted with five silicate minerals (andradite, diopside, fayalite, forsterite, nepheline). The goal of the study was to validate the model and to test the buffering capacity of the candidate minerals identified previously. These five minerals increased the pH from acidic to neutral and slightly basic values. The model was revised and improved to represent better the experimental observations. In particular, the experiments revealed the importance of secondary mineral precipitation on the buffering potential of silicates, a process not included in the original formulation. The main secondary phases likely to precipitate were identified through model calibration, as well as the degree of saturation at which they formed. The predictions of the revised geochemical model were in good agreement with the observations, with a correlation coefficient higher than 0.9 in most cases. This study confirmed the potential of silicates to act as pH control agents and showed the reliability of the geochemical model, which can be used as a design tool for field applications.

  2. Control of groundwater pH during bioremediation: improvement and validation of a geochemical model to assess the buffering potential of ground silicate minerals.

    Science.gov (United States)

    Lacroix, Elsa; Brovelli, Alessandro; Holliger, Christof; Barry, D A

    2014-05-01

    Accurate control of groundwater pH is of critical importance for in situ biological treatment of chlorinated solvents. The use of ground silicate minerals mixed with groundwater is an appealing buffering strategy as silicate minerals may act as long-term sources of alkalinity. In a previous study, we developed a geochemical model for evaluation of the pH buffering capacity of such minerals. The model included the main microbial processes driving groundwater acidification as well as mineral dissolution. In the present study, abiotic mineral dissolution experiments were conducted with five silicate minerals (andradite, diopside, fayalite, forsterite, nepheline). The goal of the study was to validate the model and to test the buffering capacity of the candidate minerals identified previously. These five minerals increased the pH from acidic to neutral and slightly basic values. The model was revised and improved to represent better the experimental observations. In particular, the experiments revealed the importance of secondary mineral precipitation on the buffering potential of silicates, a process not included in the original formulation. The main secondary phases likely to precipitate were identified through model calibration, as well as the degree of saturation at which they formed. The predictions of the revised geochemical model were in good agreement with the observations, with a correlation coefficient higher than 0.9 in most cases. This study confirmed the potential of silicates to act as pH control agents and showed the reliability of the geochemical model, which can be used as a design tool for field applications.

  3. The role of lateral boundary conditions in simulations of mineral aerosols by a regional climate model of Southwest Asia

    Energy Technology Data Exchange (ETDEWEB)

    Marcella, Marc Pace [Ralph M. Parsons Laboratory, Department of Civil and Environmental Engineering, Cambridge, MA (United States); Massachusetts Institute of Technology, Cambridge, Massachusetts (United States); Eltahir, Elfatih A.B. [Massachusetts Institute of Technology, Cambridge, Massachusetts (United States)

    2012-01-15

    The importance of specifying realistic lateral boundary conditions in the regional modeling of mineral aerosols has not been examined previously. This study examines the impact of assigning values for mineral aerosol (dust) concentrations at the lateral boundaries of Regional Climate Model version 3 (RegCM3) and its aerosol model over Southwest Asia. Currently, the dust emission module of RegCM3 operates over the interior of the domain, allowing dust to be transported to the boundaries, but neglecting any dust emitted at these points or from outside the domain. To account for possible dust occurring at, or entering from the boundaries, mixing ratios of dust concentrations from a larger domain RegCM3 simulation are specified at the boundaries of a smaller domain over Southwest Asia. The lateral boundary conditions are monthly averaged concentration values ({mu}g of dust per kg of dry air) resolved in the vertical for all four dust bin sizes within RegCM3's aerosol model. RegCM3 simulations with the aerosol/dust model including lateral boundary conditions for dust are performed for a five year period and compared to model simulations without prescribed dust concentrations at the boundaries. Results indicate that specifying boundary conditions has a significant impact on dust loading across the entire domain over Southwest Asia. More specifically, a nearly 30% increase in aerosol optical depth occurs during the summer months from specifying realistic dust boundary conditions, bringing model results closer to observations such as MISR. In addition, smaller dust particles at the boundaries have a more important impact than large particles in affecting the dust loading within the interior of this domain. Moreover, increases in aerosol optical depth and dust concentrations within the interior domain are not entirely caused by inflow from the boundaries; results indicate that an increase in the gradient of concentration at the boundaries causes an increase of

  4. The mineral dissolution rate conundrum: Insights from reactive transport modeling of U isotopes and pore fluid chemistry in marine sediments

    Science.gov (United States)

    Maher, Kate; Steefel, Carl I.; DePaolo, Donald J.; Viani, Brian E.

    2006-01-01

    Pore water chemistry and 234U/ 238U activity ratios from fine-grained sediment cored by the Ocean Drilling Project at Site 984 in the North Atlantic were used as constraints in modeling in situ rates of plagioclase dissolution with the multicomponent reactive transport code Crunch. The reactive transport model includes a solid-solution formulation to enable the use of the 234U/ 238U activity ratios in the solid and fluid as a tracer of mineral dissolution. The isotopic profiles are combined with profiles of the major element chemistry (especially alkalinity and calcium) to determine whether the apparent discrepancy between laboratory and field dissolution rates still exists when a mechanistic reactive transport model is used to interpret rates in a natural system. A suite of reactions, including sulfate reduction and methane production, anaerobic methane oxidation, CaCO 3 precipitation, dissolution of plagioclase, and precipitation of secondary clay minerals, along with diffusive transport and fluid and solid burial, control the pore fluid chemistry in Site 984 sediments. The surface area of plagioclase in intimate contact with the pore fluid is estimated to be 6.9 m 2/g based on both grain geometry and on the depletion of 234U/ 238U in the sediment via α-recoil loss. Various rate laws for plagioclase dissolution are considered in the modeling, including those based on (1) a linear transition state theory (TST) model, (2) a nonlinear dependence on the undersaturation of the pore water with respect to plagioclase, and (3) the effect of inhibition by dissolved aluminum. The major element and isotopic methods predict similar dissolution rate constants if additional lowering of the pore water 234U/ 238U activity ratio is attributed to isotopic exchange via recrystallization of marine calcite, which makes up about 10-20% of the Site 984 sediment. The calculated dissolution rate for plagioclase corresponds to a rate constant that is about 10 2 to 10 5 times smaller than

  5. Identification of Hammerstein Model Based on Quantum Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Zhang Hai Li

    2013-07-01

    Full Text Available Nonlinear system identification is a main topic of modern identification. A new method for nonlinear system identification is presented by using Quantum Genetic Algorithm(QGA.The problems of nonlinear system identification are cast as function optimization overprameter space,and the Quantum Genetic Algorithm is adopted to solve the optimization problem. Simulation experiments show that: compared with the genetic algorithm, quantum genetic algorithm is an effective swarm intelligence algorithm, its salient features of the algorithm parameters, small population size, and the use of Quantum gate update populations, greatly improving the recognition in the optimization of speed and accuracy. Simulation results show the effectiveness of the proposed method.

  6. Applications of Systems Genetics and Biology for Obesity Using Pig Models

    DEFF Research Database (Denmark)

    Kogelman, Lisette J. A.; Kadarmideen, Haja N.

    2016-01-01

    In many biomedical research areas, animals have been used as a model to increase the understanding of molecular mechanisms involved in human diseases. One of those areas is human obesity, where porcine models are increasingly used. The pig shows genetic and physiological features that are very...... similar to humans and have shown to be an excellent model for human obesity. Using pig populations, many genetic studies have been performed to unravel the genetic architecture of human obesity. Most of them are pinpointing toward single genes, but more and more studies focus on a systems genetics...... approach, a branch of systems biology. In this chapter, we will describe the state of the art of genetic studies on human obesity, using pig populations. We will describe the features of using the pig as a model for human obesity and briefly discuss the genetics of obesity, and we will focus on systems...

  7. Hierarchical linear modeling of longitudinal pedigree data for genetic association analysis.

    Science.gov (United States)

    Tan, Qihua; B Hjelmborg, Jacob V; Thomassen, Mads; Jensen, Andreas Kryger; Christiansen, Lene; Christensen, Kaare; Zhao, Jing Hua; Kruse, Torben A

    2014-01-01

    Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees, which could affect statistical assessment of the genetic effects. Approaches have been proposed to integrate kinship correlation into the mixed-effect models to explicitly model the genetic relationship. These have proved to be an efficient way of dealing with sample clustering in pedigree data. Although current algorithms implemented in popular statistical packages are useful for adjusting relatedness in the mixed modeling of genetic effects on the mean level of a phenotype, they are not sufficiently straightforward to handle the kinship correlation on the time-dependent trajectories of a phenotype. We introduce a 2-level hierarchical linear model to separately assess the genetic associations with the mean level and the rate of change of a phenotype, integrating kinship correlation in the analysis. We apply our method to the Genetic Analysis Workshop 18 genome-wide association studies data on chromosome 3 to estimate the genetic effects on systolic blood pressure measured over time in large pedigrees. Our method identifies genetic variants associated with blood pressure with estimated inflation factors of 0.99, suggesting that our modeling of random effects efficiently handles the genetic relatedness in pedigrees. Application to simulated data captures important variants specified in the simulation. Our results show that the method is useful for genetic association studies in related samples using longitudinal design.

  8. Form Follows Function: A Model for Clinical Supervision of Genetic Counseling Students.

    Science.gov (United States)

    Wherley, Colleen; Veach, Patricia McCarthy; Martyr, Meredith A; LeRoy, Bonnie S

    2015-10-01

    Supervision plays a vital role in genetic counselor training, yet models describing genetic counseling supervision processes and outcomes are lacking. This paper describes a proposed supervision model intended to provide a framework to promote comprehensive and consistent clinical supervision training for genetic counseling students. Based on the principle "form follows function," the model reflects and reinforces McCarthy Veach et al.'s empirically derived model of genetic counseling practice - the "Reciprocal Engagement Model" (REM). The REM consists of mutually interactive educational, relational, and psychosocial components. The Reciprocal Engagement Model of Supervision (REM-S) has similar components and corresponding tenets, goals, and outcomes. The 5 REM-S tenets are: Learning and applying genetic information are key; Relationship is integral to genetic counseling supervision; Student autonomy must be supported; Students are capable; and Student emotions matter. The REM-S outcomes are: Student understands and applies information to independently provide effective services, develop professionally, and engage in self-reflective practice. The 16 REM-S goals are informed by the REM of genetic counseling practice and supported by prior literature. A review of models in medicine and psychology confirms the REM-S contains supervision elements common in healthcare fields, while remaining unique to genetic counseling. The REM-S shows promise for enhancing genetic counselor supervision training and practice and for promoting research on clinical supervision. The REM-S is presented in detail along with specific examples and training and research suggestions.

  9. Modelling of the physico-chemical behaviour of clay minerals with a thermo-kinetic model taking into account particles morphology in compacted material.

    Science.gov (United States)

    Sali, D.; Fritz, B.; Clément, C.; Michau, N.

    2003-04-01

    Modelling of fluid-mineral interactions is largely used in Earth Sciences studies to better understand the involved physicochemical processes and their long-term effect on the materials behaviour. Numerical models simplify the processes but try to preserve their main characteristics. Therefore the modelling results strongly depend on the data quality describing initial physicochemical conditions for rock materials, fluids and gases, and on the realistic way of processes representations. The current geo-chemical models do not well take into account rock porosity and permeability and the particle morphology of clay minerals. In compacted materials like those considered as barriers in waste repositories, low permeability rocks like mudstones or compacted powders will be used : they contain mainly fine particles and the geochemical models used for predicting their interactions with fluids tend to misjudge their surface areas, which are fundamental parameters in kinetic modelling. The purpose of this study was to improve how to take into account the particles morphology in the thermo-kinetic code KINDIS and the reactive transport code KIRMAT. A new function was integrated in these codes, considering the reaction surface area as a volume depending parameter and the calculated evolution of the mass balance in the system was coupled with the evolution of reactive surface areas. We made application exercises for numerical validation of these new versions of the codes and the results were compared with those of the pre-existing thermo-kinetic code KINDIS. Several points are highlighted. Taking into account reactive surface area evolution during simulation modifies the predicted mass transfers related to fluid-minerals interactions. Different secondary mineral phases are also observed during modelling. The evolution of the reactive surface parameter helps to solve the competition effects between different phases present in the system which are all able to fix the chemical

  10. Estimating mineral abundances of clay and gypsum mixtures using radiative transfer models applied to visible-near infrared reflectance spectra

    Science.gov (United States)

    Robertson, K. M.; Milliken, R. E.; Li, S.

    2016-10-01

    Quantitative mineral abundances of lab derived clay-gypsum mixtures were estimated using a revised Hapke VIS-NIR and Shkuratov radiative transfer model. Montmorillonite-gypsum mixtures were used to test the effectiveness of the model in distinguishing between subtle differences in minor absorption features that are diagnostic of mineralogy in the presence of strong H2O absorptions that are not always diagnostic of distinct phases or mineral abundance. The optical constants (k-values) for both endmembers were determined from bi-directional reflectance spectra measured in RELAB as well as on an ASD FieldSpec3 in a controlled laboratory setting. Multiple size fractions were measured in order to derive a single k-value from optimization of the optical path length in the radiative transfer models. It is shown that with careful experimental conditions, optical constants can be accurately determined from powdered samples using a field spectrometer, consistent with previous studies. Variability in the montmorillonite hydration level increased the uncertainties in the derived k-values, but estimated modal abundances for the mixtures were still within 5% of the measured values. Results suggest that the Hapke model works well in distinguishing between hydrated phases that have overlapping H2O absorptions and it is able to detect gypsum and montmorillonite in these simple mixtures where they are present at levels of ∼10%. Care must be taken however to derive k-values from a sample with appropriate H2O content relative to the modeled spectra. These initial results are promising for the potential quantitative analysis of orbital remote sensing data of hydrated minerals, including more complex clay and sulfate assemblages such as mudstones examined by the Curiosity rover in Gale crater.

  11. MODELING OF NAPHTHA PYROLYSIS WITH USING GENETIC ALGORITM

    Directory of Open Access Journals (Sweden)

    V. K. Bityukov

    2015-01-01

    Full Text Available Summary. In operation of industrial pyrolysis furnaces, the main task is the selection of the optimal mode of thermal decomposition of the feedstock, depending on the yield of the desired products under conditions of technological limitations on the process. To solve this problem for an operating reactor, this paper considers the SRT-VI Large-Capacity industrial Furnace , the mathematical model of the pyrolysis process was constructed, using a kinetic scheme which consists of primary reaction of decomposition of raw materials and secondary elementary reactions of interaction of the considered mixture components, the heat balance equation and hydrodynamics of flow in the coil. The raw material for the selected installation type is naphtha (straight-run petrol. Output parameters of the model are the molar costs of marketable hydrocarbons. The reactor is described by the equation of ideal displacement in the static mode of operation. It is assumed that all reactions have a temperature dependence that follows the Arrhenius law. The activation energies of chemical processes were estimated using the PolanyiSemenov equation and identification of pre-exponential factors was carried out using a genetic algorithm (GA. This task requires solving simultaneous system of differential equations describing the pyrolysis process and a search for a large number of unknown parameters, and therefore it is proposed to modify the GA. Optimal scheme includes Gray encoding arithmetic operators, tournament selection, with tournament ranking more than 4, crossover with partial random choice of alleys, mutations with a high probability of occurring and elitism with competitive global competition. Using the proposed approach, the parametric identification of model process is accomplished. The analysis of the simulation results with the data of operating reactor showed its suitability for use in order to control the pyrolysis process.

  12. Modeling of genetic algorithms with a finite population

    NARCIS (Netherlands)

    Kemenade, C.H.M. van

    1997-01-01

    Cross-competition between non-overlapping building blocks can strongly influence the performance of evolutionary algorithms. The choice of the selection scheme can have a strong influence on the performance of a genetic algorithm. This paper describes a number of different genetic algorithms, all in

  13. Modeling of genetic algorithms with a finite population

    NARCIS (Netherlands)

    C.H.M. van Kemenade

    1997-01-01

    textabstractCross-competition between non-overlapping building blocks can strongly influence the performance of evolutionary algorithms. The choice of the selection scheme can have a strong influence on the performance of a genetic algorithm. This paper describes a number of different genetic

  14. The effect of genetic selection for Johne's disease resistance n dairy cattle: Results of a genetic-epidemiological model

    NARCIS (Netherlands)

    Hulzen, van K.J.E.; Koets, A.P.; Nielen, M.; Heuven, H.C.M.; Arendonk, van J.A.M.; Klinkenberg, D.

    2014-01-01

    The objective of this study was to model genetic selection for Johne’s disease resistance and to study the effect of different selection strategies on the prevalence in the dairy cattle population. In the Netherlands, a certification-and-surveillance program is in use to reduce prevalence and presen

  15. Osteogenesis and mineralization in a rabbit mandibular distraction osteogenesis model is promoted by the human LMP-1 gene.

    Science.gov (United States)

    Jiang, Xiaowen; Chen, Yanzhe; Fan, Xiaosheng; Zhang, Hao; Kun, Lu

    2015-04-01

    To observe the effects of LIM mineralization protein-1 (LMP-1) on bone regeneration in the distraction zone based on gene transduction, 36 New Zealand white rabbits underwent mandibular lengthening with a distraction rate of 2 mm/day. The animals were then randomly divided into group A and group B (n = 18, each). At the end of the distraction, Ad5-EGFP viruses and Ad5-LMP-1/EGFP viruses were injected into the distraction gaps in groups A and B, respectively. Seven days later, five randomly selected animals from each group were sacrificed to evaluate the survival of the virus. Four and 8 weeks after distraction osteogenesis (DO), six samples randomly selected from each group underwent CT scanning and dual energy X-ray absorptiometry detection. Eight weeks after DO, the rabbits were sacrificed, and the distracted mandibles were harvested. Six animals from each group processed for radiography, micro-CT, histology, and the rest samples were taken three-point bend testing. Using this model, better bone formation and mineralization in the distracted callus were observed in group B when compared with those in group A. The results suggest local transduction with LMP-1 gene promotes osteogenesis and mineralization in DO.

  16. Heterogeneous reactions of NO2 and HNO3 on oxides and mineral dust: A combined laboratory and modeling study

    Science.gov (United States)

    Underwood, G. M.; Song, C. H.; Phadnis, M.; Carmichael, G. R.; Grassian, V. H.

    2001-08-01

    This study combines laboratory measurements and modeling analysis to quantify the role of heterogeneous reactions of gaseous nitrogen dioxide and nitric acid on mineral oxide and mineral dust particles in tropospheric ozone formation. At least two types of heterogeneous reactions occur on the surface of these particles. Upon initial exposure of the oxide to NO2 there is a loss of NO2 from the gas phase by adsorption on the particle surface, i.e., NO2(g) → NO2(a). As the reaction proceeds, a reduction of gaseous NO2 to NO, NO2 (g) → NO (g) is found to occur. Initial uptake coefficients γ0 for NO2 on the surface of these particles have been measured at 298 K using a Knudsen cell reactor coupled to a mass spectrometer. For the oxides studied, α,γ-Al2O3, α,γ-Fe2O3, TiO2, SiO2, CaO, and MgO, γ0 ranges from dry surfaces are just below the lower limit to have an impact on the photochemical oxidant cycle, while the heterogeneous reactivity of HNO3 is sufficiently large to have an effect. Under conditions of high mineral dust mass loadings and/or smaller size distributions the importance of these reactions (both NO2 and HNO3) is expected to increase.

  17. Validation of a plant-wide phosphorus modelling approach with minerals precipitation in a full-scale WWTP.

    Science.gov (United States)

    Kazadi Mbamba, Christian; Flores-Alsina, Xavier; John Batstone, Damien; Tait, Stephan

    2016-09-01

    The focus of modelling in wastewater treatment is shifting from single unit to plant-wide scale. Plant-wide modelling approaches provide opportunities to study the dynamics and interactions of different transformations in water and sludge streams. Towards developing more general and robust simulation tools applicable to a broad range of wastewater engineering problems, this paper evaluates a plant-wide model built with sub-models from the Benchmark Simulation Model No. 2-P (BSM2-P) with an improved/expanded physico-chemical framework (PCF). The PCF includes a simple and validated equilibrium approach describing ion speciation and ion pairing with kinetic multiple minerals precipitation. Model performance is evaluated against data sets from a full-scale wastewater treatment plant, assessing capability to describe water and sludge lines across the treatment process under steady-state operation. With default rate kinetic and stoichiometric parameters, a good general agreement is observed between the full-scale datasets and the simulated results under steady-state conditions. Simulation results show differences between measured and modelled phosphorus as little as 4-15% (relative) throughout the entire plant. Dynamic influent profiles were generated using a calibrated influent generator and were used to study the effect of long-term influent dynamics on plant performance. Model-based analysis shows that minerals precipitation strongly influences composition in the anaerobic digesters, but also impacts on nutrient loading across the entire plant. A forecasted implementation of nutrient recovery by struvite crystallization (model scenario only), reduced the phosphorus content in the treatment plant influent (via centrate recycling) considerably and thus decreased phosphorus in the treated outflow by up to 43%. Overall, the evaluated plant-wide model is able to jointly describe the physico-chemical and biological processes, and is advocated for future use as a tool for

  18. The Integration of Cooperation Model and Genetic Algorithm

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    In the photogrammetry,some researchers have applied genetic algorithms in aerial image texture classification and reducing hyper-spectrum remote sensing data.Genetic algorithm can rapidly find the solutions which are close to the optimal solution.But it is not easy to find the optimal solution.In order to solve the problem,a cooperative evolution idea integrating genetic algorithm and ant colony algorithm is presented in this paper.On the basis of the advantages of ant colony algorithm,this paper proposes the method integrating genetic algorithms and ant colony algorithm to overcome the drawback of genetic algorithms.Moreover,the paper takes designing texture classification masks of aerial images as an example to illustrate the integration theory and procedures.

  19. Modeling plant, microorganisms, and mineral surface competition for soil nitrogen and phosphorus: Competition representations and ecological significance

    Science.gov (United States)

    Zhu, Q.; Riley, W. J.; Chambers, J. Q.; Tang, J.

    2014-12-01

    It is widely accepted that terrestrial ecosystem carbon dynamics are strongly coupled and controlled by soil nutrients status. Nutrient availability serves as an indicator of aboveground carbon productivity and ecosystem stability, especially when soils are infertile. In these conditions, plants have to outcompete microorganism and mineral surfaces to acquire nutrients required for photosynthesis, respiration, seed production, defense, etc. It is usually hypothesized that microbes are short-term winners but long-term losers in nutrient competition. Microbes quickly trap available soil nitrogen and phosphorous, thereby preventing nutrient inaccessibility through hydrological leaching and mineral surface adsorption. Over longer temporal scales, nutrients are released into the soil and become available for plant uptake. Despite its ecological significance, nutrient competition is either absent or over-simplified (e.g., assuming all consumers are equally competitive) in terrestrial biogeochemistry models. Here, we aim to test the representation of different competitive strategies and to investigate their ecological consequences with a newly developed biogeochemical model structure. The new model includes three major soil nutrients (ammonia, nitrate, and phosphate) and multiple consumers (plants, microbes, mineral surfaces, nitrifiers, and denitrifiers). We analyze predicted soil carbon, nitrogen, and phosphorus dynamics with three different competitive strategies: (1) plants compete poorly against microorganisms; (2) all consumers are equally competitive; and (3) an explicit Equilibrium Chemical Approximation (ECA; Tang and Riley (2013)) treatment. We find that very different ecosystem states are predicted when assuming different competitive structures, and that the ECA approach provides the best match with a large suite of observational constraints from tropical experimental and transect studies. We conclude that terrestrial biogeochemical models should represent a

  20. 3-D Numerical Modeling as a Tool for Managing Mineral Water Extraction from a Complex Groundwater Basin in Italy

    Science.gov (United States)

    Zanini, A.; Tanda, M.

    2007-12-01

    The groundwater in Italy plays an important role as drinking water; in fact it covers about the 30% of the national demand (70% in Northern Italy). The mineral water distribution in Italy is an important business with an increasing demand from abroad countries. The mineral water Companies have a great interest in order to increase the water extraction, but for the delicate and complex geology of the subsoil, where such very high quality waters are contained, a particular attention must be paid in order to avoid an excessive lowering of the groundwater reservoirs or great changes in the groundwater flow directions. A big water Company asked our University to set up a numerical model of the groundwater basin, in order to obtain a useful tool which allows to evaluate the strength of the aquifer and to design new extraction wells. The study area is located along Appennini Mountains and it covers a surface of about 18 km2; the topography ranges from 200 to 600 m a.s.l.. In ancient times only a spring with naturally sparkling water was known in the area, but at present the mineral water is extracted from deep pumping wells. The area is characterized by a very complex geology: the subsoil structure is described by a sequence of layers of silt-clay, marl-clay, travertine and alluvial deposit. Different groundwater layers are present and the one with best quality flows in the travertine layer; the natural flow rate seems to be not subjected to seasonal variations. The water age analysis revealed a very old water which means that the mineral aquifers are not directly connected with the meteoric recharge. The Geologists of the Company suggest that the water supply of the mineral aquifers comes from a carbonated unit located in the deep layers of the mountains bordering the spring area. The valley is crossed by a river that does not present connections to the mineral aquifers. Inside the area there are about 30 pumping wells that extract water at different depths. We built a 3

  1. A review of animal models used to evaluate potential allergenicity of genetically modified organisms (GMOs)

    DEFF Research Database (Denmark)

    Marsteller, Nathan; Bøgh, Katrine Lindholm; Goodman, Richard E.

    2017-01-01

    Food safety regulators request prediction of allergenicity for newly expressed proteins in genetically modified (GM) crops and in novel foods. Some have suggested using animal models to assess potential allergenicity. A variety of animal models have been used in research to evaluate sensitisation...... of genetically modified organisms (GMOs)....

  2. Cat Mammary Tumors: Genetic Models for the Human Counterpart

    Directory of Open Access Journals (Sweden)

    Filomena Adega

    2016-08-01

    Full Text Available The records are not clear, but Man has been sheltering the cat inside his home for over 12,000 years. The close proximity of this companion animal, however, goes beyond sharing the same roof; it extends to the great similarity found at the cellular and molecular levels. Researchers have found a striking resemblance between subtypes of feline mammary tumors and their human counterparts that goes from the genes to the pathways involved in cancer initiation and progression. Spontaneous cat mammary pre-invasive intraepithelial lesions (hyperplasias and neoplasias and malignant lesions seem to share a wide repertoire of molecular features with their human counterparts. In the present review, we tried to compile all the genetics aspects published (i.e., chromosomal alterations, critical cancer genes and their expression regarding cat mammary tumors, which support the cat as a valuable alternative in vitro cell and animal model (i.e., cat mammary cell lines and the spontaneous tumors, respectively, but also to present a critical point of view of some of the issues that really need to be investigated in future research.

  3. Genetic mouse models for behavioral analysis through transgenic RNAi technology.

    Science.gov (United States)

    Delic, S; Streif, S; Deussing, J M; Weber, P; Ueffing, M; Hölter, S M; Wurst, W; Kühn, R

    2008-10-01

    Pharmacological inhibitors and knockout mice have developed into routine tools to analyze the role of specific genes in behavior. Both strategies have limitations like the availability of inhibitors for only a subset of proteins and the large efforts required to construct specific mouse mutants. The recent emergence of RNA interference (RNAi)-mediated gene silencing provides a fast alternative that can be applied to any coding gene. We established an approach for the efficient generation of transgenic knockdown mice by targeted insertion of short hairpin (sh) RNA vectors into a defined genomic locus and studied the efficiency of gene silencing in the adult brain and the utility of such mice for behavioral analysis. We generated shRNA knockdown mice for the corticotropin-releasing hormone receptor type 1 (Crhr1), the leucine-rich repeat kinase 2 (Lrkk2) and the purinergic receptor P2X ligand-gated ion channel 7 (P2rx7) genes and show the ubiquitous expression of shRNA and efficient suppression of the target mRNA and protein in the brain of young and 11-month-old knockdown mice. Knockdown mice for the Crhr1 gene exhibited decreased anxiety-related behavior, an impaired stress response, and thereby recapitulate the phenotype of CRHR1 knockout mice. Our results show the feasibility of gene silencing in the adult brain and validate knockdown mice as new genetic models suitable for behavioral analysis.

  4. Modelling Agro-Met Station Observations Using Genetic Algorithm

    Directory of Open Access Journals (Sweden)

    Prashant Kumar

    2014-01-01

    Full Text Available The present work discusses the development of a nonlinear data-fitting technique based on genetic algorithm (GA for the prediction of routine weather parameters using observations from Agro-Met Stations (AMS. The algorithm produces the equations that best describe the temporal evolutions of daily minimum and maximum near-surface (at 2.5-meter height air temperature and relative humidity and daily averaged wind speed (at 10-meter height at selected AMS locations. These enable the forecasts of these weather parameters, which could have possible use in crop forecast models. The forecast equations developed in the present study use only the past observations of the above-mentioned parameters. This approach, unlike other prediction methods, provides explicit analytical forecast equation for each parameter. The predictions up to 3 days in advance have been validated using independent datasets, unknown to the training algorithm, with impressive results. The power of the algorithm has also been demonstrated by its superiority over persistence forecast used as a benchmark.

  5. Discrete channel modelling based on genetic algorithm and simulated annealing for training hidden Markov model

    Institute of Scientific and Technical Information of China (English)

    Zhao Zhi-Jin; Zheng Shi-Lian; Xu Chun-Yun; Kong Xian-Zheng

    2007-01-01

    Hidden Markov models (HMMs) have been used to model burst error sources of wireless channels. This paper proposes a hybrid method of using genetic algorithm (GA) and simulated annealing (SA) to train HMM for discrete channel modelling. The proposed method is compared with pure GA, and experimental results show that the HMMs trained by the hybrid method can better describe the error sequences due to SA's ability of facilitating hill-climbing at the later stage of the search. The burst error statistics of the HMMs trained by the proposed method and the corresponding error sequences are also presented to validate the proposed method.

  6. Genetic simplex modeling of Eysenck's dimensions of personality in a sample of young Australian twins.

    Science.gov (United States)

    Gillespie, Nathan A; Evans, David E; Wright, Margie M; Martin, Nicholas G

    2004-12-01

    The relative stability and magnitude of genetic and environmental effects underlying major dimensions of adolescent personality across time were investigated. The Junior Eysenck Personality Questionnaire was administered to over 540 twin pairs at ages 12, 14 and 16 years. Their personality scores were analyzed using genetic simplex modeling which explicitly took into account the longitudinal nature of the data. With the exception of the dimension lie, multivariate model fitting results revealed that familial aggregation was entirely explained by additive genetic effects. Results from simplex model fitting suggest that large proportions of the additive genetic variance observed at ages 14 and 16 years could be explained by genetic effects present at the age of 12 years. There was also evidence for smaller but significant genetic innovations at 14 and 16 years of age for male and female neuroticism, at 14 years for male extraversion, at 14 and 16 years for female psychoticism, and at 14 years for male psychoticism.

  7. Reactive transport modeling of coupled feldspar dissolution and secondary mineral precipitation and its implication for diagenetic interaction in sandstones

    Science.gov (United States)

    Yuan, Guanghui; Cao, Yingchang; Gluyas, Jon; Jia, Zhenzhen

    2017-06-01

    Dissolution of feldspars and precipitation of secondary minerals (kaolinite, illite and quartz) are significant diagenetic processes in arkosic sandstones. We examined moderately buried sandstones in the Eocene Shahejie Formation from two sags in the Bohai Bay Basin, East China. Three different types of mineral assemblages (MA) were identified: extensively leached feldspars with a large amount of authigenic kaolinite and quartz cement (MA-1), extensively leached feldspars with a large amount of authigenic kaolinite and minor quartz cement (MA-2), and extensively leached feldspars with a small amount of both authigenic kaolinite and quartz cement (MA-3). Numerical simulations at the continuum scale using Geochemist's Workbench 9.0 were conducted to decipher the origin of the different mineral assemblages. The physicochemical reactions including feldspar dissolution, transport of Al3+ and SiO2(aq), and precipitation of kaolinite and quartz are coupled together in these simulations, with constraints of chemical reactions, kinetic law, dispersion, and advection. Modeling results suggest that a dissolution zone, a transitional zone, and a precipitation zone can be formed in a sandstone unit with suitable constraints of temperature, flow rate, fluid composition and mineral reaction rate. And MA-3, MA-2, and MA-1 assemblages develop in these three zones respectively. The higher SiO2(aq) concentration required for the saturation of quartz than for kaolinite and the low Al3+ concentration needed for the saturation of kaolinite lead to the precipitation of only kaolinite in the transitional zone in a geochemical system with feldspar dissolution serving as the dominant source of SiO2(aq) and Al3+. Comparisons between modeling results and observations of natural sandstone diagenesis suggest that an MA-1 assemblage is likely to occur in buried sandstones at high temperatures (>70-80 °C) and low flow rates. An MA-2 assemblage may occur in moderately buried sandstones at

  8. Prediction and Research on Vegetable Price Based on Genetic Algorithm and Neural Network Model

    Institute of Scientific and Technical Information of China (English)

    2011-01-01

    Considering the complexity of vegetables price forecast,the prediction model of vegetables price was set up by applying the neural network based on genetic algorithm and using the characteristics of genetic algorithm and neural work.Taking mushrooms as an example,the parameters of the model are analyzed through experiment.In the end,the results of genetic algorithm and BP neural network are compared.The results show that the absolute error of prediction data is in the scale of 10%;in the scope that the absolute error in the prediction data is in the scope of 20% and 15%.The accuracy of genetic algorithm based on neutral network is higher than the BP neutral network model,especially the absolute error of prediction data is within the scope of 20%.The accuracy of genetic algorithm based on neural network is obviously better than BP neural network model,which represents the favorable generalization capability of the model.

  9. Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests

    Directory of Open Access Journals (Sweden)

    Q. Zhu

    2015-03-01

    Full Text Available Soil is a complex system where biotic (e.g., plant roots, micro-organisms and abiotic (e.g., mineral surfaces consumers compete for resources necessary for life (e.g., nitrogen, phosphorus. This competition is ecologically significant, since it regulates the dynamics of soil nutrients and controls aboveground plant productivity. Here we develop, calibrate, and test a nutrient competition model that accounts for multiple soil nutrients interacting with multiple biotic and abiotic consumers. As applied here for tropical forests, the Nutrient COMpetition model (N-COM includes three primary soil nutrients (NH4+, NO3−, and POx (representing the sum of PO43−, HPO42−, and H2PO4− and five potential competitors (plant roots, decomposing microbes, nitrifiers, denitrifiers, and mineral surfaces. The competition is formulated with a quasi-steady-state chemical equilibrium approximation to account for substrate (multiple substrates share one consumer and consumer (multiple consumers compete for one substrate effects. N-COM successfully reproduced observed soil heterotrophic respiration, N2O emissions, free phosphorus, sorbed phosphorus, and free NH4+ at a tropical forest site (Tapajos. The overall model posterior uncertainty was moderately well constrained. Our sensitivity analysis revealed that soil nutrient competition was primarily regulated by consumer-substrate affinity rather than environmental factors such as soil temperature or soil moisture. Our results imply that the competitiveness (from most to least competitive followed this order: (1 for NH4+, nitrifiers ~ decomposing microbes > plant roots, (2 for NO3−, denitrifiers ~ decomposing microbes > plant roots, (3 for POx, mineral surfaces > decomposing microbes ~ plant roots. Although smaller, plant relative competitiveness is of the same order of magnitude as microbes. We then applied the N-COM model to analyze field nitrogen and phosphorus perturbation experiments in two tropical forest

  10. Factor analysis models for structuring covariance matrices of additive genetic effects: a Bayesian implementation

    Directory of Open Access Journals (Sweden)

    Gianola Daniel

    2007-09-01

    Full Text Available Abstract Multivariate linear models are increasingly important in quantitative genetics. In high dimensional specifications, factor analysis (FA may provide an avenue for structuring (covariance matrices, thus reducing the number of parameters needed for describing (codispersion. We describe how FA can be used to model genetic effects in the context of a multivariate linear mixed model. An orthogonal common factor structure is used to model genetic effects under Gaussian assumption, so that the marginal likelihood is multivariate normal with a structured genetic (covariance matrix. Under standard prior assumptions, all fully conditional distributions have closed form, and samples from the joint posterior distribution can be obtained via Gibbs sampling. The model and the algorithm developed for its Bayesian implementation were used to describe five repeated records of milk yield in dairy cattle, and a one common FA model was compared with a standard multiple trait model. The Bayesian Information Criterion favored the FA model.

  11. Picroilmenites in Yakutian kimberlites: variations and genetic models

    Science.gov (United States)

    Ashchepkov, I. V.; Alymova, N. V.; Logvinova, A. M.; Vladykin, N. V.; Kuligin, S. S.; Mityukhin, S. I.; Downes, H.; Stegnitsky, Yu. B.; Prokopiev, S. A.; Salikhov, R. F.; Palessky, V. S.; Khmel'nikova, O. S.

    2014-09-01

    Major and trace element variations in picroilmenites from Late Devonian kimberlite pipes in Siberia reveal similarities within the region in general, but show individual features for ilmenites from different fields and pipes. Empirical ilmenite thermobarometry (Ashchepkov et al., 2010), as well as common methods of mantle thermobarometry and trace element geochemical modeling, shows long compositional trends for the ilmenites. These are a result of complex processes of polybaric fractionation of protokimberlite melts, accompanied by the interaction with mantle wall rocks and dissolution of previous wall rock and metasomatic associations. Evolution of the parental magmas for the picroilmenites was determined for the three distinct phases of kimberlite activity from Yubileynaya and nearby Aprelskaya pipes, showing heating and an increase of Fe# (Fe# = Fe / (Fe + Mg) a.u.) of mantle peridotite minerals from stage to stage and splitting of the magmatic system in the final stages. High-pressure (5.5-7.0 GPa) Cr-bearing Mg-rich ilmenites (group 1) reflect the conditions of high-temperature metasomatic rocks at the base of the mantle lithosphere. Trace element patterns are enriched to 0.1-10/relative to primitive mantle (PM) and have flattened, spoon-like or S- or W-shaped rare earth element (REE) patterns with Pb > 1. These result from melting and crystallization in melt-feeding channels in the base of the lithosphere, where high-temperature dunites, harzburgites and pyroxenites were formed. Cr-poor ilmenite megacrysts (group 2) trace the high-temperature path of protokimberlites developed as result of fractional crystallization and wall rock assimilation during the creation of the feeder systems prior to the main kimberlite eruption. Inflections in ilmenite compositional trends probably reflect the mantle layering and pulsing melt intrusion during melt migration within the channels. Group 2 ilmenites have inclined REE enriched patterns (10-100)/PM with La / Ybn ~ 10

  12. Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network and pathway analyses

    Directory of Open Access Journals (Sweden)

    Lisette J. A. Kogelman

    2014-07-01

    Full Text Available Obesity is a complex condition with world-wide exponentially rising prevalence rates, linked with severe diseases like Type 2 Diabetes. Economic and welfare consequences have led to a raised interest in a better understanding of the biological and genetic background. To date, whole genome investigations focusing on single genetic variants have achieved limited success, and the importance of including genetic interactions is becoming evident. Here, the aim was to perform an integrative genomic analysis in an F2 pig resource population that was constructed with an aim to maximize genetic variation of obesity-related phenotypes and genotyped using the 60K SNP chip. Firstly, Genome Wide Association (GWA analysis was performed on the Obesity Index to locate candidate genomic regions that were further validated using combined Linkage Disequilibrium Linkage Analysis and investigated by evaluation of haplotype blocks. We built Weighted Interaction SNP Hub (WISH and differentially wired (DW networks using genotypic correlations amongst obesity-associated SNPs resulting from GWA analysis. GWA results and SNP modules detected by WISH and DW analyses were further investigated by functional enrichment analyses. The functional annotation of SNPs revealed several genes associated with obesity, e.g. NPC2 and OR4D10. Moreover, gene enrichment analyses identified several significantly associated pathways, over and above the GWA study results, that may influence obesity and obesity related diseases, e.g. metabolic processes. WISH networks based on genotypic correlations allowed further identification of various gene ontology terms and pathways related to obesity and related traits, which were not identified by the GWA study. In conclusion, this is the first study to develop a (genetic obesity index and employ systems genetics in a porcine model to provide important insights into the complex genetic architecture associated with obesity and many biological pathways

  13. Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network, and pathway analyses.

    Science.gov (United States)

    Kogelman, Lisette J A; Pant, Sameer D; Fredholm, Merete; Kadarmideen, Haja N

    2014-01-01

    Obesity is a complex condition with world-wide exponentially rising prevalence rates, linked with severe diseases like Type 2 Diabetes. Economic and welfare consequences have led to a raised interest in a better understanding of the biological and genetic background. To date, whole genome investigations focusing on single genetic variants have achieved limited success, and the importance of including genetic interactions is becoming evident. Here, the aim was to perform an integrative genomic analysis in an F2 pig resource population that was constructed with an aim to maximize genetic variation of obesity-related phenotypes and genotyped using the 60K SNP chip. Firstly, Genome Wide Association (GWA) analysis was performed on the Obesity Index to locate candidate genomic regions that were further validated using combined Linkage Disequilibrium Linkage Analysis and investigated by evaluation of haplotype blocks. We built Weighted Interaction SNP Hub (WISH) and differentially wired (DW) networks using genotypic correlations amongst obesity-associated SNPs resulting from GWA analysis. GWA results and SNP modules detected by WISH and DW analyses were further investigated by functional enrichment analyses. The functional annotation of SNPs revealed several genes associated with obesity, e.g., NPC2 and OR4D10. Moreover, gene enrichment analyses identified several significantly associated pathways, over and above the GWA study results, that may influence obesity and obesity related diseases, e.g., metabolic processes. WISH networks based on genotypic correlations allowed further identification of various gene ontology terms and pathways related to obesity and related traits, which were not identified by the GWA study. In conclusion, this is the first study to develop a (genetic) obesity index and employ systems genetics in a porcine model to provide important insights into the complex genetic architecture associated with obesity and many biological pathways that underlie

  14. Reviews and new metallogenic models of mineral deposits in South China: An introduction

    Science.gov (United States)

    Hu, Rui-Zhong; Chen, Wei Terry; Xu, De-Ru; Zhou, Mei-Fu

    2017-04-01

    In South China, the Yangtze and Cathaysia blocks were welded together along the Jiangnan Fold Belt during Neoproterozoic time (∼830 Ma). Large-scale mineralization in these two blocks occurred from Proterozoic to Cenozoic, making the region one of the most important polymetallic metallogenic provinces in the world. Of particular importance are world-class deposits of iron-oxide copper gold (IOCG), sediment-hosted Mn-P-Al-(Ni, Mo, PGE), syenite-carbonatite-related REE, felsic intrusion-related Sn-W-Mo-Cu-Fe-Pb-Zn, mafic intrusion-related V-Ti-Fe and Cu-Ni-PGE and low-temperature hydrothermal Pb, Zn, Au, and Sb (Fig. 1). In addition, the Ta-Nb, Hg, As, Tl and U deposits in South China are among the world largest of these kinds. Because of these deposits, South China has been a focus of researches for many years. Publications before 2005 were mostly restricted in Chinese. In the past decade, some case studies on some world-class deposits in South China are available in international journals. These recent studies have advanced our understanding of their mode of formation. However, some important issues regarding the timing, tectonic setting and mechanisms of metal concentration still remain poorly understood. This special issue brings together some of the latest information on these topics, including major review papers on specific types of mineralization and several papers dealing with some specific deposits in the region. We anticipate that this issue will generate more interests in the studies of mineral deposits in South China. In this introduction, we outline the tectonic framework and associated deposits.

  15. The composition of fluid inclusions in ore and gangue minerals from the Silesian-Cracow Mississippi Valley-type Zn-Pb deposits Poland: Genetic and environmental implications

    Science.gov (United States)

    Viets, J.G.; Hofstra, A.H.; Emsbo, P.; Kozlowski, A.

    1996-01-01

    The composition of fluids extracted from ore and gangue sulfide minerals that span most of the paragenesis of the Silesian-Cracow district was determined using a newly developed ion chromatographic (IC) technique. Ionic species determined were Na+, NH+4, Ca2+, Mg2+, K+, Rb+, Sr2+, Ba2+, Cl-, Br-, F-, I-, PO3-4, CO2-3, HS-, S2O2-3, SO2-4, NO-3, and acetate. Mineral samples included six from the Pomorzany mine and one from the Trzebionka mine which are hosted in the Triassic Muschelkalk Formation, and two samples of drill core from mineralized Upper Devonian strata. Nine paragenetically identifiable sulfide minerals occur throughout the Silesian-Cracow district. These include from earliest to latest: early iron sulfides, granular sphalerite, early galena, light-banded sphalerite, galena, dark-banded sphalerite, iron sulfides, late dark-banded sphalerite with late galena, and late iron sulfides. Seven of the minerals were sampled for fluid inclusion analysis in this study. Only the early iron sulfides and the last galena stage were not sampled. Although the number of analyses are limited to nine samples and two replicates and there is uncertainty about the characteristics of the fluid inclusions analyzed, the data show clear temporal trends in the composition of the fluids that deposited these minerals. Fluid inclusions in minerals deposited later in the paragenesis have significantly more K+, Br-, NH+4, and acetate but less Sr2+ than those deposited earlier in the paragenesis. The later minerals are also characterized by isotopically lighter sulfur and significantly more Tl and As in the solid minerals. The change in ore-fluid chemistry is interpreted to reflect a major change in the hydrologic regime of the district. Apparently, the migrational paths of ore fluids from the Upper Silesian basin changed during ore deposition and the fluids which deposited early minerals reacted with aquifers with very different geochemical characteristics than those that deposited

  16. Mathematical model formation of the process of deriving boric acid from ulexite mineral by full factorial design method

    OpenAIRE

    DURAK, Halil; GENEL, Yasar; BASHIROV, Novruz; KERIMOV, Genber

    2012-01-01

    Ulexite is a sodium calcium boron hydrate used in producing compounds, its chemical formula is Na2O2CaO5B2O3.16H2O, and it superabounds in Turkey. One of the significant boron compounds derived from boron minerals is boric acid. The aim of this study is producing boric acid in the wake of interaction of ulexite with hydrochloric acid solution, and offering an alternative process to producing boric acid by forming the mathematical model of this processing. F...

  17. Mathematical model formation of the process of deriving boric acid from ulexite mineral by full factorial design method

    OpenAIRE

    DURAK, Halil; GENEL, Yasar; BASHIROV, Novruz; KERIMOV, Genber

    2013-01-01

    Ulexite is a sodium calcium boron hydrate used in producing compounds, its chemical formula is Na2O2CaO5B2O3.16H2O, and it superabounds in Turkey. One of the significant boron compounds derived from boron minerals is boric acid. The aim of this study is producing boric acid in the wake of interaction of ulexite with hydrochloric acid solution, and offering an alternative process to producing boric acid by forming the mathematical model of this processing. Full factorial de...

  18. [The discussion of the infiltrative model of mathematical knowledge to genetics teaching].

    Science.gov (United States)

    Liu, Jun; Luo, Pei-Gao

    2011-11-01

    Genetics, the core course of biological field, is an importance major-basic course in curriculum of many majors related with biology. Due to strong theoretical and practical as well as abstract of genetics, it is too difficult to study on genetics for many students. At the same time, mathematics is one of the basic courses in curriculum of the major related natural science, which has close relationship with the establishment, development and modification of genetics. In this paper, to establish the intrinsic logistic relationship and construct the integral knowledge network and to help students improving the analytic, comprehensive and logistic abilities, we applied some mathematical infiltrative model genetic knowledge in genetics teaching, which could help students more deeply learn and understand genetic knowledge.

  19. Modeling the effects of mineral nutrition for improving growth and development of micropropagated red raspberries

    Science.gov (United States)

    In vitro propagation is important for rapid multiplication of a wide range of nursery crops, including red raspberries. The genetic variation of the many red raspberry cultivars makes it difficult to use one growth medium for all. Although some cultivars grow well on Murashige and Skoog (1962) mediu...

  20. PM Synchronous Motor Dynamic Modeling with Genetic Algorithm ...

    African Journals Online (AJOL)

    Adel

    intelligence like neural network, genetic algorithm, etc (El Shahat and El Shewy, ..... maximum power factor has the most powerful effect on all various machine .... Artificial Intelligence, Renewable Energy, Power System, Control Systems, PV ...

  1. Potential climate effect of mineral aerosols over West Africa. Part I: model validation and contemporary climate evaluation

    Science.gov (United States)

    Ji, Zhenming; Wang, Guiling; Pal, Jeremy S.; Yu, Miao

    2016-02-01

    Mineral dusts present in the atmosphere can play an important role in climate over West Africa and surrounding regions. However, current understanding regarding how dust aerosols influence climate of West Africa is very limited. In this study, a regional climate model is used to investigate the potential climatic impacts of dust aerosols. Two sets of simulations driven by reanalysis and Earth System Model boundary conditions are performed with and without the representation of dust processes. The model, regardless of the boundary forcing, captures the spatial and temporal variability of the aerosol optical depth and surface concentration. The shortwave radiative forcing of dust is negative at the surface and positive in the atmosphere, with greater changes in the spring and summer. The presence of mineral dusts causes surface cooling and lower troposphere heating, resulting in a stabilization effect and reduction in precipitation in the northern portion of the monsoon close to the dust emissions region. This results in an enhancement of precipitation to the south. While dusts cause the lower troposphere to stabilize, upper tropospheric cooling makes the region more prone to intense deep convection as is evident by a simulated increase in extreme precipitation. In a companion paper, the impacts of dust emissions on future West African climate are investigated.

  2. Implications of modelled radioactivity measurements along coastal Odisha, Eastern India for heavy mineral resources

    Science.gov (United States)

    Ghosal, S.; Agrahari, S.; Guin, R.; Sengupta, D.

    2017-01-01

    A radioelemental assemblage assessment of two beaches of Odisha is performed for the first time. The radiation is measured in two ways, both on field with the help of a hand held environmental survey meter and in the laboratory, where the concentrations of radionuclide's 238U, 232Th and 4K have been determined with the help of High Purity Germanium detector (HPGe). Mineralogical analysis of selected samples has been performed with the help of X-Ray Fluorescence Spectrometry (XRF). A marked difference between the concentration of Uranium (274 Bq kg-1) and Thorium (2489 Bq kg-1) is observed and discussed based on the geology of the area. The placer deposits showing an enrichment of thorium can be an important source of nuclear fuel for the thorium based nuclear reactors. The ratio of thorium and uranium concentrations gives us an idea about the coastal processes associated with the beach. Statistical analysis of the data shows a positive correlation between 238U and 232Th and a strong negative correlation is indicated between 4 K and 238U, 232Th. A cross plot between the equivalent thorium and the equivalent uranium and the equivalent thorium and potassium, represents the nature of deposition and its association with the heavy mineral along with the radioactive elements. Heavy minerals exhibit an increasing trend towards Northeast-Southwest along the south eastern coast of India.

  3. Genetic and genomic analysis of RNases in model cyanobacteria.

    Science.gov (United States)

    Cameron, Jeffrey C; Gordon, Gina C; Pfleger, Brian F

    2015-10-01

    Cyanobacteria are diverse photosynthetic microbes with the ability to convert CO2 into useful products. However, metabolic engineering of cyanobacteria remains challenging because of the limited resources for modifying the expression of endogenous and exogenous biochemical pathways. Fine-tuned control of protein production will be critical to optimize the biological conversion of CO2 into desirable molecules. Messenger RNAs (mRNAs) are labile intermediates that play critical roles in determining the translation rate and steady-state protein concentrations in the cell. The majority of studies on mRNA turnover have focused on the model heterotrophic bacteria Escherichia coli and Bacillus subtilis. These studies have elucidated many RNA modifying and processing enzymes and have highlighted the differences between these Gram-negative and Gram-positive bacteria, respectively. In contrast, much less is known about mRNA turnover in cyanobacteria. We generated a compendium of the major ribonucleases (RNases) and provide an in-depth analysis of RNase III-like enzymes in commonly studied and diverse cyanobacteria. Furthermore, using targeted gene deletion, we genetically dissected the RNases in Synechococcus sp. PCC 7002, one of the fastest growing and industrially attractive cyanobacterial strains. We found that all three cyanobacterial homologs of RNase III and a member of the RNase II/R family are not essential under standard laboratory conditions, while homologs of RNase E/G, RNase J1/J2, PNPase, and a different member of the RNase II/R family appear to be essential for growth. This work will enhance our understanding of native control of gene expression and will facilitate the development of an RNA-based toolkit for metabolic engineering in cyanobacteria.

  4. Advances in behavioral genetics modeling using Mplus: applications of factor mixture modeling to twin data.

    Science.gov (United States)

    Muthén, Bengt; Asparouhov, Tihomir; Rebollo, Irene

    2006-06-01

    This article discusses new latent variable techniques developed by the authors. As an illustration, a new factor mixture model is applied to the monozygotic-dizygotic twin analysis of binary items measuring alcohol-use disorder. In this model, heritability is simultaneously studied with respect to latent class membership and within-class severity dimensions. Different latent classes of individuals are allowed to have different heritability for the severity dimensions. The factor mixture approach appears to have great potential for the genetic analyses of heterogeneous populations. Generalizations for longitudinal data are also outlined.

  5. Marine Mineral Exploration

    DEFF Research Database (Denmark)

    The past 20 years have seen extensive marine exploration work by the major industrialized countries. Studies have, in part, been concentrated on Pacific manganese nodule occurrences and on massive sulfides on mid-oceanic ridges. An international jurisdictional framework of the sea-bed mineral...... in EEZ areas are fairly unknown; many areas need detailed mapping and mineral exploration, and the majority of coastal or island states with large EEZ areas have little experience in exploration for marine hard minerals. This book describes the systematic steps in marine mineral exploration....... Such exploration requires knowledge of mineral deposits and models of their formation, of geophysical and geochemical exploration methods, and of data evaluation and interpretation methods. These topics are described in detail by an international group of authors. A short description is also given of marine...

  6. A model for family-based case–control studies of genetic imprinting and epistasis

    Science.gov (United States)

    Li, Xin; Sui, Yihan; Liu, Tian; Wang, Jianxin; Li, Yongci; Lin, Zhenwu; Hegarty, John; Koltun, Walter A.; Wang, Zuoheng

    2014-01-01

    Genetic imprinting, or called the parent-of-origin effect, has been recognized to play an important role in the formation and pathogenesis of human diseases. Although the epigenetic mechanisms that establish genetic imprinting have been a focus of many genetic studies, our knowledge about the number of imprinting genes and their chromosomal locations and interactions with other genes is still scarce, limiting precise inference of the genetic architecture of complex diseases. In this article, we present a statistical model for testing and estimating the effects of genetic imprinting on complex diseases using a commonly used case–control design with family structure. For each subject sampled from a case and control population, we not only genotype its own single nucleotide polymorphisms (SNPs) but also collect its parents’ genotypes. By tracing the transmission pattern of SNP alleles from parental to offspring generation, the model allows the characterization of genetic imprinting effects based on Pearson tests of a 2 × 2 contingency table. The model is expanded to test the interactions between imprinting effects and additive, dominant and epistatic effects in a complex web of genetic interactions. Statistical properties of the model are investigated, and its practical usefulness is validated by a real data analysis. The model will provide a useful tool for genome-wide association studies aimed to elucidate the picture of genetic control over complex human diseases. PMID:23887693

  7. Economic filters for evaluating porphyry copper deposit resource assessments using grade-tonnage deposit models, with examples from the U.S. Geological Survey global mineral resource assessment: Chapter H in Global mineral resource assessment

    Science.gov (United States)

    Robinson,, Gilpin R.; Menzie, W. David

    2012-01-01

    An analysis of the amount and location of undiscovered mineral resources that are likely to be economically recoverable is important for assessing the long-term adequacy and availability of mineral supplies. This requires an economic evaluation of estimates of undiscovered resources generated by traditional resource assessments (Singer and Menzie, 2010). In this study, simplified engineering cost models were used to estimate the economic fraction of resources contained in undiscovered porphyry copper deposits, predicted in a global assessment of copper resources. The cost models of Camm (1991) were updated with a cost index to reflect increases in mining and milling costs since 1989. The updated cost models were used to perform an economic analysis of undiscovered resources estimated in porphyry copper deposits in six tracts located in North America. The assessment estimated undiscovered porphyry copper deposits within 1 kilometer of the land surface in three depth intervals.

  8. Mainstreaming cancer genetics: A model integrating germline BRCA testing into routine ovarian cancer clinics.

    Science.gov (United States)

    Kentwell, Maira; Dow, Eryn; Antill, Yoland; Wrede, C David; McNally, Orla; Higgs, Emily; Hamilton, Anne; Ananda, Sumitra; Lindeman, Geoffrey J; Scott, Clare L

    2017-04-01

    Owing to the rapid increase in clinical need, we aimed to implement and review the performance of a mainstreaming model of germline BRCA1/2 genetic testing in eligible women with high grade non-mucinous epithelial ovarian cancer via a Genetic Counselor embedded in the gynecology oncology clinic. The model implemented involved a specialized referral form, weekly genetics-lead multidisciplinary review of referrals, and pre- and post-test genetic counseling provided by an embedded genetic counselor during chemotherapy chair time. Performance and outcomes were retrospectively audited over the following two consecutive one year periods, including survey data on medical specialist comfort with mainstreaming and the model. Sixty-four women underwent mainstreamed BRCA1/2 testing over the two year post-implementation period with a rate of detection of BRCA1/2 pathogenic variants of 17%. The referral rate for eligible women significantly increased to over 90% (pgenetic testing results was less than five months, with >90% of patients receiving results during first line chemotherapy. Genetic counseling time decreased from 120 to 54min. Cancer specialists were comfortable with the model. The mainstreaming model proved effective, increasing uptake of genetic testing in eligible patients to over 90%; it was efficient for patients, genetic counselors and cancer specialists and acceptable to cancer specialists. It facilitated co-location of genetic and oncology service delivery but separation of clinical responsibility for genetic testing to a specialist genetics service, ensuring accurate and robust patient-centred care. Copyright © 2017 Elsevier Inc. All rights reserved.

  9. EXTERNALITIES AND THE SIX FACETS MODEL OF TECHNOLOGY MANAGEMENT: GENETICALLY MODIFIED ORGANISMS IN AGRIBUSINESS

    OpenAIRE

    STEPHEN R. LUXMORE; CLYDE EIRÍKUR HULL

    2010-01-01

    The Six Facets Model of technology management has previously only been applied to process innovation at the firm and the industry level. In this article, the model is applied to product innovation for the first time. In the context of genetically-modified organisms in the agribusiness industry, we examine radical product innovation through the Six Facets Model. We propose, based on the history of genetically-modified organisms in agribusiness, that when applied to product innovation the Six F...

  10. Application of Markov chain Monte Carlo analysis to biomathematical modeling of respirable dust in US and UK coal miners.

    Science.gov (United States)

    Sweeney, Lisa M; Parker, Ann; Haber, Lynne T; Tran, C Lang; Kuempel, Eileen D

    2013-06-01

    A biomathematical model was previously developed to describe the long-term clearance and retention of particles in the lungs of coal miners. The model structure was evaluated and parameters were estimated in two data sets, one from the United States and one from the United Kingdom. The three-compartment model structure consists of deposition of inhaled particles in the alveolar region, competing processes of either clearance from the alveolar region or translocation to the lung interstitial region, and very slow, irreversible sequestration of interstitialized material in the lung-associated lymph nodes. Point estimates of model parameter values were estimated separately for the two data sets. In the current effort, Bayesian population analysis using Markov chain Monte Carlo simulation was used to recalibrate the model while improving assessments of parameter variability and uncertainty. When model parameters were calibrated simultaneously to the two data sets, agreement between the derived parameters for the two groups was very good, and the central tendency values were similar to those derived from the deterministic approach. These findings are relevant to the proposed update of the ICRP human respiratory tract model with revisions to the alveolar-interstitial region based on this long-term particle clearance and retention model.

  11. Factors influencing QTL mapping accuracy under complicated genetic models by computer simulation.

    Science.gov (United States)

    Su, C F; Wang, W; Gong, S L; Zuo, J H; Li, S J

    2016-12-19

    The accuracy of quantitative trait loci (QTLs) identified using different sample sizes and marker densities was evaluated in different genetic models. Model I assumed one additive QTL; Model II assumed three additive QTLs plus one pair of epistatic QTLs; and Model III assumed two additive QTLs with opposite genetic effects plus two pairs of epistatic QTLs. Recombinant inbred lines (RILs) (50-1500 samples) were simulated according to the Models to study the influence of different sample sizes under different genetic models on QTL mapping accuracy. RILs with 10-100 target chromosome markers were simulated according to Models I and II to evaluate the influence of marker density on QTL mapping accuracy. Different marker densities did not significantly influence accurate estimation of genetic effects with simple additive models, but influenced QTL mapping accuracy in the additive and epistatic models. The optimum marker density was approximately 20 markers when the recombination fraction between two adjacent markers was 0.056 in the additive and epistatic models. A sample size of 150 was sufficient for detecting simple additive QTLs. Thus, a sample size of approximately 450 is needed to detect QTLs with additive and epistatic models. Sample size must be approximately 750 to detect QTLs with additive, epistatic, and combined effects between QTLs. The sample size should be increased to >750 if the genetic models of the data set become more complicated than Model III. Our results provide a theoretical basis for marker-assisted selection breeding and molecular design breeding.

  12. Identification of common genetic modifiers of neurodegenerative diseases from an integrative analysis of diverse genetic screens in model organisms

    Directory of Open Access Journals (Sweden)

    Chen Xi

    2012-02-01

    Full Text Available Abstract Background An array of experimental models have been developed in the small model organisms C. elegans, S. cerevisiae and D. melanogaster for the study of various neurodegenerative diseases including Alzheimer's disease, Parkinson's disease, and expanded polyglutamine diseases as exemplified by Huntington's disease (HD and related ataxias. Genetic approaches to determine the nature of regulators of the disease phenotypes have ranged from small scale to essentially whole genome screens. The published data covers distinct models in all three organisms and one important question is the extent to which shared genetic factors can be uncovered that affect several or all disease models. Surprisingly it has appeared that there may be relatively little overlap and that many of the regulators may be organism or disease-specific. There is, however, a need for a fully integrated analysis of the available genetic data based on careful comparison of orthologues across the species to determine the real extent of overlap. Results We carried out an integrated analysis using C. elegans as the baseline model organism since this is the most widely studied in this context. Combination of data from 28 published studies using small to large scale screens in all three small model organisms gave a total of 950 identifications of genetic regulators. Of these 624 were separate genes with orthologues in C. elegans. In addition, 34 of these genes, which all had human orthologues, were found to overlap across studies. Of the common genetic regulators some such as chaperones, ubiquitin-related enzymes (including the E3 ligase CHIP which directly links the two pathways and histone deacetylases were involved in expected pathways whereas others such as the peroxisomal acyl CoA-oxidase suggest novel targets for neurodegenerative disease therapy Conclusions We identified a significant number of overlapping regulators of neurodegenerative disease models. Since the diseases

  13. Genetic hotels for the standard genetic code: evolutionary analysis based upon novel three-dimensional algebraic models.

    Science.gov (United States)

    José, Marco V; Morgado, Eberto R; Govezensky, Tzipe

    2011-07-01

    Herein, we rigorously develop novel 3-dimensional algebraic models called Genetic Hotels of the Standard Genetic Code (SGC). We start by considering the primeval RNA genetic code which consists of the 16 codons of type RNY (purine-any base-pyrimidine). Using simple algebraic operations, we show how the RNA code could have evolved toward the current SGC via two different intermediate evolutionary stages called Extended RNA code type I and II. By rotations or translations of the subset RNY, we arrive at the SGC via the former (type I) or via the latter (type II), respectively. Biologically, the Extended RNA code type I, consists of all codons of the type RNY plus codons obtained by considering the RNA code but in the second (NYR type) and third (YRN type) reading frames. The Extended RNA code type II, comprises all codons of the type RNY plus codons that arise from transversions of the RNA code in the first (YNY type) and third (RNR) nucleotide bases. Since the dimensions of remarkable subsets of the Genetic Hotels are not necessarily integer numbers, we also introduce the concept of algebraic fractal dimension. A general decoding function which maps each codon to its corresponding amino acid or the stop signals is also derived. The Phenotypic Hotel of amino acids is also illustrated. The proposed evolutionary paths are discussed in terms of the existing theories of the evolution of the SGC. The adoption of 3-dimensional models of the Genetic and Phenotypic Hotels will facilitate the understanding of the biological properties of the SGC.

  14. The WAG/Rij strain: A genetic animal model of absence epilepsy with comorbidity of depressiony

    NARCIS (Netherlands)

    Sarkisova, K.Y.; Luijtelaar, E.L.J.M. van

    2011-01-01

    A great number of clinical observations show a relationship between epilepsy and depression. Idiopathic generalized epilepsy, including absence epilepsy, has a genetic basis. The review provides evidence that WAG/Rij rats can be regarded as a valid genetic animal model of absence epilepsy with comor

  15. How Reliable is Your Detrital Geothermochronological Data? Quantifying the Influence of Abrasion on Detrital Heavy Minerals Through Numerical Modelling

    Science.gov (United States)

    Lavarini, C.; Attal, M.; Kirstein, L. A.

    2016-12-01

    Detrital heavy minerals, particularly zircon, have been used to learn about the early evolution of the Earth and are often the only record we have of events that have affected the geological evolution of rocks at the Earth's surface (Watson and Harrison, 2005). Recently, many studies have focused on the investigation of natural and artificial bias in detrital mineral analysis in order to enhance the technique's reliability (e.g., Moecher and Samson, 2006). However, in spite of the widely-known influence of physical abrasion, no attempts have been made to quantitatively assess how it potentially biases abrasion-driven products such as the mineral assemblages on which geothermochronology relies. Here, through numerical modelling, we explore how varying a series of parameters (rock erodibility, zircon fertility, sediment travel distance, source area lithology, and initial bedload ratio) yields different river loads and zircon signatures over the fluvial system. We assume that pebbles are abraded according to the commonly used Sternberg's law (1875) and that fining due to selective sorting is negligible as well as all abrasion products are in the sand size fraction. Our results highlight that the spatial location of lithologies and variations in erodibility strongly influence the release of zircon grains into the sand fraction. Even in a scenario where a catchment is made of two lithologies with identical properties, the one further from the outlet contributes relatively more zircon to the sand fraction collected at the outlet. The experiments also show the strong influence of fertility on zircon abundance in sands, and that bias increases with basin size due to the exponential nature of abrasion. These results highlight that abrasion must be carefully accounted as a natural bias in the investigation of detrital zircons for provenance research.

  16. An implementation of continuous genetic algorithm in parameter estimation of predator-prey model

    Science.gov (United States)

    Windarto

    2016-03-01

    Genetic algorithm is an optimization method based on the principles of genetics and natural selection in life organisms. The main components of this algorithm are chromosomes population (individuals population), parent selection, crossover to produce new offspring, and random mutation. In this paper, continuous genetic algorithm was implemented to estimate parameters in a predator-prey model of Lotka-Volterra type. For simplicity, all genetic algorithm parameters (selection rate and mutation rate) are set to be constant along implementation of the algorithm. It was found that by selecting suitable mutation rate, the algorithms can estimate these parameters well.

  17. Carbon Mineral Ecology: Predicting the Undiscovered Minerals of Carbon

    Science.gov (United States)

    Hazen, R. M.; Hummer, D. R.; Downs, R. T.; Hystad, G.; Golden, J.

    2015-12-01

    The diversity and distribution of Earth's minerals through deep time reflects key events in our planet's crustal evolution. Studies in mineral ecology exploit mineralogical databases to document diversity-distribution relationships of minerals, which reveal that all carbon-bearing minerals, as well as subsets containing C with O, H, Ca, or Na, conform to Large Number of Rare Events (LNRE) distributions. LNRE models facilitate prediction of total mineral diversity, and thus point to minerals that exist on Earth but have not yet been discovered and described. Our model predicts that at least 548 C minerals exist on Earth today, indicating that at least 145 carbon-bearing mineral species have yet to be discovered. Furthermore, by analyzing subsets of the most common additional elements in carbon-bearing minerals (i.e., 378 C + O species; 282 C + H species; 133 C + Ca species; and 100 C + Na species), we predict that 129 of these missing carbon minerals contain oxygen, 118 contain hydrogen, 52 contain calcium, and more than 60 contain sodium. The majority of these as yet undescribed minerals are predicted to be hydrous carbonates, many of which may have been overlooked because they are colorless, poorly crystalized, and/or water-soluble. We propose the identities of plausible as yet undescribed carbon minerals, as well as search strategies for their discovery. Some of these minerals will be natural examples of known synthetic compounds, including carbides such as calcium carbide (CaC2), crystalline hydrocarbons such as pyrene (C16H10), and numerous oxalates, anhydrous carbonates, and hydrous carbonates. Many other missing carbon minerals will be isomorphs of known carbon minerals, notably of the more than 100 different hydrous carbonate structures. An understanding of Earth's "missing" minerals provides a more complete picture of geochemical processes that influence crustal evolution.

  18. Using genetic mouse models to gain insight into glaucoma: Past results and future possibilities.

    Science.gov (United States)

    Fernandes, Kimberly A; Harder, Jeffrey M; Williams, Pete A; Rausch, Rebecca L; Kiernan, Amy E; Nair, K Saidas; Anderson, Michael G; John, Simon W M; Howell, Gareth R; Libby, Richard T

    2015-12-01

    While all forms of glaucoma are characterized by a specific pattern of retinal ganglion cell death, they are clinically divided into several distinct subclasses, including normal tension glaucoma, primary open angle glaucoma, congenital glaucoma, and secondary glaucoma. For each type of glaucoma there are likely numerous molecular pathways that control susceptibility to the disease. Given this complexity, a single animal model will never precisely model all aspects of all the different types of human glaucoma. Therefore, multiple animal models have been utilized to study glaucoma but more are needed. Because of the powerful genetic tools available to use in the laboratory mouse, it has proven to be a highly useful mammalian system for studying the pathophysiology of human disease. The similarity between human and mouse eyes coupled with the ability to use a combination of advanced cell biological and genetic tools in mice have led to a large increase in the number of studies using mice to model specific glaucoma phenotypes. Over the last decade, numerous new mouse models and genetic tools have emerged, providing important insight into the cell biology and genetics of glaucoma. In this review, we describe available mouse genetic models that can be used to study glaucoma-relevant disease/pathobiology. Furthermore, we discuss how these models have been used to gain insights into ocular hypertension (a major risk factor for glaucoma) and glaucomatous retinal ganglion cell death. Finally, the potential for developing new mouse models and using advanced genetic tools and resources for studying glaucoma are discussed.

  19. A Novel Statistical Model to Estimate Host Genetic Effects Affecting Disease Transmission

    Science.gov (United States)

    Anacleto, Osvaldo; Garcia-Cortés, Luis Alberto; Lipschutz-Powell, Debby; Woolliams, John A.; Doeschl-Wilson, Andrea B.

    2015-01-01

    There is increasing recognition that genetic diversity can affect the spread of diseases, potentially affecting plant and livestock disease control as well as the emergence of human disease outbreaks. Nevertheless, even though computational tools can guide the control of infectious diseases, few epidemiological models can simultaneously accommodate the inherent individual heterogeneity in multiple infectious disease traits influencing disease transmission, such as the frequently modeled propensity to become infected and infectivity, which describes the host ability to transmit the infection to susceptible individuals. Furthermore, current quantitative genetic models fail to fully capture the heritable variation in host infectivity, mainly because they cannot accommodate the nonlinear infection dynamics underlying epidemiological data. We present in this article a novel statistical model and an inference method to estimate genetic parameters associated with both host susceptibility and infectivity. Our methodology combines quantitative genetic models of social interactions with stochastic processes to model the random, nonlinear, and dynamic nature of infections and uses adaptive Bayesian computational techniques to estimate the model parameters. Results using simulated epidemic data show that our model can accurately estimate heritabilities and genetic risks not only of susceptibility but also of infectivity, therefore exploring a trait whose heritable variation is currently ignored in disease genetics and can greatly influence the spread of infectious diseases. Our proposed methodology offers potential impacts in areas such as livestock disease control through selective breeding and also in predicting and controlling the emergence of disease outbreaks in human populations. PMID:26405030

  20. Estimating the impact of mineral aerosols on crop yields in food insecure regions using statistical crop models

    Science.gov (United States)

    Hoffman, A.; Forest, C. E.; Kemanian, A.

    2016-12-01

    A significant number of food-insecure nations exist in regions of the world where dust plays a large role in the climate system. While the impacts of common climate variables (e.g. temperature, precipitation, ozone, and carbon dioxide) on crop yields are relatively well understood, the impact of mineral aerosols on yields have not yet been thoroughly investigated. This research aims to develop the data and tools to progress our understanding of mineral aerosol impacts on crop yields. Suspended dust affects crop yields by altering the amount and type of radiation reaching the plant, modifying local temperature and precipitation. While dust events (i.e. dust storms) affect crop yields by depleting the soil of nutrients or by defoliation via particle abrasion. The impact of dust on yields is modeled statistically because we are uncertain which impacts will dominate the response on national and regional scales considered in this study. Multiple linear regression is used in a number of large-scale statistical crop modeling studies to estimate yield responses to various climate variables. In alignment with previous work, we develop linear crop models, but build upon this simple method of regression with machine-learning techniques (e.g. random forests) to identify important statistical predictors and isolate how dust affects yields on the scales of interest. To perform this analysis, we develop a crop-climate dataset for maize, soybean, groundnut, sorghum, rice, and wheat for the regions of West Africa, East Africa, South Africa, and the Sahel. Random forest regression models consistently model historic crop yields better than the linear models. In several instances, the random forest models accurately capture the temperature and precipitation threshold behavior in crops. Additionally, improving agricultural technology has caused a well-documented positive trend that dominates time series of global and regional yields. This trend is often removed before regression with

  1. Multiple soil nutrient competition between plants, microbes, and mineral surfaces: model development, parameterization, and example applications in several tropical forests

    Science.gov (United States)

    Zhu, Q.; Riley, W. J.; Tang, J.; Koven, C. D.

    2016-01-01

    Soil is a complex system where biotic (e.g., plant roots, micro-organisms) and abiotic (e.g., mineral surfaces) consumers compete for resources necessary for life (e.g., nitrogen, phosphorus). This competition is ecologically significant, since it regulates the dynamics of soil nutrients and controls aboveground plant productivity. Here we develop, calibrate and test a nutrient competition model that accounts for multiple soil nutrients interacting with multiple biotic and abiotic consumers. As applied here for tropical forests, the Nutrient COMpetition model (N-COM) includes three primary soil nutrients (NH4+, NO3- and POx; representing the sum of PO43-, HPO42- and H2PO4-) and five potential competitors (plant roots, decomposing microbes, nitrifiers, denitrifiers and mineral surfaces). The competition is formulated with a quasi-steady-state chemical equilibrium approximation to account for substrate (multiple substrates share one consumer) and consumer (multiple consumers compete for one substrate) effects. N-COM successfully reproduced observed soil heterotrophic respiration, N2O emissions, free phosphorus, sorbed phosphorus and NH4+ pools at a tropical forest site (Tapajos). The overall model uncertainty was moderately well constrained. Our sensitivity analysis revealed that soil nutrient competition was primarily regulated by consumer-substrate affinity rather than environmental factors such as soil temperature or soil moisture. Our results also imply that under strong nutrient limitation, relative competitiveness depends strongly on the competitor functional traits (affinity and nutrient carrier enzyme abundance). We then applied the N-COM model to analyze field nitrogen and phosphorus perturbation experiments in two tropical forest sites (in Hawaii and Puerto Rico) not used in model development or calibration. Under soil inorganic nitrogen and phosphorus elevated conditions, the model accurately replicated the experimentally observed competition among

  2. Developing Novel Therapeutic Approaches in Small Cell Lung Carcinoma Using Genetically Engineered Mouse Models and Human Circulating Tumor Cells

    Science.gov (United States)

    2015-10-01

    Using Genetically Engineered Mouse Models and Human Circulating Tumor Cells PRINCIPAL INVESTIGATOR: Jeffrey Engelman MD PhD CONTRACTING...SUBTITLE Developiing Novel Therapeutic Approaches in Small Cell Lung 5a. CONTRACT NUMBER Carcinoma Using Genetically Engineered Mouse Models and 5b...biomarkers. 15. SUBJECT TERMS Small cell lung cancer (SCLC), Genetically engineered mouse model (GEMM), BH3 mimetic, TORC inhibitor, Apoptosis

  3. Computer Aided Modeling to Determine the Effectiveness of Resistive Exercises as Countermeasures for Bone Mineral Density Loss

    Science.gov (United States)

    Murphy, Benjamin M.

    1999-01-01

    Due to the loss of gravitational loading, astronauts have a tendency to lose bone mineral density in their lumbar spine and lower extremities on orbit. NASA requires astronauts to perform exercises during space flight to help reduce the amount of demineralization. To test these exercises on earth, 17 week bed rest studies are conducted that consist of specific diet and exercise regimes. Developing a finite element model of these exercises will help to quantify the stress distribution imposed by of each of these exercises. To help develop this model, MRI images are acquired from individuals participating in the bed rest studies. The MRIs can be used to create a subject specific model of each individual for testing. The MRIs are processed in the Magnetic Resonance Imaging Data Transfer System program to develop a three-dimensional finite element model of the femur for evaluation. Modifications were made to the MRIDTS that simplified the model creation process. These modifications made it possible to construct two separate models of different portions of a bone simultaneously and then later connect them manually. This helped alleviate the warping problem associated with the drastic changes in geometry found in some body parts, such as the joints. The code was also modified to incorporate material properties of various bone components into the model. Interior meshing was also incorporated into the program to allow for both the cortical shell and the entire bone to be modeled. A prototype model of the right femur of an adult female is being constructed and tested to determine the feasibility of finite element analysis as a tool for evaluating exercise effectiveness. The model is being run through the ANSYS finite element program on the Alabama Super Computer Network. After the model is validated, models of bedrest subjects can be generated to investigate exercise countermeasures.

  4. Multi-year model simulations of mineral dust distribution and transport over the Indian subcontinent during summer monsoon seasons

    Science.gov (United States)

    Sijikumar, S.; Aneesh, S.; Rajeev, K.

    2016-08-01

    Aerosol distribution over the Arabian Sea and the Indian subcontinent during the northern hemispheric summer is dominated by mineral dust transport from the West Asian desert regions. The radiative impact of these dust plumes is expected to have a prominent role in regulating the Asian Summer Monsoon circulation. While satellite observations have provided information in the spatial distribution of aerosols over the oceanic regions during the season, their utility over the land is rather limited. This study examines the transport of mineral dust over the West Asian desert, the Indian subcontinent and the surrounding oceanic regions during the summer monsoon season with the help of a regional scale model, WRF-Chem. Geographical locations of prominent dust sources, altitude ranges of mineral dust transport and their inter-annual variations are examined in detail. Multi-year model simulations were carried out during 2007 to 2012 with a model integration from 15 May to 31 August of each year. Six-year seasonal mean (June to August) vertically integrated dust amount from 1000 to 300 hPa level shows prominent dust loading over the eastern parts of Arabian desert and the northwestern part of India which are identified as two major sources of dust production. Large latitudinal gradient in dust amount is observed over the Arabian Sea with the largest dust concentration over the northwestern part and is primarily caused by the prevailing northwesterly wind at 925 hPa level from the Arabian desert. The model simulations clearly show that most of the dust distributed over the Indo-Gangetic plane originates from the Rajasthan desert located in the northwestern part of India, whereas dust observed over the central and south peninsular India and over the Arabian Sea are mainly transported from the Arabian desert. Abnormal dust loading is observed over the north Arabian Sea during June 2008. This has been produced as a result of the low pressure system (associated with the onset of

  5. A parametric model for analyzing anticipation in genetically predisposed families

    DEFF Research Database (Denmark)

    Larsen, Klaus; Petersen, Janne; Bernstein, Inge

    2009-01-01

    Anticipation, i.e. a decreasing age-at-onset in subsequent generations has been observed in a number of genetically triggered diseases. The impact of anticipation is generally studied in affected parent-child pairs. These analyses are restricted to pairs in which both individuals have been affect...

  6. A realistic model under which the genetic code is optimal.

    Science.gov (United States)

    Buhrman, Harry; van der Gulik, Peter T S; Klau, Gunnar W; Schaffner, Christian; Speijer, Dave; Stougie, Leen

    2013-10-01

    The genetic code has a high level of error robustness. Using values of hydrophobicity scales as a proxy for amino acid character, and the mean square measure as a function quantifying error robustness, a value can be obtained for a genetic code which reflects the error robustness of that code. By comparing this value with a distribution of values belonging to codes generated by random permutations of amino acid assignments, the level of error robustness of a genetic code can be quantified. We present a calculation in which the standard genetic code is shown to be optimal. We obtain this result by (1) using recently updated values of polar requirement as input; (2) fixing seven assignments (Ile, Trp, His, Phe, Tyr, Arg, and Leu) based on aptamer considerations; and (3) using known biosynthetic relations of the 20 amino acids. This last point is reflected in an approach of subdivision (restricting the random reallocation of assignments to amino acid subgroups, the set of 20 being divided in four such subgroups). The three approaches to explain robustness of the code (specific selection for robustness, amino acid-RNA interactions leading to assignments, or a slow growth process of assignment patterns) are reexamined in light of our findings. We offer a comprehensive hypothesis, stressing the importance of biosynthetic relations, with the code evolving from an early stage with just glycine and alanine, via intermediate stages, towards 64 codons carrying todays meaning.

  7. Linguini Models of Molecular Genetic Mapping and Fingerprinting.

    Science.gov (United States)

    Thompson, James N., Jr.; Gray, Stanton B.; Hellack, Jenna J.

    1997-01-01

    Presents an exercise using linguini noodles to demonstrate an aspect of DNA fingerprinting. DNA maps that show genetic differences can be produced by digesting a certain piece of DNA with two or more restriction enzymes both individually and in combination. By rearranging and matching linguini fragments, students can recreate the original pattern…

  8. Tendon Mineralization Is Progressive and Associated with Deterioration of Tendon Biomechanical Properties, and Requires BMP-Smad Signaling in the Mouse Achilles Tendon Injury Model

    Science.gov (United States)

    Zhang, Kairui; Asai, Shuji; Hast, Michael W.; Liu, Min; Usami, Yu; Iwamoto, Masahiro; Soslowsky, Louis J.; Enomoto-Iwamoto, Motomi

    2016-01-01

    Ectopic tendon mineralization can develop following tendon rupture or trauma surgery. The pathogenesis of ectopic tendon mineralization and its clinical impact have not been fully elucidated yet. In this study, we utilized a mouse Achilles tendon injury model to determine whether ectopic tendon mineralization alters the biomechanical properties of the tendon and whether BMP signaling is involved in this condition. A complete transverse incision was made at the midpoint of the right Achilles tendon in 8-week-old CD1 mice and the gap was left open. Ectopic cartilaginous mass formation was found in the injured tendon by 4 weeks post-surgery and ectopic mineralization was detected at 8–10 weeks post-surgery. Ectopic mineralization grew over time and volume of the mineralized materials of 25-weeks samples was about 2.5 fold bigger than that of 10-weeks samples, indicating that injury-induced ectopic tendon mineralization is progressive. In vitro mechanical testing showed that max force, max stress and mid-substance modulus in the 25-weeks samples were significantly lower than the 10-weeks samples. We observed substantial increases in expression of bone morphogenetic protein family genes in injured tendons 1 week post-surgery. Immunohistochemical analysis showed that phosphorylation of both Smad1 and Smad3 were highly increased in injured tendons as early as 1 week post-injury and remained high in ectopic chondrogenic lesions 4 weeks post-injury. Treatment with the BMP receptor kinase inhibitor (LDN193189) significantly inhibited injury-induced tendon mineralization. These findings indicate that injury-induced ectopic tendon mineralization is progressive, involves BMP signaling and associated with deterioration of tendon biomechanical properties. PMID:26825318

  9. Finding model parameters: Genetic algorithms and the numerical modelling of quartz luminescence

    Energy Technology Data Exchange (ETDEWEB)

    Adamiec, Grzegorz [Department of Radioisotopes, Institute of Physics, Silesian University of Technology, ul. Krzywoustego 2, 44-100 Gliwice (Poland)]. E-mail: grzegorz.adamiec@polsl.pl; Bluszcz, Andrzej [Department of Radioisotopes, Institute of Physics, Silesian University of Technology, ul. Krzywoustego 2, 44-100 Gliwice (Poland); Bailey, Richard [Department of Geography, Royal Holloway, University of London, Egham, Surrey, TW20 0EX (United Kingdom); Garcia-Talavera, Marta [LIBRA, Centro I-D, Campus Miguel Delibes, 47011 Valladolid (Spain)

    2006-08-15

    The paper presents an application of genetic algorithms (GAs) to the problem of finding appropriate parameter values for the numerical simulation of quartz thermoluminescence (TL). We show that with the use of GAs it is possible to achieve a very good match between simulated and experimentally measured characteristics of quartz, for example the thermal activation characteristics of fired quartz. The rate equations of charge transport in the numerical model of luminescence in quartz contain a large number of parameters (trap depths, frequency factors, populations, charge capture probabilities, optical detrapping probabilities, and recombination probabilities). Given that comprehensive models consist of over 10 traps, finding model parameters proves a very difficult task. Manual parameter changes are very time consuming and allow only a limited degree of accuracy. GAs provide a semi-automatic way of finding appropriate parameters.

  10. Atomistic modeling of oil shale kerogens and asphaltenes along with their interactions with the inorganic mineral matrix

    Energy Technology Data Exchange (ETDEWEB)

    Facelli, Julio [Univ. of Utah, Salt Lake City, UT (United States); Pugmire, Ronald [Univ. of Utah, Salt Lake City, UT (United States); Pimienta, Ian [Univ. of Utah, Salt Lake City, UT (United States)

    2011-03-31

    The goal of this project is to obtain and validate three dimensional atomistic models for the organic matter in both oil shales and oil sands. In the case of oil shales the modeling was completed for kerogen, the insoluble portion of the organic matter; for oil sands it was for asphaltenes, a class of molecules found in crude oil. The three dimensional models discussed in this report were developed starting from existing literature two dimensional models. The models developed included one kerogen, based on experimental data on a kerogen isolated from a Green River oil shale, and a set of six representative asphaltenes. Subsequently, the interactions between these organic models and an inorganic matrix was explored in order to gain insight into the chemical nature of this interaction, which could provide vital information in developing efficient methods to remove the organic material from inorganic mineral substrate. The inorganic substrate used to model the interaction was illite, an aluminum silicate oxide clay. In order to obtain the feedback necessary to validate the models, it is necessary to be able to calculate different observable quantities and to show that these observables both reproduce the results of experimental measurements on actual samples as well as that the observables are sensitive to structural differences between models. The observables that were calculated using the models include 13C NMR spectra, the IR vibrational spectra, and the atomic pair wise distribution function; these were chosen as they are among the methods for which both experimental and calculated values can be readily obtained. Where available, comparison was made to experiment results. Finally, molecular dynamic simulations of pyrolysis were completed on the models to gain an understanding into the nature of the decomposition of these materials when heated.

  11. Reactive fluid flow models and applications to diagenesis, mineral deposits and crustal rocks

    Energy Technology Data Exchange (ETDEWEB)

    Lasaga, A.C.; Rye, D.M.

    1993-08-01

    Funds are requested for a combined theoretical and field study of coupled fluid flow, heat and mass transport, and chemical reaction in hydrothermal and metamorphic systems. An existing computer code developed by the applicants which numerically treats multi-component, finite-rate reactions combined with advective and dispersive transport in one and two dimensions and which incorporates isotopic exchange and heat and mass transfer will continue to be developed and applied in a variety of geological settings. The code we have developed simultaneously solves for mass transport and reaction, thus offering a significant improvement in computational efficiency over existing ``batch`` reaction path codes. By coupling flow and chemical reaction in a hydrothermal system, we can explicitly investigate the extent to which characteristic flow-reaction paths govern the chemical evolution of the fluids in a hydrothermal system. The concept of a flow-reaction path is particularly important where certain portions of mature hydrothermal systems may exhaust the buffer capacity of the rock as the primary mineralogy is consumed. In these instances 7 fluids traversing distinct regions within the hydrothermal system may experience very different reaction histories, even where the system can be described as nearly isothermal. The study of paleo-hydrothermal systems can yield some important insights into the chemical dynamics of hydrothermal systems in general. As an example of a paleo-hydrothermal system, we have considered the geochemical evolution of ``porphyry-copper`` type mineralization.

  12. Modelling and genetic algorithm based optimisation of inverse supply chain

    Science.gov (United States)

    Bányai, T.

    2009-04-01

    (Recycling of household appliances with emphasis on reuse options). The purpose of this paper is the presentation of a possible method for avoiding the unnecessary environmental risk and landscape use through unprovoked large supply chain of collection systems of recycling processes. In the first part of the paper the author presents the mathematical model of recycling related collection systems (applied especially for wastes of electric and electronic products) and in the second part of the work a genetic algorithm based optimisation method will be demonstrated, by the aid of which it is possible to determine the optimal structure of the inverse supply chain from the point of view economical, ecological and logistic objective functions. The model of the inverse supply chain is based on a multi-level, hierarchical collection system. In case of this static model it is assumed that technical conditions are permanent. The total costs consist of three parts: total infrastructure costs, total material handling costs and environmental risk costs. The infrastructure-related costs are dependent only on the specific fixed costs and the specific unit costs of the operation points (collection, pre-treatment, treatment, recycling and reuse plants). The costs of warehousing and transportation are represented by the material handling related costs. The most important factors determining the level of environmental risk cost are the number of out of time recycled (treated or reused) products, the number of supply chain objects and the length of transportation routes. The objective function is the minimization of the total cost taking into consideration the constraints. However a lot of research work discussed the design of supply chain [8], but most of them concentrate on linear cost functions. In the case of this model non-linear cost functions were used. The non-linear cost functions and the possible high number of objects of the inverse supply chain leaded to the problem of choosing a

  13. MEPE-derived ASARM peptide inhibits odontogenic differentiation of dental pulp stem cells and impairs mineralization in tooth models of X-linked hypophosphatemia.

    Directory of Open Access Journals (Sweden)

    Benjamin Salmon

    Full Text Available Mutations in PHEX (phosphate-regulating gene with homologies to endopeptidases on the X-chromosome cause X-linked familial hypophosphatemic rickets (XLH, a disorder having severe bone and tooth dentin mineralization defects. The absence of functional PHEX leads to abnormal accumulation of ASARM (acidic serine- and aspartate-rich motif peptide - a substrate for PHEX and a strong inhibitor of mineralization - derived from MEPE (matrix extracellular phosphoglycoprotein and other matrix proteins. MEPE-derived ASARM peptide accumulates in tooth dentin of XLH patients where it may impair dentinogenesis. Here, we investigated the effects of ASARM peptides in vitro and in vivo on odontoblast differentiation and matrix mineralization. Dental pulp stem cells from human exfoliated deciduous teeth (SHEDs were seeded into a 3D collagen scaffold, and induced towards odontogenic differentiation. Cultures were treated with synthetic ASARM peptides (phosphorylated and nonphosphorylated derived from the human MEPE sequence. Phosphorylated ASARM peptide inhibited SHED differentiation in vitro, with no mineralized nodule formation, decreased odontoblast marker expression, and upregulated MEPE expression. Phosphorylated ASARM peptide implanted in a rat molar pulp injury model impaired reparative dentin formation and mineralization, with increased MEPE immunohistochemical staining. In conclusion, using complementary models to study tooth dentin defects observed in XLH, we demonstrate that the MEPE-derived ASARM peptide inhibits both odontogenic differentiation and matrix mineralization, while increasing MEPE expression. These results contribute to a partial mechanistic explanation of XLH pathogenesis: direct inhibition of mineralization by ASARM peptide leads to the mineralization defects in XLH teeth. This process appears to be positively reinforced by the increased MEPE expression induced by ASARM. The MEPE-ASARM system can therefore be considered as a potential

  14. MEPE-Derived ASARM Peptide Inhibits Odontogenic Differentiation of Dental Pulp Stem Cells and Impairs Mineralization in Tooth Models of X-Linked Hypophosphatemia

    Science.gov (United States)

    Khaddam, Mayssam; Naji, Jiar; Coyac, Benjamin R.; Baroukh, Brigitte; Letourneur, Franck; Lesieur, Julie; Decup, Franck; Le Denmat, Dominique; Nicoletti, Antonino; Poliard, Anne; Rowe, Peter S.; Huet, Eric; Vital, Sibylle Opsahl; Linglart, Agnès; McKee, Marc D.; Chaussain, Catherine

    2013-01-01

    Mutations in PHEX (phosphate-regulating gene with homologies to endopeptidases on the X-chromosome) cause X-linked familial hypophosphatemic rickets (XLH), a disorder having severe bone and tooth dentin mineralization defects. The absence of functional PHEX leads to abnormal accumulation of ASARM (acidic serine- and aspartate-rich motif) peptide − a substrate for PHEX and a strong inhibitor of mineralization − derived from MEPE (matrix extracellular phosphoglycoprotein) and other matrix proteins. MEPE-derived ASARM peptide accumulates in tooth dentin of XLH patients where it may impair dentinogenesis. Here, we investigated the effects of ASARM peptides in vitro and in vivo on odontoblast differentiation and matrix mineralization. Dental pulp stem cells from human exfoliated deciduous teeth (SHEDs) were seeded into a 3D collagen scaffold, and induced towards odontogenic differentiation. Cultures were treated with synthetic ASARM peptides (phosphorylated and nonphosphorylated) derived from the human MEPE sequence. Phosphorylated ASARM peptide inhibited SHED differentiation in vitro, with no mineralized nodule formation, decreased odontoblast marker expression, and upregulated MEPE expression. Phosphorylated ASARM peptide implanted in a rat molar pulp injury model impaired reparative dentin formation and mineralization, with increased MEPE immunohistochemical staining. In conclusion, using complementary models to study tooth dentin defects observed in XLH, we demonstrate that the MEPE-derived ASARM peptide inhibits both odontogenic differentiation and matrix mineralization, while increasing MEPE expression. These results contribute to a partial mechanistic explanation of XLH pathogenesis: direct inhibition of mineralization by ASARM peptide leads to the mineralization defects in XLH teeth. This process appears to be positively reinforced by the increased MEPE expression induced by ASARM. The MEPE-ASARM system can therefore be considered as a potential therapeutic

  15. Using the concentration-volume (C-V) fractal model in the delineation of gold mineralized zones within the Tepeoba porphyry Cu-Mo-Au, Balikesir, NW Turkey

    Science.gov (United States)

    Kumral, Mustafa; Abdelnasser, Amr; Karaman, Muhittin; Budakoglu, Murat

    2016-04-01

    The Tepeoba porphyry Cu-Mo-Au mineralization that located at the Biga peninsula (W Turkey) developed around the Eybek pluton concentrated at its southern contact. This mineralization that hosted in the hornfels rocks of Karakaya Complex is associated with three main alteration zones; potassic, phyllic and propylitic alterations along the fault controlled margins of the Eybek pluton and quartz stockwork veining as well as brecciation zones. As well as two mineralized zones were occurred in the mine area; hypogene and oxidation/supergene zone. The hypogene zone has differentiated alteration types; high potassic and low phyllic alteration, while the oxidation/supergene zone has high phyllic and propylitic alterations. This work deals with the delineation of gold mineralized zone within this porphyry deposit using the concentration-volume (C-V) fractal model. Five zones of gold were calculated using its power-law C-V relationship that revealed that the main phase of gold mineralization stated at 5.3083 ppm Au concentration. In addition, the C-V log-log plot shows that the highly and moderately Au mineralization zone developed in western part of deposit correlated with oxidation zone related to propylitic alteration. On the other hand, its weakly mineralization zone has a widespread in the hypogene zone related to potassic alteration. This refers to the enrichment of gold and depletion of copper at the oxidation/supergene zone is due to the oxidation/supergene alteration processes that enrich the deposits by the meteoric water. Keywords: Concentration-volume (C-V) fractal model; gold mineralized zone; Tepeoba porphyry Cu-Mo-Au; Balikesir; NW Turkey.

  16. Genetic mouse models to study blood–brain barrier development and function

    OpenAIRE

    Sohet, Fabien; Daneman, Richard

    2013-01-01

    The blood–brain barrier (BBB) is a complex physiological structure formed by the blood vessels of the central nervous system (CNS) that tightly regulates the movement of substances between the blood and the neural tissue. Recently, the generation and analysis of different genetic mouse models has allowed for greater understanding of BBB development, how the barrier is regulated during health, and its response to disease. Here we discuss: 1) Genetic mouse models that have been used to study th...

  17. Progress and Prospects for Genetic Modification of Nonhuman Primate Models in Biomedical Research

    OpenAIRE

    Chan, Anthony W. S.

    2013-01-01

    The growing interest of modeling human diseases using genetically modified (transgenic) nonhuman primates (NHPs) is a direct result of NHPs (rhesus macaque, etc.) close relation to humans. NHPs share similar developmental paths with humans in their anatomy, physiology, genetics, and neural functions; and in their cognition, emotion, and social behavior. The NHP model within biomedical research has played an important role in the development of vaccines, assisted reproductive technologies, and...

  18. A p-Adic Model of DNA Sequence and Genetic Code

    CERN Document Server

    Dragovich, Branko

    2007-01-01

    Using basic properties of p-adic numbers, we consider a simple new approach to describe main aspects of DNA sequence and genetic code. Central role in our investigation plays an ultrametric p-adic information space which basic elements are nucleotides, codons and genes. We show that a 5-adic model is appropriate for DNA sequence. This 5-adic model, combined with 2-adic distance, is also suitable for genetic code and for a more advanced employment in genomics. We find that genetic code degeneracy is related to the p-adic distance between codons.

  19. New canine models of copper toxicosis: diagnosis, treatment, and genetics.

    Science.gov (United States)

    Fieten, Hille; Penning, Louis C; Leegwater, Peter A J; Rothuizen, Jan

    2014-05-01

    The One Health principle recognizes that human health, animal health, and environmental health are inextricably linked. An excellent example is the study of naturally occurring copper toxicosis in dogs to help understand human disorders of copper metabolism. Besides the Bedlington terrier, where copper toxicosis is caused by a mutation in the COMMD1 gene, more complex hereditary forms of copper-associated hepatitis were recognized recently in other dog breeds. The Labrador retriever is one such breed, where an interplay between genetic susceptibility and exposure to copper lead to clinical copper toxicosis. Purebred dog populations are ideal for gene mapping studies, and because genes involved in copper metabolism are highly conserved across species, newly identified gene mutations in the dog may help unravel the genetic complexity of different human forms of copper toxicosis. Furthermore, increasing knowledge with respect to diagnosis and treatment strategies will benefit both species.

  20. Random regressions models to describe the genetic variation of milk yield over multiple parities in Buffaloes

    Directory of Open Access Journals (Sweden)

    H. Tonhati

    2010-02-01

    Full Text Available The objectives of this study were to estimate (covariance functions for additive genetic and permanent environmental effects, as well as the genetic parameters for milk yield over multiple parities, using random regressions models (RRM. Records of 4,757 complete lactations of Murrah breed buffaloes from 12 herds were analyzed. Ages at calving were between 2 and 11 years. The model included the additive genetic and permanent environmental random effects and the fixed effects of contemporary groups (herd, year and calving season and milking frequency (1 or 2. A cubic regression on Legendre orthogonal polynomials of ages was used to model the mean trend. The additive genetic and permanent environmental effects were modeled by Legendre orthogonal polynomials. Residual variances were considered homogenous or heterogeneous, modeled through variance functions or step functions with 5, 7 or 10 classes. Results from Akaike’s and Schwarz’s Bayesian information criterion indicated that a RRM considering a third order polynomial for the additive genetic and permanent environmental effects and a step function with 5 classes for residual variances fitted best. Heritability estimates obtained by this model varied from 0.10 to 0.28. Genetic correlations were high between consecutive ages, but decreased when intervals between ages increased

  1. Using genetically engineered animal models in the postgenomic era to understand gene function in alcoholism.

    Science.gov (United States)

    Reilly, Matthew T; Harris, R Adron; Noronha, Antonio

    2012-01-01

    Over the last 50 years, researchers have made substantial progress in identifying genetic variations that underlie the complex phenotype of alcoholism. Not much is known, however, about how this genetic variation translates into altered biological function. Genetic animal models recapitulating specific characteristics of the human condition have helped elucidate gene function and the genetic basis of disease. In particular, major advances have come from the ability to manipulate genes through a variety of genetic technologies that provide an unprecedented capacity to determine gene function in the living organism and in alcohol-related behaviors. Even newer genetic-engineering technologies have given researchers the ability to control when and where a specific gene or mutation is activated or deleted, allowing investigators to narrow the role of the gene's function to circumscribed neural pathways and across development. These technologies are important for all areas of neuroscience, and several public and private initiatives are making a new generation of genetic-engineering tools available to the scientific community at large. Finally, high-throughput "next-generation sequencing" technologies are set to rapidly increase knowledge of the genome, epigenome, and transcriptome, which, combined with genetically engineered mouse mutants, will enhance insight into biological function. All of these resources will provide deeper insight into the genetic basis of alcoholism.

  2. Empirical valence bond models for reactive potential energy surfaces: a parallel multilevel genetic program approach.

    Science.gov (United States)

    Bellucci, Michael A; Coker, David F

    2011-07-28

    We describe a new method for constructing empirical valence bond potential energy surfaces using a parallel multilevel genetic program (PMLGP). Genetic programs can be used to perform an efficient search through function space and parameter space to find the best functions and sets of parameters that fit energies obtained by ab initio electronic structure calculations. Building on the traditional genetic program approach, the PMLGP utilizes a hierarchy of genetic programming on two different levels. The lower level genetic programs are used to optimize coevolving populations in parallel while the higher level genetic program (HLGP) is used to optimize the genetic operator probabilities of the lower level genetic programs. The HLGP allows the algorithm to dynamically learn the mutation or combination of mutations that most effectively increase the fitness of the populations, causing a significant increase in the algorithm's accuracy and efficiency. The algorithm's accuracy and efficiency is tested against a standard parallel genetic program with a variety of one-dimensional test cases. Subsequently, the PMLGP is utilized to obtain an accurate empirical valence bond model for proton transfer in 3-hydroxy-gamma-pyrone in gas phase and protic solvent.

  3. Baboons as a model to study genetics and epigenetics of human disease.

    Science.gov (United States)

    Cox, Laura A; Comuzzie, Anthony G; Havill, Lorena M; Karere, Genesio M; Spradling, Kimberly D; Mahaney, Michael C; Nathanielsz, Peter W; Nicolella, Daniel P; Shade, Robert E; Voruganti, Saroja; VandeBerg, John L

    2013-01-01

    A major challenge for understanding susceptibility to common human diseases is determining genetic and environmental factors that influence mechanisms underlying variation in disease-related traits. The most common diseases afflicting the US population are complex diseases that develop as a result of defects in multiple genetically controlled systems in response to environmental challenges. Unraveling the etiology of these diseases is exceedingly difficult because of the many genetic and environmental factors involved. Studies of complex disease genetics in humans are challenging because it is not possible to control pedigree structure and often not practical to control environmental conditions over an extended period of time. Furthermore, access to tissues relevant to many diseases from healthy individuals is quite limited. The baboon is a well-established research model for the study of a wide array of common complex diseases, including dyslipidemia, hypertension, obesity, and osteoporosis. It is possible to acquire tissues from healthy, genetically characterized baboons that have been exposed to defined environmental stimuli. In this review, we describe the genetic and physiologic similarity of baboons with humans, the ability and usefulness of controlling environment and breeding, and current genetic and genomic resources. We discuss studies on genetics of heart disease, obesity, diabetes, metabolic syndrome, hypertension, osteoporosis, osteoarthritis, and intrauterine growth restriction using the baboon as a model for human disease. We also summarize new studies and resources under development, providing examples of potential translational studies for targeted interventions and therapies for human disease.

  4. EURASIAN MINERAL WATER: MATHEMATICAL MODELING, CLASSIFICATION AND ASSESSMENT OF THEIR IMPACT ON THE BIOCHEMICAL COMPOSITION OF HUMAN BLOOD

    Directory of Open Access Journals (Sweden)

    Nikolay Kornilov

    2014-06-01

    Full Text Available In the article the results of comparative analysis of the composition of the Eurasian hydromineral resources and the assessment of their impact on the physiological condition of a human organism according to biochemical studies of venous blood are presented. Processing of initial data on the composition and properties of mineral waters chloride-hydrocarbonate, sulphate- hydrocarbonate and chloride-sulphate types and venous blood are made using the method of mathematical modeling, developed by the authors of this article. It is shown that in the balneological impact of hydromineral resources on the body in the blood increases the hemoglobin and oxygen, decreases glucose, and acid-base pH shifted to high alkalinity.

  5. Investigation of mineral aerosols radiative effects over High Mountain Asia in 1990-2009 using a regional climate model

    Science.gov (United States)

    Ji, Zhenming; Kang, Shichang; Zhang, Qianggong; Cong, Zhiyuan; Chen, Pengfei; Sillanpää, Mika

    2016-09-01

    Mineral aerosols scatter and absorb incident solar radiation in the atmosphere, and play an important role in the regional climate of High Mountain Asia (the domain includes the Himalayas, Tibetan Plateau, Pamir, Hindu-kush, Karakorum and Tienshan Mountains). Dust deposition on snow/ice can also change the surface albedo, resulting in perturbations in the surface radiation balance. However, most studies that have made quantitative assessments of the climatic effect of mineral aerosols over the High Mountain Asia region did not consider the impact of dust on snow/ice at the surface. In this study, a regional climate model coupled with an aerosol-snow/ice feedback module was used to investigate the emission, distribution, and deposition of dust and the climatic effects of aerosols over High Mountain Asia. Two sets of simulations driven by a reanalysis boundary condition were performed, i.e., with and without dust-climate feedback. Results indicated that the model captured the spatial and temporal features of the climatology and aerosol optical depth (AOD). High dust emission fluxes were simulated in the interior of the Tibetan Plateau (TP) and the Yarlung Tsangpo Valley in March-April-May (MAM), with a decreasing trend during 1990-2009. Dry deposition was controlled by the topography, and its spatial and seasonal features agreed well with the dust emission fluxes. The maximum wet deposition occurred in the western (southern and central) TP in MAM (JJA). A positive surface radiative forcing was induced by dust, including aerosol-snow/ice feedback, resulting in 2-m temperature increases of 0.1-0.5 °C over the western TP and Kunlun Mountains in MAM. Mineral dust also caused a decrease of 5-25 mm in the snow water equivalent (SWE) over the western TP, Himalayas, and Pamir Mountains in DJF and MAM. The long-term regional mean radiative forcing via dust deposition on snow showed an rising trend during 1990-2009, which suggested the contribution of aerosols surface

  6. Ontology driven modeling for the knowledge of genetic susceptibility to disease.

    Science.gov (United States)

    Lin, Yu; Sakamoto, Norihiro

    2009-05-12

    For the machine helped exploring the relationships between genetic factors and complex diseases, a well-structured conceptual framework of the background knowledge is needed. However, because of the complexity of determining a genetic susceptibility factor, there is no formalization for the knowledge of genetic susceptibility to disease, which makes the interoperability between systems impossible. Thus, the ontology modeling language OWL was used for formalization in this paper. After introducing the Semantic Web and OWL language propagated by W3C, we applied text mining technology combined with competency questions to specify the classes of the ontology. Then, an N-ary pattern was adopted to describe the relationships among these defined classes. Based on the former work of OGSF-DM (Ontology of Genetic Susceptibility Factors to Diabetes Mellitus), we formalized the definition of "Genetic Susceptibility", "Genetic Susceptibility Factor" and other classes by using OWL-DL modeling language; and a reasoner automatically performed the classification of the class "Genetic Susceptibility Factor". The ontology driven modeling is used for formalization the knowledge of genetic susceptibility to complex diseases. More importantly, when a class has been completely formalized in an ontology, the OWL reasoning can automatically compute the classification of the class, in our case, the class of "Genetic Susceptibility Factors". With more types of genetic susceptibility factors obtained from the laboratory research, our ontologies always needs to be refined, and many new classes must be taken into account to harmonize with the ontologies. Using the ontologies to develop the semantic web needs to be applied in the future.

  7. Aggregate and Mineral Resources - Minerals

    Data.gov (United States)

    NSGIC State | GIS Inventory — This point occurrence data set represents the current mineral and selected energy resources of Utah. The data set coordinates were derived from USGS topographic maps...

  8. Towards a formal design model based on a genetic design model system

    DEFF Research Database (Denmark)

    Storga, Mario; Andreasen, Mogens Myrup; Marjanovic, Dorian

    2005-01-01

    The research presented in this article is aimed to the investigation of the nature, building and practical role of a Design Ontology as a potential framework for the more efficient product development data-, information- and knowledge- description, -explanation, -understanding and -reusing...... by IEEE, provides us definitions for the most general and universal concepts, that we used in our research for derivation of terms definitions and axioms in the Design Ontology. The Design Ontology was evaluated using the OntoEdit® ontology engineering environment, on a real product example, and based....... In this article, we briefly summarize our experience of converting informal definitions of the concepts from the product development domain based on the existing theoretical background into formal design model. As a main data source for extracting the content of a design ontology, Genetic Design Model System...

  9. Towards a formal design model based on a genetic design model system

    DEFF Research Database (Denmark)

    Storga, Mario; Andreasen, Mogens Myrup; Marjanovic, Dorian

    2005-01-01

    . In this article, we briefly summarize our experience of converting informal definitions of the concepts from the product development domain based on the existing theoretical background into formal design model. As a main data source for extracting the content of a design ontology, Genetic Design Model System......The research presented in this article is aimed to the investigation of the nature, building and practical role of a Design Ontology as a potential framework for the more efficient product development data-, information- and knowledge- description, -explanation, -understanding and -reusing...... by IEEE, provides us definitions for the most general and universal concepts, that we used in our research for derivation of terms definitions and axioms in the Design Ontology. The Design Ontology was evaluated using the OntoEdit® ontology engineering environment, on a real product example, and based...

  10. Modelling the loss of genetic diversity in vole populations in a spatially and temporally varying environment

    DEFF Research Database (Denmark)

    Topping, Christopher John; Østergaard, Siri; Pertoldi, Cino

    2003-01-01

    a genetically explicit individual-based model (IBM) coupled to a dynamic landscape model was used to obtain measures for the genetic status of simulated vole populations. The rate of loss of expected heterozygosity (He) was calculated for simulated populations using two levels of spatial and temporal...... heterogeneity. Results showed that both spatial and temporal heterogeneity exerted an influence on the rate of loss of genetic diversity, but the precise effect was a balance between the effects of population sub-structuring, the frequency of founder effects and population size. These were in turn related...... of heterozygosity was corrected for the harmonic mean of the population size, the rate of loss was almost identical in the four scenarios. Unlike classical genetic models, IBMs are flexible enough to mimic real population processes under a range of environmental and behavioural conditions. We conclude that IBMs...

  11. Two-level mixed modeling of longitudinal pedigree data for genetic association analysis

    DEFF Research Database (Denmark)

    Tan, Q.

    2013-01-01

    assess the genetic associations with the mean level and the rate of change in a phenotype both with kinship correlation integrated in the mixed effect models. We apply our method to longitudinal pedigree data to estimate the genetic effects on systolic blood pressure measured over time in large pedigrees...... of follow-up. Approaches have been proposed to integrate kinship correlation into the mixed effect models to explicitly model the genetic relationship which have been proven as an efficient way for dealing with sample clustering in pedigree data. Although useful for adjusting relatedness in the mixed....... Our results show that the method efficiently handles relatedness in detecting genetic variations that affect the mean level or the rate of change for a phenotype of interest....

  12. A New Modeling Method Based on Genetic Neural Network for Numeral Eddy Current Sensor

    Institute of Scientific and Technical Information of China (English)

    Along Yu; Zheng Li

    2006-01-01

    In this paper, we present a method used to the numeral eddy current sensor modeling based on genetic neural network to settle its nonlinear problem. The principle and algorithms of genetic neural network are introduced. In this method,the nonlinear model parameters of the numeral eddy current sensor are optimized by genetic neural network (GNN) according to measurement data. So the method remains both the global searching ability of genetic algorithm and the good local searching ability of neural network. The nonlinear model has the advantages of strong robustness, on-line scaling and high precision. The maximum nonlinearity error can be reduced to 0.037% using GNN. However, the maximum nonlinearity error is 0.075% using least square method (LMS).

  13. Model-based problem solving through symbolic regression via pareto genetic programming

    NARCIS (Netherlands)

    Vladislavleva, E.

    2008-01-01

    Pareto genetic programming methodology is extended by additional generic model selection and generation strategies that (1) drive the modeling engine to creation of models of reduced non-linearity and increased generalization capabilities, and (2) improve the effectiveness of the search for robust m

  14. Genetic algorithms and genetic programming for multiscale modeling: Applications in materials science and chemistry and advances in scalability

    Science.gov (United States)

    Sastry, Kumara Narasimha

    2007-03-01

    Effective and efficient rnultiscale modeling is essential to advance both the science and synthesis in a, wide array of fields such as physics, chemistry, materials science; biology, biotechnology and pharmacology. This study investigates the efficacy and potential of rising genetic algorithms for rnultiscale materials modeling and addresses some of the challenges involved in designing competent algorithms that solve hard problems quickly, reliably and accurately. In particular, this thesis demonstrates the use of genetic algorithms (GAs) and genetic programming (GP) in multiscale modeling with the help of two non-trivial case studies in materials science and chemistry. The first case study explores the utility of genetic programming (GP) in multi-timescaling alloy kinetics simulations. In essence, GP is used to bridge molecular dynamics and kinetic Monte Carlo methods to span orders-of-magnitude in simulation time. Specifically, GP is used to regress symbolically an inline barrier function from a limited set of molecular dynamics simulations to enable kinetic Monte Carlo that simulate seconds of real time. Results on a non-trivial example of vacancy-assisted migration on a surface of a face-centered cubic (fcc) Copper-Cobalt (CuxCo 1-x) alloy show that GP predicts all barriers with 0.1% error from calculations for less than 3% of active configurations, independent of type of potentials used to obtain the learning set of barriers via molecular dynamics. The resulting method enables 2--9 orders-of-magnitude increase in real-time dynamics simulations taking 4--7 orders-of-magnitude less CPU time. The second case study presents the application of multiobjective genetic algorithms (MOGAs) in multiscaling quantum chemistry simulations. Specifically, MOGAs are used to bridge high-level quantum chemistry and semiempirical methods to provide accurate representation of complex molecular excited-state and ground-state behavior. Results on ethylene and benzene---two common

  15. Genetic Parameters for Milk Yield and Lactation Persistency Using Random Regression Models in Girolando Cattle.

    Science.gov (United States)

    Canaza-Cayo, Ali William; Lopes, Paulo Sávio; da Silva, Marcos Vinicius Gualberto Barbosa; de Almeida Torres, Robledo; Martins, Marta Fonseca; Arbex, Wagner Antonio; Cobuci, Jaime Araujo

    2015-10-01

    A total of 32,817 test-day milk yield (TDMY) records of the first lactation of 4,056 Girolando cows daughters of 276 sires, collected from 118 herds between 2000 and 2011 were utilized to estimate the genetic parameters for TDMY via random regression models (RRM) using Legendre's polynomial functions whose orders varied from 3 to 5. In addition, nine measures of persistency in milk yield (PSi) and the genetic trend of 305-day milk yield (305MY) were evaluated. The fit quality criteria used indicated RRM employing the Legendre's polynomial of orders 3 and 5 for fitting the genetic additive and permanent environment effects, respectively, as the best model. The heritability and genetic correlation for TDMY throughout the lactation, obtained with the best model, varied from 0.18 to 0.23 and from -0.03 to 1.00, respectively. The heritability and genetic correlation for persistency and 305MY varied from 0.10 to 0.33 and from -0.98 to 1.00, respectively. The use of PS7 would be the most suitable option for the evaluation of Girolando cattle. The estimated breeding values for 305MY of sires and cows showed significant and positive genetic trends. Thus, the use of selection indices would be indicated in the genetic evaluation of Girolando cattle for both traits.

  16. Ocean circulation model predicts high genetic structure observed in a long-lived pelagic developer.

    Science.gov (United States)

    Sunday, J M; Popovic, I; Palen, W J; Foreman, M G G; Hart, M W

    2014-10-01

    Understanding the movement of genes and individuals across marine seascapes is a long-standing challenge in marine ecology and can inform our understanding of local adaptation, the persistence and movement of populations, and the spatial scale of effective management. Patterns of gene flow in the ocean are often inferred based on population genetic analyses coupled with knowledge of species' dispersive life histories. However, genetic structure is the result of time-integrated processes and may not capture present-day connectivity between populations. Here, we use a high-resolution oceanographic circulation model to predict larval dispersal along the complex coastline of western Canada that includes the transition between two well-studied zoogeographic provinces. We simulate dispersal in a benthic sea star with a 6-10 week pelagic larval phase and test predictions of this model against previously observed genetic structure including a strong phylogeographic break within the zoogeographical transition zone. We also test predictions with new genetic sampling in a site within the phylogeographic break. We find that the coupled genetic and circulation model predicts the high degree of genetic structure observed in this species, despite its long pelagic duration. High genetic structure on this complex coastline can thus be explained through ocean circulation patterns, which tend to retain passive larvae within 20-50 km of their parents, suggesting a necessity for close-knit design of Marine Protected Area networks. © 2014 John Wiley & Sons Ltd.

  17. Identifying future models for delivering genetic services: a nominal group study in primary care

    Directory of Open Access Journals (Sweden)

    Davies Peter

    2005-04-01

    Full Text Available Background To enable primary care medical practitioners to generate a range of possible service delivery models for genetic counselling services and critically assess their suitability. Methods Modified nominal group technique using in primary care professional development workshops. Results 37 general practitioners in Wales, United Kingdom too part in the nominal group process. The practitioners who attended did not believe current systems were sufficient to meet anticipated demand for genetic services. A wide range of different service models was proposed, although no single option emerged as a clear preference. No argument was put forward for genetic assessment and counselling being central to family practice, neither was there a voice for the view that the family doctor should become skilled at advising patients about predictive genetic testing and be able to counsel patients about the wider implications of genetic testing for patients and their family members, even for areas such as common cancers. Nevertheless, all the preferred models put a high priority on providing the service in the community, and often co-located in primary care, by clinicians who had developed expertise. Conclusion There is a need for a wider debate about how healthcare systems address individual concerns about genetic concerns and risk, especially given the increasing commercial marketing of genetic tests.

  18. Joint modeling of genetically correlated diseases and functional annotations increases accuracy of polygenic risk prediction.

    Directory of Open Access Journals (Sweden)

    Yiming Hu

    2017-06-01

    Full Text Available Accurate prediction of disease risk based on genetic factors is an important goal in human genetics research and precision medicine. Advanced prediction models will lead to more effective disease prevention and treatment strategies. Despite the identification of thousands of disease-associated genetic variants through genome-wide association studies (GWAS in the past decade, accuracy of genetic risk prediction remains moderate for most diseases, which is largely due to the challenges in both identifying all the functionally relevant variants and accurately estimating their effect sizes. In this work, we introduce PleioPred, a principled framework that leverages pleiotropy and functional annotations in genetic risk prediction for complex diseases. PleioPred uses GWAS summary statistics as its input, and jointly models multiple genetically correlated diseases and a variety of external information including linkage disequilibrium and diverse functional annotations to increase the accuracy of risk prediction. Through comprehensive simulations and real data analyses on Crohn's disease, celiac disease and type-II diabetes, we demonstrate that our approach can substantially increase the accuracy of polygenic risk prediction and risk population stratification, i.e. PleioPred can significantly better separate type-II diabetes patients with early and late onset ages, illustrating its potential clinical application. Furthermore, we show that the increment in prediction accuracy is significantly correlated with the genetic correlation between the predicted and jointly modeled diseases.

  19. Theoretical study of statistical fractal model with applications to mineral resource prediction

    Science.gov (United States)

    Wei, Shen; Pengda, Zhao

    2002-04-01

    The statistical estimation of fractal dimensions is an important topic of investigation. Current solutions emphsize visual straight-line fitting, but nonlinear statistical modeling has the potential of making valuable contributions in this field. In this paper, we present the concepts of generalized fractal models and generalized fractal dimension and conclude that many geological models are special cases of the generalized models. We show that the power-function distribution possesses the fractal property of scaling invariance under upper truncation, which may help in lead statistical fractal modeling. A new method is developed on the basis of nonlinear regression to estimate fractal parameters. This method has advantages with respect to the traditional method based on linear regression for estimating the fractal dimension. Finally, the new method is illustrated by means of application to a real data set.

  20. Adaptive fixation in two-locus models of stabilizing selection and genetic drift.

    Science.gov (United States)

    Wollstein, Andreas; Stephan, Wolfgang

    2014-10-01

    The relationship between quantitative genetics and population genetics has been studied for nearly a century, almost since the existence of these two disciplines. Here we ask to what extent quantitative genetic models in which selection is assumed to operate on a polygenic trait predict adaptive fixations that may lead to footprints in the genome (selective sweeps). We study two-locus models of stabilizing selection (with and without genetic drift) by simulations and analytically. For symmetric viability selection we find that ∼16% of the trajectories may lead to fixation if the initial allele frequencies are sampled from the neutral site-frequency spectrum and the effect sizes are uniformly distributed. However, if the population is preadapted when it undergoes an environmental change (i.e., sits in one of the equilibria of the model), the fixation probability decreases dramatically. In other two-locus models with general viabilities or an optimum shift, the proportion of adaptive fixations may increase to >24%. Similarly, genetic drift leads to a higher probability of fixation. The predictions of alternative quantitative genetics models, initial conditions, and effect-size distributions are also discussed.

  1. A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait

    Directory of Open Access Journals (Sweden)

    Damgaard Lars

    2005-12-01

    Full Text Available Abstract With the increasing use of survival models in animal breeding to address the genetic aspects of mainly longevity of livestock but also disease traits, the need for methods to infer genetic correlations and to do multivariate evaluations of survival traits and other types of traits has become increasingly important. In this study we derived and implemented a bivariate quantitative genetic model for a linear Gaussian and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted. Model parameters were inferred from their marginal posterior distributions. The required fully conditional posterior distributions were derived and issues on implementation are discussed. The twoWeibull baseline parameters were updated jointly using a Metropolis-Hastingstep. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. Simulation results showed that the estimated marginal posterior distributions covered well and placed high density to the true parameter values used in the simulation of data. In conclusion, the proposed method allows inferring additive genetic and environmental correlations, and doing multivariate genetic evaluation of a linear Gaussian trait and a survival trait.

  2. A bivariate quantitative genetic model for a linear Gaussian trait and a survival trait.

    Science.gov (United States)

    Damgaard, Lars Holm; Korsgaard, Inge Riis

    2006-01-01

    With the increasing use of survival models in animal breeding to address the genetic aspects of mainly longevity of livestock but also disease traits, the need for methods to infer genetic correlations and to do multivariate evaluations of survival traits and other types of traits has become increasingly important. In this study we derived and implemented a bivariate quantitative genetic model for a linear Gaussian and a survival trait that are genetically and environmentally correlated. For the survival trait, we considered the Weibull log-normal animal frailty model. A Bayesian approach using Gibbs sampling was adopted. Model parameters were inferred from their marginal posterior distributions. The required fully conditional posterior distributions were derived and issues on implementation are discussed. The two Weibull baseline parameters were updated jointly using a Metropolis-Hasting step. The remaining model parameters with non-normalized fully conditional distributions were updated univariately using adaptive rejection sampling. Simulation results showed that the estimated marginal posterior distributions covered well and placed high density to the true parameter values used in the simulation of data. In conclusion, the proposed method allows inferring additive genetic and environmental correlations, and doing multivariate genetic evaluation of a linear Gaussian trait and a survival trait.

  3. Matching Index-of-Refraction for 3D Printing Model Using Mixture of Herb Essential Oil and Light Mineral Oil

    Energy Technology Data Exchange (ETDEWEB)

    Song, Min Seop; Choi, Hae Yoon; Kim, Eung Soo [Seoul National Univ., Seoul (Korea, Republic of)

    2013-10-15

    This study has extensively investigated the emerging 3-D printing technologies for use of MIR-based flow field visualization methods such as PIV and LDV. As a result, mixture of Herb essential oil and light mineral oil has been evaluated to be great working fluid due to its adequate properties. Using this combination, the RIs between 1.45 and 1.55 can be accurately matched, and most of the transparent materials are found to be ranged in here. Conclusively, the proposed MIR method are expected to provide large flexibility of model materials and geometries for laser based optical measurements. Particle Image Velocimetry (PIV) and Laser Doppler Velocimetry (LDV) are the two major optical technologies used for flow field visualization in the latest fundamental thermal-hydraulics researches. Those techniques seriously require minimizing optical distortions for enabling high quality data. Therefore, matching index of refraction (MIR) between model materials and working fluids are an essential part of minimizing measurement uncertainty. This paper proposes to use 3-D Printing technology for manufacturing models for the MIR-based optical measurements. Because of the large flexibility in geometries and materials of the 3-D Printing, its application is obviously expected to provide tremendous advantages over the traditional MIR-based optical measurements. This study focuses on the 3-D printing models and investigates their optical properties, transparent printing techniques, and index-matching fluids.

  4. Effect of Bone Mineral Density on Rotator Cuff Tear: An Osteoporotic Rabbit Model.

    Directory of Open Access Journals (Sweden)

    Xiaobin Chen

    Full Text Available An increased bone mineral density (BMD in the proximity to tendon insertion can improve rotator cuff repair and healing. However, how a decrease of BMD in the humeral head affects the biomechanical properties of the rotator cuff tendon is still unclear. Previous studies have demonstrated ovariectomy in animals to lead to osteoporosis and decreased BMD, and Teriparatide (PTH administration to improve BMD and strength of bone. This study aimed to explore the correlation between humeral head BMD and infraspinatus (ISP tendon insertion strength, and if an increase in bone quantity of the humeral head can improve the strength of the rotator cuff.Eighteen New England white rabbits were divided into the 3 groups: Control, Ovariectomy-Saline (OVX-Saline, and Ovariectomy-PTH (OVX-PTH. The OVX-Saline group and the OVX-PTH were administered daily saline and Teriparatide injections for 8 weeks starting at 17 weeks of OVX. BMD of the humeral head was measured, the ISP tendon failure load was tested and the failure stress was calculated. One specimen from each group was used for histological analysis. Linear regression analysis was used to derive equations for the BMD and failure stress.Significant differences were observed in the measured humeral head BMD of the Control and OVX-PTH groups compared to the OVX-Saline group (P = 0.0004 and P = 0.0024, respectively. No significant difference was found in failure stress among the three groups, but an expected trend with the control group and OVX-PTH group presenting higher failure strength compared to the OVX-Saline group. BMD at the humeral head showed a positive linear correlation with stress (r2 = 0.54. Histology results showed the superiority in OVX-PTH group ISP enthesis compared to the OVX-Saline group.Bone loss of the humeral head leads to decreased tendon/bone insertion strength of the infraspinatus tendon enthesis. Teriparatide administration can increase bone density of the humeral head and may improve

  5. Effect of Bone Mineral Density on Rotator Cuff Tear: An Osteoporotic Rabbit Model.

    Science.gov (United States)

    Chen, Xiaobin; Giambini, Hugo; Ben-Abraham, Ephraim; An, Kai-Nan; Nassr, Ahmad; Zhao, Chunfeng

    2015-01-01

    An increased bone mineral density (BMD) in the proximity to tendon insertion can improve rotator cuff repair and healing. However, how a decrease of BMD in the humeral head affects the biomechanical properties of the rotator cuff tendon is still unclear. Previous studies have demonstrated ovariectomy in animals to lead to osteoporosis and decreased BMD, and Teriparatide (PTH) administration to improve BMD and strength of bone. This study aimed to explore the correlation between humeral head BMD and infraspinatus (ISP) tendon insertion strength, and if an increase in bone quantity of the humeral head can improve the strength of the rotator cuff. Eighteen New England white rabbits were divided into the 3 groups: Control, Ovariectomy-Saline (OVX-Saline), and Ovariectomy-PTH (OVX-PTH). The OVX-Saline group and the OVX-PTH were administered daily saline and Teriparatide injections for 8 weeks starting at 17 weeks of OVX. BMD of the humeral head was measured, the ISP tendon failure load was tested and the failure stress was calculated. One specimen from each group was used for histological analysis. Linear regression analysis was used to derive equations for the BMD and failure stress. Significant differences were observed in the measured humeral head BMD of the Control and OVX-PTH groups compared to the OVX-Saline group (P = 0.0004 and P = 0.0024, respectively). No significant difference was found in failure stress among the three groups, but an expected trend with the control group and OVX-PTH group presenting higher failure strength compared to the OVX-Saline group. BMD at the humeral head showed a positive linear correlation with stress (r2 = 0.54). Histology results showed the superiority in OVX-PTH group ISP enthesis compared to the OVX-Saline group. Bone loss of the humeral head leads to decreased tendon/bone insertion strength of the infraspinatus tendon enthesis. Teriparatide administration can increase bone density of the humeral head and may improve the

  6. Revising explanatory models to accommodate anomalous genetic phenomena: Problem solving in the context of discovery

    Science.gov (United States)

    Hafner, Robert; Stewart, Jim

    Past problem-solving research has provided a basis for helping students structure their knowledge and apply appropriate problem-solving strategies to solve problems for which their knowledge (or mental models) of scientific phenomena is adequate (model-using problem solving). This research examines how problem solving in the domain of Mendelian genetics proceeds in situations where solvers' mental models are insufficient to solve problems at hand (model-revising problem solving). Such situations require solvers to use existing models to recognize anomalous data and to revise those models to accommodate the data. The study was conducted in the context of 9-week high school genetics course and addressed: the heuristics charactenstic of successful model-revising problem solving: the nature of the model revisions, made by students as well as the nature of model development across problem types; and the basis upon which solvers decide that a revised model is sufficient (that t has both predictive and explanatory power).

  7. Two-level mixed modeling of longitudinal pedigree data for genetic association analysis

    DEFF Research Database (Denmark)

    Tan, Q.

    2013-01-01

    Genetic association analysis on complex phenotypes under a longitudinal design involving pedigrees encounters the problem of correlation within pedigrees which could affect statistical assessment of the genetic effects on both the mean level of the phenotype and its rate of change over the time...... assess the genetic associations with the mean level and the rate of change in a phenotype both with kinship correlation integrated in the mixed effect models. We apply our method to longitudinal pedigree data to estimate the genetic effects on systolic blood pressure measured over time in large pedigrees....... Our results show that the method efficiently handles relatedness in detecting genetic variations that affect the mean level or the rate of change for a phenotype of interest....

  8. Query Optimization Using Genetic Algorithms in the Vector Space Model

    CERN Document Server

    Mashagba, Eman Al; Nassar, Mohammad Othman

    2011-01-01

    In information retrieval research; Genetic Algorithms (GA) can be used to find global solutions in many difficult problems. This study used different similarity measures (Dice, Inner Product) in the VSM, for each similarity measure we compared ten different GA approaches based on different fitness functions, different mutations and different crossover strategies to find the best strategy and fitness function that can be used when the data collection is the Arabic language. Our results shows that the GA approach which uses one-point crossover operator, point mutation and Inner Product similarity as a fitness function is the best IR system in VSM.

  9. Forward and backward models for fault diagnosis based on parallel genetic algorithms

    Institute of Scientific and Technical Information of China (English)

    Yi LIU; Ying LI; Yi-jia CAO; Chuang-xin GUO

    2008-01-01

    In this paper, a mathematical model consisting of forward and backward models is built on parallel genetic algorithms (PGAs) for fault diagnosis in a transmission power system. A new method to reduce the scale of fault sections is developed in the forward model and the message passing interface (MPI) approach is chosen to parallel the genetic algorithms by global sin-gle-population master-slave method (GPGAs). The proposed approach is applied to a sample system consisting of 28 sections, 84 protective relays and 40 circuit breakers. Simulation results show that the new model based on GPGAs can achieve very fast computation in online applications of large-scale power systems.

  10. DEVELOPMENT OF MULTI-PHASE AND MULTI-COMPONENT FLOW MODEL WITH REACTION IN POROUS MEDIA FOR RISK ASSESSMENT ON SOIL CONTAMINATION DUE TO MINERAL OIL

    Science.gov (United States)

    Sakamoto, Yasuhide; Nishiwaki, Junko; Hara, Junko; Kawabe, Yoshishige; Sugai, Yuichi; Komai, Takeshi

    In late years, soil contamination due to mineral oil in vacant lots of oil factory and oil field has become obvious. Measure for soil contamina tion and risk assessment are neces sary for sustainable development of industrial activity. Especially, in addition to contaminated sites, various exposure paths for human body such as well water, soil and farm crop are supposed. So it is very important to comprehend the transport phenomena of contaminated material under the environments of soil and ground water. In this study, mineral oil as c ontaminated material consisting of mu lti-component such as aliphatic and aromatic series was modeled. Then numerical mode l for transport phenomena in surface soil and aquifer was constructed. On the basis of modeling for mineral oil, our numerical model consists of three-phase (oil, water and gas) forty three-component. This numerical model becomes base program for risk assessment system on soil contamination due to mineral oil. Using this numerical model, we carried out some numerical simulation for a laboratory-scale experiment on oil-water multi-phase flow. Relative permeability that dominate flow behavior in multi-phase condition was formulated and the validity of the numerical model developed in this study was considered.

  11. Spatial analysis and modelling of glaciogenic geochemical dispersion - Implication for mineral exploration in Finland

    Science.gov (United States)

    Sarala, Pertti; Nykänen, Vesa

    2017-04-01

    Spatial modelling for prospectivity mapping involves the integration of various geoscientific digital map data. It is essential that the quality of data is high class and that the geological processes involved are well understood. Effects of glacial dynamics and glaciogenic geochemical dispersion need to be taken into consideration when using till geochemistry as one of such input dataset for prospectivity modelling. This paper investigates this issue by developing a fuzzy logic prospectivity model that integrates airborne geophysical data with two different till geochemical datasets. First we use the original geochemical sample set and secondly a spatially corrected dataset that is based on the knowledge of glacial dynamics on the regional scale within the study area. The effect of this correction is tested by comparing the modelling results of both cases using the receiver operating characteristics (ROC) technique to validate the models by using the location of known gold deposits represented by exploration drilling. This study confirms that by taking into consideration the transport caused by the glaciation we can significantly improve the performance of a prospectivity model using till geochemical data.

  12. Fumarolic minerals

    DEFF Research Database (Denmark)

    Balic Zunic, Tonci; Garavelli, Anna; Jakobsson, Sveinn Peter

    2016-01-01

    The fumarolic mineralogy of the Icelandic active volcanoes, the Tyrrhenian volcanic belt (Italy) and the Aegean active arc (Greece) is investigated, and literature data surveyed in order to define the characteristics of the European fumarolic systems. They show broad diversity of mineral...... associations, with Vesuvius and Vulcano being also among the world localities richest in mineral species. Volcanic systems, which show recession over a longer period, show fumarolic development from the hightemperature alkaline halide/sulphate, calcic sulphate or sulphidic parageneses, synchronous...... fluctuations in activity, illustrated by the example of Vulcano where the high-temperature association appears intermittently. A full survey of the mineral groups and species is given in respect to their importance and appearance in fumarolic associations....

  13. Application of a single-objective, hybrid genetic algorithm approach to pharmacokinetic model building.

    Science.gov (United States)

    Sherer, Eric A; Sale, Mark E; Pollock, Bruce G; Belani, Chandra P; Egorin, Merrill J; Ivy, Percy S; Lieberman, Jeffrey A; Manuck, Stephen B; Marder, Stephen R; Muldoon, Matthew F; Scher, Howard I; Solit, David B; Bies, Robert R

    2012-08-01

    A limitation in traditional stepwise population pharmacokinetic model building is the difficulty in handling interactions between model components. To address this issue, a method was previously introduced which couples NONMEM parameter estimation and model fitness evaluation to a single-objective, hybrid genetic algorithm for global optimization of the model structure. In this study, the generalizability of this approach for pharmacokinetic model building is evaluated by comparing (1) correct and spurious covariate relationships in a simulated dataset resulting from automated stepwise covariate modeling, Lasso methods, and single-objective hybrid genetic algorithm approaches to covariate identification and (2) information criteria values, model structures, convergence, and model parameter values resulting from manual stepwise versus single-objective, hybrid genetic algorithm approaches to model building for seven compounds. Both manual stepwise and single-objective, hybrid genetic algorithm approaches to model building were applied, blinded to the results of the other approach, for selection of the compartment structure as well as inclusion and model form of inter-individual and inter-occasion variability, residual error, and covariates from a common set of model options. For the simulated dataset, stepwise covariate modeling identified three of four true covariates and two spurious covariates; Lasso identified two of four true and 0 spurious covariates; and the single-objective, hybrid genetic algorithm identified three of four true covariates and one spurious covariate. For the clinical datasets, the Akaike information criterion was a median of 22.3 points lower (range of 470.5 point decrease to 0.1 point decrease) for the best single-objective hybrid genetic-algorithm candidate model versus the final manual stepwise model: the Akaike information criterion was lower by greater than 10 points for four compounds and differed by less than 10 points for three

  14. Improving Control of Microbially-Induced Mineral Precipitation in Flow Systems - Experiments and Modelling

    Science.gov (United States)

    Gerlach, R.; Phillips, A. J.; Lauchnor, E.; Ebigbo, A.; Connolly, J.; Mitchell, A. C.; Helmig, R.; Cunningham, A. B.; Spangler, L.

    2012-12-01

    Batch and flow experiments at atmospheric and geologic CO2 storage-relevant pressures in our laboratories have demonstrated the ability of microbial biofilms and biofilm produced calcium carbonate precipitates to decrease the permeability of natural and artificial porous media as well as improve the stability of unconsolidated porous media. Two overarching challenges in effectively implementing microbially induced calcium carbonate precipitation (MICP) are controlling (1) the spatial and temporal distribution of the formed precipitates and (2) the inactivation of microbes during the calcium carbonate precipitation process. Failure to control either one of those could result in injection well plugging or the necessity to implement costly cell-reinjection or -resuscitation strategies. Our recent work has focused on optimizing strategies for MICP in small (capillaries and micromodels), small columns (1 to 2.5 cm diameter, up to 5 cm in length), meso- (2 ft columns and 4 cm x 8 cm 2-d reactors) and large-scale (75 cm diameter, 38 cm high sandstone radial flow) systems. Results of these experiments have been modelled using two different approaches. (1) a microscale phase-field approach and (2) a large scale volume averaging approach. Close interaction between experimenters and modellers have resulted in improved injection strategies and the models are currently being used as experimental design tools. This presentation will focus on our recent efforts that combined 2 ft column experimentation with Darcy-scale modelling to calibrate and validate a model before utilizing the model for the optimization of biomineralization strategies in radial flow demonstrations in meso-scale sand stone cores at ambient and high pressures. Schematic pore-scale representation of MICP model

  15. Modeling genetic imprinting effects of DNA sequences with multilocus polymorphism data

    Directory of Open Access Journals (Sweden)

    Staud Roland

    2009-08-01

    Full Text Available Abstract Single nucleotide polymorphisms (SNPs represent the most widespread type of DNA sequence variation in the human genome and they have recently emerged as valuable genetic markers for revealing the genetic architecture of complex traits in terms of nucleotide combination and sequence. Here, we extend an algorithmic model for the haplotype analysis of SNPs to estimate the effects of genetic imprinting expressed at the DNA sequence level. The model provides a general procedure for identifying the number and types of optimal DNA sequence variants that are expressed differently due to their parental origin. The model is used to analyze a genetic data set collected from a pain genetics project. We find that DNA haplotype GAC from three SNPs, OPRKG36T (with two alleles G and T, OPRKA843G (with alleles A and G, and OPRKC846T (with alleles C and T, at the kappa-opioid receptor, triggers a significant effect on pain sensitivity, but with expression significantly depending on the parent from which it is inherited (p = 0.008. With a tremendous advance in SNP identification and automated screening, the model founded on haplotype discovery and statistical inference may provide a useful tool for genetic analysis of any quantitative trait with complex inheritance.

  16. Learning genetic inquiry through the use, revision, and justification of explanatory models

    Science.gov (United States)

    Cartier, Jennifer Lorraine

    Central to the process of inquiry in science is the construction and assessment of models that can be used to explain (and in some cases, predict) natural phenomena. This dissertation is a qualitative study of student learning in a high school biology course that was designed to give students opportunities to learn about genetic inquiry in part by providing them with authentic experiences doing inquiry in the discipline. With the aid of a computer program that generates populations of "fruit flies", the students in this class worked in groups structured like scientific communities to build, revise, and defend explanatory models for various inheritance phenomena. Analysis of the ways in which the first cohort of students assessed their inheritance models revealed that all students assessed models based upon empirical fit (data/model match). However, in contrast to the practice of scientists and despite explicit instruction, students did not consistently apply conceptual assessment criteria to their models. That is, they didn't seek consistency between underlying concepts or processes in their models and those of other important genetic models, such as meiosis. This is perhaps in part because they lacked an understanding of models as conceptual rather than physical entities. Subsequently, the genetics curriculum was altered in order to create more opportunities for students to address epistemological issues associated with model assessment throughout the course. The second cohort of students' understanding of models changed over the nine-week period: initially the majority of students equated scientific models with "proof" (generally physical) of "theories"; at the end of the course, most students demonstrated understanding of the conceptual nature of scientific models and the need to justify such knowledge according to both its empirical utility and conceptual consistency. Through model construction and assessment (i.e. scientific inquiry), students were able to

  17. Modeling phosphate transport and removal in a compact bed filled with a mineral-based sorbent for domestic wastewater treatment

    Science.gov (United States)

    Herrmann, Inga; Jourak, Amir; Gustafsson, Jon Petter; Hedström, Annelie; Lundström, T. Staffan; Viklander, Maria

    2013-11-01

    Phosphorus filter units containing mineral-based sorbents with a high phosphate (PO4) binding capacity have been shown to be appropriate for removing PO4 in the treatment of domestic wastewater in on-site facilities. However, a better understanding of their PO4 removal mechanisms, and reactions that could lead to the formation of PO4 compounds, is required to evaluate the potential utility of candidate sorbents. Models based on data obtained from laboratory-scale experiments with columns of selected materials can be valuable for acquiring such understanding. Thus, in this study the transport and removal of PO4 in experiments with a laboratory-scale column filled with a commercial silicate-based sorbent were modeled, using the hydro-geochemical transport code PHREEQC. The resulting models, that incorporated the dissolution of calcite, kinetic constrains for the dissolution of calcium oxide (CaO) and wollastonite (CaSiO3), and the precipitation of amorphous tricalcium phosphate, Ca3(PO4)2, successfully simulated the removal of PO4 observed in the experiments.

  18. FraudMiner: A Novel Credit Card Fraud Detection Model Based on Frequent Itemset Mining

    Directory of Open Access Journals (Sweden)

    K. R. Seeja

    2014-01-01

    Full Text Available This paper proposes an intelligent credit card fraud detection model for detecting fraud from highly imbalanced and anonymous credit card transaction datasets. The class imbalance problem is handled by finding legal as well as fraud transaction patterns for each customer by using frequent itemset mining. A matching algorithm is also proposed to find to which pattern (legal or fraud the incoming transaction of a particular customer is closer and a decision is made accordingly. In order to handle the anonymous nature of the data, no preference is given to any of the attributes and each attribute is considered equally for finding the patterns. The performance evaluation of the proposed model is done on UCSD Data Mining Contest 2009 Dataset (anonymous and imbalanced and it is found that the proposed model has very high fraud detection rate, balanced classification rate, Matthews correlation coefficient, and very less false alarm rate than other state-of-the-art classifiers.

  19. FraudMiner: A Novel Credit Card Fraud Detection Model Based on Frequent Itemset Mining

    Science.gov (United States)

    Seeja, K. R.; Zareapoor, Masoumeh

    2014-01-01

    This paper proposes an intelligent credit card fraud detection model for detecting fraud from highly imbalanced and anonymous credit card transaction datasets. The class imbalance problem is handled by finding legal as well as fraud transaction patterns for each customer by using frequent itemset mining. A matching algorithm is also proposed to find to which pattern (legal or fraud) the incoming transaction of a particular customer is closer and a decision is made accordingly. In order to handle the anonymous nature of the data, no preference is given to any of the attributes and each attribute is considered equally for finding the patterns. The performance evaluation of the proposed model is done on UCSD Data Mining Contest 2009 Dataset (anonymous and imbalanced) and it is found that the proposed model has very high fraud detection rate, balanced classification rate, Matthews correlation coefficient, and very less false alarm rate than other state-of-the-art classifiers. PMID:25302317

  20. Modeling the sorption kinetics of divalent metal ions onto mineral adsorbent using integral method.

    Science.gov (United States)

    Singhal, Nidhi; Prasad, Murari; Gupta, Neelmani; Kumar, Vineet

    2007-09-15

    A mathematical model has been developed that could predict kinetic parameters for the adsorption of divalent cations (lead, copper and zinc) onto low-grade rock phosphate using experimental data. The experiments were conducted with the initial concentrations of metal ions ranging from 10 to 100 mg/L. The mathematical model is based on application of Freundlich isotherm to mass transfer across the film surrounding the adsorbent. A code in C programming is used to numerically integrate the model equation, and to obtain the best simulated values of Freundlich constants K, N, order of reaction n, and film transfer coefficient, alpha. It is observed that the adsorption of metal ions on rock phosphate is more sensitive to N,n, and alpha in comparison to K, and lead is adsorbed more favorably than copper and zinc.