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Sample records for genetic models mineralization

  1. Genetic aspects of uranium mineralization in the Himalaya

    International Nuclear Information System (INIS)

    Saraswat, A.C.; Mahadevan, T.M.

    1989-01-01

    The Himalayan Uranium Province hosts five major types of uranium mineralization: (1) stratiform remobilized (Proterozoic), (2) structurally controlled hydrothermal (Proterozoic), (3) black shale-phosphorite (Palaeozoic-Mesozoic), (4) sandstone (Siwalik belt, Tertiary), and (5) primary disseminations in granitoids (Tertiary). Evaluation of the genetic aspects of these types has led to the identification of distinct spatial (lithostratigraphic and tectonic units) and temporal relations among them. The sandstone types are confined to the Tertiary (Middle Miocene to Pleistocene) molasse formations found south of th Main Boundary Thrust (MBT). Between the MBT and the Main Central Thrust, in the Lesser Himalaya, mineralization hosted in the Chail quartzite-phyllite ± metabasic sequences is of stratiform remobilized type. The structurally controlled hydrothermal type is confined to Dalings and gneisses. Syngenetic uranium in black shale-phosphorite sequences of Palaeozoic-Mesozoic age is found on the southern fringes of the Lesser Himalaya, bordering the MBT. Disseminated uranium occurs in the Tertiary and Proterozoic(?) granitoids of the Greater Himalaya and Ladakh. Rb-Sr geochronological data on host rocks and U-Pb dates on uraninites from some areas indicate that uranium mineralization in stratiform remobilized and structurally controlled types hosted by the Chails, Dalings and gneisses is essentially Precambrian and thus existed much before the Himalayan Orogeny. The Himalayan Orogeny, however, appears to have aided in further remobilization. The sandstone type mineralization in the Siwalik, on the other hand, is directly related to the process of formation of the foredeep and molasse sedimentation and subsequent uplift and epigenesis of the uranium mineralization, all of which are directly relatable to the evolution of the Himalaya. The relevance of deep seated lineament structures to mineralization, particularly of uranium, needs to be evaluated critically, as most

  2. 40Ar-39Ar dating of Archean iron oxide Cu-Au and Paleoproterozoic granite-related Cu-Au deposits in the Carajás Mineral Province, Brazil: implications for genetic models

    Science.gov (United States)

    Pollard, Peter J.; Taylor, Roger G.; Peters, Lisa; Matos, Fernando; Freitas, Cantidiano; Saboia, Lineu; Huhn, Sergio

    2018-05-01

    40Ar-39Ar dating of biotite from IOCG and granite-related Cu-Au deposits in the Carajás Mineral Province provides evidence for the timing of mineralization and constraints on genetic models of ore formation. Ages of biotite from greisen and quartz-rich vein and breccia deposits, Alvo 118—1885 ± 4 Ma, Breves—1886 ± 5 Ma, Estrela—1896 ± 7 Ma, and Gameleira—1908 ± 7 Ma, demonstrate the close temporal relationship between Cu-Au mineralization and subjacent A-type granites. Mineralization is hosted within granite cupolas (Breves) or in vein/breccia systems emanating from the cupolas (Estrela and Gameleira), consistent with a genetic relationship of mineralization to the B-Li-F-rich granites. Plateau and minimum ages of biotite from IOCG deposits, including Igarapé Bahia, Cristalino, Corta Goela, and GT34, range from 2537 ± 6 Ma to 2193 ± 4 Ma. The 40Ar-39Ar age of biotite from Igarapé Bahia (2537 ± 6 Ma) is similar to a previous SHRIMP 207Pb-206Pb age for monazite of 2575 ± 12 Ma when the uncertainties in the respective analyses and standards are taken into account. The age spectrum for biotite from Cristalino shows increasing ages for successive steps, consistent with post-crystallization Ar loss, and the age of 2388 ± 5 Ma for the last three steps is considered a minimum age for Cu-Au mineralization. The age of biotite from the GT34 prospect (2512 ± 7 Ma) coincides with a previously identified period of basement reactivation and may indicate the formation of Cu-Au mineralization at this time or resetting of biotite from an older mineralization event at this time. At Corta Goela, within the Canaã Shear Zone, the biotite age of 2193 ± 4 Ma lies between the ages of IOCG (2.57-2.76 Ga) and granite-related Cu-Au ( 1.88 Ga) deposits elsewhere in the Carajás district but is similar to previously reported 40Ar-39Ar ages for amphibole from Sossego, possibly indicating that mineralization at both Sossego and Corta Goela was affected by a thermal event at

  3. A genetic model based on evapoconcentration for sediment-hosted exotic-Cu mineralization in arid environments: the case of the El Tesoro Central copper deposit, Atacama Desert, Chile

    Science.gov (United States)

    Fernández-Mort, A.; Riquelme, R.; Alonso-Zarza, A. M.; Campos, E.; Bissig, T.; Mpodozis, C.; Carretier, S.; Herrera, C.; Tapia, M.; Pizarro, H.; Muñoz, S.

    2017-12-01

    Although the formation of exotic-Cu deposits is controlled by multiple factors, the role of the sedimentary environment has not been well defined. We present a case study of the El Tesoro Central exotic-Cu deposit located in the Atacama Desert of northern Chile. This deposit consists of two mineralized bodies hosted within Late Cenozoic gravels deposited in an arid continental environment dominated by alluvial fans with sub-surficial ponded water bodies formed at the foot of these fans or within the interfan areas. Both exotic-Cu orebodies mostly consist of chrysocolla, copper wad, atacamite, paratacamite, quartz, opal, and calcite. The most commonly observed paragenesis comprises chrysocolla, silica minerals, and calcite and records a progressive increase in pH, which is notably influenced by evaporation. The results of stable isotope analyses (δ13C and δ18O) and hydrogeochemical simulations confirm that evapoconcentration is the main controlling factor in the exotic-Cu mineralization at El Tesoro Central. This conclusion complements the traditional genetic model based on the gradual neutralization of highly oversaturated Cu-bearing solutions that progressively cement the gravels and underlying bedrock regardless of the depositional environment. This study concludes that in exotic-Cu deposits formed relatively far from the source, a favorable sedimentary environment and particular hydrologic and climatic conditions are essential to trap, accumulate, evapoconcentrate, neutralize and saturate Cu-bearing solutions to trigger mineralization. Thus, detailed sedimentological studies should be incorporated when devising exploration strategies in order to discover new exotic-Cu resources, particularly if they are expected to have formed relatively far from the metal sources.

  4. Statistical models for optimizing mineral exploration

    International Nuclear Information System (INIS)

    Wignall, T.K.; DeGeoffroy, J.

    1987-01-01

    The primary purpose of mineral exploration is to discover ore deposits. The emphasis of this volume is on the mathematical and computational aspects of optimizing mineral exploration. The seven chapters that make up the main body of the book are devoted to the description and application of various types of computerized geomathematical models. These chapters include: (1) the optimal selection of ore deposit types and regions of search, as well as prospecting selected areas, (2) designing airborne and ground field programs for the optimal coverage of prospecting areas, and (3) delineating and evaluating exploration targets within prospecting areas by means of statistical modeling. Many of these statistical programs are innovative and are designed to be useful for mineral exploration modeling. Examples of geomathematical models are applied to exploring for six main types of base and precious metal deposits, as well as other mineral resources (such as bauxite and uranium)

  5. Genetic African Ancestry and Markers of Mineral Metabolism in CKD.

    Science.gov (United States)

    Gutiérrez, Orlando M; Parsa, Afshin; Isakova, Tamara; Scialla, Julia J; Chen, Jing; Flack, John M; Nessel, Lisa C; Gupta, Jayanta; Bellovich, Keith A; Steigerwalt, Susan; Sondheimer, James H; Wright, Jackson T; Feldman, Harold I; Kusek, John W; Lash, James P; Wolf, Myles

    2016-04-07

    Disorders of mineral metabolism are more common in African Americans with CKD than in European Americans with CKD. Previous studies have focused on the differences in mineral metabolism by self-reported race, making it difficult to delineate the importance of environmental compared with biologic factors. In a cross-sectional analysis of 3013 participants of the Chronic Renal Insufficiency Cohort study with complete data, we compared markers of mineral metabolism (phosphorus, calcium, alkaline phosphatase, parathyroid hormone, fibroblast growth factor 23, and urine calcium and phosphorus excretion) in European Americans versus African Americans and separately, across quartiles of genetic African ancestry in African Americans (n=1490). Compared with European Americans, African Americans had higher blood concentrations of phosphorus, alkaline phosphatase, fibroblast growth factor 23, and parathyroid hormone, lower 24-hour urinary excretion of calcium and phosphorus, and lower urinary fractional excretion of calcium and phosphorus at baseline (PAfrican Americans, a higher percentage of African ancestry was associated with lower 24-hour urinary excretion of phosphorus (PtrendAfrican ancestry was significantly associated with lower 24-hour urinary phosphorus excretion (each 10% higher African ancestry was associated with 39.6 mg lower 24-hour urinary phosphorus, PAfrican ancestry was associated with an absolute 1.1% lower fractional excretion of phosphorus, P=0.01). A higher percentage of African ancestry was independently associated with lower 24-hour urinary phosphorus excretion and lower fractional excretion of phosphorus among African Americans with CKD. These findings suggest that genetic variability might contribute to racial differences in urinary phosphorus excretion in CKD. Copyright © 2016 by the American Society of Nephrology.

  6. Nature of parent rocks, mineralization styles and ore genesis of regolith-hosted REE deposits in South China: An integrated genetic model

    Science.gov (United States)

    Li, Yan Hei Martin; Zhao, Wen Winston; Zhou, Mei-Fu

    2017-10-01

    Regolith-hosted rare earth element (REE) deposits, also called ion-adsorption or weathered crust elution-deposited REE deposits are distributed over Jiangxi, Guangdong, Fujian, Hunan, Guangxi and Yunnan provinces in South China. In general, these deposits can be categorized into the HREE-dominated type, for example the famous Zudong deposit in southern Jiangxi province and the LREE-dominated type, such as the Heling and Dingnan deposits in southern Jiangxi province. Most of these deposits form from weathering of biotite and muscovite granites, syenites, monzogranites, granodiorites, granite porphyries, and rhyolitic tuffs. The parent rocks are generally peraluminous, siliceous, alkaline and contain a variety of REE-bearing minerals. Mostly, REE patterns of regolith are inherited from the parent rocks, and therefore, characteristics of the parent rocks impose a significant control on the ore formation. Data compilation shows that autometasomatism during the latest stage of granite crystallization is likely essential in forming the HREE-enriched granites, whereas LREE-enriched granites could form through magmatic differentiation. These deposits are normally two- to three-fold, but could be up to ten-fold enrichment in REE compared to the parent granites, where the maximum enrichment usually occurs from the lower B to the upper C horizon. Ce shows different behavior with the other REEs. Strongly positive Ce anomalies commonly occur at the upper part of weathering profiles, likely due to oxidation of Ce3+ to Ce4+ and removal of Ce from soil solutions through precipitation of cerianite. Vertical pH and redox gradients in weathering crusts facilitate dissolution of REE-bearing minerals at shallow level and fixation of REE at depth through either adsorption on clay minerals or precipitation of secondary minerals. At the same time, mass removal of major elements plays an important role in concentrating REE in regolith. Combination of mass removal and eluviation

  7. 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....

  8. Minerals

    Science.gov (United States)

    Minerals are important for your body to stay healthy. Your body uses minerals for many different jobs, including keeping your bones, muscles, heart, and brain working properly. Minerals are also important for making enzymes and hormones. ...

  9. Methods of modeling and optimization of work effects for chosen mineral processing systems

    Directory of Open Access Journals (Sweden)

    Tomasz Niedoba

    2005-11-01

    Full Text Available The methods being used in the mineral processing modeling are reviewed in this paper. Particularly, the heuristic approach was presented. The new, modern techniques of modeling and optimization were proposed, including the least median squares method and genetic algorithms. The rules of the latter were described in details.

  10. Mineral vein dynamics modelling (FRACS II)

    International Nuclear Information System (INIS)

    Urai, J.; Virgo, S.; Arndt, M.

    2016-08-01

    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.

  11. 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.

  12. Evolutionary genetics: the Drosophila model

    Indian Academy of Sciences (India)

    Unknown

    Evolutionary genetics straddles the two fundamental processes of life, ... of the genus Drosophila have been used extensively as model systems in experimental ... issue will prove interesting, informative and thought-provoking for both estab-.

  13. Mineral vein dynamics modeling (FRACS). Phase 1

    Energy Technology Data Exchange (ETDEWEB)

    Urai, J.; Virgo, S.; Arndt, M. [RWTH Aachen (Germany). Geologie-Endogene Dynamik] [and others

    2013-07-15

    The Mineral Vein Dynamics Modeling group ''FRACS'' is a team of 7 research groups from the Universities of Mainz, Aachen, Tuebingen, Karlsruhe, Bayreuth, ETH Zuerich and Glasgow working on an understanding of the dynamic development of fracturing, fluid flow and fracture sealing. World-class field laboratories, especially carbonate sequences from the Oman Mountains are studied and classified. State of the art numerical programs are written, expanded and used to simulate the dynamic interaction of fracturing, flow and resealing and the results are compared with the natural examples. Newest analytical technologies including laser scanning, high resolution X-ray microtomography, fluid inclusion and isotope analysis are performed to understand and compare the results of simulations with natural examples. A new statistical program was developed to classify the natural fracture and vein systems and compare them with dynamic numerical simulations and analytical models. The results of the first project phase are extremely promising. Most of the numerical models have been developed up to the stage where they can be used to simulate the natural examples. The models allow a definition of the first proxies for high fluid pressure and tectonic stresses. It was found out that the Oman Mountains are a complex and very dynamic system that constantly fractures and reseals from the scale of small veins up to the scale of large normal and strike slip faults. The numerical simulations also indicate that the permeability of such systems is not a constant but that the system adjusts to the driving force, for ex-ample high fluid pressure. When the system reseals fast a fluctuating behavior can be observed in the models where the system constantly fractures and reseals, which is in accordance with the observation of the natural laboratory.

  14. Behavior genetics: Bees as model

    International Nuclear Information System (INIS)

    Nates Parra, Guiomar

    2011-01-01

    The honeybee Apis mellifera (Apidae) is a model widely used in behavior because of its elaborate social life requiring coordinate actions among the members of the society. Within a colony, division of labor, the performance of tasks by different individuals, follows genetically determined physiological changes that go along with aging. Modern advances in tools of molecular biology and genomics, as well as the sequentiation of A. mellifera genome, have enabled a better understanding of honeybee behavior, in particular social behavior. Numerous studies show that aspects of worker behavior are genetically determined, including defensive, hygienic, reproductive and foraging behavior. For example, genetic diversity is associated with specialization to collect water, nectar and pollen. Also, control of worker reproduction is associated with genetic differences. In this paper, I review the methods and the main results from the study of the genetic and genomic basis of some behaviors in bees.

  15. 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); 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 (Huib); 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 (Cornelia); 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 (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.

  16. Genetic Process Mining: Alignment-based Process Model Mutation

    NARCIS (Netherlands)

    Eck, van M.L.; Buijs, J.C.A.M.; Dongen, van B.F.; Fournier, F.; Mendling, J.

    2015-01-01

    The Evolutionary Tree Miner (ETM) is a genetic process discovery algorithm that enables the user to guide the discovery process based on preferences with respect to four process model quality dimensions: replay fitness, precision, generalization and simplicity. Traditionally, the ETM algorithm uses

  17. Minerals

    Science.gov (United States)

    ... Aren't minerals something you find in the earth, like iron and quartz? Well, yes, but small ... canned salmon and sardines with bones leafy green vegetables, such as broccoli calcium-fortified foods — from orange ...

  18. 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.

  19. 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.

  20. Genetic Screening of WNT4 and WNT5B in Two Populations with Deviating Bone Mineral Densities

    DEFF Research Database (Denmark)

    Hendrickx, Gretl; Boudin, Eveline; Steenackers, Ellen

    2017-01-01

    A role for WNT4 and WNT5B in bone metabolism was indicated by genome-wide association studies (GWAS) and a Wnt4 knockout mouse model. The aim of this study was therefore to replicate and further investigate the causality between genetic variation in WNT4 and WNT5B and deviating bone mineral density...... (BMD) values. A WNT4 and WNT5B mutation screening was performed in patients with craniotubular hyperostosis using Sanger sequencing. Here, no putative causal mutations were detected. Moreover, a high and low BMD cohort was selected from the Odense Androgen Study population for re-sequencing. In WNT4 we...

  1. 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.

  2. Genetic Aspects of Gold Mineralization at Some Occurrences in the Eastern Desert of Egypt

    Science.gov (United States)

    Abd El Monsef, M.; Slobodník, M.; Salem, I. A.

    2012-04-01

    The Eastern Desert of Egypt is well known as a gold-mining area since ancient times, there're more than 95 gold deposits and occurrences spread the whole area covered by the basement rocks of Precambrian age. The basement rocks of the Eastern Desert of Egypt constitute the Nubian Shield that has formed a continuous part of the Arabian-Nubian Shield before the opening of Red Sea (Oligocene-Early Miocene). Commonly, the system of gold-bearing quartz veins in the Eastern Desert is clearly structural controlled related to brittle-ductile shear zones that mostly developed during late deformational stages of the evolution history for basement rocks in the Eastern Desert. This running study principally aims to contribute the mineral resource potential of the gold deposits in Egypt, so particularly Fatira, Gidami and Atalla occurrences have been involved into a comprehensive study based on field, structural, mineralogical, geochemical and genetic investigations. It is intended to better understanding for the characteristics, distribution controls, conditions and age of mineralization in relation to the age of the hosting rocks intrusion to find if there're genetic links between the gold mineralization and the evolution of the host intrusive complex. Several authors suggested that the gold mineralization was related to the intrusion of the (postorogenic) Younger granites. Other authors interpret these deposits as products of hydrothermal activity induced either by metamorphism or cooling effects of early Paleozoic magmatism or as combined metamorphic/magmatic episodes. The prime focus will be directed to the ore itself and the associated hydrothermal alteration zones based on detailed maps and well-distributed samples network and geochemical anomalies distribution. The laboratory studies included microscopic examination (reflecting and transmitting microscopy) to allow for determination of the hosting rocks types and mineralogical changes related to the gold mineralization

  3. 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

  4. Prevalence and Genetic Diversity of Enterococcus faecalis Isolates from Mineral Water and Spring Water in China

    Directory of Open Access Journals (Sweden)

    Lei Wei

    2017-06-01

    Full Text Available Enterococcus faecalis is an important opportunistic pathogen which is frequently detected in mineral water and spring water for human consumption and causes human urinary tract infections, endocarditis and neonatal sepsis. The aim of this study was to determine the prevalence, virulence genes, antimicrobial resistance and genetic diversity of E. faecalis from mineral water and spring water in China. Of 314 water samples collected from January 2013 to January 2014, 48 samples (15.3% were contaminated E. faecalis. The highest contamination rate occurred in activated carbon filtered water of spring water (34.5%, followed by source water of spring water (32.3% and source water of mineral water (6.4%. The virulence gene test of 58 E. faecalis isolates showed that the detection rates of asa1, ace, cylA, gelE and hyl were 79.3, 39.7, 0, 100, 0%, respectively. All 58 E. faecalis isolates were not resistant to 12 kinds of antibiotics (penicillin, ampicillin, linezolid, quinupristin/dalfopristin, vancomycin, gentamicin, streptomycin, ciprofloxacin, levofloxacin, norfloxacin, nitrofurantoin, and tetracycline. Enterobacterial repetitive intergenic consensus-PCR classified 58 isolates and three reference strains into nine clusters with a similarity of 75%. This study is the first to investigate the prevalence of E. faecalis in mineral water and spring water in China. The results of this study suggested that spring water could be potential vehicles for transmission of E. faecalis.

  5. Measurement and Modelling of Scaling Minerals

    DEFF Research Database (Denmark)

    Villafafila Garcia, Ada

    2005-01-01

    -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......-, )-H2O, are presented. M2+ stands for Ba2+, Ca2+, or Sr2+. Chapter 5 is devoted to the correlation and prediction of vapour-liquid-solid equilibria for different carbonate systems causing scale problems (CaCO3, BaCO3, SrCO3, and MgCO3), covering the temperature range from 0 to 250ºC and pressures up......-NaCl-Na2SO4-H2O are given. M2+ stands for Ca2+, Mg2+, Ba2+, and Sr2+. This chapter also includes an analysis of the CaCO3-MgCO3-CO2-H2O system. Chapter 6 deals with the system NaCl-H2O. Available data for that system at high temperatures and/or pressures are addressed, and sodium chloride solubility...

  6. Genetic Sharing with Cardiovascular Disease Risk Factors and Diabetes Reveals Novel Bone Mineral Density Loci.

    Directory of Open Access Journals (Sweden)

    Sjur Reppe

    Full Text Available Bone 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. We used a novel genetic pleiotropy-informed conditional False Discovery Rate (FDR method to identify single nucleotide polymorphisms (SNPs associated with BMD by leveraging cardiovascular disease (CVD associated disorders and metabolic traits. By conditioning on SNPs associated with the CVD-related phenotypes, type 1 diabetes, type 2 diabetes, systolic blood pressure, diastolic blood pressure, high density lipoprotein, low density lipoprotein, triglycerides and waist hip ratio, we identified 65 novel independent BMD loci (26 with femoral neck BMD and 47 with lumbar spine BMD at conditional FDR < 0.01. Many of the loci were confirmed in genetic expression studies. Genes validated at the mRNA levels were characteristic for the osteoblast/osteocyte lineage, Wnt signaling pathway and bone metabolism. The results provide new insight into genetic mechanisms of variability in BMD, and a better understanding of the genetic underpinnings of clinical comorbidity.

  7. Model Predictive Control of Mineral Column Flotation Process

    Directory of Open Access Journals (Sweden)

    Yahui Tian

    2018-06-01

    Full Text Available Column flotation is an efficient method commonly used in the mineral industry to separate useful minerals from ores of low grade and complex mineral composition. Its main purpose is to achieve maximum recovery while ensuring desired product grade. This work addresses a model predictive control design for a mineral column flotation process modeled by a set of nonlinear coupled heterodirectional hyperbolic partial differential equations (PDEs and ordinary differential equations (ODEs, which accounts for the interconnection of well-stirred regions represented by continuous stirred tank reactors (CSTRs and transport systems given by heterodirectional hyperbolic PDEs, with these two regions combined through the PDEs’ boundaries. The model predictive control considers both optimality of the process operations and naturally present input and state/output constraints. For the discrete controller design, spatially varying steady-state profiles are obtained by linearizing the coupled ODE–PDE model, and then the discrete system is obtained by using the Cayley–Tustin time discretization transformation without any spatial discretization and/or without model reduction. The model predictive controller is designed by solving an optimization problem with input and state/output constraints as well as input disturbance to minimize the objective function, which leads to an online-solvable finite constrained quadratic regulator problem. Finally, the controller performance to keep the output at the steady state within the constraint range is demonstrated by simulation studies, and it is concluded that the optimal control scheme presented in this work makes this flotation process more efficient.

  8. A genetic link between magnetite mineralization and diorite intrusion at the El Romeral iron oxide-apatite deposit, northern Chile

    Science.gov (United States)

    Rojas, Paula A.; Barra, Fernando; Reich, Martin; Deditius, Artur; Simon, Adam; Uribe, Francisco; Romero, Rurik; Rojo, Mario

    2018-01-01

    El Romeral is one of the largest iron oxide-apatite (IOA) deposits in the Coastal Cordillera of northern Chile. The Cerro Principal magnetite ore body at El Romeral comprises massive magnetite intergrown with actinolite, with minor apatite, scapolite, and sulfides (pyrite ± chalcopyrite). Several generations of magnetite were identified by using a combination of optical and electron microscopy techniques. The main mineralization event is represented by zoned magnetite grains with inclusion-rich cores and inclusion-poor rims, which form the massive magnetite ore body. This main magnetite stage was followed by two late hydrothermal events that are represented by magnetite veinlets that crosscut the massive ore body and by disseminated magnetite in the andesite host rock and in the Romeral diorite. The sulfur stable isotope signature of the late hydrothermal sulfides indicates a magmatic origin for sulfur (δ34S between - 0.8 and 2.9‰), in agreement with previous δ34S data reported for other Chilean IOA and iron oxide-copper-gold deposits. New 40Ar/39Ar dating of actinolite associated with the main magnetite ore stage yielded ages of ca. 128 Ma, concordant within error with a U-Pb zircon age for the Romeral diorite (129.0 ± 0.9 Ma; mean square weighted deviation = 1.9, n = 28). The late hydrothermal magnetite-biotite mineralization is constrained at ca. 118 Ma by 40Ar/39Ar dating of secondary biotite. This potassic alteration is about 10 Ma younger than the main mineralization episode, and it may be related to post-mineralization dikes that crosscut and remobilize Fe from the main magnetite ore body. These data reveal a clear genetic association between magnetite ore formation, sulfide mineralization, and the diorite intrusion at El Romeral (at 129 Ma), followed by a late and more restricted stage of hydrothermal alteration associated with the emplacement of post-ore dikes at ca. 118 Ma. Therefore, this new evidence supports a magmatic-hydrothermal model for the

  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.

    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. Mineral Precipitation in Fractures: Multiscale Imaging and Geochemical Modeling

    Science.gov (United States)

    Hajirezaie, S.; Peters, C. A.; Swift, A.; Sheets, J. M.; Cole, D. R.; Crandall, D.; Cheshire, M.; Stack, A. G.; Anovitz, L. M.

    2017-12-01

    For subsurface energy technologies such as geologic carbon sequestration, fractures are potential pathways for fluid migration from target formations. Highly permeable fractures may become sealed by mineral precipitation. In this study, we examined shale specimens with existing cemented fractures as natural analogues, using an array of imaging methods to characterize mineralogy and porosity at several spatial scales. In addition, we used reactive transport modeling to investigate geochemical conditions that can lead to extensive mineral precipitation and to simulate the impacts on fracture hydraulic properties. The naturally-cemented fractured rock specimens were from the Upper Wolfcamp formation in Texas, at 10,000 ft depth. The specimens were scanned using x-ray computed tomography (xCT) at resolution of 13 microns. The xCT images revealed an original fracture aperture of 1.9 mm filled with several distinct mineral phases and vuggy void regions, and the mineral phase volumes and surface areas were quantified and mapped in 3D. Specimens were thin-sectioned and examined at micron- and submicron-scales using petrographic microscopy (PM), scanning electron microscopy (SEM), energy dispersive X-ray spectroscopy (EDX), and small angle X-ray scattering (SAXS). Collectively these methods revealed crystals of dolomite as large as 900 microns in length overlain with a heterogeneous mixture of carbonate minerals including calcite, dolomite, and Fe-rich dolomite, interspersed at spatial scales as small as 5 microns. In addition, secondary precipitation of SiO2 was found to fill some of the void space. This multiscale imaging was used to inform the reactive transport modeling employed to examine the conditions that can cause the observed mineral precipitation in fractures at a larger scale. Two brines containing solutions that when mixed would lead to precipitation of various carbonate minerals were simulated as injectants into a fracture domain. In particular, the competing

  11. Preliminary conceptual model for mineral evolution in Yucca Mountain

    International Nuclear Information System (INIS)

    Duffy, C.J.

    1993-12-01

    A model is presented for mineral alteration in Yucca Mountain, Nevada, that suggests that the mineral transformations observed there are primarily controlled by the activity of aqueous silica. The rate of these reactions is related to the rate of evolution of the metastable silica polymorphs opal-CT and cristobalite assuming that a SiO 2(aq) is fixed at the equilibrium solubility of the most soluble silica polymorph present. The rate equations accurately predict the present depths of disappearance of opal-CT and cristobalite. The rate equations have also been used to predict the extent of future mineral alteration that may result from emplacement of a high-level nuclear waste repository in Yucca Mountain. Relatively small changes in mineralogy are predicted, but these predictions are based on the assumption that emplacement of a repository would not increase the pH of water in Yucca Mountain nor increase its carbonate content. Such changes may significantly increase mineral alteration. Some of the reactions currently occurring in Yucca Mountain consume H + and CO 3 2- . Combining reaction rate models for these reactions with water chemistry data may make it possible to estimate water flux through the basal vitrophyre of the Topopah Spring Member and to help confirm the direction and rate of flow of groundwater in Yucca Mountain

  12. Phenotypic Dissection of Bone Mineral Density Reveals Skeletal Site Specificity and Facilitates the Identification of Novel Loci in the Genetic Regulation of Bone Mass Attainment

    NARCIS (Netherlands)

    J.P. Kemp (John); M.C. Medina-Gomez (Carolina); K. Estrada Gil (Karol); B. St Pourcain (Beate); D.H.M. Heppe (Denise); N.M. Warrington (Nicole); L. Oei (Ling); S.M. Ring (Susan); C.J. Kruithof (Claudia); N.J. Timpson (Nicholas); L.E. Wolber (Lisa); S. Reppe (Sjur); K.M. Gautvik (Kaare); E. Grundberg (Elin); B. Ge (Bing); B.C.J. van der Eerden (Bram); J. van de Peppel (Jeroen); M.A. Hibbs (Matthew); C.L. Ackert-Bicknell (Cheryl); K. Choi (Kunho); D.L. Koller (Daniel); M.J. Econs (Michael); F.M. Williams (Frances); T. Foroud (Tatiana); M.C. Zillikens (Carola); C. Ohlsson (Claes); A. Hofman (Albert); A.G. Uitterlinden (André); G. Davey-Smith (George); V.W.V. Jaddoe (Vincent); J.H. Tobias (Jon); F. Rivadeneira Ramirez (Fernando); D.M. Evans (David)

    2014-01-01

    textabstractHeritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we

  13. Behavior genetic modeling of human fertility

    DEFF Research Database (Denmark)

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

    2001-01-01

    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......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....... A bivariate analysis indicated significant shared genetic variance between NumCh and FirstTry....

  14. Genetic coding and gene expression - new Quadruplet genetic coding model

    Science.gov (United States)

    Shankar Singh, Rama

    2012-07-01

    Successful demonstration of human genome project has opened the door not only for developing personalized medicine and cure for genetic diseases, but it may also answer the complex and difficult question of the origin of life. It may lead to making 21st century, a century of Biological Sciences as well. Based on the central dogma of Biology, genetic codons in conjunction with tRNA play a key role in translating the RNA bases forming sequence of amino acids leading to a synthesized protein. This is the most critical step in synthesizing the right protein needed for personalized medicine and curing genetic diseases. So far, only triplet codons involving three bases of RNA, transcribed from DNA bases, have been used. Since this approach has several inconsistencies and limitations, even the promise of personalized medicine has not been realized. The new Quadruplet genetic coding model proposed and developed here involves all four RNA bases which in conjunction with tRNA will synthesize the right protein. The transcription and translation process used will be the same, but the Quadruplet codons will help overcome most of the inconsistencies and limitations of the triplet codes. Details of this new Quadruplet genetic coding model and its subsequent potential applications including relevance to the origin of life will be presented.

  15. Modelling of acid-base titration curves of mineral assemblages

    Directory of Open Access Journals (Sweden)

    Stamberg Karel

    2016-01-01

    Full Text Available The modelling of acid-base titration curves of mineral assemblages was studied with respect to basic parameters of their surface sites to be obtained. The known modelling approaches, component additivity (CA and generalized composite (GC, and three types of different assemblages (fucoidic sandstones, sedimentary rock-clay and bentonite-magnetite samples were used. In contrary to GC-approach, application of which was without difficulties, the problem of CA-one consisted in the credibility and accessibility of the parameters characterizing the individual mineralogical components.

  16. 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.

  17. Animal models for human genetic diseases

    African Journals Online (AJOL)

    Sharif Sons

    The study of human genetic diseases can be greatly aided by animal models because of their similarity .... and gene targeting in embryonic stem cells) has been a powerful tool in .... endonucleases that are designed to make a doublestrand.

  18. THE ALLOMETRIC-AUTOREGRESSIVE MODEL IN GENETIC ...

    African Journals Online (AJOL)

    The application of an allometric-autoregressive model for the quantification of growth and efficiency of feed utilization for purposes of selection for ... be of value in genetic studies. ... mass) gives a fair indication of the cumulative preweaning.

  19. 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. © 2013.

  20. 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...

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

    Science.gov (United States)

    Kristensen, K E; Jacobsen, C S; Hansen, L H; Aamand, J; Morgan, J A W; Sternberg, C; Sørensen, S R

    2006-09-01

    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. 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. We successfully constructed a genetically labelled isoproturon-mineralizing-strain SRS2 and demonstrated its ability to survive in soil and its colonization of rhizosphere. The construction of a luxAB-labelled strain SRS2 maintaining the degradative ability, provides a powerful tool for ecological studies serving as the basis for evaluating SRS2 as a bioremediation agent.

  2. Noise in Genetic Toggle Switch Models

    Directory of Open Access Journals (Sweden)

    Andrecut M.

    2006-06-01

    Full Text Available In this paper we study the intrinsic noise effect on the switching behavior of a simple genetic circuit corresponding to the genetic toggle switch model. The numerical results obtained from a noisy mean-field model are compared to those obtained from the stochastic Gillespie simulation of the corresponding system of chemical reactions. Our results show that by using a two step reaction approach for modeling the transcription and translation processes one can make the system to lock in one of the steady states for exponentially long times.

  3. On the mineralization model of 'three sources--heat, water and uranium'

    International Nuclear Information System (INIS)

    Li Xueli

    1992-01-01

    In response to the relations between geological and geothermal settings, geothermal water and uranium mineralizations in the Southeastern China, the model of uranium mineralization in discharge area (depressurization area) of fossil geothermal systems in Mesozoic-Cenozoic Volcanic-magmatic active areas has been put forward and expounded in the view of mineral-formation by the 'three sources'-heat, water and uranium

  4. Modeling CO2-Water-Mineral Wettability and Mineralization for Carbon Geosequestration.

    Science.gov (United States)

    Liang, Yunfeng; Tsuji, Shinya; Jia, Jihui; Tsuji, Takeshi; Matsuoka, Toshifumi

    2017-07-18

    Carbon dioxide (CO 2 ) capture and storage (CCS) is an important climate change mitigation option along with improved energy efficiency, renewable energy, and nuclear energy. CO 2 geosequestration, that is, to store CO 2 under the subsurface of Earth, is feasible because the world's sedimentary basins have high capacity and are often located in the same region of the world as emission sources. How CO 2 interacts with the connate water and minerals is the focus of this Account. There are four trapping mechanisms that keep CO 2 in the pores of subsurface rocks: (1) structural trapping, (2) residual trapping, (3) dissolution trapping, and (4) mineral trapping. The first two are dominated by capillary action, where wettability controls CO 2 and water two-phase flow in porous media. We review state-of-the-art studies on CO 2 /water/mineral wettability, which was found to depend on pressure and temperature conditions, salt concentration in aqueous solutions, mineral surface chemistry, and geometry. We then review some recent advances in mineral trapping. First, we show that it is possible to reproduce the CO 2 /water/mineral wettability at a wide range of pressures using molecular dynamics (MD) simulations. As the pressure increases, CO 2 gas transforms into a supercritical fluid or liquid at ∼7.4 MPa depending on the environmental temperature. This transition leads to a substantial decrease of the interfacial tension between CO 2 and reservoir brine (or pure water). However, the wettability of CO 2 /water/rock systems depends on the type of rock surface. Recently, we investigated the contact angle of CO 2 /water/silica systems with two different silica surfaces using MD simulations. We found that contact angle increased with pressure for the hydrophobic (siloxane) surface while it was almost constant for the hydrophilic (silanol) surface, in excellent agreement with experimental observations. Furthermore, we found that the CO 2 thin films at the CO 2 -hydrophilic

  5. Quartz-pebble-conglomerate gold deposits: Chapter P in Mineral deposit models for resource assessment

    Science.gov (United States)

    Taylor, Ryan D.; Anderson, Eric D.

    2018-05-17

    Quartz-pebble-conglomerate gold deposits represent the largest repository of gold on Earth, largely due to the deposits of the Witwatersrand Basin, which account for nearly 40 percent of the total gold produced throughout Earth’s history. This deposit type has had a controversial history in regards to genetic models. However, most researchers conclude that they are paleoplacer deposits that have been modified by metamorphism and hydrothermal fluid flow subsequent to initial sedimentation.The deposits are found exclusively within fault-bounded depositional basins. The periphery of these basins commonly consists of granite-greenstone terranes, classic hosts for lode gold that source the detrital material infilling the basin. The gold reefs are typically located along unconformities or, less commonly, at the top of sedimentary beds. Large quartz pebbles and heavy-mineral concentrates are found associated with the gold. Deposits that formed prior to the Great Oxidation Event (circa 2.4 giga-annum [Ga]) contain pyrite, whereas younger deposits contain iron oxides. Uranium minerals and hydrocarbons are also notable features of some deposits.Much of the gold in these types of deposits forms crystalline features that are the product of local remobilization. However, some gold grains preserve textures that are undoubtedly of detrital origin. Other heavy minerals, such as pyrite, contain growth banding that is truncated along broken margins, which indicates that they were transported into place as opposed to forming by in situ growth in a hydrothermal setting.The ore tailings associated with these deposits commonly contain uranium-rich minerals and sulfides. Oxidation of the sulfides releases sulfuric acid and mobilizes various metals into the environment. The neutralizing potential of the tailings is minimal, since carbonate minerals are rare. The continuity of the tabular ore bodies, such as those of the Witwatersrand Basin, has allowed these mines to be the deepest in

  6. Shaping asteroid models using genetic evolution (SAGE)

    Science.gov (United States)

    Bartczak, P.; Dudziński, G.

    2018-02-01

    In this work, we present SAGE (shaping asteroid models using genetic evolution), an asteroid modelling algorithm based solely on photometric lightcurve data. It produces non-convex shapes, orientations of the rotation axes and rotational periods of asteroids. The main concept behind a genetic evolution algorithm is to produce random populations of shapes and spin-axis orientations by mutating a seed shape and iterating the process until it converges to a stable global minimum. We tested SAGE on five artificial shapes. We also modelled asteroids 433 Eros and 9 Metis, since ground truth observations for them exist, allowing us to validate the models. We compared the derived shape of Eros with the NEAR Shoemaker model and that of Metis with adaptive optics and stellar occultation observations since other models from various inversion methods were available for Metis.

  7. 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 ...

  8. Model comparisons and genetic and environmental parameter ...

    African Journals Online (AJOL)

    arc

    Model comparisons and genetic and environmental parameter estimates of growth and the ... breeding strategies and for accurate breeding value estimation. The objectives ...... Sci. 23, 72-76. Van Wyk, J.B., Fair, M.D. & Cloete, S.W.P., 2003.

  9. 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 pressur...

  10. Biologically enhanced mineral weathering: what does it look like, can we model it?

    Science.gov (United States)

    Schulz, M. S.; Lawrence, C. R.; Harden, J. W.; White, A. F.

    2011-12-01

    The interaction between plants and minerals in soils is hugely important and poorly understood as it relates to the fate of soil carbon. Plant roots, fungi and bacteria inhabit the mineral soil and work symbiotically to extract nutrients, generally through low molecular weight exudates (organic acids, extracelluar polysachrides (EPS), siderophores, etc.). Up to 60% of photosynthetic carbon is allocated below ground as roots and exudates, both being important carbon sources in soils. Some exudates accelerate mineral weathering. To test whether plant exudates are incorporated into poorly crystalline secondary mineral phases during precipitation, we are investigating the biologic-mineral interface. We sampled 5 marine terraces along a soil chronosequence (60 to 225 ka), near Santa Cruz, CA. The effects of the biologic interactions with mineral surfaces were characterized through the use of Scanning Electron Microscopy (SEM). Morphologically, mycorrhizal fungi were observed fully surrounding minerals, fungal hyphae were shown to tunnel into primary silicate minerals and we have observed direct hyphal attachment to mineral surfaces. Fungal tunneling was seen in all 5 soils by SEM. Additionally, specific surface area (using a nitrogen BET method) of primary minerals was measured to determine if the effects of mineral tunneling are quantifiable in older soils. Results suggest that fungal tunneling is more extensive in the primary minerals of older soils. We have also examined the influence of organic acids on primary mineral weathering during soil development using a geochemical reactive transport model (CrunchFlow). Addition of organic acids in our models of soil development at Santa Cruz result in decreased activity of Fe and Al in soil pore water, which subsequently alters the spatial extent of primary mineral weathering and kaolinite precipitation. Overall, our preliminary modeling results suggest biological processes may be an important but underrepresented aspect of

  11. Relative risk models of lung cancer in uranium miners

    Energy Technology Data Exchange (ETDEWEB)

    Tomasek, L [National Radiation Protection Institute, Prague (Czech Republic); Placek, V [Inst. for Expertises and Emergencies, Pribram-Kamenna (Czech Republic)

    1996-12-31

    The study population of the S cohort (studies of underground miners of uranium and other substances as the source of information on long term effects of exposure to radon and its progeny) involve uranium miners, that started underground work at the Jachymov and Horni Slavkov mines in the period 1978-1959, and had worked at least for four years. A total 4320 men satisfied these criteria. During the decade up to 1990, follow-up of the cohort mainly relied on the national population registry. In order to improve the follow-u, a series of additional checks were conducted: in the files of the Czech and Slovak Pensions Offices, by local enquires, and by direct correspondence. These additional efforts resulted in an increase of more than 10% in the numbers of known men to have died or emigrated. An exceptional feature of the S study is the large number of measurements of radon concentrations made in each mine-shaft (mean number per year and shaft was 223 in the period 1949-1960). Each man`s annual exposures to radon progeny in terms of working levels were estimated combining measurement data with men`s employment details. The excess relative risk models were used in the form RR = c(1 + ERR(w,x)), where ERR is excess relative risk, w and x denote exposure history and modifying variable, and c is an intercept term that allows the mortality rate for `unexposed` cohort to differ from that in the general population. The increased mortality (O/E=1.58; where O is observed and E is expected cases among collected death cases in the cohort) in the cohort, generally, somewhat lower ratios than one reflect the non-industrial character of the region, with the exception of lung cancer in man. The differences in the O/E ratios for lung cancer among the separate communities indicate that even in the situation of generally lower mortality, the dependence of lung cancer mortality on radon exposure cannot be excluded. 3 tabs., 6 refs.

  12. THE GEOLOGY, GEOCHEMISTRY AND GENETICAL FEATURES OF THE ORMANBAŞI HILL (SİNCİK, ADIYAMAN COPPER MINERALIZATION

    Directory of Open Access Journals (Sweden)

    Nail YILDIRIM

    2012-06-01

    Full Text Available - The study area covers Ormanbaşı Hill of Adıyaman–Sincik County and its vicinity. Regional geological locations of Cu mineralizations that lie between the Southeastern Anatolian Foothill Belt and Taurus Orogenic Belt are conformable with thrust planes approximately extending in E-W directions. Cu mineralizations are observed in the form of lenses and layers within mudstone, diabase, spilite, and claystone - shales of the Koçali complex. The primary genetic relations of these formations have completely been disappeared but have only been traced along thrust planes that are conformable with general tectonic lineaments. The ore structure is generally massive but is stockwork and disseminated in some zones. The ore-bearing layer with pyrite towards deeper parts is observed, while the mineralization is observed in the form of iron ore cap (gossan at the surface. Ore paragenesis consists of pyrite, marcasite, chalcopyrite, sphalerite, bornite, chalcocite - covelline and native copper. All samples belonging to ore mineralizations plot on Cyprus type volcanogenic massive sulfide (VMS area in Cu – Pb - Zn and Au - (Cu + Pb + Zn - Ag ternary diagrams. All samples in Pb, Cu, Ag, Au and Zn spider diagrams which were normalized to primary mantle show a trend similar to VMS deposits. Besides, analyses carried out in massive pyrites indicated that these had Ni/Co ratio higher than 1% and less Ni content. Therefore; it was detected that hydrothermal processes had been effective in ore mineralizations. S32 /S34 ratios were obtained as 6.9 and 7.6 in sulfur isotope analyses performed by using pyrite and chalcopyrite samples. These values are both compatible with sulfur ratios in hydrothermal solutions related to volcanism and show a similar composition with that of Cyprus type VMS deposits on the world.

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

    DEFF Research Database (Denmark)

    Chapelle, Lucie

    2016-01-01

    and as a consequence focus on the mechanical properties of mineral wool has intensified. Also understanding the deformation mechanisms during compression of low density mineral wool is crucial since better thickness recovery after compression will result in significant savings on transport costs. The mechanical...... 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...... of the structure on mechanical properties can be explored. The size of the representative volume elements for the prediction of the elastic properties is determined for two types of applied boundary conditions. For sufficiently large volumes, the predicted elastic properties are consistent with results from...

  14. 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.

  15. Barite-polymetallic mineralization of Zmeinogorsk ore district and some genetic aspects of its formation

    Science.gov (United States)

    Bestemianova, K. V.; Grinev, O. M.

    2017-12-01

    Zmeinogorsky ore district is located in the northwest part of Ore Altai megatrough, which has long-lasting history of its development and complicated geological structure. Within the ore district, which is the northwest part of the devonian Zmeinogorsk-Bystrushinsky trough, ore mineralization is associated with the system of northwest border faults and cross branch faults. There were four main stages and five phases of minerogenesis. The first stage is the stage of oregenesis beginning and quartz-chlorite-sericite wall-rock alteration rocks formation. Ore deposition and intense tectonics took place during the second stage. The third stage is the most longstanding and productive ore formation stage. There are five distinct minerogenesis phases within this stage. The fourth stage expressed in erosion development and supergene alteration of already formed ore bodies with oxidation zone formation. Main ore minerals are pyrite, chalcopyrite, sphalerite and galena. Minor minerals are tetrahedrite, bornite, tennantite and chalcocite. Precious metals minerals are acanthite, gold, electrum, gold and silver amalgams. Barren minerals are barite, quartz, calcite, gypsum. According to obtained data average isotopic composition of third stage sulphides is: pyrite -0,2‰, chalcopyrite 0‰, galena +0,5‰, sphalerite -1,2‰ for the first complex; chalcopyrite -1,9‰, galena -3,4‰, sphalerite -2,3‰, tetrahedrite -3,7‰ for the second complex; tennantite -12,8‰, bornite -8,9‰ for the third complex. Sulfur isotopic compoisiton variations indicate source inhomogeneity. Thus, there was dominant source change from mantle one in the beginning to crustal one in the end. Main oregenesis stages took place in the range of temperatures between 170 and 210°С and in the mineral-forming solutions salinity range between 3 and 10 wt % NaCl equiv.

  16. 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.

  17. Genetic demographic networks: Mathematical model and applications.

    Science.gov (United States)

    Kimmel, Marek; Wojdyła, Tomasz

    2016-10-01

    Recent improvement in the quality of genetic data obtained from extinct human populations and their ancestors encourages searching for answers to basic questions regarding human population history. The most common and successful are model-based approaches, in which genetic data are compared to the data obtained from the assumed demography model. Using such approach, it is possible to either validate or adjust assumed demography. Model fit to data can be obtained based on reverse-time coalescent simulations or forward-time simulations. In this paper we introduce a computational method based on mathematical equation that allows obtaining joint distributions of pairs of individuals under a specified demography model, each of them characterized by a genetic variant at a chosen locus. The two individuals are randomly sampled from either the same or two different populations. The model assumes three types of demographic events (split, merge and migration). Populations evolve according to the time-continuous Moran model with drift and Markov-process mutation. This latter process is described by the Lyapunov-type equation introduced by O'Brien and generalized in our previous works. Application of this equation constitutes an original contribution. In the result section of the paper we present sample applications of our model to both simulated and literature-based demographies. Among other we include a study of the Slavs-Balts-Finns genetic relationship, in which we model split and migrations between the Balts and Slavs. We also include another example that involves the migration rates between farmers and hunters-gatherers, based on modern and ancient DNA samples. This latter process was previously studied using coalescent simulations. Our results are in general agreement with the previous method, which provides validation of our approach. Although our model is not an alternative to simulation methods in the practical sense, it provides an algorithm to compute pairwise

  18. Genetic Affiliation of Gold and Uranium Mineralization in El-Missikat Granite, Central Eastern Desert, Egypt

    International Nuclear Information System (INIS)

    Ammar, F.A.; Omar, S.A.M.; El Sawey, El.H.

    2016-01-01

    Gabal El-Missikat granitic pluton is affected by two fault systems trending NW-SE (the oldest) and ENE-WSW directions. It is one of the uranium occurrences in the Eastern Desert of Egypt. The northwestern margins of El-Missikat pluton, along its contact with the gneissose quartz diorite, are dissected by numerous reactivated fractured shear zones running generally ENE-WSW to NE-SW and dipping about 60°-70° to SE. Many white (oldest), smoky or black and jasperoid (youngest) silica veinlets fill the fractures of these shear zones. These veins are of irregular shape and variable thickness ranging from few centimeters to about three meters. They are chiefly affected by silicification, sericitization, hematitization , kaolinization and hydrothermal alterations processes. The smoky black veins are hosting secondary uranium and fluorite-, sulphide-gold mineralizations. Polished surface studies, ICP-ES and Atomic Absorption as well as Scanning Electron Microscope measurements recorded galena, pyrite chalcopyrite, sphalerite and molybdenite in the black and jasperoid mineralized veins. Gold associated with ore mineral assemblage as pyrite, chalcopyrite, sphalerite, galena, sheelite and iron oxides. The identified sulphide minerals not bearing gold are recorded. Gold are relatively coarse-grained, massive and metallic yellow or stretched bronze colored particles. The recorded secondary U minerals associates the sulphide gold-mineralization in the black and jasperoid silica veins. Regarding the mobility of both uranium and gold, U 4+ mobilized in oxidizing medium and migrate and transport as U 6+ , then deposited later as U 4+ when the medium changes to be reducing characterized by high /O 2 . On contrary, gold mobilized when the medium is complex AuCl 3- ion bearing. Consequently, El- Missikat granitic pluton affected by oxidizing Au and Cl 3- bearing high temperature hydrothermal solutions that leached U 4+ , W and Mo from the granitic mass as U 6 + , later decrease of

  19. Somatic cell genetics of uranium miners and plutonium workers. A biological dose-response indicator

    International Nuclear Information System (INIS)

    Brandom, W.F.; Bloom, A.D.; Bistline, R.W.; Saccomanno, G.

    1978-01-01

    Two populations of underground uranium miners and plutonium workers work in the state of Colorado, United States of America. We have explored the prevalence of structural chromosome aberrations in peripheral blood lymphocytes as a possible biological indicator of absorbed radiation late-effects in these populations. The uranium miners are divided into four exposure groups expressed in Working Level Months (WLM), the plutonium workers into six groups with estimated 239 Pu burdens expressed in nCi. Comparison of chromosome aberration frequency data between controls, miners, and plutonium workers demonstrate: (1) a cytogenetic response to occupational ionizing radiation at low estimated doses; and (2) an increasing monotonic dose-response in the prevalence of complex (all exchange) or total aberrations in all exposure groups in these populations. We also compared trends in the prevalence of aberrations per exposure unit (WLM and nCi) in each exposure subgroup for each population. In the uranium miners, the effects per WLM seem to decrease monotonically with increasing dose, whereas in the Pu workers the change per nCi appears abrupt, with all exposure groups over 1.3 nCi (minimum detectable level) having essentially similar rates. The calculations of aberrations per respective current maximum permissible dose (120 WLM and 40 nCi) for the two populations yield 4.8 X 10 -2 /100 cells for uranium miners and 90.6 X 10 -2 /100 cells for Pu workers. Factors which may have influenced this apparent 20-fold increase in the effectiveness of plutonium in the production of complex aberrations (9-fold increase in total aberrations) are discussed. (author)

  20. 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...

  1. Population genetics models of local ancestry.

    Science.gov (United States)

    Gravel, Simon

    2012-06-01

    Migrations have played an important role in shaping the genetic diversity of human populations. Understanding genomic data thus requires careful modeling of historical gene flow. Here we consider the effect of relatively recent population structure and gene flow and interpret genomes of individuals that have ancestry from multiple source populations as mosaics of segments originating from each population. This article describes general and tractable models for local ancestry patterns with a focus on the length distribution of continuous ancestry tracts and the variance in total ancestry proportions among individuals. The models offer improved agreement with Wright-Fisher simulation data when compared to the state-of-the art and can be used to infer time-dependent migration rates from multiple populations. Considering HapMap African-American (ASW) data, we find that a model with two distinct phases of "European" gene flow significantly improves the modeling of both tract lengths and ancestry variances.

  2. Context trees for privacy-preserving modeling of genetic data

    NARCIS (Netherlands)

    Kusters, C.J.; Ignatenko, T.

    2016-01-01

    In this work, we use context trees for privacypreserving modeling of genetic sequences. The resulting estimated models are applied for functional comparison of genetic sequences in a privacy preserving way. Here we define privacy as uncertainty about the genetic source sequence given its model and

  3. Using parallel computing in modeling and optimization of mineral ...

    African Journals Online (AJOL)

    Then to solve ultimate pit limit problem it is required to find such a sub graph in a graph whose sum of weights will be maximal. One of the possible solutions of this problem is using genetic algorithms. We use a ... Details of implementation parallel genetic algorithm for searching open pit limits are provided. Comparison with ...

  4. 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.

  5. Evolutionary model with genetics, aging, and knowledge

    Science.gov (United States)

    Bustillos, Armando Ticona; de Oliveira, Paulo Murilo

    2004-02-01

    We represent a process of learning by using bit strings, where 1 bits represent the knowledge acquired by individuals. Two ways of learning are considered: individual learning by trial and error, and social learning by copying knowledge from other individuals or from parents in the case of species with parental care. The age-structured bit string allows us to study how knowledge is accumulated during life and its influence over the genetic pool of a population after many generations. We use the Penna model to represent the genetic inheritance of each individual. In order to study how the accumulated knowledge influences the survival process, we include it to help individuals to avoid the various death situations. Modifications in the Verhulst factor do not show any special feature due to its random nature. However, by adding years to life as a function of the accumulated knowledge, we observe an improvement of the survival rates while the genetic fitness of the population becomes worse. In this latter case, knowledge becomes more important in the last years of life where individuals are threatened by diseases. Effects of offspring overprotection and differences between individual and social learning can also be observed. Sexual selection as a function of knowledge shows some effects when fidelity is imposed.

  6. A Follow-up Association Study of Genetic Variants for Bone Mineral Density in a Korean Population

    Directory of Open Access Journals (Sweden)

    Seokjin Ham

    2014-09-01

    Full Text Available Bone mineral density (BMD is one of the quantitative traits that are genetically inherited and affected by various factors. Over the past years, genome-wide association studies (GWASs have searched for many genetic loci that influence BMD. A recent meta-analysis of 17 GWASs for BMD of the femoral neck and lumbar spine is the largest GWAS for BMD to date and offers 64 single-nucleotide polymorphisms (SNPs in 56 associated loci. We investigated these BMD loci in a Korean population called Korea Association REsource (KARE to identify their validity in an independent study. The KARE population contains genotypes from 8,842 individuals, and their BMD levels were measured at the distal radius (BMD-RT and midshaft tibia (BMD-TT. Thirteen genomic loci among 56 loci were significantly associated with BMD variations, and 3 loci were involved in known biological pathways related to BMD. In order to find putative functional variants, nearby SNPs in relation to linkage equilibrium were annotated, and their possible functional effects were predicted. These findings reveal that tens of variants, not a single factor, may contribute to the genetic architecture of BMD; have an important role regardless of ethnic group; and may highlight the importance of a replication study in GWASs to validate genuine loci for BMD variation.

  7. Evaluation of geological structure and uranium mineralization model in West Lemajung Sector, Kalan Basin, West Kalimantan

    International Nuclear Information System (INIS)

    Ngadenin; Sularto, P.

    2000-01-01

    The fieldwork is based on the data of strike (S0) and schistosity (S1) of cores that could not penetrate the geological structure model and result of observation on some cores has shown that U mineralization veins are not always parallel to S1. The problems were encountered in core drill data to improve the estimation of U resources from indication category to measured category. The purpose of the evaluation is to establish the advisability of geological structure model and U mineralization model which was applied by this time. The research used remapping of geological structure with surface method in the scale of 1:1000. The result of remapping shows the difference of the dipping between new geological structure model and the old model. The dipping of the new model is to South East until vertical and the old model is to North West until vertical and to South East until vertical. Despite the difference between both of them, the substantive of folding system is identical so that the new and old models can be applied in drilling in West Lemajung sector. U mineralization model of remapping result consists of 3 types : type 1 U mineralization lens form with West-East direction and vertical dipping which is associated with tourmaline, type 2 U mineralization filling in the open fractures with West-East direction and 70 o to North dipping and parallel with S1, and type 3 U mineralization fill in opening fractures with N 110 o - 130 o E the direction and 60 o to North East until subvertical dipping while the old model is only one type. It is U mineralization filling in the open fractures with West-East the direction and 70 o to North the dipping and parallel with S1. Because of this significant difference, data collection of drill core must follow the new mineralization model. (author)

  8. 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.

  9. 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.

  10. A coupled hydrodynamic-hydrochemical modeling for predicting mineral transport in a natural acid drainage system.

    Science.gov (United States)

    Zegers Risopatron, G., Sr.; Navarro, L.; Montserrat, S., Sr.; McPhee, J. P.; Niño, Y.

    2017-12-01

    The geochemistry of water and sediments, coupled with hydrodynamic transport in mountainous channels, is of particular interest in central Chilean Andes due to natural occurrence of acid waters. In this paper, we present a coupled transport and geochemical model to estimate and understand transport processes and fate of minerals at the Yerba Loca Basin, located near Santiago, Chile. In the upper zone, water presentes low pH ( 3) and high concentrations of iron, aluminum, copper, manganese and zinc. Acidity and minerals are the consequence of water-rock interactions in hydrothermal alteration zones, rich in sulphides and sulphates, covered by seasonal snow and glaciers. Downstream, as a consequence of neutral to alkaline lateral water contributions (pH >7) along the river, pH increases and concentration of solutes decreases. The mineral transport model has three components: (i) a hydrodynamic model, where we use HEC-RAS to solve 1D Saint-Venant equations, (ii) a sediment transport model to estimate erosion and sedimentation rates, which quantify minerals transference between water and riverbed and (iii) a solute transport model, based on the 1D OTIS model which takes into account the temporal delay in solutes transport that typically is observed in natural channels (transient storage). Hydrochemistry is solved using PHREEQC, a software for speciation and batch reaction. Our results show that correlation between mineral precipitation and dissolution according to pH values changes along the river. Based on pH measurements (and according to literature) we inferred that main minerals in the water system are brochantite, ferrihydrite, hydrobasaluminite and schwertmannite. Results show that our model can predict the transport and fate of minerals and metals in the Yerba Loca Basin. Mineral dissolution and precipitation process occur for limited ranges of pH values. When pH values are increased, iron minerals (schwertmannite) are the first to precipitate ( 2.5

  11. 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.

  12. Beaufort group uranium mineralization - a model that may aid exploration

    International Nuclear Information System (INIS)

    Stuart-Williams, V.

    1982-01-01

    The ore bodies examined while working on the Pristerognathus Diictodon Assemblage Zone West of Beaufort West are of the URAVAN type (URA - uranium, VAN - vanadium). It was found that uranium mineralization in any one ore body was not strictly random and tends to be associated with a fairly consistent sandstone and siltstone geometry. Mineralization is only found where coalescence between the two sandstones has occurred and it disappears where the sandstones remain coalesced. At a point of coalescence the fluids from the upper and lower sandstone are mixed, the oxidizing fluid penetrating progressively deeper in the sandstone couplet until the entire couplet is oxidizing. This generates a weakly dipping REDOX front. The REDOX front is not considered strong enough to have precipitated uranyl carbonate complexes in transport

  13. 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

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

    Science.gov (United States)

    Kazadi Mbamba, Christian; Tait, Stephan; Flores-Alsina, Xavier; Batstone, Damien J

    2015-11-15

    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 existing wastewater treatment models. The present study systematically tested a semi-mechanistic modelling approach, using various experimental platforms with multiple minerals precipitation. Experiments included dynamic titration with addition of sodium hydroxide to synthetic wastewater, and aeration to progressively increase pH and induce precipitation in real piggery digestate and sewage sludge digestate. The model approach consisted of an equilibrium part for aqueous phase reactions and a kinetic part for minerals precipitation. The model was fitted to dissolved calcium, magnesium, total inorganic carbon and phosphate. Results indicated that precipitation was dominated by the mineral struvite, forming together with varied and minor amounts of calcium phosphate and calcium carbonate. The model approach was noted to have the advantage of requiring a minimal number of fitted parameters, so the model was readily identifiable. Kinetic rate coefficients, which were statistically fitted, were generally in the range 0.35-11.6 h(-1) with confidence intervals of 10-80% relative. Confidence regions for the kinetic rate coefficients were often asymmetric with model-data residuals increasing more gradually with larger coefficient values. This suggests that a large kinetic coefficient could be used when actual measured data is lacking for a particular precipitate-matrix combination. Correlation between the kinetic rate coefficients of different minerals was low, indicating that parameter values for individual minerals could be independently fitted (keeping all other model parameters constant). Implementation was therefore relatively flexible, and would be readily expandable to include other

  15. Chromate Adsorption on Selected Soil Minerals: Surface Complexation Modeling Coupled with Spectroscopic Investigation.

    Czech Academy of Sciences Publication Activity Database

    Veselská, V.; Fajgar, Radek; Číhalová, S.; Bolanz, R.M.; Göttlicher, J.; Steininger, R.; Siddique, J.A.; Komárek, M.

    2016-01-01

    Roč. 318, NOV 15 (2016), s. 433-442 ISSN 0304-3894 Institutional support: RVO:67985858 Keywords : surface complexation modeling * chromate * soil minerals Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 6.065, year: 2016

  16. Mineral-modeled ceramics for long-term storage of high-level nuclear wastes

    International Nuclear Information System (INIS)

    Vance, E.R.

    1980-01-01

    Over the past ten years, Penn State's Materials Research Laboratory has done extensive work on mineral-modeled ceramics for high-level nuclear waste storage. These ceramics are composed of several mineral analogues that form a monolithic polycrystalline aggregate. Mineral-modeling can be made in a similar fashion to nuclear waste glasses, and their naturally occurring analogues are known to last millions, and even billions, of years in hot, wet conditions. It is believed that such ceramics could reduce dispersal of radionuclides by leaching to a minimum

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

    OpenAIRE

    Ignat Ignatov; Oleg Mosin

    2014-01-01

    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 deh...

  18. Central Ukraine Uranium Province: The genetic model

    International Nuclear Information System (INIS)

    Emetz, A.; Cuney, M.

    2014-01-01

    ramifications or intersections. In such places albitites are often altered by superimposed calcic and potassic metasomatism resulting in the replacement of aegirine and riebeckite by garnet, epidote, actinolite, calcite and lamellar phlogopite accompanying U-mineralization. All types of the metasomatic alterations gradually pinch out with depth. U-mineralized metasomatites are enriched in a complex of elements typically accumulated in the crust during regional metamorphism, and partial melting as indicated by pegmatite dike swarms in the Ingul Megablock. From seismic data interpretation, all U deposits in the CUUP are located over latitudinal mantle “deeps” or in the zones where the base of the lithosphere contrastingly subsides. In conclusion, Na-metasomatism is interpreted as a regional process resulting from the deep penetration of marine waters down along crustal scale shear zones during an extensional tectonic regime causing the regional collapse of the Ingul Megablock. Calcic and potassic alterations and U-mineralization are possibly connected with the crust dehydration and probable hotspot partial melting in the mantle initiated by the most unstable P-T conditions within zones of contrasting thickness of the lithosphere. The proposed models of Na-metasomatism and U-accumulation are useful for delineation of prospective territories having the potential to host U deposits associated with Na-metasomatites in Proterozoic terrains. (author)

  19. Spatial arrangement of organic compounds on a model mineral surface: implications for soil organic matter stabilization.

    Science.gov (United States)

    Petridis, Loukas; Ambaye, Haile; Jagadamma, Sindhu; Kilbey, S Michael; Lokitz, Bradley S; Lauter, Valeria; Mayes, Melanie A

    2014-01-01

    The complexity of the mineral-organic carbon interface may influence the extent of stabilization of organic carbon compounds in soils, which is important for global climate futures. The nanoscale structure of a model interface was examined here by depositing films of organic carbon compounds of contrasting chemical character, hydrophilic glucose and amphiphilic stearic acid, onto a soil mineral analogue (Al2O3). Neutron reflectometry, a technique which provides depth-sensitive insight into the organization of the thin films, indicates that glucose molecules reside in a layer between Al2O3 and stearic acid, a result that was verified by water contact angle measurements. Molecular dynamics simulations reveal the thermodynamic driving force behind glucose partitioning on the mineral interface: The entropic penalty of confining the less mobile glucose on the mineral surface is lower than for stearic acid. The fundamental information obtained here helps rationalize how complex arrangements of organic carbon on soil mineral surfaces may arise.

  20. A Rational Model In Theoretical Genetics

    Directory of Open Access Journals (Sweden)

    Karl Javorszky

    2008-07-01

    Full Text Available This model connects information processing in biological organisms with methods and concepts used in classical, technical information processing. The central concept shows copying and regulatory interaction between a logical sequence consisting of triplets and the amount of constituents of a set. The basic mathematical model of information processing within a biological cell has been worked out. The cell in the model copies its present state into a sequence and reads it off the sequence. The sequence comes in triplets and is not one sequence but appears in two almost identical varieties. We treat consecutive and contemporary assemblies of information carrying media as equally suited to contain information. Methods used so far utilised the consecutive property of media, while in biology one observes the concurrent existence of specific realisations of possibilities. Genetics connects the two approaches by using an interplay between consecutively (sequentially ordered logical markers (the DNA and the state of the set engulfing the DNA. Several mathematical tools have been evolved to assemble an interface between sequentially ordered carriers and the same number of carriers if they arrive contemporaneously. Using linguistic theory and formal logic one concludes that measurement(s on a cell are a (set of logical sentence(s relating to an assembly of n objects with group structures among each other. We linearise and count all possible group relations on a set of n objects and introduce the concept of multidimensional partitions hitherto left undefined. We introduce the concept of a maximally structured set by establishing an upper limit to the information carrying capacity of n objects used commutatively and sequentially at the same time (like genetics does. The copying and re-copying mechanism which is the core matter with genetics appears in the model as differing transmission efficiency coefficients of media if the media are used once sequentially

  1. 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.

  2. 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.

  3. A facile in vitro model to study rapid mineralization in bone tissues.

    Science.gov (United States)

    Deegan, Anthony J; Aydin, Halil M; Hu, Bin; Konduru, Sandeep; Kuiper, Jan Herman; Yang, Ying

    2014-09-16

    Mineralization in bone tissue involves stepwise cell-cell and cell-ECM interaction. Regulation of osteoblast culture microenvironments can tailor osteoblast proliferation and mineralization rate, and the quality and/or quantity of the final calcified tissue. An in vitro model to investigate the influencing factors is highly required. We developed a facile in vitro model in which an osteoblast cell line and aggregate culture (through the modification of culture well surfaces) were used to mimic intramembranous bone mineralization. The effect of culture environments including culture duration (up to 72 hours for rapid mineralization study) and aggregates size (monolayer culture as control) on mineralization rate and mineral quantity/quality were examined by osteogenic gene expression (PCR) and mineral markers (histological staining, SEM-EDX and micro-CT). Two size aggregates (on average, large aggregates were 745 μm and small 79 μm) were obtained by the facile technique with high yield. Cells in aggregate culture generated visible and quantifiable mineralized matrix within 24 hours, whereas cells in monolayer failed to do so by 72 hours. The gene expression of important ECM molecules for bone formation including collagen type I, alkaline phosphatase, osteopontin and osteocalcin, varied temporally, differed between monolayer and aggregate cultures, and depended on aggregate size. Monolayer specimens stayed in a proliferation phase for the first 24 hours, and remained in matrix synthesis up to 72 hours; whereas the small aggregates were in the maturation phase for the first 24 and 48 hour cultures and then jumped to a mineralization phase at 72 hours. Large aggregates were in a mineralization phase at all these three time points and produced 36% larger bone nodules with a higher calcium content than those in the small aggregates after just 72 hours in culture. This study confirms that aggregate culture is sufficient to induce rapid mineralization and that aggregate

  4. 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.

  5. Linear Mixed Models in Statistical Genetics

    NARCIS (Netherlands)

    R. de Vlaming (Ronald)

    2017-01-01

    markdownabstractOne of the goals of statistical genetics is to elucidate the genetic architecture of phenotypes (i.e., observable individual characteristics) that are affected by many genetic variants (e.g., single-nucleotide polymorphisms; SNPs). A particular aim is to identify specific SNPs that

  6. 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

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

    Science.gov (United States)

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

    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

  8. 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

    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

  9. Testing the structure of a hydrological model using Genetic Programming

    Science.gov (United States)

    Selle, Benny; Muttil, Nitin

    2011-01-01

    SummaryGenetic Programming is able to systematically explore many alternative model structures of different complexity from available input and response data. We hypothesised that Genetic Programming can be used to test the structure of hydrological models and to identify dominant processes in hydrological systems. To test this, Genetic Programming was used to analyse a data set from a lysimeter experiment in southeastern Australia. The lysimeter experiment was conducted to quantify the deep percolation response under surface irrigated pasture to different soil types, watertable depths and water ponding times during surface irrigation. Using Genetic Programming, a simple model of deep percolation was recurrently evolved in multiple Genetic Programming runs. This simple and interpretable model supported the dominant process contributing to deep percolation represented in a conceptual model that was published earlier. Thus, this study shows that Genetic Programming can be used to evaluate the structure of hydrological models and to gain insight about the dominant processes in hydrological systems.

  10. Mouse genome-wide association and systems genetics identify Asxl2 as a regulator of bone mineral density and osteoclastogenesis.

    Directory of Open Access Journals (Sweden)

    Charles R Farber

    2011-04-01

    Full Text Available Significant advances have been made in the discovery of genes affecting bone mineral density (BMD; however, our understanding of its genetic basis remains incomplete. In the current study, genome-wide association (GWA and co-expression network analysis were used in the recently described Hybrid Mouse Diversity Panel (HMDP to identify and functionally characterize novel BMD genes. In the HMDP, a GWA of total body, spinal, and femoral BMD revealed four significant associations (-log10P>5.39 affecting at least one BMD trait on chromosomes (Chrs. 7, 11, 12, and 17. The associations implicated a total of 163 genes with each association harboring between 14 and 112 genes. This list was reduced to 26 functional candidates by identifying those genes that were regulated by local eQTL in bone or harbored potentially functional non-synonymous (NS SNPs. This analysis revealed that the most significant BMD SNP on Chr. 12 was a NS SNP in the additional sex combs like-2 (Asxl2 gene that was predicted to be functional. The involvement of Asxl2 in the regulation of bone mass was confirmed by the observation that Asxl2 knockout mice had reduced BMD. To begin to unravel the mechanism through which Asxl2 influenced BMD, a gene co-expression network was created using cortical bone gene expression microarray data from the HMDP strains. Asxl2 was identified as a member of a co-expression module enriched for genes involved in the differentiation of myeloid cells. In bone, osteoclasts are bone-resorbing cells of myeloid origin, suggesting that Asxl2 may play a role in osteoclast differentiation. In agreement, the knockdown of Asxl2 in bone marrow macrophages impaired their ability to form osteoclasts. This study identifies a new regulator of BMD and osteoclastogenesis and highlights the power of GWA and systems genetics in the mouse for dissecting complex genetic traits.

  11. 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.

  12. Discussion on geochemical characteristics, mechanism and prospecting model of gluey type sandstone uranium mineralization--taking Redwell uranium deposit as an example

    International Nuclear Information System (INIS)

    Wang Jinping

    1998-01-01

    Redwell uranium deposit hosted in the red clastic rock formation, is a typical example of gluey type uranium mineralization, which has not been reported so far in China. Based on the study of geochemical characteristics of Redwell deposit, the author discusses the genetic mechanism of this type deposits, and proposes the prospecting model of 4 in 1 of red bed-fault-oil gas-uranium source

  13. 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.

    2014-01-01

    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. PMID:24352669

  14. 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.

  15. Simplified models of rates of CO2 mineralization in Geologic Carbon Storage

    Science.gov (United States)

    DePaolo, D. J.; Zhang, S.

    2017-12-01

    Geologic carbon storage (GCS) reverses the flow of carbon to the atmosphere, returning the carbon to long-term geologic storage. Models suggest that most of the injected CO2 will be "trapped" in the subsurface by physical means, but the most risk-free and permanent form of carbon storage is as carbonate minerals (Ca,Mg,Fe)CO3. The transformation of CO2 to carbonate minerals requires supply of divalent cations by dissolution of silicate minerals. Available data suggest that rates of transformation are difficult to predict. We show that the chemical kinetic observations and experimental results, when reduced to a single timescale that describes the fractional rate at which cations are released to solution by mineral dissolution, show sufficiently systematic behavior that the rates of mineralization can be estimated with reasonable certainty. Rate of mineralization depends on both the abundance (determined by the reservoir rock mineralogy) and the rate at which cations are released by dissolution into pore fluid that has been acidified with dissolved CO2. Laboratory-measured rates and field observations give values spanning 8 to 10 orders of magnitude, but when evaluated in the context of reservoir-scale reactive transport simulations, this range becomes much smaller. Reservoir scale simulations indicate that silicate mineral dissolution and subsequent carbonate mineral precipitation occur at pH 4.5 to 6, fluid flow velocity less than 5m/yr, and 50-100 years or more after the start of injection. These constraints lead to estimates of 200 to 2000 years for conversion of 60-90% of injected CO2 when the reservoir rock has a sufficient volume fraction of divalent cation-bearing silicate minerals (ca. 20%), and confirms that when reservoir rock mineralogy is not favorable the fraction of CO2 converted to carbonate minerals is minimal over 104 years. A sufficient amount of reactive minerals represents the condition by which the available cations per volume of rock plus pore

  16. Testing the Structure of Hydrological Models using Genetic Programming

    Science.gov (United States)

    Selle, B.; Muttil, N.

    2009-04-01

    Genetic Programming is able to systematically explore many alternative model structures of different complexity from available input and response data. We hypothesised that genetic programming can be used to test the structure hydrological models and to identify dominant processes in hydrological systems. To test this, genetic programming was used to analyse a data set from a lysimeter experiment in southeastern Australia. The lysimeter experiment was conducted to quantify the deep percolation response under surface irrigated pasture to different soil types, water table depths and water ponding times during surface irrigation. Using genetic programming, a simple model of deep percolation was consistently evolved in multiple model runs. This simple and interpretable model confirmed the dominant process contributing to deep percolation represented in a conceptual model that was published earlier. Thus, this study shows that genetic programming can be used to evaluate the structure of hydrological models and to gain insight about the dominant processes in hydrological systems.

  17. Determination of bone mineral volume fraction using impedance analysis and Bruggeman model

    Energy Technology Data Exchange (ETDEWEB)

    Ciuchi, Ioana Veronica; Olariu, Cristina Stefania, E-mail: oocristina@yahoo.com; Mitoseriu, Liliana, E-mail: lmtsr@uaic.ro

    2013-11-20

    Highlights: • Mineral volume fraction of a bone sample was determined. • Dielectric properties for bone sample and for the collagen type I were determined by impedance spectroscopy. • Bruggeman effective medium approximation was applied in order to evaluate mineral volume fraction of the sample. • The computed values were compared with ones derived from a histogram test performed on SEM micrographs. -- Abstract: Measurements by impedance spectroscopy and Bruggeman effective medium approximation model were employed in order to determine the mineral volume fraction of dry bone. This approach assumes that two or more phases are present into the composite: the matrix (environment) and the other ones are inclusion phases. A fragment of femur diaphysis dense bone from a young pig was investigated in its dehydrated state. Measuring the dielectric properties of bone and its main components (hydroxyapatite and collagen) and using the Bruggeman approach, the mineral volume filling factor was determined. The computed volume fraction of the mineral volume fraction was confirmed by a histogram test analysis based on the SEM microstructures. In spite of its simplicity, the method provides a good approximation for the bone mineral volume fraction. The method which uses impedance spectroscopy and EMA modeling can be further developed by considering the conductive components of the bone tissue as a non-invasive in situ impedance technique for bone composition evaluation and monitoring.

  18. Determination of bone mineral volume fraction using impedance analysis and Bruggeman model

    International Nuclear Information System (INIS)

    Ciuchi, Ioana Veronica; Olariu, Cristina Stefania; Mitoseriu, Liliana

    2013-01-01

    Highlights: • Mineral volume fraction of a bone sample was determined. • Dielectric properties for bone sample and for the collagen type I were determined by impedance spectroscopy. • Bruggeman effective medium approximation was applied in order to evaluate mineral volume fraction of the sample. • The computed values were compared with ones derived from a histogram test performed on SEM micrographs. -- Abstract: Measurements by impedance spectroscopy and Bruggeman effective medium approximation model were employed in order to determine the mineral volume fraction of dry bone. This approach assumes that two or more phases are present into the composite: the matrix (environment) and the other ones are inclusion phases. A fragment of femur diaphysis dense bone from a young pig was investigated in its dehydrated state. Measuring the dielectric properties of bone and its main components (hydroxyapatite and collagen) and using the Bruggeman approach, the mineral volume filling factor was determined. The computed volume fraction of the mineral volume fraction was confirmed by a histogram test analysis based on the SEM microstructures. In spite of its simplicity, the method provides a good approximation for the bone mineral volume fraction. The method which uses impedance spectroscopy and EMA modeling can be further developed by considering the conductive components of the bone tissue as a non-invasive in situ impedance technique for bone composition evaluation and monitoring

  19. 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 co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......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...

  20. 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 co...... applications. The methods presented are implemented in such a way that large and complex quantitative genetic data can be analyzed......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...

  1. The stratigraphy of the Malmani dolomite subgroup in the Carletonville area, Transvaal: genetic implications for lead-zinc mineralization

    International Nuclear Information System (INIS)

    Clay, A.N.

    1986-01-01

    The geological setting of a borehole intersection of lead-zinc mineralization in the Malmani Dolomite Subgroup in the Carletonville area is discussed. It is suggested that the lead and zinc ions were derived from the overlying shales, transported as bisulphide complexes in silica-enriched, alkaline solutions, and deposited during silicification in the upper part of the dolomite succession which contains relic evaporites. Lead isotope data suggests that the known lead-zinc deposits in the Transvaal sequence are not of major importance. However, the dolomites are regarded as very probable hosts for Mississippi Valley type base metal deposits and offer important exploration targets. This study includes lead isotopic data. Lead isotope compositions and model lead ages for galenas in the zinc deposits are shown. It is concluded that the leads have undergone either a two-stage evolution process, or have mixed with 206 Pb-enriched ores. Model ages suggest that the lead was derived from an approximate 2,7 Ga source and that mineralization took place at 1,7 Ga

  2. Animal models for human genetic diseases | Sharif | African Journal ...

    African Journals Online (AJOL)

    The study of human genetic diseases can be greatly aided by animal models because of their similarity to humans in terms of genetics. In addition to understand diverse aspects of basic biology, model organisms are extensively used in applied research in agriculture, industry, and also in medicine, where they are used to ...

  3. Teaching Genetic Counseling Skills: Incorporating a Genetic Counseling Adaptation Continuum Model to Address Psychosocial Complexity.

    Science.gov (United States)

    Shugar, Andrea

    2017-04-01

    Genetic counselors are trained health care professionals who effectively integrate both psychosocial counseling and information-giving into their practice. Preparing genetic counseling students for clinical practice is a challenging task, particularly when helping them develop effective and active counseling skills. Resistance to incorporating these skills may stem from decreased confidence, fear of causing harm or a lack of clarity of psycho-social goals. The author reflects on the personal challenges experienced in teaching genetic counselling students to work with psychological and social complexity, and proposes a Genetic Counseling Adaptation Continuum model and methodology to guide students in the use of advanced counseling skills.

  4. 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.

  5. Research on interactive genetic-geological models to evaluate favourability for undiscovered uranium resources

    International Nuclear Information System (INIS)

    Finch, W.I.; Granger, H.C.; Lupe, R.; McCammon, R.B.

    1980-01-01

    Current methods of evaluating favourability for undiscovered uranium resources are unduly subjective, quite possibly inconsistent and, as a consequence, of questionable reliability. This research is aimed at reducing the subjectivity and increasing the reliability by designing an improved method that depends largely on geological data and their statistical frequency of occurrence. This progress report outlines a genetic approach to modelling the geological factors that controlled uranium mineralization in order to evaluate the favourability for the occurrence of undiscovered uranium deposits of the type modelled. A genetic model is constructed from all the factors that describe the processes, in chronological sequence, that formed uranium deposits thought to have a common origin. The field and laboratory evidence for the processes constitute a geologic-occurrence base that parallels the chronological sequence of events. The genetic model and the geologic-occurrence base are portrayed as two columns of an interactive matrix called the ''genetic-geologic model''. For each column, eight chronological stages are used to describe the overall formation of the uranium deposits. These stages consist of (1) precursor processes; (2) host-rock formation; (3) preparation of host-rock; (4) uranium-source development; (5) transport of uranium; (6) primary uranium deposition; (7) post-deposition modification; and (8) preservation. To apply the genetic-geological model to evaluate favourability, a question is posed that determines the presence or absence of each attribute listed under the geologic-occurrence base. By building a logic circuit of the attributes according to either their essential or non-essential nature, the resultant match between a well-documented control area and the test area may be determined. The degree of match is a measure of favourability for uranium occurrence as hypothesized in the genetic model

  6. Evaluating Ice Nucleating Particle Concentrations From Prognostic Dust Minerals in an Earth System Model

    Science.gov (United States)

    Perlwitz, J. P.; Knopf, D. A.; Fridlind, A. M.; Miller, R. L.; Pérez García-Pando, C.; DeMott, P. J.

    2016-12-01

    The effect of aerosol particles on the radiative properties of clouds, the so-called, indirect effect of aerosols, is recognized as one of the largest sources of uncertainty in climate prediction. The distribution of water vapor, precipitation, and ice cloud formation are influenced by the atmospheric ice formation, thereby modulating cloud albedo and thus climate. It is well known that different particle types possess different ice formation propensities with mineral dust being a superior ice nucleating particle (INP) compared to soot particles. Furthermore, some dust mineral types are more proficient INP than others, depending on temperature and relative humidity.In recent work, we have presented an improved dust aerosol module in the NASA GISS Earth System ModelE2 with prognostic mineral composition of the dust aerosols. Thus, there are regional variations in dust composition. We evaluated the predicted mineral fractions of dust aerosols by comparing them to measurements from a compilation of about 60 published literature references. Additionally, the capability of the model to reproduce the elemental composition of the simulated dusthas been tested at Izana Observatory at Tenerife, Canary Islands, which is located off-shore of Africa and where frequent dust events are observed. We have been able to show that the new approach delivers a robust improvement of the predicted mineral fractions and elemental composition of dust.In the current study, we use three-dimensional dust mineral fields and thermodynamic conditions, which are simulated using GISS ModelE, to calculate offline the INP concentrations derived using different ice nucleation parameterizations that are currently discussed. We evaluate the calculated INP concentrations from the different parameterizations by comparing them to INP concentrations from field measurements.

  7. 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.

  8. Explanatory models of black lung: understanding the health-related behavior of Appalachian coal miners.

    Science.gov (United States)

    Friedl, J

    1982-03-01

    Many retired coal miners who are eligible for care in a black lung treatment center at little or no cost to themselves do not enter into available programs or discontinue soon after beginning therapy. Reasons for this behavior are related to the prevalent beliefs among Appalachians concerning the course of black lung and the appropriate treatment for it. The miners' health beliefs are clearly at odds with those of the health care providers who work in the centers. Using the concept of explanatory model, popular and professional health cultures are analyzed, focusing on course of disease, sick role, appropriate treatment, and expected outcome. Differences in explanatory models are discussed with regard to implications for the organization and delivery of care to retired coal miners with black lung.

  9. Geology of gemstone deposit Ugljarevats (Central Serbia) and contributions to genetic model

    International Nuclear Information System (INIS)

    Kureshevicj, Lidija; Vushovicj, Olivera; Delicj-Nikolicj, Ivana

    2017-01-01

    Silica gemstone deposit Ugljarevats is situated within the ophiolite sequence of the Vardar zone central deep fault. Genetic processes of this deposit are connected to the Neogene calc-alkaline magmatic activity of the Vardar zone and hydrothermal activity triggered by it. Based on surface occurrences of listwenitized serpentinite containing silica mineralization, it can be inferred that the ore body is an elongated oval stock. Within the stock of hydrothermally altered serpentinite, the gemstone mineralization occurs as veins, stock works and irregular bodies. Present gemstone types include chalcedony varieties (jasper, colourless and greenish chalcedony, carnelian and sard) and opal (opalized serpentinite). Homogenous pieces are very rare. Most often, various types of silica are intimately intermixed and combined. The mineralization has formed in two distinct hydrothermal phases, apparently in close time succession. Jasper and coloured chalcedony (and rare magnesite) are the products of the first phase of hydro- thermal activity, while the colourless chalcedony is formed in the second phase. Newly discovered type of silica vein with central-symmetrical parallel banding gives new contributions to a genetic model, proving the precipitation process and its products are unpredictably changeable, heterogeneous and depending on the evolution of the local environment physico-chemical conditions, notably the contents of impurities and system's openness degree. (author)

  10. Toward a mineral physics reference model for the Moon's core.

    Science.gov (United States)

    Antonangeli, Daniele; Morard, Guillaume; Schmerr, Nicholas C; Komabayashi, Tetsuya; Krisch, Michael; Fiquet, Guillaume; Fei, Yingwei

    2015-03-31

    The physical properties of iron (Fe) at high pressure and high temperature are crucial for understanding the chemical composition, evolution, and dynamics of planetary interiors. Indeed, the inner structures of the telluric planets all share a similar layered nature: a central metallic core composed mostly of iron, surrounded by a silicate mantle, and a thin, chemically differentiated crust. To date, most studies of iron have focused on the hexagonal closed packed (hcp, or ε) phase, as ε-Fe is likely stable across the pressure and temperature conditions of Earth's core. However, at the more moderate pressures characteristic of the cores of smaller planetary bodies, such as the Moon, Mercury, or Mars, iron takes on a face-centered cubic (fcc, or γ) structure. Here we present compressional and shear wave sound velocity and density measurements of γ-Fe at high pressures and high temperatures, which are needed to develop accurate seismic models of planetary interiors. Our results indicate that the seismic velocities proposed for the Moon's inner core by a recent reanalysis of Apollo seismic data are well below those of γ-Fe. Our dataset thus provides strong constraints to seismic models of the lunar core and cores of small telluric planets. This allows us to propose a direct compositional and velocity model for the Moon's core.

  11. Modelling the incongruent dissolution of hydrated cement minerals

    International Nuclear Information System (INIS)

    Berner, U.R.

    1988-01-01

    Hydrated calciumsilicates are the main constituents of hydrated portland cements. Their chemistry will strongly influence the longterm behaviour of a concrete system envisioned in use in radioactive waste repositories. Experimental data show that hydrated calciumsilicates dissolve incongruently, depending on the calcium/silicon ratio of the solid. A model that simulates the incongruent dissolution behaviour of these hydrated calciumsilicates is presented. In the model the hydrated calciumcilicates are represented as a mixture of two congruently soluble components. The dissolution of the particular components is described using the concept of variable activities in the solid state. Each component's activity in the solid state is obtained from a large body of solubility data by applying the Gibbs-Duhem equation for nonideal mixtures. Using this approach a simplified set of equations, which describe the solubility of the components as a function of the calcium/silicon ratio of the solid, is derived. As an application, the degradation of a standard portland cement in pure water and in a carbonate-rich groundwater is modelled. (orig.)

  12. Mineral potential modelling of gold and silver mineralization in the Nevada Great Basin - a GIS-based analysis using weights of evidence

    Science.gov (United States)

    Mihalasky, Mark J.

    2001-01-01

    The distribution of 2,690 gold-silver-bearing occurrences in the Nevada Great Basin was examined in terms of spatial association with various geological phenomena. Analysis of these relationships, using GIS and weights of evidence modelling techniques, has predicted areas of high mineral potential where little or no mining activity exists. Mineral potential maps for sedimentary (?disseminated?) and volcanic (?epithermal?) rock-hosted gold-silver mineralization revealed two distinct patterns that highlight two sets of crustal-scale geologic features that likely control the regional distribution of these deposit types. The weights of evidence method is a probability-based technique for mapping mineral potential using the spatial distribution of known mineral occurrences. Mineral potential maps predicting the distribution of gold-silver-bearing occurrences were generated from structural, geochemical, geomagnetic, gravimetric, lithologic, and lithotectonic-related deposit-indicator factors. The maps successfully predicted nearly 70% of the total number of known occurrences, including ~83% of sedimentary and ~60% of volcanic rock-hosted types. Sedimentary and volcanic rockhosted mineral potential maps showed high spatial correlation (an area cross-tabulation agreement of 85% and 73%, respectively) with expert-delineated mineral permissive tracts. In blind tests, the sedimentary and volcanic rock-hosted mineral potential maps predicted 10 out of 12 and 5 out of 5 occurrences, respectively. The key mineral predictor factors, in order of importance, were determined to be: geology (including lithology, structure, and lithotectonic terrane), geochemistry (indication of alteration), and geophysics. Areas of elevated sedimentary rock-hosted mineral potential are generally confined to central, north-central, and north-eastern Nevada. These areas form a conspicuous ?V?-shape pattern that is coincident with the Battle Mountain-Eureka (Cortez) and Carlin mineral trends and a

  13. 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

    is appropriate if the study design has a hierarchical structure as in our scenario. We used the Estonian National Soil Monitoring data on arable lands to predict SOC concentrations of mineral soils. Subsequently, the model with the best prediction accuracy was applied to the Estonian digital soil map...

  14. Simulating pattern-process relationships to validate landscape genetic models

    Science.gov (United States)

    A. J. Shirk; S. A. Cushman; E. L. Landguth

    2012-01-01

    Landscapes may resist gene flow and thereby give rise to a pattern of genetic isolation within a population. The mechanism by which a landscape resists gene flow can be inferred by evaluating the relationship between landscape models and an observed pattern of genetic isolation. This approach risks false inferences because researchers can never feasibly test all...

  15. Developing robotic behavior using a genetic programming model

    International Nuclear Information System (INIS)

    Pryor, R.J.

    1998-01-01

    This report describes the methodology for using a genetic programming model to develop tracking behaviors for autonomous, microscale robotic vehicles. The use of such vehicles for surveillance and detection operations has become increasingly important in defense and humanitarian applications. Through an evolutionary process similar to that found in nature, the genetic programming model generates a computer program that when downloaded onto a robotic vehicle's on-board computer will guide the robot to successfully accomplish its task. Simulations of multiple robots engaged in problem-solving tasks have demonstrated cooperative behaviors. This report also discusses the behavior model produced by genetic programming and presents some results achieved during the study

  16. Eco-genetic modeling of contemporary life-history evolution.

    Science.gov (United States)

    Dunlop, Erin S; Heino, Mikko; Dieckmann, Ulf

    2009-10-01

    We present eco-genetic modeling as a flexible tool for exploring the course and rates of multi-trait life-history evolution in natural populations. We build on existing modeling approaches by combining features that facilitate studying the ecological and evolutionary dynamics of realistically structured populations. In particular, the joint consideration of age and size structure enables the analysis of phenotypically plastic populations with more than a single growth trajectory, and ecological feedback is readily included in the form of density dependence and frequency dependence. Stochasticity and life-history trade-offs can also be implemented. Critically, eco-genetic models permit the incorporation of salient genetic detail such as a population's genetic variances and covariances and the corresponding heritabilities, as well as the probabilistic inheritance and phenotypic expression of quantitative traits. These inclusions are crucial for predicting rates of evolutionary change on both contemporary and longer timescales. An eco-genetic model can be tightly coupled with empirical data and therefore may have considerable practical relevance, in terms of generating testable predictions and evaluating alternative management measures. To illustrate the utility of these models, we present as an example an eco-genetic model used to study harvest-induced evolution of multiple traits in Atlantic cod. The predictions of our model (most notably that harvesting induces a genetic reduction in age and size at maturation, an increase or decrease in growth capacity depending on the minimum-length limit, and an increase in reproductive investment) are corroborated by patterns observed in wild populations. The predicted genetic changes occur together with plastic changes that could phenotypically mask the former. Importantly, our analysis predicts that evolutionary changes show little signs of reversal following a harvest moratorium. This illustrates how predictions offered by

  17. Can genetics help psychometrics? Improving dimensionality assessment through genetic factor modeling.

    Science.gov (United States)

    Franić, Sanja; Dolan, Conor V; Borsboom, Denny; Hudziak, James J; van Beijsterveldt, Catherina E M; Boomsma, Dorret I

    2013-09-01

    In the present article, we discuss the role that quantitative genetic methodology may play in assessing and understanding the dimensionality of psychological (psychometric) instruments. Specifically, we study the relationship between the observed covariance structures, on the one hand, and the underlying genetic and environmental influences giving rise to such structures, on the other. We note that this relationship may be such that it hampers obtaining a clear estimate of dimensionality using standard tools for dimensionality assessment alone. One situation in which dimensionality assessment may be impeded is that in which genetic and environmental influences, of which the observed covariance structure is a function, differ from each other in structure and dimensionality. We demonstrate that in such situations settling dimensionality issues may be problematic, and propose using quantitative genetic modeling to uncover the (possibly different) dimensionalities of the underlying genetic and environmental structures. We illustrate using simulations and an empirical example on childhood internalizing problems.

  18. Comparing estimates of genetic variance across different relationship models.

    Science.gov (United States)

    Legarra, Andres

    2016-02-01

    Use of relationships between individuals to estimate genetic variances and heritabilities via mixed models is standard practice in human, plant and livestock genetics. Different models or information for relationships may give different estimates of genetic variances. However, comparing these estimates across different relationship models is not straightforward as the implied base populations differ between relationship models. In this work, I present a method to compare estimates of variance components across different relationship models. I suggest referring genetic variances obtained using different relationship models to the same reference population, usually a set of individuals in the population. Expected genetic variance of this population is the estimated variance component from the mixed model times a statistic, Dk, which is the average self-relationship minus the average (self- and across-) relationship. For most typical models of relationships, Dk is close to 1. However, this is not true for very deep pedigrees, for identity-by-state relationships, or for non-parametric kernels, which tend to overestimate the genetic variance and the heritability. Using mice data, I show that heritabilities from identity-by-state and kernel-based relationships are overestimated. Weighting these estimates by Dk scales them to a base comparable to genomic or pedigree relationships, avoiding wrong comparisons, for instance, "missing heritabilities". Copyright © 2015 Elsevier Inc. All rights reserved.

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

    International Nuclear Information System (INIS)

    Yu Along

    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

  20. PM Synchronous Motor Dynamic Modeling with Genetic Algorithm ...

    African Journals Online (AJOL)

    Adel

    This paper proposes dynamic modeling simulation for ac Surface Permanent Magnet Synchronous ... Simulations are implemented using MATLAB with its genetic algorithm toolbox. .... selection, the process that drives biological evolution.

  1. 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

  2. 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

  3. Short communication: Genetic lag represents commercial herd genetic merit more accurately than the 4-path selection model.

    Science.gov (United States)

    Dechow, C D; Rogers, G W

    2018-05-01

    Expectation of genetic merit in commercial dairy herds is routinely estimated using a 4-path genetic selection model that was derived for a closed population, but commercial herds using artificial insemination sires are not closed. The 4-path model also predicts a higher rate of genetic progress in elite herds that provide artificial insemination sires than in commercial herds that use such sires, which counters other theoretical assumptions and observations of realized genetic responses. The aim of this work is to clarify whether genetic merit in commercial herds is more accurately reflected under the assumptions of the 4-path genetic response formula or by a genetic lag formula. We demonstrate by tracing the transmission of genetic merit from parents to offspring that the rate of genetic progress in commercial dairy farms is expected to be the same as that in the genetic nucleus. The lag in genetic merit between the nucleus and commercial farms is a function of sire and dam generation interval, the rate of genetic progress in elite artificial insemination herds, and genetic merit of sires and dams. To predict how strategies such as the use of young versus daughter-proven sires, culling heifers following genomic testing, or selective use of sexed semen will alter genetic merit in commercial herds, genetic merit expectations for commercial herds should be modeled using genetic lag expectations. Copyright © 2018 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  4. U-Pb age for some base-metal sulfide deposits in Ireland: genetic implications for Mississippi Valley-type mineralization

    International Nuclear Information System (INIS)

    Duane, M.J.; Welke, H.J.; Allsopp, H.L.

    1986-01-01

    Evidence is presented that links the timing of vein-type (Cu-Ag(U)) to stratiform Mississippi Valley-type (MVT, Pb-Zn) ore events in Ireland. The rare occurrence of pitchblende, coffinite(?), and brannerite mineralization, which is regarded as a precursor component to the sulfide mineralization in the Gortdrum deposit (Ireland), provides the first direct radiometric dating tool for these carbonate-hosted deposits. The U-Pb (340 +25/-20 Ma) and Pb-Pb (359 +/- 26 Ma) whole-rock ages constrain the uranium and base-metal mineralizing events to the Early Carboniferous. The data support a model according to which MVT and earlier uranium mineralization stages of some major ore bodies resulted from fracturing coincident with large basin-dewatering events. The Pb-Pb and concordia data are consistent with an Early Carboniferous age for the mineralization at Gortdrum and agree closely with a previously published Rb-Sr age of 359 +/- 22 Ma, obtained for Missouri glauconites. Furthermore, other comparative geologic data from Ireland and from North American MVT mineral provinces support a model of Pb-Zn-Cu(U) mobilization on a regional scale that implicates the later closing stages of the proto-Atlantic. 40 references, 3 figures, 1 table

  5. Use of mineral physics, with geodynamic modelling and seismology, to investigate flow in the Earth's mantle

    International Nuclear Information System (INIS)

    Blackman, D K

    2007-01-01

    Seismologists and mineral physicists have known for decades that anisotropy inherent in mantle minerals could provide a means to relate surface seismic measurements to deformation patterns at great depth in the Earth, where direct geologic observations would never be possible. Prior to the past decade, only qualitative relationships or simple symmetry assumptions between mantle flow (deformation), mineral alignment and seismic anisotropy were possible. Recent numerical methods now allow quantitative incorporation of constraints from mineral physics to flow/deformation models and, thereby, direct estimates of the resulting pattern of seismic anisotropy can be made and compared with observed signatures. Numerical methods for simulating microstructural deformation within an aggregate of minerals subjected to an arbitrary stress field make it possible to quantitatively link crystal-scale processes with large-scale Earth processes of mantle flow and seismic wave propagation, on regional (100s of kilometres) and even global scales. Such linked numerical investigations provide a rich field for exploring inter-dependences of micro and macro processes, as well as a means to determine the extents to which viable seismic experiments could discern between different models of Earth structure and dynamics. The aim of this review is to provide an overview of why and how linked numerical models are useful for exploring processes in the mantle and how they relate to surface tectonics. A brief introduction to the basic concepts of deformation of mantle minerals and the limits of knowledge currently available are designed to serve both the subsequent discussions in this review and as an entry point to more detailed literature for readers interested in pursuing the topic further. The reference list includes both primary sources and pertinent review articles on individual aspects of the combined subjects covered in the review. A series of flow/texturing models illustrate the

  6. Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma) in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

    Science.gov (United States)

    Sánchez-de la Vega, Guillermo; Castellanos-Morales, Gabriela; Gámez, Niza; Hernández-Rosales, Helena S.; Vázquez-Lobo, Alejandra; Aguirre-Planter, Erika; Jaramillo-Correa, Juan P.; Montes-Hernández, Salvador; Lira-Saade, Rafael; Eguiarte, Luis E.

    2018-01-01

    Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites) to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs) for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago) to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma). Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST) among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango). We detected low levels of gene

  7. Genetic Resources in the “Calabaza Pipiana” Squash (Cucurbita argyrosperma in Mexico: Genetic Diversity, Genetic Differentiation and Distribution Models

    Directory of Open Access Journals (Sweden)

    Guillermo Sánchez-de la Vega

    2018-03-01

    Full Text Available Analyses of genetic variation allow understanding the origin, diversification and genetic resources of cultivated plants. Domesticated taxa and their wild relatives are ideal systems for studying genetic processes of plant domestication and their joint is important to evaluate the distribution of their genetic resources. Such is the case of the domesticated subspecies C. argyrosperma ssp. argyrosperma, known in Mexico as calabaza pipiana, and its wild relative C. argyrosperma ssp. sororia. The main aim of this study was to use molecular data (microsatellites to assess the levels of genetic variation and genetic differentiation within and among populations of domesticated argyrosperma across its distribution in Mexico in comparison to its wild relative, sororia, and to identify environmental suitability in previously proposed centers of domestication. We analyzed nine unlinked nuclear microsatellite loci to assess levels of diversity and distribution of genetic variation within and among populations in 440 individuals from 19 populations of cultivated landraces of argyrosperma and from six wild populations of sororia, in order to conduct a first systematic analysis of their genetic resources. We also used species distribution models (SDMs for sororia to identify changes in this wild subspecies’ distribution from the Holocene (∼6,000 years ago to the present, and to assess the presence of suitable environmental conditions in previously proposed domestication sites. Genetic variation was similar among subspecies (HE = 0.428 in sororia, and HE = 0.410 in argyrosperma. Nine argyrosperma populations showed significant levels of inbreeding. Both subspecies are well differentiated, and genetic differentiation (FST among populations within each subspecies ranged from 0.152 to 0.652. Within argyrosperma we found three genetic groups (Northern Mexico, Yucatan Peninsula, including Michoacan and Veracruz, and Pacific coast plus Durango. We detected low

  8. The genetic analysis of repeated measures I: Simplex models

    NARCIS (Netherlands)

    Molenaar, P.C.M.; Boomsma, D.I.

    1987-01-01

    Extends the simplex model to a model that may be used for the genetic and environmental analysis of covariance (ANCOVA) structures. This "double" simplex structure can be specified as a linear structural relationships model. It is shown that data that give rise to a simplex correlation structure,

  9. 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.

  10. Probabilistic failure analysis of bone using a finite element model of mineral-collagen composites.

    Science.gov (United States)

    Dong, X Neil; Guda, Teja; Millwater, Harry R; Wang, Xiaodu

    2009-02-09

    Microdamage accumulation is a major pathway for energy dissipation during the post-yield deformation of bone. In this study, a two-dimensional probabilistic finite element model of a mineral-collagen composite was developed to investigate the influence of the tissue and ultrastructural properties of bone on the evolution of microdamage from an initial defect in tension. The probabilistic failure analyses indicated that the microdamage progression would be along the plane of the initial defect when the debonding at mineral-collagen interfaces was either absent or limited in the vicinity of the defect. In this case, the formation of a linear microcrack would be facilitated. However, the microdamage progression would be scattered away from the initial defect plane if interfacial debonding takes place at a large scale. This would suggest the possible formation of diffuse damage. In addition to interfacial debonding, the sensitivity analyses indicated that the microdamage progression was also dependent on the other material and ultrastructural properties of bone. The intensity of stress concentration accompanied with microdamage progression was more sensitive to the elastic modulus of the mineral phase and the nonlinearity of the collagen phase, whereas the scattering of failure location was largely dependent on the mineral to collagen ratio and the nonlinearity of the collagen phase. The findings of this study may help understanding the post-yield behavior of bone at the ultrastructural level and shed light on the underlying mechanism of bone fractures.

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

    International Nuclear Information System (INIS)

    Smith, David E.

    2000-01-01

    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

  12. The dissolution rate of silicate glasses and minerals: an alternative model based on several activated complexes

    International Nuclear Information System (INIS)

    Berger, G.

    1997-01-01

    Most of the mineral reactions in natural water-rock systems progress at conditions close to the chemical equilibrium. The kinetics of these reactions, in particular the dissolution rate of the primary minerals, is a major constrain for the numerical modelling of diagenetic and hydrothermal processes. In the case of silicates, recent experimental studies have pointed out the necessity to better understand the elementary reactions which control the dissolution process. This article presents several models that have been proposed to account for the observed dissolution rate/chemical affinity relationships. The case of glasses (R7T7), feldspars and clays, in water, in near neutral pH aqueous solutions and in acid/basic media, are reviewed. (A.C.)

  13. Probabilistic Failure Analysis of Bone Using a Finite Element Model of Mineral-Collagen Composites

    OpenAIRE

    Dong, X. Neil; Guda, Teja; Millwater, Harry R.; Wang, Xiaodu

    2008-01-01

    Microdamage accumulation is a major pathway for energy dissipation during the post-yield deformation of bone. In this study, a two-dimensional probabilistic finite element model of a mineral-collagen composite was developed to investigate the influence of the tissue and ultrastructural properties of bone on the evolution of microdamage from an initial defect in tension. The probabilistic failure analyses indicated that the microdamage progression would be along the plane of the initial defect...

  14. Impact of organic-mineral matter interactions on thermal reaction pathways for coal model compounds

    Energy Technology Data Exchange (ETDEWEB)

    Buchanan, A.C. III; Britt, P.F.; Struss, J.A. [Oak Ridge National Lab., TN (United States). Chemical and Analytical Sciences Div.

    1995-07-01

    Coal is a complex, heterogeneous solid that includes interdispersed mineral matter. However, knowledge of organic-mineral matter interactions is embryonic, and the impact of these interactions on coal pyrolysis and liquefaction is incomplete. Clay minerals, for example, are known to be effective catalysts for organic reactions. Furthermore, clays such as montmorillonite have been proposed to be key catalysts in the thermal alteration of lignin into vitrinite during the coalification process. Recent studies by Hatcher and coworkers on the evolution of coalified woods using microscopy and NMR have led them to propose selective, acid-catalyzed, solid state reaction chemistry to account for retained structural integrity in the wood. However, the chemical feasibility of such reactions in relevant solids is difficult to demonstrate. The authors have begun a model compound study to gain a better molecular level understanding of the effects in the solid state of organic-mineral matter interactions relevant to both coal formation and processing. To satisfy the need for model compounds that remain nonvolatile solids at temperatures ranging to 450 C, model compounds are employed that are chemically bound to the surface of a fumed silica (Si-O-C{sub aryl}linkage). The organic structures currently under investigation are phenethyl phenyl ether (C{sub 6}H{sub 5}CH{sub 2}CH{sub 2}OC{sub 6}H{sub 5}) derivatives, which serve as models for {beta}-alkyl aryl ether units that are present in lignin and lignitic coals. The solid-state chemistry of these materials at 200--450 C in the presence of interdispersed acid catalysts such as small particle size silica-aluminas and montmorillonite clay will be reported. Initial focus will be on defining the potential impact of these interactions on coal pyrolysis and liquefaction.

  15. 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.

  16. Population genetics of Setaria viridis, a new model system.

    Science.gov (United States)

    Huang, Pu; Feldman, Maximilian; Schroder, Stephan; Bahri, Bochra A; Diao, Xianmin; Zhi, Hui; Estep, Matt; Baxter, Ivan; Devos, Katrien M; Kellogg, Elizabeth A

    2014-10-01

    An extensive survey of the standing genetic variation in natural populations is among the priority steps in developing a species into a model system. In recent years, green foxtail (Setaria viridis), along with its domesticated form foxtail millet (S. italica), has rapidly become a promising new model system for C4 grasses and bioenergy crops, due to its rapid life cycle, large amount of seed production and small diploid genome, among other characters. However, remarkably little is known about the genetic diversity in natural populations of this species. In this study, we survey the genetic diversity of a worldwide sample of more than 200 S. viridis accessions, using the genotyping-by-sequencing technique. Two distinct genetic groups in S. viridis and a third group resembling S. italica were identified, with considerable admixture among the three groups. We find the genetic variation of North American S. viridis correlates with both geography and climate and is representative of the total genetic diversity in this species. This pattern may reflect several introduction/dispersal events of S. viridis into North America. We also modelled demographic history and show signal of recent population decline in one subgroup. Finally, we show linkage disequilibrium decay is rapid (<45 kb) in our total sample and slow in genetic subgroups. These results together provide an in-depth understanding of the pattern of genetic diversity of this new model species on a broad geographic scale. They also provide key guidelines for on-going and future work including germplasm preservation, local adaptation, crossing designs and genomewide association studies. © 2014 John Wiley & Sons Ltd.

  17. Random forest predictive modeling of mineral prospectivity with small number of prospects and data with missing values in Abra (Philippines)

    Science.gov (United States)

    Carranza, Emmanuel John M.; Laborte, Alice G.

    2015-01-01

    Machine learning methods that have been used in data-driven predictive modeling of mineral prospectivity (e.g., artificial neural networks) invariably require large number of training prospect/locations and are unable to handle missing values in certain evidential data. The Random Forests (RF) algorithm, which is a machine learning method, has recently been applied to data-driven predictive mapping of mineral prospectivity, and so it is instructive to further study its efficacy in this particular field. This case study, carried out using data from Abra (Philippines), examines (a) if RF modeling can be used for data-driven modeling of mineral prospectivity in areas with a few (i.e., individual layers of evidential data. Furthermore, RF modeling can handle missing values in evidential data through an RF-based imputation technique whereas in WofE modeling values are simply represented by zero weights. Therefore, the RF algorithm is potentially more useful than existing methods that are currently used for data-driven predictive mapping of mineral prospectivity. In particular, it is not a purely black-box method like artificial neural networks in the context of data-driven predictive modeling of mineral prospectivity. However, further testing of the method in other areas with a few mineral occurrences is needed to fully investigate its usefulness in data-driven predictive modeling of mineral prospectivity.

  18. Intrusion-Related Gold Deposits: New insights from gravity and hydrothermal integrated 3D modeling applied to the Tighza gold mineralization (Central Morocco)

    Science.gov (United States)

    Eldursi, Khalifa; Branquet, Yannick; Guillou-Frottier, Laurent; Martelet, Guillaume; Calcagno, Philippe

    2018-04-01

    The Tighza (or Jebel Aouam) district is one of the most important polymetallic districts in Morocco. It belongs to the Variscan Belt of Central Meseta, and includes W-Au, Pb-Zn-Ag, and Sb-Ba mineralization types that are spatially related to late-Carboniferous granitic stocks. One of the proposed hypotheses suggests that these granitic stocks are connected to a large intrusive body lying beneath them and that W-Au mineralization is directly related to this magmatism during a 287-285 Ma time span. A more recent model argues for a disconnection between the older barren outcropping magmatic stocks and a younger hidden magmatic complex responsible for the W-Au mineralization. Independently of the magmatic scenario, the W-Au mineralization is consensually recognized as of intrusion-related gold deposit (IRGD) type, W-rich. In addition to discrepancies between magmatic sceneries, the IRGD model does not account for published older age corresponding to a high-temperature hydrothermal event at ca. 291 Ma. Our study is based on gravity data inversion and hydro-thermal modeling, and aims to test this model of IRGD and its related magmatic geometries, with respect to subsurface geometries, favorable physical conditions for deposition and time record of hydrothermal processes. Combined inversion of geology and gravity data suggests that an intrusive body is rooted mainly at the Tighza fault in the north and that it spreads horizontally toward the south during a trans-tensional event (D2). Based on the numerical results, two types of mineralization can be distinguished: 1) the "Pre-Main" type appears during the emplacement of the magmatic body, and 2) the "Main" type appears during magma crystallization and the cooling phase. The time-lag between the two mineralization types depends on the cooling rate of magma. Although our numerical model of thermally-driven fluid flow around the Tighza pluton is simplified, as it does not take into account the chemical and deformation

  19. 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

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

    NARCIS (Netherlands)

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

    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

  1. 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.

  2. Applicability of genetic algorithms to parameter estimation of economic models

    Directory of Open Access Journals (Sweden)

    Marcel Ševela

    2004-01-01

    Full Text Available The paper concentrates on capability of genetic algorithms for parameter estimation of non-linear economic models. In the paper we test the ability of genetic algorithms to estimate of parameters of demand function for durable goods and simultaneously search for parameters of genetic algorithm that lead to maximum effectiveness of the computation algorithm. The genetic algorithms connect deterministic iterative computation methods with stochastic methods. In the genteic aůgorithm approach each possible solution is represented by one individual, those life and lifes of all generations of individuals run under a few parameter of genetic algorithm. Our simulations resulted in optimal mutation rate of 15% of all bits in chromosomes, optimal elitism rate 20%. We can not set the optimal extend of generation, because it proves positive correlation with effectiveness of genetic algorithm in all range under research, but its impact is degreasing. The used genetic algorithm was sensitive to mutation rate at most, than to extend of generation. The sensitivity to elitism rate is not so strong.

  3. 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. Copyright © 2013 Elsevier Ltd. All rights reserved.

  4. Applying a health action model to predict and improve healthy behaviors in coal miners.

    Science.gov (United States)

    Vahedian-Shahroodi, Mohammad; Tehrani, Hadi; Mohammadi, Faeze; Gholian-Aval, Mahdi; Peyman, Nooshin

    2018-05-01

    One of the most important ways to prevent work-related diseases in occupations such as mining is to promote healthy behaviors among miners. This study aimed to predict and promote healthy behaviors among coal miners by using a health action model (HAM). The study was conducted on 200 coal miners in Iran in two steps. In the first step, a descriptive study was implemented to determine predictive constructs and effectiveness of HAM on behavioral intention. The second step involved a quasi-experimental study to determine the effect of an HAM-based education intervention. This intervention was implemented by the researcher and the head of the safety unit based on the predictive construct specified in the first step over 12 sessions of 60 min. The data was collected using an HAM questionnaire and a checklist of healthy behavior. The results of the first step of the study showed that attitude, belief, and normative constructs were meaningful predictors of behavioral intention. Also, the results of the second step revealed that the mean score of attitude and behavioral intention increased significantly after conducting the intervention in the experimental group, while the mean score of these constructs decreased significantly in the control group. The findings of this study showed that HAM-based educational intervention could improve the healthy behaviors of mine workers. Therefore, it is recommended to extend the application of this model to other working groups to improve healthy behaviors.

  5. Genetic pathways to Neurodegeneration Models and mechanisms ...

    Indian Academy of Sciences (India)

    Paige Rudich

    Models and mechanisms of repeat expansion disorders: a worm's eye view ..... retardation 1 gene FMR1 gives rise to a spectrum of neurological disorders (Saul and Tarleton ... autism. Shorter repeat expansion lengths from 55-200 cause the.

  6. 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.

  7. ENU mutagenesis to generate genetically modified rat models.

    Science.gov (United States)

    van Boxtel, Ruben; Gould, Michael N; Cuppen, Edwin; Smits, Bart M G

    2010-01-01

    The rat is one of the most preferred model organisms in biomedical research and has been extremely useful for linking physiology and pathology to the genome. However, approaches to genetically modify specific genes in the rat germ line remain relatively scarce. To date, the most efficient approach for generating genetically modified rats has been the target-selected N-ethyl-N-nitrosourea (ENU) mutagenesis-based technology. Here, we describe the detailed protocols for ENU mutagenesis and mutant retrieval in the rat model organism.

  8. Introduction to genetic algorithms as a modeling tool

    International Nuclear Information System (INIS)

    Wildberger, A.M.; Hickok, K.A.

    1990-01-01

    Genetic algorithms are search and classification techniques modeled on natural adaptive systems. This is an introduction to their use as a modeling tool with emphasis on prospects for their application in the power industry. It is intended to provide enough background information for its audience to begin to follow technical developments in genetic algorithms and to recognize those which might impact on electric power engineering. Beginning with a discussion of genetic algorithms and their origin as a model of biological adaptation, their advantages and disadvantages are described in comparison with other modeling tools such as simulation and neural networks in order to provide guidance in selecting appropriate applications. In particular, their use is described for improving expert systems from actual data and they are suggested as an aid in building mathematical models. Using the Thermal Performance Advisor as an example, it is suggested how genetic algorithms might be used to make a conventional expert system and mathematical model of a power plant adapt automatically to changes in the plant's characteristics

  9. 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...

  10. Modelling lung cancer due to radon and smoking in WISMUT miners: Preliminary results

    International Nuclear Information System (INIS)

    Bijwaard, H.; Dekkers, F.; Van Dillen, T.

    2011-01-01

    A mechanistic two-stage carcinogenesis model has been applied to model lung-cancer mortality in the largest uranium-miner cohort available. Models with and without smoking action both fit the data well. As smoking information is largely missing from the cohort data, a method has been devised to project this information from a case-control study onto the cohort. Model calculations using 256 projections show that the method works well. Preliminary results show that if an explicit smoking action is absent in the model, this is compensated by the values of the baseline parameters. This indicates that in earlier studies performed without smoking information, the results obtained for the radiation parameters are still valid. More importantly, the inclusion of smoking-related parameters shows that these mainly influence the later stages of lung-cancer development. (authors)

  11. Geochemical modeling of the influence of silicate mineral alteration on alkalinity production and carbonate precipitation

    Science.gov (United States)

    Herda, Gerhard; Kraemer, Stephan M.; Gier, Susanne; Meister, Patrick

    2016-04-01

    High CO2 partial pressure (pCO2) in deep rock reservoirs causes acidification of the porefluid. Such conditions occur during injection and subsurface storage of CO2 (to prevent the release of greenhouse gas) but also naturally in zones of strong methanogenic microbial activity in organic matter-rich ocean margin sediments. The acidic fluids are corrosive to carbonates and bear the risk of leakage of CO2 gas to the surface. Porefluid acidification may be moderated by processes that increase the alkalinity, i.e. that produce weak acid anions capable of buffering the acidification imposed by the CO2. Often, alkalinity increases as a result of anaerobic microbial activity, such as anaerobic oxidation of methane. However, on a long term the alteration of silicates, in particular, clay minerals, may be a more efficient mechanism of alkalinity production. Under altered temperature, pressure and porefluid composition at depth, clay minerals may change to thermodynamically more stable states, thereby increasing the alkalinity of the porefluid by partial leaching of Mg-(OH)2 and Ca-(OH)2 (e.g. Wallmann et al., 2008; Mavromatis et al., 2014). This alteration may even be enhanced by a high pCO2. Thus, silicate alteration can be essential for a long-term stabilization of volatile CO2 in the form of bicarbonate or may even induce precipitation of carbonate minerals, but these processes are not fully understood yet. The goal of this study is to simulate the alkalinity effect of silicate alteration under diagenetic conditions and high pCO2 by geochemical modeling. We are using the program PHREEQC (Parkhurst and Appelo, 2013) to generate high rock/fluid ratio characteristics for deep subsurface rock reservoirs. Since we are interested in the long-term evolution of diagenetic processes, over millions of years, we do not consider kinetics but calculate the theoretically possible equilibrium conditions. In a first step we are calculating the saturation state of different clay minerals

  12. Modeling groundwater age using tritium and groundwater mineralization processes - Morondava sedimentary basin, Southwestern Madagascar

    International Nuclear Information System (INIS)

    RAMAROSON, V.

    2007-01-01

    The tritium method in the lumped parameter approach was used for groundwater dating in the Morondava sedimentary basin, Southwestern Madagascar. Tritium data were interpreted by the dispersion model. The modeling results, with P D values between 0.05 and 0.7, show that shallow groundwater age is ranging from 17 to 56 years. Different types of chemical composition were determined for these shallow ground waters, among others, Ca-HCO 3 , Ca-Na-HCO 3 , Ca-Na-Mg-HCO 3 , Ca-K-HCO 3 -NO 3 -SO 4 , Na-Cl, or Ca-Na-Mg-Cl. Likewise, deeper ground waters show various chemical type such as Ca-Na-HCO 3 , Ca-Mg-Na H CO 3 , Ca-Na-Mg-HCO 3 , Ca-Na-Mg-HCO 3 -Cl-SO 4 , Ca-Mg-HCO 3 , Na-Ca-Mg-HCO 3 -SO 4 -Cl, Na-Cl-HCO 3 or Na-HCO 3 -Cl. To evaluate the geochemical processes, the NETPATH inverse geochemical modeling type was implemented. The modeling results show that silicate minerals dissolution , including olivine, plagioclase, and pyroxene is more important than calcite or dolomite dissolution, for both shallow and deeper groundwater . In the Southern part of the study area, while halite dissolution is likely to be the source of shallow groundwater chloride concentration rise, the mineral precipitation seems to be responsible for less chloride content in deeper groundwater. Besides, ion exchange contributes to the variations of major cations concentrations in groundwater. The major difference between shallow and deep groundwater mineralization process lies in the leaching of marine aerosols deposits by local precipitation, rapidly infiltrated through the sandy formation and giving marine chemical signature to shallow groundwater [fr

  13. Identification of mineralized zones in the Zardu area, Kushk SEDEX deposit (Central Iran, based on geological and multifractal modeling

    Directory of Open Access Journals (Sweden)

    Dahooei Ahmad Heidari

    2016-02-01

    Full Text Available The aim of this paper is to delineate the different lead–zinc mineralized zones in the Zardu area of the Kushk zinc–lead stratabound SEDEX deposit, Central Iran, through concentration–volume (C–V modeling of geological and lithogeochemical drillcore data. The geological model demonstrated that the massive sulfide and pyrite+dolomite ore types as main rock types hosting mineralization. The C–V fractal modeling used lead, zinc and iron geochemical data to outline four types of mineralized zones, which were then compared to the mineralized rock types identified in the geological model. ‘Enriched’ mineralized zones contain lead and zinc values higher than 6.93% and 19.95%, respectively, with iron values lower than 12.02%. Areas where lead and zinc values were higher than 1.58% and 5.88%, respectively, and iron grades lower than 22% are labelled “high-grade” mineralized zones, and these zones are linked to massive sulfide and pyrite+dolomite lithologies of the geological model. Weakly mineralized zones, labelled ‘low-grade’ in the C– V model have 0–0.63% lead, 0–3.16% zinc and > 30.19% iron, and are correlated to those lithological units labeled as gangue in the geological model, including shales and dolomites, pyritized dolomites. Finally, a log-ratio matrix was employed to validate the results obtained and check correlations between the geological and fractal modeling. Using this method, a high overall accuracy (OA was confirmed for the correlation between the enriched and high-grade mineralized zones and two lithological units — the massive sulfide and pyrite+dolomite ore types.

  14. Sleep and Development in Genetically Tractable Model Organisms.

    Science.gov (United States)

    Kayser, Matthew S; Biron, David

    2016-05-01

    Sleep is widely recognized as essential, but without a clear singular function. Inadequate sleep impairs cognition, metabolism, immune function, and many other processes. Work in genetic model systems has greatly expanded our understanding of basic sleep neurobiology as well as introduced new concepts for why we sleep. Among these is an idea with its roots in human work nearly 50 years old: sleep in early life is crucial for normal brain maturation. Nearly all known species that sleep do so more while immature, and this increased sleep coincides with a period of exuberant synaptogenesis and massive neural circuit remodeling. Adequate sleep also appears critical for normal neurodevelopmental progression. This article describes recent findings regarding molecular and circuit mechanisms of sleep, with a focus on development and the insights garnered from models amenable to detailed genetic analyses. Copyright © 2016 by the Genetics Society of America.

  15. Genetic engineering in nonhuman primates for human disease modeling.

    Science.gov (United States)

    Sato, Kenya; Sasaki, Erika

    2018-02-01

    Nonhuman primate (NHP) experimental models have contributed greatly to human health research by assessing the safety and efficacy of newly developed drugs, due to their physiological and anatomical similarities to humans. To generate NHP disease models, drug-inducible methods, and surgical treatment methods have been employed. Recent developments in genetic and developmental engineering in NHPs offer new options for producing genetically modified disease models. Moreover, in recent years, genome-editing technology has emerged to further promote this trend and the generation of disease model NHPs has entered a new era. In this review, we summarize the generation of conventional disease model NHPs and discuss new solutions to the problem of mosaicism in genome-editing technology.

  16. An approximate multitrait model for genetic evaluation in dairy cattle with a robust estimation of genetic trends (Open Access publication

    Directory of Open Access Journals (Sweden)

    Madsen Per

    2007-07-01

    Full Text Available Abstract In a stochastic simulation study of a dairy cattle population three multitrait models for estimation of genetic parameters and prediction of breeding values were compared. The first model was an approximate multitrait model using a two-step procedure. The first step was a single trait model for all traits. The solutions for fixed effects from these analyses were subtracted from the phenotypes. A multitrait model only containing an overall mean, an additive genetic and a residual term was applied on these preadjusted data. The second model was similar to the first model, but the multitrait model also contained a year effect. The third model was a full multitrait model. Genetic trends for total merit and for the individual traits in the breeding goal were compared for the three scenarios to rank the models. The full multitrait model gave the highest genetic response, but was not significantly better than the approximate multitrait model including a year effect. The inclusion of a year effect into the second step of the approximate multitrait model significantly improved the genetic trend for total merit. In this study, estimation of genetic parameters for breeding value estimation using models corresponding to the ones used for prediction of breeding values increased the accuracy on the breeding values and thereby the genetic progress.

  17. Disease modeling in genetic kidney diseases: zebrafish.

    Science.gov (United States)

    Schenk, Heiko; Müller-Deile, Janina; Kinast, Mark; Schiffer, Mario

    2017-07-01

    Growing numbers of translational genomics studies are based on the highly efficient and versatile zebrafish (Danio rerio) vertebrate model. The increasing types of zebrafish models have improved our understanding of inherited kidney diseases, since they not only display pathophysiological changes but also give us the opportunity to develop and test novel treatment options in a high-throughput manner. New paradigms in inherited kidney diseases have been developed on the basis of the distinct genome conservation of approximately 70 % between zebrafish and humans in terms of existing gene orthologs. Several options are available to determine the functional role of a specific gene or gene sets. Permanent genome editing can be induced via complete gene knockout by using the CRISPR/Cas-system, among others, or via transient modification by using various morpholino techniques. Cross-species rescues succeeding knockdown techniques are employed to determine the functional significance of a target gene or a specific mutation. This article summarizes the current techniques and discusses their perspectives.

  18. Genetic Evaluation and Ranking of Different Animal Models Using ...

    African Journals Online (AJOL)

    An animal model utilizes all relationships available in a given data set. Estimates for variance components for additive direct, additive maternal, maternal environmental and direct environmental effects, and their covariances between direct and maternal genetic effects for post weaning growth traits have been obtained with ...

  19. Revised models and genetic parameter estimates for production and ...

    African Journals Online (AJOL)

    Genetic parameters for production and reproduction traits in the Elsenburg Dormer sheep stud were estimated using records of 11743 lambs born between 1943 and 2002. An animal model with direct and maternal additive, maternal permanent and temporary environmental effects was fitted for traits considered traits of the ...

  20. Use of Genetic Models to Study the Urinary Concentrating Mechanism

    DEFF Research Database (Denmark)

    Olesen, Emma Tina Bisgaard; Kortenoeven, Marleen L.A.; Fenton, Robert A.

    2015-01-01

    technology is providing critical new information about urinary concentrating processes and thus mechanisms for maintaining body water homeostasis. In this chapter we provide a brief overview of genetic mouse model generation, and then summarize findings in transgenic and knockout mice pertinent to our...

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

    NARCIS (Netherlands)

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

    2017-01-01

    The discovery, development and use of genetic rodent models of absence epilepsy have led to a new theory about the origin of absence seizures, which has gained impact within the international epilepsy community. A focal zone has been identified in the perioral region of the somatosensory cortex in

  2. ENU mutagenesis to generate genetically modified rat models

    NARCIS (Netherlands)

    van Boxtel, R.; Gould, M.; Cuppen, E.; Smits, B.M.

    2010-01-01

    The rat is one of the most preferred model organisms in biomedical research and has been extremely useful for linking physiology and pathology to the genome. However, approaches to genetically modify specific genes in the rat germ line remain relatively scarce. To date, the most efficient approach

  3. The elastic solid solution model for minerals at high pressures and temperatures

    Science.gov (United States)

    Myhill, R.

    2018-02-01

    Non-ideality in mineral solid solutions affects their elastic and thermodynamic properties, their thermobaric stability, and the equilibrium phase relations in multiphase assemblages. At a given composition and state of order, non-ideality in minerals is typically modelled via excesses in Gibbs free energy which are either constant or linear with respect to pressure and temperature. This approach has been extremely successful when modelling near-ideal solutions. However, when the lattice parameters of the solution endmembers differ significantly, extrapolations of thermodynamic properties to high pressures using these models may result in significant errors. In this paper, I investigate the effect of parameterising solution models in terms of the Helmholtz free energy, treating volume (or lattice parameters) rather than pressure as an independent variable. This approach has been previously applied to models of order-disorder, but the implications for the thermodynamics and elasticity of solid solutions have not been fully explored. Solid solution models based on the Helmholtz free energy are intuitive at a microscopic level, as they automatically include the energetic contribution from elastic deformation of the endmember lattices. A chemical contribution must also be included in such models, which arises from atomic exchange within the solution. Derivations are provided for the thermodynamic properties of n-endmember solutions. Examples of the use of the elastic model are presented for the alkali halides, pyroxene, garnet, and bridgmanite solid solutions. Elastic theory provides insights into the microscopic origins of non-ideality in a range of solutions, and can make accurate predictions of excess enthalpies, entropies, and volumes as a function of volume and temperature. In solutions where experimental data are sparse or contradictory, the Helmholtz free energy approach can be used to assess the magnitude of excess properties and their variation as a function

  4. Lung cancer from radon and smoking: a multistage model for the WISMUT uranium miners

    International Nuclear Information System (INIS)

    Dillen, Teun van; Bijwaard, Harmen; Schnelzer, Maria; Kreuzer, Michaela; Grosche, Bernd

    2008-01-01

    Full text: In the world's third-largest uranium-mining province located in areas of Saxony and Thuringia in the former German Democratic Republic, the WISMUT Company conducted extensive uranium mining starting in 1946. Up to 1990, when mining activities were discontinued, most of the 400,000 employees had been exposed to uranium ore dust and radon and its progeny. It is well established that, besides smoking, such exposures are associated with an increased risk of lung cancer. From about 130,000 known miners a huge cohort of 59,000 miners has been formed and in an epidemiological analysis lung cancer risks have been evaluated (Grosche et al., 2006). We will present an alternative approach using a biologically-based multistage carcinogenesis model quantifying the lung-cancer risk related to both the exposure to radon and smoking habits. This mechanistic technique allows for extrapolation to the low exposures that are important for present-day radiation protection purposes and the transfer of risk across populations. The model is applied to a sub-cohort of about 35,000 persons who were employed at WISMUT after 1955, with known annual exposures estimated from the job-exposure matrix (Lehmann et al., 2004). Unfortunately, detailed information on smoking is missing for most miners. However, this information has been retrieved in two case-control studies, one of which was nested in the cohort while the other was not (Brueske-Hohlfeld et al., 2006). For these studies, the relevant smoking parameters are assembled in so-called smoking spectra that are next projected onto the entire cohort using a Monte-Carlo sampling method. Individual smoking habits that are randomly assigned to the cohort members, together with the information on annual exposure to radon, is used as an input for the multistage model. Model parameters related to radon and tobacco exposure are fitted with a maximum-likelihood technique. We will show results of the observed and expected lung

  5. CMCpy: Genetic Code-Message Coevolution Models in Python

    Science.gov (United States)

    Becich, Peter J.; Stark, Brian P.; Bhat, Harish S.; Ardell, David H.

    2013-01-01

    Code-message coevolution (CMC) models represent coevolution of a genetic code and a population of protein-coding genes (“messages”). Formally, CMC models are sets of quasispecies coupled together for fitness through a shared genetic code. Although CMC models display plausible explanations for the origin of multiple genetic code traits by natural selection, useful modern implementations of CMC models are not currently available. To meet this need we present CMCpy, an object-oriented Python API and command-line executable front-end that can reproduce all published results of CMC models. CMCpy implements multiple solvers for leading eigenpairs of quasispecies models. We also present novel analytical results that extend and generalize applications of perturbation theory to quasispecies models and pioneer the application of a homotopy method for quasispecies with non-unique maximally fit genotypes. Our results therefore facilitate the computational and analytical study of a variety of evolutionary systems. CMCpy is free open-source software available from http://pypi.python.org/pypi/CMCpy/. PMID:23532367

  6. Modelling of niobium sorption on clay minerals in sodium and calcium perchlorate solutions

    Energy Technology Data Exchange (ETDEWEB)

    Ervanne, Heini; Hakanen, Martti; Lehto, Jukka [Helsinki Univ. (Finland). Laboratory of Radiochemistry

    2014-11-01

    The sorption behaviour of niobium on kaolinite and illite minerals in sodium and calcium perchlorate solutions was evaluated with use of the mass distribution coefficient, Rd, obtained in batch sorption experiments. Very high distribution coefficient values, about 100 m{sup 3}/kg, were obtained for both minerals in the neutral pH range between 6 and 8. Values were somewhat lower at pH 5. In NaClO{sub 4} solution, the sorption of niobium starts to decrease at pH higher than 8. This is in agreement with the increase, with pH, in the proportion of anionic niobate species, which are presumed to be low or non-sorbing. A similar decrease was not observed in Ca(ClO{sub 4}){sub 2} solution, probably owing to the influence of Ca on niobium solution speciation and surface species. The surface complexation model was applied to model the Rd values. The model fitted well for the NaClO{sub 4} solution but only at pH below 9 for the Ca(ClO{sub 4}){sub 2} solution. The discrepancy between the strong sorption of niobium in calcium-bearing solution at high pH and the calculated speciation is due in part to the non-inclusion of calcium niobate solution species and Ca-Nb compounds in the present NEA and other similar thermodynamic databases.

  7. 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.

  8. Application of genetic algorithm in radio ecological models parameter determination

    Energy Technology Data Exchange (ETDEWEB)

    Pantelic, G. [Institute of Occupatioanl Health and Radiological Protection ' Dr Dragomir Karajovic' , Belgrade (Serbia)

    2006-07-01

    The method of genetic algorithms was used to determine the biological half-life of 137 Cs in cow milk after the accident in Chernobyl. Methodologically genetic algorithms are based on the fact that natural processes tend to optimize themselves and therefore this method should be more efficient in providing optimal solutions in the modeling of radio ecological and environmental events. The calculated biological half-life of 137 Cs in milk is (32 {+-} 3) days and transfer coefficient from grass to milk is (0.019 {+-} 0.005). (authors)

  9. Application of genetic algorithm in radio ecological models parameter determination

    International Nuclear Information System (INIS)

    Pantelic, G.

    2006-01-01

    The method of genetic algorithms was used to determine the biological half-life of 137 Cs in cow milk after the accident in Chernobyl. Methodologically genetic algorithms are based on the fact that natural processes tend to optimize themselves and therefore this method should be more efficient in providing optimal solutions in the modeling of radio ecological and environmental events. The calculated biological half-life of 137 Cs in milk is (32 ± 3) days and transfer coefficient from grass to milk is (0.019 ± 0.005). (authors)

  10. 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.

  11. Comparison of models of automatic classification of textural patterns of mineral presents in Colombian coals

    International Nuclear Information System (INIS)

    Lopez Carvajal, Jaime; Branch Bedoya, John Willian

    2005-01-01

    The automatic classification of objects is a very interesting approach under several problem domains. This paper outlines some results obtained under different classification models to categorize textural patterns of minerals using real digital images. The data set used was characterized by a small size and noise presence. The implemented models were the Bayesian classifier, Neural Network (2-5-1), support vector machine, decision tree and 3-nearest neighbors. The results after applying crossed validation show that the Bayesian model (84%) proved better predictive capacity than the others, mainly due to its noise robustness behavior. The neuronal network (68%) and the SVM (67%) gave promising results, because they could be improved increasing the data amount used, while the decision tree (55%) and K-NN (54%) did not seem to be adequate for this problem, because of their sensibility to noise

  12. Genetic demixing and evolution in linear stepping stone models

    Science.gov (United States)

    Korolev, K. S.; Avlund, Mikkel; Hallatschek, Oskar; Nelson, David R.

    2010-04-01

    Results for mutation, selection, genetic drift, and migration in a one-dimensional continuous population are reviewed and extended. The population is described by a continuous limit of the stepping stone model, which leads to the stochastic Fisher-Kolmogorov-Petrovsky-Piscounov equation with additional terms describing mutations. Although the stepping stone model was first proposed for population genetics, it is closely related to “voter models” of interest in nonequilibrium statistical mechanics. The stepping stone model can also be regarded as an approximation to the dynamics of a thin layer of actively growing pioneers at the frontier of a colony of micro-organisms undergoing a range expansion on a Petri dish. The population tends to segregate into monoallelic domains. This segregation slows down genetic drift and selection because these two evolutionary forces can only act at the boundaries between the domains; the effects of mutation, however, are not significantly affected by the segregation. Although fixation in the neutral well-mixed (or “zero-dimensional”) model occurs exponentially in time, it occurs only algebraically fast in the one-dimensional model. An unusual sublinear increase is also found in the variance of the spatially averaged allele frequency with time. If selection is weak, selective sweeps occur exponentially fast in both well-mixed and one-dimensional populations, but the time constants are different. The relatively unexplored problem of evolutionary dynamics at the edge of an expanding circular colony is studied as well. Also reviewed are how the observed patterns of genetic diversity can be used for statistical inference and the differences are highlighted between the well-mixed and one-dimensional models. Although the focus is on two alleles or variants, q -allele Potts-like models of gene segregation are considered as well. Most of the analytical results are checked with simulations and could be tested against recent spatial

  13. 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.

  14. Uranium fission track length distribution modelling for retracing chronothermometrical history of minerals

    International Nuclear Information System (INIS)

    Rebetez, M.

    1987-01-01

    Spontaneous fission of uranium 238 isotope contained in certain minerals creates damage zones called latent tracks, that can be etched chemically. The observation of these etched tracks and the measurement of their characteristics using an optical microscope are the basis of several applications in the domain of the earth sciences. First, the determination of their densities permits dating a mineral and establishing uranium mapping of rocks. Second, the measurement of their lengths can be a good source of information for retracing the thermal and tectonic history of the sample. The study of the partial annealing of tracks in apatite appears to be the ideal indicator for the evaluation of petroleum potential of a sedimentary basin. To allow the development of this application, it is necessary to devise a theoretical model of track length distributions. The model which is proposed takes into account the most realistic hypotheses concerning registration, etching and observation of tracks. The characteristics of surface tracks (projected lengths, depths, inclination angles, real lengths) and confined tracks (Track IN Track and Track IN Cleavage) are calculated. Surface tracks and confined tracks are perfectly complementary for chrono-thermometric interpretation of complex geological histories. The method is applied to the case of two samples with different tectonic history, issued from the cretaceous alcalin magmatism from the Pyrenees (Bilbao, Spain). A graphic method of distribution deconvolution is proposed. Finally, the uranium migration, depending on the hydrothermal alteration, is studied on the granite from Auriat (France) [fr

  15. A New Murine Model of Chronic Kidney Disease-Mineral and Bone Disorder

    Directory of Open Access Journals (Sweden)

    Bianca Frauscher

    2017-01-01

    Full Text Available Chronic kidney disease (CKD is associated with mineral and bone disorder (MBD, which is the main cause of the extensively increased cardiovascular mortality in the CKD population. We now aimed to establish a new murine experimental CKD-MBD model. Dilute brown non-Agouti (DBA/2 mice were fed with high-phosphate diet for 4 (HPD4 or 7 (HPD7 days, then with standard chow diet (SCD and subsequently followed until day 84. They were compared to DBA/2 mice maintained on SCD during the whole study period. Both 4 and 7 days HPD-fed mice developed phosphate nephropathy with tubular atrophy, interstitial fibrosis, decreased glomerular filtration rate, and increased serum urea levels. The abdominal aorta of HPD-treated mice showed signs of media calcification. Histomorphometric analysis of HPD-treated mice showed decreased bone volume/tissue volume, low mineral apposition rate, and low bone formation rate as compared to SCD-fed mice, despite increased parathyroid hormone levels. Overall, the observed phenotype was more pronounced in the HPD7 group. In summary, we established a new, noninvasive, and therefore easy to perform reproducible CKD-MBD model, which showed media calcification, secondary hyperparathyroidism, and low-turnover bone disease.

  16. 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.; 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

  17. Genetic enhancement of macroautophagy in vertebrate models of neurodegenerative diseases.

    Science.gov (United States)

    Ejlerskov, Patrick; Ashkenazi, Avraham; Rubinsztein, David C

    2018-04-03

    Most of the neurodegenerative diseases that afflict humans manifest with the intraneuronal accumulation of toxic proteins that are aggregate-prone. Extensive data in cell and neuronal models support the concept that such proteins, like mutant huntingtin or alpha-synuclein, are substrates for macroautophagy (hereafter autophagy). Furthermore, autophagy-inducing compounds lower the levels of such proteins and ameliorate their toxicity in diverse animal models of neurodegenerative diseases. However, most of these compounds also have autophagy-independent effects and it is important to understand if similar benefits are seen with genetic strategies that upregulate autophagy, as this strengthens the validity of this strategy in such diseases. Here we review studies in vertebrate models using genetic manipulations of core autophagy genes and describe how these improve pathology and neurodegeneration, supporting the validity of autophagy upregulation as a target for certain neurodegenerative diseases. Copyright © 2018 Elsevier Inc. All rights reserved.

  18. Developing the lithotectonic framework and model for sulphide mineralization in the Jebilet Massif, Morocco: implications for regional exploration

    OpenAIRE

    Lusty, Paul A.J.; Goodenough, Kathryn M.; Essaifi, Abderrahim; Maacha, Lhou

    2015-01-01

    The central Jebilet massif, part of the North African Variscan Belt, hosts significant polymetallic sulphide mineralization. It is generally considered syngenetic and has many features of volcanogenic massive sulphide (VMS) mineralization. However, some characteristics are not compatible with a classic VMS model and two alternative scenarios for formation have been proposed. Our preliminary research favours a complex, multi-stage development of the sulphide deposits...

  19. [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.

  20. 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

  1. 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

  2. Determination of the relationship between major fault and zinc mineralization using fractal modeling in the Behabad fault zone, central Iran

    Science.gov (United States)

    Adib, Ahmad; Afzal, Peyman; Mirzaei Ilani, Shapour; Aliyari, Farhang

    2017-10-01

    The aim of this study is to determine a relationship between zinc mineralization and a major fault in the Behabad area, central Iran, using the Concentration-Distance to Major Fault (C-DMF), Area of Mineralized Zone-Distance to Major Fault (AMZ-DMF), and Concentration-Area (C-A) fractal models for Zn deposit/mine classification according to their distance from the Behabad fault. Application of the C-DMF and the AMZ-DMF models for Zn mineralization classification in the Behabad fault zone reveals that the main Zn deposits have a good correlation with the major fault in the area. The distance from the known zinc deposits/mines with Zn values higher than 29% and the area of the mineralized zone of more than 900 m2 to the major fault is lower than 1 km, which shows a positive correlation between Zn mineralization and the structural zone. As a result, the AMZ-DMF and C-DMF fractal models can be utilized for the delineation and the recognition of different mineralized zones in different types of magmatic and hydrothermal deposits.

  3. 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…

  4. Evolution of models for conversion of smectite to non-expandable minerals

    International Nuclear Information System (INIS)

    Pusch, R.

    1993-12-01

    Hydrothermal alteration of smectite has long been regarded as conversion to illite and chlorite as concluded from investigations of Gulf sediments. As manifested by statements given earlier at various international scientific meetings and in the literature, smectite-to-illite conversion (S→I) has been assumed to be a solid-state reaction with layer-by-layer alteration via mixed layer I/S to illite. In the last 10 years this opinion has successively changed and in recent years the concept of dissolution of smectite and accessory minerals and precipitation of illite and possibly I/S has been favored by many investigators. The present report reports laboratory and field investigations on bentonite and also calculations based on geochemical codes, which all support the dissolution/precipitation process. Applying Pytte's model for calculating the rate of conversion to illite, one finds good agreement with a number of experiments and field data, and this model is therefore recommended for practical use

  5. Calibration of the century, apsim and ndicea models of decomposition and n mineralization of plant residues in the humid tropics

    Directory of Open Access Journals (Sweden)

    Alexandre Ferreira do Nascimento

    2011-06-01

    Full Text Available The aim of this study was to calibrate the CENTURY, APSIM and NDICEA simulation models for estimating decomposition and N mineralization rates of plant organic materials (Arachis pintoi, Calopogonium mucunoides, Stizolobium aterrimum, Stylosanthes guyanensis for 360 days in the Atlantic rainforest bioma of Brazil. The models´ default settings overestimated the decomposition and N-mineralization of plant residues, underlining the fact that the models must be calibrated for use under tropical conditions. For example, the APSIM model simulated the decomposition of the Stizolobium aterrimum and Calopogonium mucunoides residues with an error rate of 37.62 and 48.23 %, respectively, by comparison with the observed data, and was the least accurate model in the absence of calibration. At the default settings, the NDICEA model produced an error rate of 10.46 and 14.46 % and the CENTURY model, 21.42 and 31.84 %, respectively, for Stizolobium aterrimum and Calopogonium mucunoides residue decomposition. After calibration, the models showed a high level of accuracy in estimating decomposition and N- mineralization, with an error rate of less than 20 %. The calibrated NDICEA model showed the highest level of accuracy, followed by the APSIM and CENTURY. All models performed poorly in the first few months of decomposition and N-mineralization, indicating the need of an additional parameter for initial microorganism growth on the residues that would take the effect of leaching due to rainfall into account.

  6. 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.

  7. 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.

  8. Genetic algorithms and experimental discrimination of SUSY models

    International Nuclear Information System (INIS)

    Allanach, B.C.; Quevedo, F.; Grellscheid, D.

    2004-01-01

    We introduce genetic algorithms as a means to estimate the accuracy required to discriminate among different models using experimental observables. We exemplify the technique in the context of the minimal supersymmetric standard model. If supersymmetric particles are discovered, models of supersymmetry breaking will be fit to the observed spectrum and it is beneficial to ask beforehand: what accuracy is required to always allow the discrimination of two particular models and which are the most important masses to observe? Each model predicts a bounded patch in the space of observables once unknown parameters are scanned over. The questions can be answered by minimising a 'distance' measure between the two hypersurfaces. We construct a distance measure that scales like a constant fraction of an observable, since that is how the experimental errors are expected to scale. Genetic algorithms, including concepts such as natural selection, fitness and mutations, provide a solution to the minimisation problem. We illustrate the efficiency of the method by comparing three different classes of string models for which the above questions could not be answered with previous techniques. The required accuracy is in the range accessible to the Large Hadron Collider (LHC) when combined with a future linear collider (LC) facility. The technique presented here can be applied to more general classes of models or observables. (author)

  9. Dynamic modeling of genetic networks using genetic algorithm and S-system.

    Science.gov (United States)

    Kikuchi, Shinichi; Tominaga, Daisuke; Arita, Masanori; Takahashi, Katsutoshi; Tomita, Masaru

    2003-03-22

    The modeling of system dynamics of genetic networks, metabolic networks or signal transduction cascades from time-course data is formulated as a reverse-problem. Previous studies focused on the estimation of only network structures, and they were ineffective in inferring a network structure with feedback loops. We previously proposed a method to predict not only the network structure but also its dynamics using a Genetic Algorithm (GA) and an S-system formalism. However, it could predict only a small number of parameters and could rarely obtain essential structures. In this work, we propose a unified extension of the basic method. Notable improvements are as follows: (1) an additional term in its evaluation function that aims at eliminating futile parameters; (2) a crossover method called Simplex Crossover (SPX) to improve its optimization ability; and (3) a gradual optimization strategy to increase the number of predictable parameters. The proposed method is implemented as a C program called PEACE1 (Predictor by Evolutionary Algorithms and Canonical Equations 1). Its performance was compared with the basic method. The comparison showed that: (1) the convergence rate increased about 5-fold; (2) the optimization speed was raised about 1.5-fold; and (3) the number of predictable parameters was increased about 5-fold. Moreover, we successfully inferred the dynamics of a small genetic network constructed with 60 parameters for 5 network variables and feedback loops using only time-course data of gene expression.

  10. Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.

    Directory of Open Access Journals (Sweden)

    John P Kemp

    2014-06-01

    Full Text Available Heritability of bone mineral density (BMD varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (rg and residual (re correlations between BMD measured at the upper limbs (UL-BMD, lower limbs (LL-BMD and skull (SK-BMD, using total-body DXA scans of ∼ 4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC. Point estimates of rg indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD rg = 0.78 between them, than with the skull (UL-/SK-BMD rg = 0.58 and LL-/SK-BMD rg = 0.43. Likewise, the residual correlation between BMD at appendicular sites (r(e = 0.55 was higher than the residual correlation between SK-BMD and BMD at appendicular sites (r(e = 0.20-0.24. To explore the basis for the observed differences in rg and re, genome-wide association meta-analyses were performed (n ∼ 9,395, combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites. In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01 × 10(-37, whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31 × 10(-14. In addition, we report a novel association between RIN3 (previously associated with Paget's disease and LL-BMD (rs754388: β = 0.13, SE = 0.02, P = 1.4 × 10(-10. Our results suggest that BMD at different skeletal sites is under a mixture of shared and

  11. Phenotypic dissection of bone mineral density reveals skeletal site specificity and facilitates the identification of novel loci in the genetic regulation of bone mass attainment.

    Science.gov (United States)

    Kemp, John P; Medina-Gomez, Carolina; Estrada, Karol; St Pourcain, Beate; Heppe, Denise H M; Warrington, Nicole M; Oei, Ling; Ring, Susan M; Kruithof, Claudia J; Timpson, Nicholas J; Wolber, Lisa E; Reppe, Sjur; Gautvik, Kaare; Grundberg, Elin; Ge, Bing; van der Eerden, Bram; van de Peppel, Jeroen; Hibbs, Matthew A; Ackert-Bicknell, Cheryl L; Choi, Kwangbom; Koller, Daniel L; Econs, Michael J; Williams, Frances M K; Foroud, Tatiana; Zillikens, M Carola; Ohlsson, Claes; Hofman, Albert; Uitterlinden, André G; Davey Smith, George; Jaddoe, Vincent W V; Tobias, Jonathan H; Rivadeneira, Fernando; Evans, David M

    2014-06-01

    Heritability of bone mineral density (BMD) varies across skeletal sites, reflecting different relative contributions of genetic and environmental influences. To quantify the degree to which common genetic variants tag and environmental factors influence BMD, at different sites, we estimated the genetic (rg) and residual (re) correlations between BMD measured at the upper limbs (UL-BMD), lower limbs (LL-BMD) and skull (SK-BMD), using total-body DXA scans of ∼ 4,890 participants recruited by the Avon Longitudinal Study of Parents and their Children (ALSPAC). Point estimates of rg indicated that appendicular sites have a greater proportion of shared genetic architecture (LL-/UL-BMD rg = 0.78) between them, than with the skull (UL-/SK-BMD rg = 0.58 and LL-/SK-BMD rg = 0.43). Likewise, the residual correlation between BMD at appendicular sites (r(e) = 0.55) was higher than the residual correlation between SK-BMD and BMD at appendicular sites (r(e) = 0.20-0.24). To explore the basis for the observed differences in rg and re, genome-wide association meta-analyses were performed (n ∼ 9,395), combining data from ALSPAC and the Generation R Study identifying 15 independent signals from 13 loci associated at genome-wide significant level across different skeletal regions. Results suggested that previously identified BMD-associated variants may exert site-specific effects (i.e. differ in the strength of their association and magnitude of effect across different skeletal sites). In particular, variants at CPED1 exerted a larger influence on SK-BMD and UL-BMD when compared to LL-BMD (P = 2.01 × 10(-37)), whilst variants at WNT16 influenced UL-BMD to a greater degree when compared to SK- and LL-BMD (P = 2.31 × 10(-14)). In addition, we report a novel association between RIN3 (previously associated with Paget's disease) and LL-BMD (rs754388: β = 0.13, SE = 0.02, P = 1.4 × 10(-10)). Our results suggest that BMD at different skeletal sites is under a mixture of shared and

  12. 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.

  13. Model parameters estimation and sensitivity by genetic algorithms

    International Nuclear Information System (INIS)

    Marseguerra, Marzio; Zio, Enrico; Podofillini, Luca

    2003-01-01

    In this paper we illustrate the possibility of extracting qualitative information on the importance of the parameters of a model in the course of a Genetic Algorithms (GAs) optimization procedure for the estimation of such parameters. The Genetic Algorithms' search of the optimal solution is performed according to procedures that resemble those of natural selection and genetics: an initial population of alternative solutions evolves within the search space through the four fundamental operations of parent selection, crossover, replacement, and mutation. During the search, the algorithm examines a large amount of solution points which possibly carries relevant information on the underlying model characteristics. A possible utilization of this information amounts to create and update an archive with the set of best solutions found at each generation and then to analyze the evolution of the statistics of the archive along the successive generations. From this analysis one can retrieve information regarding the speed of convergence and stabilization of the different control (decision) variables of the optimization problem. In this work we analyze the evolution strategy followed by a GA in its search for the optimal solution with the aim of extracting information on the importance of the control (decision) variables of the optimization with respect to the sensitivity of the objective function. The study refers to a GA search for optimal estimates of the effective parameters in a lumped nuclear reactor model of literature. The supporting observation is that, as most optimization procedures do, the GA search evolves towards convergence in such a way to stabilize first the most important parameters of the model and later those which influence little the model outputs. In this sense, besides estimating efficiently the parameters values, the optimization approach also allows us to provide a qualitative ranking of their importance in contributing to the model output. The

  14. Effect of excess dietary salt on calcium metabolism and bone mineral in a spaceflight rat model

    Science.gov (United States)

    Navidi, Meena; Wolinsky, Ira; Fung, Paul; Arnaud, Sara B.

    1995-01-01

    High levels of salt promote urinary calcium (UCa) loss and have the potential to cause bone mineral deficits if intestinal Ca absorption does not compensate for these losses. To determine the effect of excess dietary salt on the osteopenia that follows skeletal unloading, we used a spaceflight model that unloads the hindlimbs of 200-g rats by tail suspension (S). Rats were studied for 2 wk on diets containing high salt (4 and 8%) and normal calcium (0.45%) and for 4 wk on diets containing 8% salt (HiNa) and 0.2% Ca (LoCa). Final body weights were 9-11% lower in S than in control rats (C) in both experiments, reflecting lower growth rates in S than in C during pair feeding. UCa represented 12% of dietary Ca on HiNA diets and was twofold higher in S than in C transiently during unloading. Net intestinal Ca absorption was consistently 11-18% lower in S than in C. Serum 1,25-dihydroxyvitamin D was unaffected by either LoCa or HiNa diets in S but was increased by LoCa and HiNa diets in C. Despite depressed intestinal Ca absoption in S and a sluggish response of the Ca endocrine system to HiNa diets, UCa loss did not appear to affect the osteopenia induced by unloading. Although any deficit in bone mineral content from HiNa diets may have been too small to detect or the duration of the study too short to manifest, there were clear differences in Ca metabolism from control levels in the response of the spaceflight model to HiNa diets, indicated by depression of intestinal Ca absorption and its regulatory hormone.

  15. Chemical event chain model of coupled genetic oscillators.

    Science.gov (United States)

    Jörg, David J; Morelli, Luis G; Jülicher, Frank

    2018-03-01

    We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

  16. Chemical event chain model of coupled genetic oscillators

    Science.gov (United States)

    Jörg, David J.; Morelli, Luis G.; Jülicher, Frank

    2018-03-01

    We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their frequency, their quality factor, and their synchrony by the oscillator cross correlation. The steady state is determined by coupling and exhibits stochastic transitions between different modes. The interplay of stochasticity and nonlinearity leads to isolated regions in parameter space in which the coupled system works best as a biological pacemaker. Key features of the stochastic oscillations can be captured by an effective model for phase oscillators that are coupled by signals with distributed delays.

  17. 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.

  18. The evolution of menstruation: A new model for genetic assimilation

    Science.gov (United States)

    Emera, D.; Romero, R.; Wagner, G.

    2012-01-01

    Why do humans menstruate while most mammals do not? Here, we present our answer to this long-debated question, arguing that (i) menstruation occurs as a mechanistic consequence of hormone-induced differentiation of the endometrium (referred to as spontaneous decidualization, or SD); (ii) SD evolved because of maternal-fetal conflict; and (iii) SD evolved by genetic assimilation of the decidualization reaction, which is induced by the fetus in non-menstruating species. The idea that menstruation occurs as a consequence of SD has been proposed in the past, but here we present a novel hypothesis on how SD evolved. We argue that decidualization became genetically stabilized in menstruating lineages, allowing females to prepare for pregnancy without any signal from the fetus. We present three models for the evolution of SD by genetic assimilation, based on recent advances in our understanding of the mechanisms of endometrial differentiation and implantation. Testing these models will ultimately shed light on the evolutionary significance of menstruation, as well as on the etiology of human reproductive disorders like endometriosis and recurrent pregnancy loss. PMID:22057551

  19. Genetic modelling in schizophrenia according to HLA typing.

    Science.gov (United States)

    Smeraldi, E; Macciardi, F; Gasperini, M; Orsini, A; Bellodi, L; Fabio, G; Morabito, A

    1986-09-01

    Studying families of schizophrenic patients, we observed that the risk of developing the overt form of the illness could be enhanced by some factors. Among these various factors we focused our attention on a biological variable, namely the presence or the absence of particular HLA antigens: partitioning our schizophrenic patients according to their HLA structure (i.e. those with HLA-A1 or CRAG-A1 antigens and those with HLA-non-CRAG-A1 antigens, respectively), revealed different illness distribution in the two groups. From a genetic point of view, this finding suggests the presence of heterogeneity in the hypothetical liability system related to schizophrenia and we evaluated the heterogeneity hypothesis by applying alternative genetic models to our data, trying to detect more biologically homogeneous subgroups of the disease.

  20. 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.

  1. 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.

  2. Analysis of genetic effects of nuclear-cytoplasmic interaction on quantitative traits: genetic model for diploid plants.

    Science.gov (United States)

    Han, Lide; Yang, Jian; Zhu, Jun

    2007-06-01

    A genetic model was proposed for simultaneously analyzing genetic effects of nuclear, cytoplasm, and nuclear-cytoplasmic interaction (NCI) as well as their genotype by environment (GE) interaction for quantitative traits of diploid plants. In the model, the NCI effects were further partitioned into additive and dominance nuclear-cytoplasmic interaction components. Mixed linear model approaches were used for statistical analysis. On the basis of diallel cross designs, Monte Carlo simulations showed that the genetic model was robust for estimating variance components under several situations without specific effects. Random genetic effects were predicted by an adjusted unbiased prediction (AUP) method. Data on four quantitative traits (boll number, lint percentage, fiber length, and micronaire) in Upland cotton (Gossypium hirsutum L.) were analyzed as a worked example to show the effectiveness of the model.

  3. Modelling of water-gas-rock geo-chemical interactions. Application to mineral diagenesis in geological reservoirs

    International Nuclear Information System (INIS)

    Bildstein, Olivier

    1998-01-01

    Mineral diagenesis in tanks results from interactions between minerals, water, and possibly gases, over geological periods of time. The associated phenomena may have a crucial importance for reservoir characterization because of their impact on petrophysical properties. The objective of this research thesis is thus to develop a model which integrates geochemical functions necessary to simulate diagenetic reactions, and which is numerically efficient enough to perform the coupling with a transport model. After a recall of thermodynamic and kinetic backgrounds, the author discusses how the nature of available analytic and experimental data influenced choices made for the formalization of physical-chemical phenomena and for behaviour laws to be considered. Numerical and computational aspects are presented in the second part. The model is validated by using simple examples. The different possible steps during the kinetic competition between two mineral are highlighted, as well the competition between mineral reaction kinetics and water flow rate across the rock. Redox reactions are also considered. In the third part, the author reports the application of new model functions, and highlights the contribution of the modelling to the understanding of some complex geochemical phenomena and to the prediction of reservoir quality. The model is applied to several diagenetic transformations: cementation of dolomitic limestone by anhydride, illite precipitation, and thermal reduction of sulphates [fr

  4. 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. © 2015 John Wiley & Sons Ltd and International Behavioural and Neural Genetics Society.

  5. 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.

  6. 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.

  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

    coefficient values. This suggests that a large kinetic coefficient could be used when actual measured data is lacking for a particular precipitate-matrix combination. Correlation between the kinetic rate coefficients of different minerals was low, indicating that parameter values for individual minerals could...

  8. Modeling AEC—New Approaches to Study Rare Genetic Disorders

    Science.gov (United States)

    Koch, Peter J.; Dinella, Jason; Fete, Mary; Siegfried, Elaine C.; Koster, Maranke I.

    2015-01-01

    Ankyloblepharon-ectodermal defects-cleft lip/palate (AEC) syndrome is a rare monogenetic disorder that is characterized by severe abnormalities in ectoderm-derived tissues, such as skin and its appendages. A major cause of morbidity among affected infants is severe and chronic skin erosions. Currently, supportive care is the only available treatment option for AEC patients. Mutations in TP63, a gene that encodes key regulators of epidermal development, are the genetic cause of AEC. However, it is currently not clear how mutations in TP63 lead to the various defects seen in the patients’ skin. In this review, we will discuss current knowledge of the AEC disease mechanism obtained by studying patient tissue and genetically engineered mouse models designed to mimic aspects of the disorder. We will then focus on new approaches to model AEC, including the use of patient cells and stem cell technology to replicate the disease in a human tissue culture model. The latter approach will advance our understanding of the disease and will allow for the development of new in vitro systems to identify drugs for the treatment of skin erosions in AEC patients. Further, the use of stem cell technology, in particular induced pluripotent stem cells (iPSC), will enable researchers to develop new therapeutic approaches to treat the disease using the patient’s own cells (autologous keratinocyte transplantation) after correction of the disease-causing mutations. PMID:24665072

  9. Genetic fuzzy system modeling and simulation of vascular behaviour

    DEFF Research Database (Denmark)

    Tang, Jiaowei; Boonen, Harrie C.M.

    Background: The purpose of our project is to identify the rule sets and their interaction within the framework of cardiovascular function. By an iterative process of computational simulation and experimental work, we strive to mimic the physiological basis for cardiovascular adaptive changes in c...... the pressure change of different blood vessels. Conclusion: Genetic fuzzy system is one of potential modeling methods in modeling and simulation of vascular behavior.......Background: The purpose of our project is to identify the rule sets and their interaction within the framework of cardiovascular function. By an iterative process of computational simulation and experimental work, we strive to mimic the physiological basis for cardiovascular adaptive changes...... 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...

  10. Genetic Programming and Standardization in Water Temperature Modelling

    Directory of Open Access Journals (Sweden)

    Maritza Arganis

    2009-01-01

    Full Text Available An application of Genetic Programming (an evolutionary computational tool without and with standardization data is presented with the aim of modeling the behavior of the water temperature in a river in terms of meteorological variables that are easily measured, to explore their explanatory power and to emphasize the utility of the standardization of variables in order to reduce the effect of those with large variance. Recorded data corresponding to the water temperature behavior at the Ebro River, Spain, are used as analysis case, showing a performance improvement on the developed model when data are standardized. This improvement is reflected in a reduction of the mean square error. Finally, the models obtained in this document were applied to estimate the water temperature in 2004, in order to provide evidence about their applicability to forecasting purposes.

  11. 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.)

  12. Using genetic algorithms to calibrate a water quality model.

    Science.gov (United States)

    Liu, Shuming; Butler, David; Brazier, Richard; Heathwaite, Louise; Khu, Soon-Thiam

    2007-03-15

    With the increasing concern over the impact of diffuse pollution on water bodies, many diffuse pollution models have been developed in the last two decades. A common obstacle in using such models is how to determine the values of the model parameters. This is especially true when a model has a large number of parameters, which makes a full range of calibration expensive in terms of computing time. Compared with conventional optimisation approaches, soft computing techniques often have a faster convergence speed and are more efficient for global optimum searches. This paper presents an attempt to calibrate a diffuse pollution model using a genetic algorithm (GA). Designed to simulate the export of phosphorus from diffuse sources (agricultural land) and point sources (human), the Phosphorus Indicators Tool (PIT) version 1.1, on which this paper is based, consisted of 78 parameters. Previous studies have indicated the difficulty of full range model calibration due to the number of parameters involved. In this paper, a GA was employed to carry out the model calibration in which all parameters were involved. A sensitivity analysis was also performed to investigate the impact of operators in the GA on its effectiveness in optimum searching. The calibration yielded satisfactory results and required reasonable computing time. The application of the PIT model to the Windrush catchment with optimum parameter values was demonstrated. The annual P loss was predicted as 4.4 kg P/ha/yr, which showed a good fitness to the observed value.

  13. 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…

  14. Interaction of radon and smoking among Czech uranium miners using model of a threshold energy

    International Nuclear Information System (INIS)

    Boehm, R.; Holy, K.; Sedlak, A.

    2014-01-01

    Exposure to radon and smoking are among the most important factors influencing the risk of lung cancer. However, the joint effect of radon and smoking has not been sufficiently investigated so far. In this paper we will try to describe by means of a threshold energy model the mechanism of synergic effect of the aforementioned factors, and compare their influence on the risk of lung cancer. The model is based on the assumption that the inactivation of cells is caused by the excess of threshold specific energy z0 in the sensitive volume of the cell. Cigarette smoking causes, among others, an increase in the synthesis of the survivin protein that protects cells from apoptosis and thereby reduces their radiosensitivity. Survivin is therefore responsible for the increase of threshold energy z0, which in turn leads to the increase of lung cancer risk. A linear relationship between the threshold energy and the number of cigarettes smoked was assumed. The effect of smoking on radon exposure was evaluated for various groups of smokers that were defined by the degree of morphometric and geometric changes in the lungs induced by smoking and various degrees of chronic obstructive pulmonary disease. We simulate various scenarios of irradiation - short-term exposure, long-term exposure, as well as various smoking habits - smoker, ex-smoker. The calculated values can be, to an extent, compared to the epidemiological analysis geometric mixture models of Tomasek, who statistically evaluated epidemiological data about lung cancer occurrence among miners working in Jachymov and Pribram mines. From the results it follows that the correlation coefficient was particularly high. Although the approach outlined in this paper is only one of the many that strive to describe in detail the synergic effect of smoking and exposition, the used model can contribute to a more precise estimate of lung cancer risk in areas with various smoking habits. (authors)

  15. Modeling the Interaction of Mineral Dust with Solar Radiation: Spherical versus Non-spherical Particles

    Science.gov (United States)

    Hoshyaripour, A.; Vogel, B.; Vogel, H.

    2017-12-01

    Mineral dust, emitted from arid and semi-arid regions, is the most dominant atmospheric aerosol by mass. Beside detrimental effect on air quality, airborne dust also influences the atmospheric radiation by absorbing and scattering solar and terrestrial radiation. As a result, while the long-term radiative impacts of dust are important for climate, the short-term effects are significant for the photovoltaic energy production. Therefore, it is a vital requirement to accurately forecast the effects of dust on energy budget of the atmosphere and surface. To this end, a major issue is the fact that dust particles are non-spherical. Thus, the optical properties of such particles cannot be calculated precisely using the conventional methods like Mie theory that are often used in climate and numerical weather forecast models. In this study, T-Matrix method is employed, which is able to treat the non-sphericity of particles. Dust particles are assumed to be prolate spheroids with aspect ratio of 1.5 distributed in three lognormal modes. The wavelength-dependent refractive indices of dust are used in T-Matrix algorithm to calculate the extinction coefficient, single scattering albedo, asymmetry parameter and backscattering ratio at different wavelengths. These parameters are then implemented in ICON-ART model (ICOsahedral Nonhydrostatic model with Aerosols and Reactive Trace gases) to conduct a global simulation with 80 km horizontal resolution and 90 vertical levels. April 2014 is selected as the simulation period during which North African dust plumes reached central Europe and Germany. Results show that treatment of non-sphericity reduces the dust AOD in the range of 10 to 30%/. The impacts on diffuse and direct radiation at global, regional and local scales show strong dependency on the size distribution of the airborne dust. The implications for modeling and remote sensing the dust impacts on solar energy are also discussed.

  16. 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.

  17. Evaluation of efficacy of mineral oil, charcoal, and smectite in a rat model of equine cantharidin toxicosis.

    Science.gov (United States)

    Qualls, H J; Holbrook, T C; Gilliam, L L; Njaa, B L; Panciera, R J; Pope, C N; Payton, M E

    2013-01-01

    The efficacy of orally administered therapeutics for the treatment of cantharidin intoxication has not been evaluated in controlled studies. To develop a model of acute cantharidin intoxication in laboratory rats and to evaluate in this model the relative efficacy of 3 gastrointestinal therapies used to treat equine cantharidin toxicosis. Sixty-four male Sprague-Dawley rats. A blinded, randomized, controlled study was performed on rats surgically implanted with telemetry transmitters for evaluating heart rate, locomotor activity, and body temperature. Orogastric administration of cantharidin was performed within 15 seconds before administration of mineral oil, activated charcoal, or smectite. Negative control groups received therapeutic agents alone. Urine was collected for cantharidin analysis. Rats were sacrificed 24 hours after intoxication, and tissues were collected for histopathologic evaluation. Data analysis included ANOVA procedures and contingency tables. Six of 8 cantharidin-intoxicated rats treated with mineral oil died; bradycardia and hypothermia developed in the animals of this group 0-8 hours after intoxication. Rats treated with mineral oil had higher urine cantharidin concentrations than rats receiving cantharidin alone or with smectite (P = .04). The most severe hypothermia (30.6°C ± 1.0) developed in rats administered mineral oil at 4-8 hours after intoxication, whereas those treated with charcoal (35.2°C ± 0.8) had mean body temperatures higher than all other treatment groups (P = .03). Survival times in the charcoal (P = .16) and smectite (P = .12) treatment groups were not statistically different from negative controls. Mineral oil is often used in the treatment of equine cantharidin toxicosis. Our findings suggest that mineral oil increases cantharidin absorption, worsening morbidity and fatality in rats. Copyright © 2013 by the American College of Veterinary Internal Medicine.

  18. 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.

  19. Cost optimization model and its heuristic genetic algorithms

    International Nuclear Information System (INIS)

    Liu Wei; Wang Yongqing; Guo Jilin

    1999-01-01

    Interest and escalation are large quantity in proportion to the cost of nuclear power plant construction. In order to optimize the cost, the mathematics model of cost optimization for nuclear power plant construction was proposed, which takes the maximum net present value as the optimization goal. The model is based on the activity networks of the project and is an NP problem. A heuristic genetic algorithms (HGAs) for the model was introduced. In the algorithms, a solution is represented with a string of numbers each of which denotes the priority of each activity for assigned resources. The HGAs with this encoding method can overcome the difficulty which is harder to get feasible solutions when using the traditional GAs to solve the model. The critical path of the activity networks is figured out with the concept of predecessor matrix. An example was computed with the HGAP programmed in C language. The results indicate that the model is suitable for the objectiveness, the algorithms is effective to solve the model

  20. Genetics

    International Nuclear Information System (INIS)

    Hubitschek, H.E.

    1975-01-01

    Progress is reported on the following research projects: genetic effects of high LET radiations; genetic regulation, alteration, and repair; chromosome replication and the division cycle of Escherichia coli; effects of radioisotope decay in the DNA of microorganisms; initiation and termination of DNA replication in Bacillus subtilis; mutagenesis in mouse myeloma cells; lethal and mutagenic effects of near-uv radiation; effect of 8-methoxypsoralen on photodynamic lethality and mutagenicity in Escherichia coli; DNA repair of the lethal effects of far-uv; and near uv irradiation of bacterial cells

  1. Validation of a plant-wide phosphorus modelling approach with minerals precipitation in a full-scale WWTP

    DEFF Research Database (Denmark)

    Mbamba, Christian Kazadi; Flores Alsina, Xavier; Batstone, Damien John

    2016-01-01

    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...... 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......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...

  2. 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...

  3. 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...

  4. 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.

  5. Helicobacter pylori genetic diversification in the Mongolian gerbil model.

    Science.gov (United States)

    Beckett, Amber C; Loh, John T; Chopra, Abha; Leary, Shay; Lin, Aung Soe; McDonnell, Wyatt J; Dixon, Beverly R E A; Noto, Jennifer M; Israel, Dawn A; Peek, Richard M; Mallal, Simon; Algood, Holly M Scott; Cover, Timothy L

    2018-01-01

    Helicobacter pylori requires genetic agility to infect new hosts and establish long-term colonization of changing gastric environments. In this study, we analyzed H. pylori genetic adaptation in the Mongolian gerbil model. This model is of particular interest because H. pylori -infected gerbils develop a high level of gastric inflammation and often develop gastric adenocarcinoma or gastric ulceration. We analyzed the whole genome sequences of H. pylori strains cultured from experimentally infected gerbils, in comparison to the genome sequence of the input strain. The mean annualized single nucleotide polymorphism (SNP) rate per site was 1.5e -5 , which is similar to the rates detected previously in H. pylori- infected humans. Many of the mutations occurred within or upstream of genes associated with iron-related functions ( fur , tonB1 , fecA2 , fecA3 , and frpB3 ) or encoding outer membrane proteins ( alpA, oipA, fecA2, fecA3, frpB3 and cagY ). Most of the SNPs within coding regions (86%) were non-synonymous mutations. Several deletion or insertion mutations led to disruption of open reading frames, suggesting that the corresponding gene products are not required or are deleterious during chronic H. pylori colonization of the gerbil stomach. Five variants (three SNPs and two deletions) were detected in isolates from multiple animals, which suggests that these mutations conferred a selective advantage. One of the mutations (FurR88H) detected in isolates from multiple animals was previously shown to confer increased resistance to oxidative stress, and we now show that this SNP also confers a survival advantage when H. pylori is co-cultured with neutrophils. Collectively, these analyses allow the identification of mutations that are positively selected during H. pylori colonization of the gerbil model.

  6. GEOSURF: a computer program for modeling adsorption on mineral surfaces from aqueous solution

    Science.gov (United States)

    Sahai, Nita; Sverjensky, Dimitri A.

    1998-11-01

    A new program, GEOSURF, has been developed for calculating aqueous and surface speciation consistent with the triple-layer model of surface complexation. GEOSURF is an extension of the original programs MINEQL, MICROQL and HYDRAQL. We present, here, the basic algorithm of GEOSURF along with a description of the new features implemented. GEOSURF is linked to internally consistent data bases for surface species (SURFK.DAT) and for aqueous species (AQSOL.DAT). SURFK.DAT contains properties of minerals such as site densities, and equilibrium constants for adsorption of aqueous protons and electrolyte ions on a variety of oxides and hydroxides. The Helgeson, Kirkham and Flowers version of the extended Debye-Huckel Equation for 1:1 electrolytes is implemented for calculating aqueous activity coefficients. This permits the calculation of speciation at ionic strengths greater than 0.5 M. The activity of water is computed explicitly from the osmotic coefficient of the solution, and the total amount of electrolyte cation (or anion) is adjusted to satisfy the electroneutrality condition. Finally, the use of standard symbols for chemical species rather than species identification numbers is included to facilitate use of the program. One of the main limitations of GEOSURF is that aqueous and surface speciation can only be calculated at fixed pH and at fixed concentration of total adsorbate. Thus, the program cannot perform reaction-path calculations: it cannot determine whether or not a solution is over- or under-saturated with respect to one or more solid phases. To check the proper running of GEOSURF, we have compared results generated by GEOSURF with those from two other programs, HYDRAQL and EQ3. The Davies equation and the "bdot" equation, respectively, are used in the latter two programs for calculating aqueous activity coefficients. An example of the model fit to experimental data for rutile in 0.001 M-2.0 M NaNO 3 is included.

  7. Constraining the Timescales of Rehydration in Nominally Anhydrous Minerals Using 3D Numerical Diffusion Models

    Science.gov (United States)

    Lynn, K. J.; Warren, J. M.

    2017-12-01

    Nominally anhydrous minerals (NAMs) are important for characterizing deep-Earth water reservoirs, but the water contents of olivine (ol), orthopyroxene (opx), and clinopyroxene (cpx) in peridotites generally do not reflect mantle equilibrium conditions. Ol is typically "dry" and decoupled from H in cpx and opx, which is inconsistent with models of partial melting and/or diffusive loss of H during upwelling beneath mid-ocean ridges. The rehydration of mantle pyroxenes via late-stage re-fertilization has been invoked to explain their relatively high water contents. Here, we use sophisticated 3D diffusion models (after Shea et al., 2015, Am Min) of H in ol, opx, and cpx to investigate the timescales of rehydration across a range of conditions relevant for melt-rock interaction and serpentinization of peridotites. Numerical crystals with 1 mm c-axis lengths and realistic crystal morphologies are modeled using recent H diffusivities that account for compositional variation and diffusion anisotropy. Models were run over timescales of minutes to millions of years and temperatures from 300 to 1200°C. Our 3D models show that, at the high-T end of the range, H concentrations in the cores of NAMs are partially re-equilibrated in as little as a few minutes, and completely re-equilibrated within hours to weeks. At low-T (300°C), serpentinization can induce considerable diffusion in cpx and opx. H contents are 30% re-equilibrated after continuous exposure to hydrothermal fluids for 102 and 105 years, respectively, which is inconsistent with previous interpretations that there is no effect on H in opx under similar conditions. Ol is unaffected after 1 Myr due to the slower diffusivity of the proton-vacancy mechanism at 300°C (2-4 log units lower than for opx). In the middle of the T range (700-1000°C), rehydration of opx and cpx occurs over hours to days, while ol is somewhat slower to respond (days to weeks), potentially allowing the decoupling observed in natural samples to

  8. 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.

  9. Variable selection in Logistic regression model with genetic algorithm.

    Science.gov (United States)

    Zhang, Zhongheng; Trevino, Victor; Hoseini, Sayed Shahabuddin; Belciug, Smaranda; Boopathi, Arumugam Manivanna; Zhang, Ping; Gorunescu, Florin; Subha, Velappan; Dai, Songshi

    2018-02-01

    Variable or feature selection is one of the most important steps in model specification. Especially in the case of medical-decision making, the direct use of a medical database, without a previous analysis and preprocessing step, is often counterproductive. In this way, the variable selection represents the method of choosing the most relevant attributes from the database in order to build a robust learning models and, thus, to improve the performance of the models used in the decision process. In biomedical research, the purpose of variable selection is to select clinically important and statistically significant variables, while excluding unrelated or noise variables. A variety of methods exist for variable selection, but none of them is without limitations. For example, the stepwise approach, which is highly used, adds the best variable in each cycle generally producing an acceptable set of variables. Nevertheless, it is limited by the fact that it commonly trapped in local optima. The best subset approach can systematically search the entire covariate pattern space, but the solution pool can be extremely large with tens to hundreds of variables, which is the case in nowadays clinical data. Genetic algorithms (GA) are heuristic optimization approaches and can be used for variable selection in multivariable regression models. This tutorial paper aims to provide a step-by-step approach to the use of GA in variable selection. The R code provided in the text can be extended and adapted to other data analysis needs.

  10. 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.

  11. Quantitative genetic models of sexual selection by male choice.

    Science.gov (United States)

    Nakahashi, Wataru

    2008-09-01

    There are many examples of male mate choice for female traits that tend to be associated with high fertility. I develop quantitative genetic models of a female trait and a male preference to show when such a male preference can evolve. I find that a disagreement between the fertility maximum and the viability maximum of the female trait is necessary for directional male preference (preference for extreme female trait values) to evolve. Moreover, when there is a shortage of available male partners or variance in male nongenetic quality, strong male preference can evolve. Furthermore, I also show that males evolve to exhibit a stronger preference for females that are more feminine (less resemblance to males) than the average female when there is a sexual dimorphism caused by fertility selection which acts only on females.

  12. 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…

  13. 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.

  14. Genetic algorithm based optimization of advanced solar cell designs modeled in Silvaco AtlasTM

    OpenAIRE

    Utsler, James

    2006-01-01

    A genetic algorithm was used to optimize the power output of multi-junction solar cells. Solar cell operation was modeled using the Silvaco ATLASTM software. The output of the ATLASTM simulation runs served as the input to the genetic algorithm. The genetic algorithm was run as a diffusing computation on a network of eighteen dual processor nodes. Results showed that the genetic algorithm produced better power output optimizations when compared with the results obtained using the hill cli...

  15. Qualification of Thermodynamic Data for Geochemical Modeling of Mineral-Water Interactions in Dilute Systems

    International Nuclear Information System (INIS)

    T. J. Wolery; C.F. Jove-Colon

    2004-01-01

    The purpose of this analysis report is to qualify the thermochemical database data0.ymp.R2 (DTN: MO0302SPATHDYN.000 [DIRS 161756], qualified by this report) and supporting calculations (DTNs: MO0302SPATHDYN.001 [DIRS 161886], and MO0303SPASPEQ2.000 [DIRS 162278]), which were originally documented in ''Data Qualification: Update and Revision of the Geochemical Thermodynamic Database, Data0.ymp'' (Steinborn et al. 2003 [DIRS 161956]). This original document still serves as the record of development of the data0.ymp.R2 database (DTN: MO0302SPATHDYN.000 [DIRS 161756]). The data0.ymp.R2 thermodynamic database (DTN: MO0302SPATHDYN.000 [DIRS 161756]) was developed for use with software code EQ3/6 (EQ3/6 V8.0, STN: 10813-8.0-00) (BSC 2003 [DIRS 162228]) and software code EQ6 (EQ6 V7.2bLV, STN: 10075-7.2bLV-02) (BSC 2002 [DIRS 159731]) to conduct geochemical modeling of mineral-fluid interactions involving aqueous solutions (ionic strengths of up to one molal; see Section 6.5) and temperatures of up to 300 C along the liquid-vapor saturation curve of pure water. The data0.ymp.R2 database (DTN: MO0302SPATHDYN.000 [DIRS 161756]) is an update of the previously qualified predecessor database data0.ymp.R0 (DTN: MO0009THRMODYN.001 [DIRS 152576]). The scope of this report is limited to qualification of the updates, as well as identification and evaluation of certain errors and discrepancies as discussed

  16. Accumulation of Biomass and Mineral Elements with Calendar Time by Corn: Application of the Expanded Growth Model

    Science.gov (United States)

    Overman, Allen R.; Scholtz, Richard V.

    2011-01-01

    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. PMID:22194842

  17. 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.

  18. On the use of the spectroscopic techniques to model the interactions between radionuclides and solid minerals

    Energy Technology Data Exchange (ETDEWEB)

    Simoni, E. [IPN, Paris XI University, 91406 Orsay (France)]. e-mail: simoni@ipno.in2p3.fr

    2004-07-01

    In order to determine the radionuclides sorption constants on solid natural minerals, both thermodynamic and structural investigations, using spectroscopic techniques, are presented. The natural clays, that could be used as engineering barrier in the nuclear waste geological repository, are rather complex minerals. Therefore, in order to understand how these natural materials retain the radionuclides, it is necessary first to perform these studies on simple substrates such as phosphates, oxides and silicates (as powder and single crystal as well) and then extrapolate the obtained results on the natural minerals. As examples, the main results on the sorption processes of the hexavalent uranium onto zircon (ZrSiO{sub 4}) and lanthanum phosphate (LaPO{sub 4}) are presented. The corresponding sorption curves are simulated using the results obtained with the following spectroscopic techniques: laser induced spectro fluorimetry, X-ray photoelectron spectroscopy (XP S), X-ray absorption spectroscopy (Exafs). Finally, the thermodynamic sorption constants are calculated. (Author)

  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. Causal models in epidemiology: past inheritance and genetic future

    Directory of Open Access Journals (Sweden)

    Kriebel David

    2006-07-01

    Full Text Available Abstract The eruption of genetic research presents a tremendous opportunity to epidemiologists to improve our ability to identify causes of ill health. Epidemiologists have enthusiastically embraced the new tools of genomics and proteomics to investigate gene-environment interactions. We argue that neither the full import nor limitations of such studies can be appreciated without clarifying underlying theoretical models of interaction, etiologic fraction, and the fundamental concept of causality. We therefore explore different models of causality in the epidemiology of disease arising out of genes, environments, and the interplay between environments and genes. We begin from Rothman's "pie" model of necessary and sufficient causes, and then discuss newer approaches, which provide additional insights into multifactorial causal processes. These include directed acyclic graphs and structural equation models. Caution is urged in the application of two essential and closely related concepts found in many studies: interaction (effect modification and the etiologic or attributable fraction. We review these concepts and present four important limitations. 1. Interaction is a fundamental characteristic of any causal process involving a series of probabilistic steps, and not a second-order phenomenon identified after first accounting for "main effects". 2. Standard methods of assessing interaction do not adequately consider the life course, and the temporal dynamics through which an individual's sufficient cause is completed. Different individuals may be at different stages of development along the path to disease, but this is not usually measurable. Thus, for example, acquired susceptibility in children can be an important source of variation. 3. A distinction must be made between individual-based and population-level models. Most epidemiologic discussions of causality fail to make this distinction. 4. At the population level, there is additional

  1. GRAVITATIONAL LENS MODELING WITH GENETIC ALGORITHMS AND PARTICLE SWARM OPTIMIZERS

    International Nuclear Information System (INIS)

    Rogers, Adam; Fiege, Jason D.

    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 automatically, which represents the trade-off between the image χ 2 and regularization effects, and allows an estimate of the optimally regularized solution for each lens parameter set. In the final step of the optimization procedure, the lens model with the lowest χ 2 is used while the global optimizer solves for the source intensity distribution directly. This allows us to accurately determine the number of degrees of freedom in the problem to facilitate comparison between lens models and enforce positivity on the source profile. In practice, we find that the GA conducts a more thorough search of the parameter space than the PSO.

  2. The use of genetic algorithms to model protoplanetary discs

    Science.gov (United States)

    Hetem, Annibal; Gregorio-Hetem, Jane

    2007-12-01

    The protoplanetary discs of T Tauri and Herbig Ae/Be stars have previously been studied using geometric disc models to fit their spectral energy distribution (SED). The simulations provide a means to reproduce the signatures of various circumstellar structures, which are related to different levels of infrared excess. With the aim of improving our previous model, which assumed a simple flat-disc configuration, we adopt here a reprocessing flared-disc model that assumes hydrostatic, radiative equilibrium. We have developed a method to optimize the parameter estimation based on genetic algorithms (GAs). This paper describes the implementation of the new code, which has been applied to Herbig stars from the Pico dos Dias Survey catalogue, in order to illustrate the quality of the fitting for a variety of SED shapes. The star AB Aur was used as a test of the GA parameter estimation, and demonstrates that the new code reproduces successfully a canonical example of the flared-disc model. The GA method gives a good quality of fit, but the range of input parameters must be chosen with caution, as unrealistic disc parameters can be derived. It is confirmed that the flared-disc model fits the flattened SEDs typical of Herbig stars; however, embedded objects (increasing SED slope) and debris discs (steeply decreasing SED slope) are not well fitted with this configuration. Even considering the limitation of the derived parameters, the automatic process of SED fitting provides an interesting tool for the statistical analysis of the circumstellar luminosity of large samples of young stars.

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

    International Nuclear Information System (INIS)

    Sogn, T.A.; Haugen, L.E.

    2011-01-01

    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 N O 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 degree C for 8 weeks. Secondly, the calibrated model was tested by use of NO 3 -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 N O model reproduced relatively well the NO 3 -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 NO 3 -leaching. To achieve a satisfactory simulation of the NO 3 -leaching, recalibration of the model had to be carried out. Thus, SOILN N O 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.

  4. 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.

  5. Cs-selective mineral adsorbents in columns: physico-chemical properties and modeling

    International Nuclear Information System (INIS)

    Michel, Caroline

    2015-01-01

    Following the nuclear disaster in Fukushima Dai-Ichi, thousands of tons of fresh water and seawater were used for cooling the reactors or contaminated as a result of groundwater seepage. Decontamination of these waters is complicated by the presence of other cations (Na + , K + , Ca 2+ , Mg 2+ ) naturally present in these waters. Decontamination process in columns packed was studied in this context with two types of mineral adsorbents: the TERMOXID 35 and the SORBMATECH 202. The first one is a commercial adsorbent and consists of mixed ferrocyanide K/Ni impregnated over a solid matrix Zr(OH) 4 . The second one was synthesized in CEA and is composed of ferrocyanide K/Cu impregnated over a solid matrix SiO 2 . Both materials have shown a high efficiency for Cs decontamination in seawater with K(d,Cs) of about 10 5 mL/g. Batch studies conducted in different solutions (pure water, fresh water and seawater) allowed determining sorption kinetics and ion exchange mechanisms responsible for the sorption of Cs + , taking into account competitive effects of the natural water cations (Na + , K + , Ca 2+ , Mg 2+ ). Modelling of batches was performed with the geochemical code CHESS considering competitive effects according to the Vanselow formalism and selectivity coefficients, developing a specific thermodynamic database. The performances of these materials were then tested in column. The operating parameters such as Darcy's velocity and the H/D ratio were studied for a proper functioning of this process. The T35 has proven to be less efficient mainly because of the slow diffusion of Cs in the pores of the material. The S 2 O 2 has proven to be a good candidate for the application of high flow rates. The breakthrough curves obtained in fresh water have been modelled with the reactive transport codes HYTEC and OPTIPUR using the CHESS thermodynamic database. This approach will eventually help to support the design of a decontamination unit by the operator. (author) [fr

  6. 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

  7. 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.

  8. Gebel Gattar prospect, an obvious model of intra granitic uranium mineralization

    Energy Technology Data Exchange (ETDEWEB)

    Salman, A A; Shalaby, H M; Noseir, L; Elkhouli, D; Roz, M; Abu Zeid, M; Mostafa, M; Amin, N; Ayoub, R; Khamis, H [Nuclear materials authority, El Maadi, Cairo, (Egypt)

    1995-10-01

    Gebel Gattar area is situated in the northern Eastern desert, SW Hurghada city and is considered as an area of high potentiality for workable uranium deposits. The field radiometric prospect has started in May 1984. The geologic, structural and radiometric studies have resulted in the northern parts of the pluton and are controlled by some important structural features, namely NNE-SSW, ENE-WSW, NW-SE and to a lesser extent the N-S faults. The uranium content of the fresh granites in the area ranges from 20 to 30 ppm and thus could be considered as uraniferous granites. The mineralized samples are ranging from 1000 to 5000 ppm, while hand piked sample could reach as much as 14000 ppm. Detailed mineralogical studies proved the presence of various types of secondary uranium minerals presented mainly by molybdates, vanadates, silicate and sulphates. Exploratory tunneling works during 1990 to 1992 demonstrated that the uranium mineralization is still persistent from level 900 m (asl) to level 660 m (asl) which is nearly the wadi level. The alteration of the rocks especially hematitization, kaolination and partial silicificant is still well noticed and the gaping of the fault zone is more open and shows an increasing width. Moreover, secondary uranium minerals are still present indicating persistence of the oxidizing conditions. 5 figs., 4 tabs.

  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.,

  10. Miners' welfare

    Energy Technology Data Exchange (ETDEWEB)

    Buckley, C

    1984-06-13

    The Miners' Welfare Committee (MWC) was formed in Britain in 1921 and initiated building programmes to provide welfare amenities for miners and families, using architecture to improve the quality of a miner's working and leisure time. The article reviews the MWC's work, and assesses the design and architecture at the Selby Coalfield. (7 refs.)

  11. Equilibrium and non-equilibrium concepts in forest genetic modelling: population- and individually-based approaches

    OpenAIRE

    Kramer, Koen; van der Werf, D. C.

    2010-01-01

    The environment is changing and so are forests, in their functioning, in species composition, and in the species’ genetic composition. Many empirical and process-based models exist to support forest management. However, most of these models do not consider the impact of environmental changes and forest management on genetic diversity nor on the rate of adaptation of critical plant processes. How genetic diversity and rates of adaptation depend on management actions is a crucial next step in m...

  12. 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

  13. Statistical analysis of results from the quantitative mapping of fracture minerals in Forsmark. 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

    so, the differences are generally shown to be small and if comparing the cumulative distribution functions for the data subsets of the 21 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 = -1.47 and sigma 0.70, chlorite mu = -0.93 and sigma = 0.46, clay minerals mu = -1.09 and sigma = 0.44, pyrite mu = -4.01 and sigma = 1.26. 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 = 0.85 and beta = 0.65, chlorite alpha =1.38 and beta = 0.51, clay minerals alpha = 1.47 and beta = 0.40, pyrite alpha = -1.52 and beta = 1.18. 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

  14. 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.

  15. International mineral economics

    International Nuclear Information System (INIS)

    Gocht, W.R.; Eggert, R.G.

    1988-01-01

    International Mineral Economics provides an integrated overview of the important concepts. The treatment is interdisciplinary, drawing on the fields of economics, geology, business, and mining engineering. Part I examines the technical concepts important for understanding the geology of ore deposits, the methods of exploration and deposit evaluation, and the activities of mining and mineral processing. Part II focuses on the economic and related concepts important for understanding mineral development, the evaluation of exploration and mining projects, and mineral markets and market models. Finally, Part III reviews and traces the historical development of the policies of international organizations, the industrialized countries, and the developing countries. (orig.)

  16. Marine Mineral Exploration

    DEFF Research Database (Denmark)

    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...

  17. 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

  18. Modelling Autistic Features in Mice Using Quantitative Genetic Approaches

    NARCIS (Netherlands)

    Molenhuis, Remco T; Bruining, Hilgo; Kas, Martien J

    2017-01-01

    Animal studies provide a unique opportunity to study the consequences of genetic variants at the behavioural level. Human studies have identified hundreds of risk genes for autism spectrum disorder (ASD) that can lead to understanding on how genetic variation contributes to individual differences in

  19. A Realistic Model under which the Genetic Code is Optimal

    NARCIS (Netherlands)

    Buhrman, H.; van der Gulik, P.T.S.; Klau, G.W.; Schaffner, C.; Speijer, D.; Stougie, L.

    2013-01-01

    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

  20. Improvements in the biokinetic model for strontium with allowance for age and gender differences in bone mineral metabolism

    International Nuclear Information System (INIS)

    Shagina, N.B.; Tolstykh, E.I.; Degteva, M.O.

    2003-01-01

    An age- and gender-dependent biokinetic model for strontium was developed based on the study of a population living along the Techa River exposed to effluents from the Mayak Production Association. To estimate parameters of a new model (Techa biokinetic model, TBM) many data sets have been assembled: our whole-body counter data on long-term retention of 90 Sr in humans, data from studies during the period of global fallout, data resulting from deliberate injections of strontium radionuclides, and non-radiological data regarding bone formation and resorption, mineral content of the body, etc. The model was developed using the basic structure of the ICRP biokinetic model for strontium, but new age- and gender-specific parameters were derived. This paper discusses the approaches applied to develop the new model. (author)

  1. 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

  2. Trace element partitioning in rock forming minerals of co-genetic, subduction-related alkaline and tholeiitic mafic rocks in the Ural Mountains, Russia

    Science.gov (United States)

    Krause, J.; Brügmann, G. E.; Pushkarev, E. V.

    2009-04-01

    The partitioning of trace elements between rock forming minerals in igneous rocks is largely controlled by physical and chemical parameters e.g. temperature, pressure and chemical composition of the minerals and the coexisting melt. In the present study partition coefficients for REE between hornblende, orthopyroxene, feldspars, apatite and clinopyroxene in a suite of co-genetic alkaline and tholeiitic mafic rocks from the Ural Mountains (Russia) were calculated. The results give insights to the influence of the chemical composition of the parental melt on the partitioning behaviour of the REE. Nepheline-bearing, alkaline melanogabbros (tilaites) are assumed to represent the most fractionated products of the melt that formed the ultramafic cumulates in zoned mafic-ultramafic complexes in the Ural Mountains. Co-genetic with the latter is a suite of olivine gabbros, gabbronorites and hornblende gabbros formed from a tholeiitic parental melt. Negative anomalies for the HFSE along with low Nb and Ta contents and a positive Sr anomaly indicate a subduction related origin of all parental melts. The nepheline gabbros consist predominantly of coarse-grained clinopyroxene phenocrysts in a matrix of fine grained clinopyroxene, olivine, plagioclase, K-feldspar and nepheline with accessory apatite. The tholeiitic gabbros have equigranular to porphyric textures with phenocrysts of olivine, pyroxene and hornblende in a plagioclase rich matrix with olivine hornblende, pyroxene and accessory apatite. Element concentrations of adjacent matrix grains and rims of phenochrysts were measured with LA-ICPMS. The distribution of REE between hornblende and clinopyroxene in the tholeiitic rocks is similar for most of the elements (DHbl•Cpx(La-Tm) = 2.7-2.8, decreasing to 2.6 and 2.4 for Yb and Lu, respectively). These values are about two times higher than published data (e.g. Ionov et al. 1997). Partition coefficients for orthopyroxene/clinopyroxene systematically decrease from the HREE

  3. Use of a genetic algorithm in a subchannel model

    International Nuclear Information System (INIS)

    Alberto Teyssedou; Armando Nava-Dominguez

    2005-01-01

    Full text of publication follows: The channel of a nuclear reactor contains the fuel bundles which are made up of fuel elements distributed in a manner that creates a series of interconnected subchannels through which the coolant flows. Subchannel codes are used to determine local flow variables; these codes consider the complex geometry of a nuclear fuel bundle as being divided in simple parallel and interconnected cells called 'subchannels'. Each subchannel is bounded by the solid walls of the fuel rods or by imaginary boundaries placed between adjacent subchannels. In each subchannel the flow is considered as one dimensional, therefore lateral mixing mechanisms between subchannels should be taken into account. These mixing mechanisms are: Diversion cross-flow, Turbulent mixing, Turbulent void diffusion, Void drift and Buoyancy drift; they are implemented as independent contribution terms in a pseudo-vectorial lateral momentum equation. These mixing terms are calculated with correlations that require the use of empirical coefficients. It has been observed, however, that there is no unique set of coefficients and or correlations that can be used to predict a complete range of experimental conditions. To avoid this drawback, in this paper a Genetic Algorithm (GA) was coupled to a subchannel model. The use of a GA in conjunction with an appropriate objective function allows the subchannel model to internally determine the optimal values of the coefficients without user intervention. The subchannel model requires two diffusion coefficients, the drift flux two-phase flow distribution coefficient, C 0 , and a coefficient used to control the lateral pressure losses. The GA algorithm was implemented in order to find the most appropriate values of these four coefficients. Genetic algorithms (GA) are based on the theory of evolution; thus, the GA manipulates a population of individuals (chromosomes) in order to evolve them towards a best adaptation (fitness criterion) to

  4. Estimation and interpretation of genetic effects with epistasis using the NOIA model.

    Science.gov (United States)

    Alvarez-Castro, José M; Carlborg, Orjan; Rönnegård, Lars

    2012-01-01

    We introduce this communication with a brief outline of the historical landmarks in genetic modeling, especially concerning epistasis. Then, we present methods for the use of genetic modeling in QTL analyses. In particular, we summarize the essential expressions of the natural and orthogonal interactions (NOIA) model of genetic effects. Our motivation for reviewing that theory here is twofold. First, this review presents a digest of the expressions for the application of the NOIA model, which are often mixed with intermediate and additional formulae in the original articles. Second, we make the required theory handy for the reader to relate the genetic concepts to the particular mathematical expressions underlying them. We illustrate those relations by providing graphical interpretations and a diagram summarizing the key features for applying genetic modeling with epistasis in comprehensive QTL analyses. Finally, we briefly review some examples of the application of NOIA to real data and the way it improves the interpretability of the results.

  5. Development of Genetic Occurrence Models for Geothermal Prospecting

    Science.gov (United States)

    Walker, J. D.; Sabin, A.; Unruh, J.; Monastero, F. C.; Combs, J.

    2007-12-01

    , including high heat flow, anomalous temperature water wells, high-temperature indications from aqueous geothermometry and geochemistry, Pliocene or younger ages from low-temperature thermochronometers, as well as more obvious factors such as geysers and fumaroles (which by definition will be missing for blind resources). Our occurrence-model strategy inverts the current approach that relies first on obvious evidence of geothermal activity. We evaluated our approach by retrospectively applying the protocol to the characteristics of producing geothermal fields, and in all cases, known resource areas fit the parameters identified from a genetic perspective.

  6. 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

  7. Quantitative genetics of Taura syndrome resistance in Pacific (Penaeus vannamei): A cure model approach

    DEFF Research Database (Denmark)

    Ødegård, Jørgen; Gitterle, Thomas; Madsen, Per

    2011-01-01

    cure survival model using Gibbs sampling, treating susceptibility and endurance as separate genetic traits. Results: Overall mortality at the end of test was 28%, while 38% of the population was considered susceptible to the disease. The estimated underlying heritability was high for susceptibility (0....... However, genetic evaluation of susceptibility based on the cure model showed clear associations with standard genetic evaluations that ignore the cure fraction for these data. Using the current testing design, genetic variation in observed survival time and absolute survival at the end of test were most...

  8. [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.

  9. Hierarchical linear modeling of longitudinal pedigree data for genetic association analysis

    DEFF Research Database (Denmark)

    Tan, Qihua; B Hjelmborg, Jacob V; Thomassen, Mads

    2014-01-01

    -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...... 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......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...

  10. 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).......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...

  11. 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.

  12. Genetic correlations among body condition score, yield and fertility in multiparous cows using random regression models

    OpenAIRE

    Bastin, Catherine; Gillon, Alain; Massart, Xavier; Bertozzi, Carlo; Vanderick, Sylvie; Gengler, Nicolas

    2010-01-01

    Genetic correlations between body condition score (BCS) in lactation 1 to 3 and four economically important traits (days open, 305-days milk, fat, and protein yields recorded in the first 3 lactations) were estimated on about 12,500 Walloon Holstein cows using 4-trait random regression models. Results indicated moderate favorable genetic correlations between BCS and days open (from -0.46 to -0.62) and suggested the use of BCS for indirect selection on fertility. However, unfavorable genetic c...

  13. Dietary fibers from mushroom sclerotia. 4. In vivo mineral absorption using ovariectomized rat model.

    Science.gov (United States)

    Wong, Ka-Hing; Katsumata, Shin-Ichi; Masuyama, Ritsuko; Uehara, Mariko; Suzuki, Kazuharu; Cheung, Peter C K

    2006-03-08

    The effect of three novel dietary fibers (DFs) prepared from mushroom sclerotia, namely, Pleurotus tuber-regium, Polyporus rhinocerus, and Wolfiporia cocos, on calcium and magnesium absorption was evaluated in ovariectomized (OVX) rats fed with sclerotial DF based and low Ca (0.3%) diets for 14 days. The animals in the W. cocos DF diet group possessed significantly (p cocos DF group were also significantly (p cocos DF could improve the overall Ca and Mg absorptions of the OVX rats fed a low Ca diet. The potential use of sclerotial DFs as a functional food ingredient for enhancing mineral absorption is also discussed.

  14. 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...

  15. Different concepts and models of information for family-relevant genetic findings: comparison and ethical analysis.

    Science.gov (United States)

    Lenk, Christian; Frommeld, Debora

    2015-08-01

    Genetic predispositions often concern not only individual persons, but also other family members. Advances in the development of genetic tests lead to a growing number of genetic diagnoses in medical practice and to an increasing importance of genetic counseling. In the present article, a number of ethical foundations and preconditions for this issue are discussed. Four different models for the handling of genetic information are presented and analyzed including a discussion of practical implications. The different models' ranges of content reach from a strictly autonomous position over self-governed arrangements in the practice of genetic counseling up to the involvement of official bodies and committees. The different models show a number of elements which seem to be very useful for the handling of genetic data in families from an ethical perspective. In contrast, the limitations of the standard medical attempt regarding confidentiality and personal autonomy in the context of genetic information in the family are described. Finally, recommendations for further ethical research and the development of genetic counseling in families are given.

  16. Re-Os, Sm-Nd, U-Pb, and stepwise lead leaching isotope systematics in shear-zone hosted gold mineralization: genetic tracing and age constraints of crustal hydrothermal activity

    Science.gov (United States)

    Frei, R.; Nägler, Th. F.; Schönberg, R.; Kramers, J. D.

    1998-06-01

    A combined Re-Os, Sm-Nd, U-Pb, and stepwise Pb leaching (PbSL) isotope study of hydrothermal (Mo-W)-bearing minerals and base metal sulfides from two adjacent shear zone hosted gold deposits (RAN, Kimberley) in the Harare-Shamva greenstone belt (Zimbabwe) constrain the timing of the mineralizing events to two periods. During an initial Late Archean event (2.60 Ga) a first molybdenite-scheelite bearing paragenesis was deposited in both shear zone systems, followed by a local reactivation of the shear systems during an Early Proterozoic (1.96 Ga) tectono-thermal overprint, during which base metal sulfides and most of the gold was (re-)deposited. While PbSL has revealed an open-system behavior of the U-Pb systematics in molybdenite and wolframite from the RAN mine, initial Archean Re-Os ages are still preserved implying that this system in these minerals was more resistant to the overprint. A similar retentivity could be shown for the Sm-Nd system in scheelite and powellite associated with the above ore minerals. Re-Os isotopic data from the Proterozoic mineralization in the Kimberley mine point to a recent gain of Re, most pronouncedly affecting Fe-rich sulfides such as pyrrhotite. A significant Re-loss in powellitic scheelite (an alteration phase of molybdenite-bearing scheelite), coupled with a marked loss of U in W-Mo ore minerals, complements the observation of a major Re uptake in Fe-sulfides during oxidizing conditions in a weathering environment. Pyrrhotite under these conditions behaves as an efficient Re-sink. Lead isotope signatures from PbSL residues of molybdenite, powellite, and quartz indicate a continental crustal source and/or contamination for the mineralizing fluid by interaction of the fluids with older sedimentary material as represented by the direct host country rocks. Our investigation reveals the potential of the Re-Os isotopic system applied to crustal hydrothermal ore minerals for genetic tracing and dating purposes. The simplified chemical

  17. Two-level mixed modeling of longitudinal pedigree data for genetic association analysis

    DEFF Research Database (Denmark)

    Tan, Q.

    2013-01-01

    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...... 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......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...

  18. 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.

  19. Invited review: Genetic and genomic mouse models for livestock research

    Directory of Open Access Journals (Sweden)

    D. Arends

    2018-02-01

    Full Text Available Knowledge about the function and functioning of single or multiple interacting genes is of the utmost significance for understanding the organism as a whole and for accurate livestock improvement through genomic selection. This includes, but is not limited to, understanding the ontogenetic and environmentally driven regulation of gene action contributing to simple and complex traits. Genetically modified mice, in which the functions of single genes are annotated; mice with reduced genetic complexity; and simplified structured populations are tools to gain fundamental knowledge of inheritance patterns and whole system genetics and genomics. In this review, we briefly describe existing mouse resources and discuss their value for fundamental and applied research in livestock.

  20. Relationships between soil and leaf mineral composition are element-specific, environment-dependent and geographically structured in the emerging model Arabidopsis halleri.

    Science.gov (United States)

    Stein, Ricardo J; Höreth, Stephan; de Melo, J Romário F; Syllwasschy, Lara; Lee, Gwonjin; Garbin, Mário L; Clemens, Stephan; Krämer, Ute

    2017-02-01

    Leaf mineral composition, the leaf ionome, reflects the complex interaction between a plant and its environment including local soil composition, an influential factor that can limit species distribution and plant productivity. Here we addressed within-species variation in plant-soil interactions and edaphic adaptation using Arabidopsis halleri, a well-suited model species as a facultative metallophyte and metal hyperaccumulator. We conducted multi-element analysis of 1972 paired leaf and soil samples from 165 European populations of A. halleri, at individual resolution to accommodate soil heterogeneity. Results were further confirmed under standardized conditions upon cultivation of 105 field-collected genotypes on an artificially metal-contaminated soil in growth chamber experiments. Soil-independent between- and within-population variation set apart leaf accumulation of zinc, cadmium and lead from all other nutrient and nonessential elements, concurring with differential hypothesized ecological roles in either biotic interaction or nutrition. For these metals, soil-leaf relationships were element-specific, differed between metalliferous and nonmetalliferous soils and were geographically structured both in the field and under standardized growth conditions, implicating complex scenarios of recent ecological adaptation. Our study provides an example and a reference for future related work and will serve as a basis for the molecular-genetic dissection and ecological analysis of the observed phenotypic variation. © 2016 The Authors. New Phytologist © 2016 New Phytologist Trust.

  1. Applications of Systems Genetics and Biology for Obesity Using Pig Models

    DEFF Research Database (Denmark)

    Kogelman, Lisette; Kadarmideen, Haja N.

    2016-01-01

    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...

  2. Climatology of nocturnal low-level jets over North Africa and implications for modeling mineral dust emission.

    Science.gov (United States)

    Fiedler, S; Schepanski, K; Heinold, B; Knippertz, P; Tegen, I

    2013-06-27

    [1] This study presents the first climatology for the dust emission amount associated with Nocturnal Low-Level Jets (NLLJs) in North Africa. These wind speed maxima near the top of the nocturnal boundary layer can generate near-surface peak winds due to shear-driven turbulence in the course of the night and the NLLJ breakdown during the following morning. The associated increase in the near-surface wind speed is a driver for mineral dust emission. A new detection algorithm for NLLJs is presented and used for a statistical assessment of NLLJs in 32 years of ERA-Interim reanalysis from the European Centre for Medium-Range Weather Forecasts. NLLJs occur in 29% of the nights in the annual and spatial mean. The NLLJ climatology shows a distinct annual cycle with marked regional differences. Maxima of up to 80% NLLJ frequency are found where low-level baroclinicity and orographic channels cause favorable conditions, e.g., over the Bodélé Depression, Chad, for November-February and along the West Saharan and Mauritanian coast for April-September. Downward mixing of NLLJ momentum to the surface causes 15% of mineral dust emission in the annual and spatial mean and can be associated with up to 60% of the total dust amount in specific areas, e.g., the Bodélé Depression and south of the Hoggar-Tibesti Channel. The sharp diurnal cycle underlines the importance of using wind speed information with high temporal resolution as driving fields for dust emission models. Citation: Fiedler, S., K. Schepanski, B. Heinold, P. Knippertz, and I. Tegen (2013), Climatology of nocturnal low-level jets over North Africa and implications for modeling mineral dust emission, J. Geophys. Res. Atmos., 118, 6100-6121, doi:10.1002/jgrd.50394.

  3. Application of stereolithographic custom models for studying the impact of biofilms and mineral precipitation on fluid flow.

    Science.gov (United States)

    Stoner, D L; Watson, S M; Stedtfeld, R D; Meakin, P; Griffel, L K; Tyler, T L; Pegram, L M; Barnes, J M; Deason, V A

    2005-12-01

    Here we introduce the use of transparent experimental models fabricated by stereolithography for studying the impacts of biomass accumulation, minerals precipitation, and physical configuration of flow paths on liquid flow in fracture apertures. The internal configuration of the models ranged in complexity from simple geometric shapes to those that incorporate replicated surfaces of natural fractures and computationally derived fracture surfaces. High-resolution digital time-lapse imaging was employed to qualitatively observe the migration of colloidal and soluble dyes through the flow models. In this study, a Sphingomonas sp. and Sporosarcina (Bacillus) pasteurii influenced the fluid dynamics by physically altering flow paths. Microbial colonization and calcite deposition enhanced the stagnant regions adjacent to solid boundaries. Microbial growth and calcite precipitation occurred to a greater extent in areas behind the fabricated obstacles and less in high-velocity orifices.

  4. Genetic evolution, plasticity, and bet-hedging as adaptive responses to temporally autocorrelated fluctuating selection: A quantitative genetic model.

    Science.gov (United States)

    Tufto, Jarle

    2015-08-01

    Adaptive responses to autocorrelated environmental fluctuations through evolution in mean reaction norm elevation and slope and an independent component of the phenotypic variance are analyzed using a quantitative genetic model. Analytic approximations expressing the mutual dependencies between all three response modes are derived and solved for the joint evolutionary outcome. Both genetic evolution in reaction norm elevation and plasticity are favored by slow temporal fluctuations, with plasticity, in the absence of microenvironmental variability, being the dominant evolutionary outcome for reasonable parameter values. For fast fluctuations, tracking of the optimal phenotype through genetic evolution and plasticity is limited. If residual fluctuations in the optimal phenotype are large and stabilizing selection is strong, selection then acts to increase the phenotypic variance (bet-hedging adaptive). Otherwise, canalizing selection occurs. If the phenotypic variance increases with plasticity through the effect of microenvironmental variability, this shifts the joint evolutionary balance away from plasticity in favor of genetic evolution. If microenvironmental deviations experienced by each individual at the time of development and selection are correlated, however, more plasticity evolves. The adaptive significance of evolutionary fluctuations in plasticity and the phenotypic variance, transient evolution, and the validity of the analytic approximations are investigated using simulations. © 2015 The Author(s). Evolution © 2015 The Society for the Study of Evolution.

  5. 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.

  6. Mineral-associated organic matter: are we now on the right path to accurately measuring and modelling it?

    Science.gov (United States)

    Cotrufo, M. F.

    2017-12-01

    Mineral-associated organic matter (MAOM) is the largest and most persistent pool of carbon in soil. Understanding and correctly modeling its dynamic is key to suggest management practices that can augment soil carbon storage for climate change mitigation, as well as increase soil organic matter (SOM) stocks to support soil health on the long-term. In the Microbial Efficiency Mineral Stabilization (MEMS) framework we proposed that, contrary to what originally thought, this form of persistent SOM is derived from the labile components of plant inputs, through their efficient microbial processing. I will present results from several experiments using dual isotope labeling of plant inputs that largely confirm this opinion, and point to the key role of dissolved organic matter in MAOM formation, and to the dynamic nature of the outer layer of MAOM. I will also show how we are incorporating this understanding in a new SOM model, which uses physically defined measurable pools rather than turnover-defined pools to forecast C cycling in soil.

  7. The surface chemistry of divalent metal carbonate minerals; a critical assessment of surface charge and potential data using the charge distribution multi-site ion complexation model

    NARCIS (Netherlands)

    Wolthers, M.; Charlet, L.; Van Cappellen, P.

    2008-01-01

    The Charge Distribution MUltiSite Ion Complexation or CD–MUSIC modeling approach is used to describe the chemical structure of carbonate mineralaqueous solution interfaces. The new model extends existing surface complexation models of carbonate minerals, by including atomic scale information on

  8. A Model for Understanding the Genetic Basis for Disparity in Prostate Cancer Risk

    Science.gov (United States)

    2017-10-01

    AWARD NUMBER: W81XWH-15-1-0529 TITLE: A Model for Understanding the Genetic Basis for Disparity in Prostate Cancer Risk PRINCIPAL INVESTIGATOR...AND SUBTITLE A Model for Understanding the Genetic Basis for Disparity in Prostate Cancer Risk 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-15-1...STATEMENT Approved for Public Release; Distribution Unlimited 13. SUPPLEMENTARY NOTES 14. ABSTRACT Prostate cancer is the most commonly diagnosed cancer in

  9. Genetic Modeling of Radiation Injury in Prostate Cancer Patients Treated with Radiotherapy

    Science.gov (United States)

    2017-10-01

    AWARD NUMBER: W81XWH-15-1-0681 TITLE: Genetic Modeling of Radiation Injury in Prostate Cancer Patients Treated with Radiotherapy PRINCIPAL...TITLE AND SUBTITLE 5a. CONTRACT NUMBER 5b. GRANT NUMBER W81XWH-15-1-0681Genetic Modeling of Radiation Injury in Prostate Cancer Patients Treated...effects, urinary morbidity, rectal injury, sexual dysfunction 16. SECURITY CLASSIFICATION OF: 17. LIMITATION OF ABSTRACT 18. NUMBER OF PAGES 19a. NAME OF

  10. Application of genetic algorithm in modeling on-wafer inductors for up to 110 Ghz

    Science.gov (United States)

    Liu, Nianhong; Fu, Jun; Liu, Hui; Cui, Wenpu; Liu, Zhihong; Liu, Linlin; Zhou, Wei; Wang, Quan; Guo, Ao

    2018-05-01

    In this work, the genetic algorithm has been introducted into parameter extraction for on-wafer inductors for up to 110 GHz millimeter-wave operations, and nine independent parameters of the equivalent circuit model are optimized together. With the genetic algorithm, the model with the optimized parameters gives a better fitting accuracy than the preliminary parameters without optimization. Especially, the fitting accuracy of the Q value achieves a significant improvement after the optimization.

  11. 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

  12. Comparison of estimation and simulation methods for modeling block 1 of anomaly no.3 in Narigan Uranium mineral deposit

    International Nuclear Information System (INIS)

    Jamali Esfahlan, D.; Madani, H.

    2011-01-01

    Geostatistical methods are applied for modeling the mineral deposits at the final stage of the detailed exploration. By applying the results of these models, the technical and economic feasibility studies are conducted for the deposits. The geostatistical modeling methods are usually consist of estimation and simulation methods. The estimation techniques, such as Kriging, construct spatial relation (geological continuation model) between data, by providing the best unique guesses for unknown features. However, when applying this technique for a grid of drill-holes over a deposit, an obvious discrepancy exists between the real geological features and the Kriging estimation map. Because of the limited number of sampled data applied for Kriging, it could not appear as the same as the real features. Also the spatial continuity estimated by the Kriging maps, are smoother than the real unknown features. On the other hand, the objective of simulation is to provide some functions or sets of variable values, to be compatible with the existing information. This means that the simulated values have an average and the variance similar to the raw data and may even be the same as the measurements. we studied the Anomaly No.3 of Narigan uranium mineral deposit, located in the central Iran region and applied the Kriging estimation and the sequential Gaussian simulation methods, and finally by comparing the results we concluded that the Kriging estimation method is more reliable for long term planning of a mine. Because of the reconstructing random structures, the results of the simulation methods indicate that they could also be applied for short term planning in mine exploitation.

  13. 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. PMID:23134044

  14. 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. © 2011 American Institute of Physics

  15. Non-linear nuclear engineering models as genetic programming application

    International Nuclear Information System (INIS)

    Domingos, Roberto P.; Schirru, Roberto; Martinez, Aquilino S.

    1997-01-01

    This work presents a Genetic Programming paradigm and a nuclear application. A field of Artificial Intelligence, based on the concepts of Species Evolution and Natural Selection, can be understood as a self-programming process where the computer is the main agent responsible for the discovery of a program able to solve a given problem. In the present case, the problem was to find a mathematical expression in symbolic form, able to express the existent relation between equivalent ratio of a fuel cell, the enrichment of fuel elements and the multiplication factor. Such expression would avoid repeatedly reactor physics codes execution for core optimization. The results were compared with those obtained by different techniques such as Neural Networks and Linear Multiple Regression. Genetic Programming has shown to present a performance as good as, and under some features superior to Neural Network and Linear Multiple Regression. (author). 10 refs., 8 figs., 1 tabs

  16. 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

  17. Assessment of environmental impact models in natural occurring radionuclides solid wastes disposal from the mineral industry

    International Nuclear Information System (INIS)

    Pontedeiro, Elizabeth May Braga Dulley

    2006-07-01

    This work evaluates the behavior of wastes with naturally occurring radionuclides as generated by the mineral industry and their final disposal in landfills. An integrated methodology is used to predict the performance of an industrial landfill for disposal of wastes containing NORM/TENORM, and to define acceptable amounts that can be disposed at the landfill using long-term environmental assessment. The governing equations for radionuclide transport are solved analytically using the generalized integral transform technique. Results obtained for each compartment of the biogeosphere are validated with experimental results or compared to other classes of solutions. An impact analysis is performed in order to define the potential consequences of a landfill to the environment, considering not only the engineering characteristics of the waste deposit but also the exposure pathways and plausible scenarios in which the contaminants could migrate and reach the environment and the human population. The present work permits the development of a safety approach that can be used to derive quantitative waste acceptance criteria for the disposal of NORM/TENORM waste in landfills. (author)

  18. Modelling the co-evolution of indirect genetic effects and inherited variability.

    Science.gov (United States)

    Marjanovic, Jovana; Mulder, Han A; Rönnegård, Lars; Bijma, Piter

    2018-03-28

    When individuals interact, their phenotypes may be affected not only by their own genes but also by genes in their social partners. This phenomenon is known as Indirect Genetic Effects (IGEs). In aquaculture species and some plants, however, competition not only affects trait levels of individuals, but also inflates variability of trait values among individuals. In the field of quantitative genetics, the variability of trait values has been studied as a quantitative trait in itself, and is often referred to as inherited variability. Such studies, however, consider only the genetic effect of the focal individual on trait variability and do not make a connection to competition. Although the observed phenotypic relationship between competition and variability suggests an underlying genetic relationship, the current quantitative genetic models of IGE and inherited variability do not allow for such a relationship. The lack of quantitative genetic models that connect IGEs to inherited variability limits our understanding of the potential of variability to respond to selection, both in nature and agriculture. Models of trait levels, for example, show that IGEs may considerably change heritable variation in trait values. Currently, we lack the tools to investigate whether this result extends to variability of trait values. Here we present a model that integrates IGEs and inherited variability. In this model, the target phenotype, say growth rate, is a function of the genetic and environmental effects of the focal individual and of the difference in trait value between the social partner and the focal individual, multiplied by a regression coefficient. The regression coefficient is a genetic trait, which is a measure of cooperation; a negative value indicates competition, a positive value cooperation, and an increasing value due to selection indicates the evolution of cooperation. In contrast to the existing quantitative genetic models, our model allows for co-evolution of

  19. Numerical modeling of the impact of temperature on the behavior of minerals in the Soultz-sous-Forêts enhanced geothermal system

    Science.gov (United States)

    Van Ngo, Viet; Lucas, Yann; Clément, Alain; Fritz, Bertrand

    2015-04-01

    Operation of the enhanced geothermal system (EGS) requires to re-inject fluid, after heat exchange at the surface to the energy production, into the geothermal reservoir. This cold re-injected fluid can cause a strong disequilibrium with the fluid and granitic rock within the geothermal reservoir and then implies the possible dissolution/precipitation of minerals. The hydrothermal alterations include the transformation of plagioclase, biotite and K-feldspar and the precipitation of various secondary minerals. The major sealing phases observed in the main fracture zones are quartz, calcite, and clay minerals. These mineralogical transformations may modify the porosity, permeability and fluid pathways of the geothermal reservoir. In the Soultz-sous-Forêts EGS (Alsace, France), the hydraulic connection between the injection well and the production well is quite poor. Therefore, understanding the impact of changes in temperature, which are caused by the re-injected fluid, on the behavior of minerals (especially for the main newly-formed minerals such as quartz, calcite and clay minerals) is a critical preliminary step for the long-term prediction of their evolution. The approach used in the present work is typically based on a geochemical code, called THERMA, which enables to calculate the changes in equilibrium constants of all primary and secondary minerals and aqueous species as a function of temperature. Our model accounted for a wide range of different mineral groups in order to make sure a large freedom for the numerical calculations. The modeling results showed that when the temperature of geothermal reservoir is cooled down, quartz, calcite, illites, galena and pyrite have tendency towards equilibrium state, which indicates that they are precipitated under the geothermal conditions. In contrast, other minerals including plagioclase, K-feldspar and biotite remained unsaturated. These behaviors of minerals were further illustrated by the Khorzinsky stability

  20. Portfolio optimization by using linear programing models based on genetic algorithm

    Science.gov (United States)

    Sukono; Hidayat, Y.; Lesmana, E.; Putra, A. S.; Napitupulu, H.; Supian, S.

    2018-01-01

    In this paper, we discussed the investment portfolio optimization using linear programming model based on genetic algorithms. It is assumed that the portfolio risk is measured by absolute standard deviation, and each investor has a risk tolerance on the investment portfolio. To complete the investment portfolio optimization problem, the issue is arranged into a linear programming model. Furthermore, determination of the optimum solution for linear programming is done by using a genetic algorithm. As a numerical illustration, we analyze some of the stocks traded on the capital market in Indonesia. Based on the analysis, it is shown that the portfolio optimization performed by genetic algorithm approach produces more optimal efficient portfolio, compared to the portfolio optimization performed by a linear programming algorithm approach. Therefore, genetic algorithms can be considered as an alternative on determining the investment portfolio optimization, particularly using linear programming models.

  1. 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

  2. 3D implicit modeling of the Sishen Mine: new resolution of the geometry and origin of Fe mineralization

    Science.gov (United States)

    Stoch, B.; Anthonissen, C. J.; McCall, M.-J.; Basson, I. J.; Deacon, J.; Cloete, E.; Botha, J.; Britz, J.; Strydom, M.; Nel, D.; Bester, M.

    2017-12-01

    The Sishen deposit is one of the largest iron ore concentrations in current production. Hematite mineralization occurs along a strike length of 14 km, with a width of 3.2 km and a maximum vertical extent of 400 m below the original surface. The 986-Mt reserve incorporates a suite of individual orebodies, beneath a locally preserved tectonized unconformity, with a wide range of geometries, depths, and orientations. Fully constrained, implicit 3D modeling of the entire mining volume (> 70 km3), was undertaken to the original, pre-mining topography. The model incorporates 5287 mapping points and > 21,000 drillholes and provides exceptional insight into the original configuration of ore and its relationship to contacts, unconformities, and structures in the enclosing country rock. The bulk of ore occurs to the west of a strike-extensive, partially inverted normal fault (Sloep Fault), within an asymmetrical synclinal structure on its western flank. This linear, N-S distribution of deep, thick ore is punctuated by palaeosinkholes, wherein base-of-ore dips of greater than 45°, are concentrically arranged. Localized ore volumes also occur along faults and in fault-bounded, downthrown blocks, to the north of NW-SE- and NE-SW-trending strike-slip faults that show relatively minor uplift to the south, probably due to the Lomanian Namaqua-Natal Orogeny. The revised model demonstrates the proximity of ore to a tectonized unconformity and highlights the structural control on ore volumes, implying that Fe mineralization at Sishen cannot be exclusively attributed to supergene enrichment and concentric palaeosinkhole formation.

  3. Remote sensing of mineral dust aerosol using AERI during the UAE2: A modeling and sensitivity study

    Science.gov (United States)

    Hansell, R. A.; Liou, K. N.; Ou, S. C.; Tsay, S. C.; Ji, Q.; Reid, J. S.

    2008-09-01

    Numerical simulations and sensitivity studies have been performed to assess the potential for using brightness temperature spectra from a ground-based Atmospheric Emitted Radiance Interferometer (AERI) during the United Arab Emirates Unified Aerosol Experiment (UAE2) for detecting/retrieving mineral dust aerosol. A methodology for separating dust from clouds and retrieving the dust IR optical depths was developed by exploiting differences between their spectral absorptive powers in prescribed thermal IR window subbands. Dust microphysical models were constructed using in situ data from the UAE2 and prior field studies while composition was modeled using refractive index data sets for minerals commonly observed around the UAE region including quartz, kaolinite, and calcium carbonate. The T-matrix, finite difference time domain (FDTD), and Lorenz-Mie light scattering programs were employed to calculate the single scattering properties for three dust shapes: oblate spheroids, hexagonal plates, and spheres. We used the Code for High-resolution Accelerated Radiative Transfer with Scattering (CHARTS) radiative transfer program to investigate sensitivity of the modeled AERI spectra to key dust and atmospheric parameters. Sensitivity studies show that characterization of the thermodynamic boundary layer is crucial for accurate AERI dust detection/retrieval. Furthermore, AERI sensitivity to dust optical depth is manifested in the strong subband slope dependence of the window region. Two daytime UAE2 cases were examined to demonstrate the present detection/retrieval technique, and we show that the results compare reasonably well to collocated AERONET Sun photometer/MPLNET micropulse lidar measurements. Finally, sensitivity of the developed methodology to the AERI's estimated MgCdTe detector nonlinearity was evaluated.

  4. 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.

  5. 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.

  6. Application of hierarchical genetic models to Raven and WAIS subtests: a Dutch twin study

    NARCIS (Netherlands)

    Rijsdijk, F.V.; Vernon, P.A.; Boomsma, D.I.

    2002-01-01

    Hierarchical models of intelligence are highly informative and widely accepted. Application of these models to twin data, however, is sparse. This paper addresses the question of how a genetic hierarchical model fits the Wechsler Adult Intelligence Scale (WAIS) subtests and the Raven Standard

  7. 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

  8. Architecture and mineral deposit settings of the Altaid orogenic collage: a revised model

    Science.gov (United States)

    Yakubchuk, Alexander

    2004-09-01

    of the Paleo-Pacific Ocean. Several world-class Cu-(Mo)-porphyry, Cu-Pb-Zn VMS and intrusion-related Au mineral camps, which formed in the Altaids at this stage, coincided with the episodes of plate reorganization and oroclinal bending of magmatic arcs. Major Pb-Zn and Cu sedimentary rock-hosted deposits of Kazakhstan and Central Asia formed in backarc rifts, which developed on the earlier amalgamated fragments. Major orogenic gold deposits are intrusion-related deposits, often occurring within black shale-bearing sutured backarc basins with oceanic crust. After amalgamation of the western Altaids, this part of the collage and adjacent cratons were affected by the Siberian superplume, which ascended at the Permian-Triassic transition. This plume-related magmatism produced various deposits, such as famous Ni-Cu-PGE deposits of Norilsk in the northwest of the Siberian craton. In the early Mesozoic, the eastern Altaids were oroclinally bent together with the overlapping Transbaikal magmatic arc in response to the northward migration and anti-clockwise rotation of the North China craton. The following collision of the eastern portion of the Altaid collage with the Siberian craton formed the Mongol-Okhotsk suture zone, which still links the accretionary wedges of central Mongolia and Circum-Pacific belts. In the late Mesozoic, a system of continent-scale conjugate northwest-trending and northeast-trending strike-slip faults developed in response to the southward propagation of the Siberian craton with subsequent post-mineral offset of some metallogenic belts for as much as 70-400 km, possibly in response to spreading in the Canadian basin. India-Asia collision rejuvenated some of these faults and generated a system of impact rifts.

  9. Roll-front uranium occurrences of the South Texas Mineral Belt: Development of a database for mineral potential modelling and quantitative resource assessment

    International Nuclear Information System (INIS)

    Mihalasky, M.

    2014-01-01

    The South Texas Mineral Belt in the United States is a broad curvilinear region of marginal-marine roll-front sandstone uranium occurrences. Located ~130 km inland, the belt parallels the Gulf of Mexico coastline and extends from southeast Texas to Mexico. It trends northeast-southwest and is about 400 km long and 10-50 km wide as delineated by alignments and clusters of occurrences, but ~100 km wide if outlying occurrences are included. The occurrences are hosted in coastal plain sediments and rocks of Tertiary age that dip gently towards the Gulf. These include the Lower Eocene Wilcox Group, Middle Eocene Claiborne Group, Upper Eocene Jackson Group, Upper Oligocene–Miocene Catahoula Tuff, Lower Miocene Oakville Sandstone, and Pliocene Goliad Sand. Older sequences are mixed fluvial-beach facies, whereas younger are dominantly fluvial. Occurrence distribution is controlled by host unit strike and dip, and permeable sequences therein, and by a combination of growth faults and locations of reductants.

  10. 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...

  11. 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.

  12. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Science.gov (United States)

    Yabe, Shiori; Yamasaki, Masanori; Ebana, Kaworu; Hayashi, Takeshi; Iwata, Hiroyoshi

    2016-01-01

    Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS), which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the potential of genomic

  13. Island-Model Genomic Selection for Long-Term Genetic Improvement of Autogamous Crops.

    Directory of Open Access Journals (Sweden)

    Shiori Yabe

    Full Text Available Acceleration of genetic improvement of autogamous crops such as wheat and rice is necessary to increase cereal production in response to the global food crisis. Population and pedigree methods of breeding, which are based on inbred line selection, are used commonly in the genetic improvement of autogamous crops. These methods, however, produce a few novel combinations of genes in a breeding population. Recurrent selection promotes recombination among genes and produces novel combinations of genes in a breeding population, but it requires inaccurate single-plant evaluation for selection. Genomic selection (GS, which can predict genetic potential of individuals based on their marker genotype, might have high reliability of single-plant evaluation and might be effective in recurrent selection. To evaluate the efficiency of recurrent selection with GS, we conducted simulations using real marker genotype data of rice cultivars. Additionally, we introduced the concept of an "island model" inspired by evolutionary algorithms that might be useful to maintain genetic variation through the breeding process. We conducted GS simulations using real marker genotype data of rice cultivars to evaluate the efficiency of recurrent selection and the island model in an autogamous species. Results demonstrated the importance of producing novel combinations of genes through recurrent selection. An initial population derived from admixture of multiple bi-parental crosses showed larger genetic gains than a population derived from a single bi-parental cross in whole cycles, suggesting the importance of genetic variation in an initial population. The island-model GS better maintained genetic improvement in later generations than the other GS methods, suggesting that the island-model GS can utilize genetic variation in breeding and can retain alleles with small effects in the breeding population. The island-model GS will become a new breeding method that enhances the

  14. 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.

  15. A model for non-isothermal flow and mineral precipitation and dissolution in a thin strip

    NARCIS (Netherlands)

    Bringedal, C.; Berre, I.; Pop, I.S.; Radu, F.A.

    2015-01-01

    Sixth International Conference on Advanced Computational Methods in Engineering (ACOMEN 2014) Motivated by porosity changes due to chemical reactions caused by injection of cold water in a geothermal reservoir, we propose a two-dimensional pore scale model of a thin strip. The pore scale model

  16. Setaria viridis as a model system to advance millet genetics and genomics

    Directory of Open Access Journals (Sweden)

    Pu Huang

    2016-11-01

    Full Text Available Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crop.

  17. Setaria viridis as a Model System to Advance Millet Genetics and Genomics.

    Science.gov (United States)

    Huang, Pu; Shyu, Christine; Coelho, Carla P; Cao, Yingying; Brutnell, Thomas P

    2016-01-01

    Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail ( Setaria viridis ) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica . These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops.

  18. Setaria viridis as a Model System to Advance Millet Genetics and Genomics

    Science.gov (United States)

    Huang, Pu; Shyu, Christine; Coelho, Carla P.; Cao, Yingying; Brutnell, Thomas P.

    2016-01-01

    Millet is a common name for a group of polyphyletic, small-seeded cereal crops that include pearl, finger and foxtail millet. Millet species are an important source of calories for many societies, often in developing countries. Compared to major cereal crops such as rice and maize, millets are generally better adapted to dry and hot environments. Despite their food security value, the genetic architecture of agronomically important traits in millets, including both morphological traits and climate resilience remains poorly studied. These complex traits have been challenging to dissect in large part because of the lack of sufficient genetic tools and resources. In this article, we review the phylogenetic relationship among various millet species and discuss the value of a genetic model system for millet research. We propose that a broader adoption of green foxtail (Setaria viridis) as a model system for millets could greatly accelerate the pace of gene discovery in the millets, and summarize available and emerging resources in S. viridis and its domesticated relative S. italica. These resources have value in forward genetics, reverse genetics and high throughput phenotyping. We describe methods and strategies to best utilize these resources to facilitate the genetic dissection of complex traits. We envision that coupling cutting-edge technologies and the use of S. viridis for gene discovery will accelerate genetic research in millets in general. This will enable strategies and provide opportunities to increase productivity, especially in the semi-arid tropics of Asia and Africa where millets are staple food crops. PMID:27965689

  19. Elevated dietary magnesium during pregnancy and postnatal life prevents ectopic mineralization in Enpp1asj mice, a model for generalized arterial calcification of infancy.

    Science.gov (United States)

    Kingman, Joshua; Uitto, Jouni; Li, Qiaoli

    2017-06-13

    Generalized arterial calcification of infancy (GACI) is an autosomal recessive disorder caused by mutations in the ENPP1 gene. It is characterized by mineralization of the arterial blood vessels, often diagnosed prenatally, and associated with death in early childhood. There is no effective treatment for this devastating disorder. We previously characterized the Enpp1asjmutant mouse as a model of GACI, and we have now explored the effect of elevated dietary magnesium (five-fold) in pregnant mothers and continuing for the first 14 weeks of postnatal life. The mothers were kept on either control diet or experimental diet supplemented with magnesium. Upon weaning at 4 weeks of age the pups were placed either on control diet or high magnesium diet. The degree of mineralization was assessed at 14 weeks of age by histopathology and a chemical calcium assay in muzzle skin, kidney and aorta. Mice placed on high magnesium diet showed little, if any, evidence of mineralization when their corresponding mothers were also placed on diet enriched with magnesium during pregnancy and nursing. The reduced ectopic mineralization in these mice was accompanied by increased calcium and magnesium content in the urine, suggesting that magnesium competes calcium-phosphate binding thereby preventing the mineral deposition. These results have implications for dietary management of pregnancies in which the fetus is suspected of having GACI. Moreover, augmenting a diet with high magnesium may be beneficial for other ectopic mineralization diseases, including nephrocalcinosis.

  20. Matching Index-of-Refraction for 3D Printing Model Using Mixture of Herb Essential Oil and Light Mineral Oil

    International Nuclear Information System (INIS)

    Song, Min Seop; Choi, Hae Yoon; Kim, Eung Soo

    2013-01-01

    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

  1. 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.

  2. Alternate service delivery models in cancer genetic counseling: a mini-review

    Directory of Open Access Journals (Sweden)

    Adam Hudson Buchanan

    2016-05-01

    Full Text Available Demand for cancer genetic counseling has grown rapidly in recent years as germline genomic information has become increasingly incorporated into cancer care and the field has entered the public consciousness through high-profile celebrity publications. Increased demand and existing variability in the availability of trained cancer genetics clinicians place a priority on developing and evaluating alternate service delivery models for genetic counseling. This mini-review summarizes the state of science regarding service delivery models such as telephone counseling, telegenetics and group counseling. Research on comparative effectiveness of these models in traditional individual, in-person genetic counseling has been promising for improving access to care in a manner acceptable to patients. Yet, it has not fully evaluated the short- and long-term patient- and system-level outcomes that will help answer the question of whether these models achieve the same beneficial psychosocial and behavioral outcomes as traditional cancer genetic counseling. We propose a research agenda focused on comparative effectiveness of available service delivery models and how to match models to patients and practice settings. Only through this rigorous research can clinicians and systems find the optimal balance of clinical quality, ready and secure access to care, and financial sustainability. Such research will be integral to achieving the promise of genomic medicine in oncology.

  3. Hybrid Model Based on Genetic Algorithms and SVM Applied to Variable Selection within Fruit Juice Classification

    Directory of Open Access Journals (Sweden)

    C. Fernandez-Lozano

    2013-01-01

    Full Text Available Given the background of the use of Neural Networks in problems of apple juice classification, this paper aim at implementing a newly developed method in the field of machine learning: the Support Vector Machines (SVM. Therefore, a hybrid model that combines genetic algorithms and support vector machines is suggested in such a way that, when using SVM as a fitness function of the Genetic Algorithm (GA, the most representative variables for a specific classification problem can be selected.

  4. Genetic algorithms used for PWRs refuel management automatic optimization: a new modelling

    International Nuclear Information System (INIS)

    Chapot, Jorge Luiz C.; Schirru, Roberto; Silva, Fernando Carvalho da

    1996-01-01

    A Genetic Algorithms-based system, linking the computer codes GENESIS 5.0 and ANC through the interface ALGER, has been developed aiming the PWRs fuel management optimization. An innovative codification, the Lists Model, has been incorporated to the genetic system, which avoids the use of variants of the standard crossover operator and generates only valid loading patterns in the core. The GENESIS/ALGER/ANC system has been successfully tested in an optimization study for Angra-1 second cycle. (author)

  5. Genetic Models in Evolutionary Game Theory: The Evolution of Altruism

    NARCIS (Netherlands)

    Rubin, Hannah

    2015-01-01

    While prior models of the evolution of altruism have assumed that organisms reproduce asexually, this paper presents a model of the evolution of altruism for sexually reproducing organisms using Hardy–Weinberg dynamics. In this model, the presence of reciprocal altruists allows the population to

  6. Application of random regression models to the genetic evaluation ...

    African Journals Online (AJOL)

    The model included fixed regression on AM (range from 30 to 138 mo) and the effect of herd-measurement date concatenation. Random parts of the model were RRM coefficients for additive and permanent environmental effects, while residual effects were modelled to account for heterogeneity of variance by AY. Estimates ...

  7. Review Genetic prediction models and heritability estimates for ...

    African Journals Online (AJOL)

    edward

    2015-05-09

    May 9, 2015 ... Instead, through stepwise inclusion of type traits in the PH model, the .... Great Britain uses a bivariate animal model for all breeds, ... Štípková, 2012) and then applying linear models to the combined datasets with the ..... multivariate analyses, it is difficult to use indicator traits to estimate longevity early in life ...

  8. 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...... with or immediately following the eruptions, through mediumtemperature ammonium minerals, metal chlorides, or fluoride associations to the late low-temperature paragenesis dominated by sulphur, gypsum, alunogen, and other hydrous sulphates. The situation can be different in the systems that are not recessing but show...

  9. Disease-threat model explains acceptance of genetically modified products

    Directory of Open Access Journals (Sweden)

    Prokop Pavol

    2013-01-01

    Full Text Available Natural selection favoured survival of individuals who were able to avoid disease. The behavioural immune system is activated especially when our sensory system comes into contact with disease-connoting cues and/or when these cues resemble disease threat. We investigated whether or not perception of modern risky technologies, risky behaviour, expected reproductive goals and food neophobia are associated with the behavioural immune system related to specific attitudes toward genetically modified (GM products. We found that respondents who felt themselves more vulnerable to infectious diseases had significantly more negative attitudes toward GM products. Females had less positive attitudes toward GM products, but engaging in risky behaviours, the expected reproductive goals of females and food neophobia did not predict attitudes toward GM products. Our results suggest that evolved psychological mechanisms primarily designed to protect us against pathogen threat are activated by modern technologies possessing potential health risks.

  10. A simple algorithm to estimate genetic variance in an animal threshold model using Bayesian inference Genetics Selection Evolution 2010, 42:29

    DEFF Research Database (Denmark)

    Ødegård, Jørgen; Meuwissen, Theo HE; Heringstad, Bjørg

    2010-01-01

    Background In the genetic analysis of binary traits with one observation per animal, animal threshold models frequently give biased heritability estimates. In some cases, this problem can be circumvented by fitting sire- or sire-dam models. However, these models are not appropriate in cases where...... records exist for the parents). Furthermore, the new algorithm showed much faster Markov chain mixing properties for genetic parameters (similar to the sire-dam model). Conclusions The new algorithm to estimate genetic parameters via Gibbs sampling solves the bias problems typically occurring in animal...... individual records exist on parents. Therefore, the aim of our study was to develop a new Gibbs sampling algorithm for a proper estimation of genetic (co)variance components within an animal threshold model framework. Methods In the proposed algorithm, individuals are classified as either "informative...

  11. Parallel Genetic Algorithms for calibrating Cellular Automata models: Application to lava flows

    International Nuclear Information System (INIS)

    D'Ambrosio, D.; Spataro, W.; Di Gregorio, S.; Calabria Univ., Cosenza; Crisci, G.M.; Rongo, R.; Calabria Univ., Cosenza

    2005-01-01

    Cellular Automata are highly nonlinear dynamical systems which are suitable far simulating natural phenomena whose behaviour may be specified in terms of local interactions. The Cellular Automata model SCIARA, developed far the simulation of lava flows, demonstrated to be able to reproduce the behaviour of Etnean events. However, in order to apply the model far the prediction of future scenarios, a thorough calibrating phase is required. This work presents the application of Genetic Algorithms, general-purpose search algorithms inspired to natural selection and genetics, far the parameters optimisation of the model SCIARA. Difficulties due to the elevated computational time suggested the adoption a Master-Slave Parallel Genetic Algorithm far the calibration of the model with respect to the 2001 Mt. Etna eruption. Results demonstrated the usefulness of the approach, both in terms of computing time and quality of performed simulations

  12. Potential uses of genetic geological modelling to identify new uranium provinces

    International Nuclear Information System (INIS)

    Finch, W.I.

    1982-01-01

    Genetic-geological modelling is the placing of the various processes of the development of a uranium province into distinct stages that are ordered chronologically and made part of a matrix with corresponding geologic evidence. The models can be applied to a given region by using one of several methods to determine a numerical favorability rating. Two of the possible methods, geologic decision analysis and an oil-and-gas type of play analysis, are briefly described. Simplified genetic models are given for environments of the quartz-pebble conglomerate, unconformity-related vein, and sandstone types of deposits. Comparison of the genetic models of these three sedimentary-related environments reveals several common attributes that may define a general uranium province environment

  13. Mineral sands

    International Nuclear Information System (INIS)

    Anon.

    1990-01-01

    This paper presents an outlook of the Australian mineral sand industry and covers the major operators. It is shown that conscious of an environmentally minded public, the Australian miners have led the way in the rehabilitation of mined areas. Moreover the advanced ceramic industry is generating exciting new perspectives for zircon producers and there is a noticeable growth in the electronic market for rare earths, but in long term the success may depend as much on environmental management and communication skills as on mining and processing skills

  14. Bone mineral properties in growing Col1a2(+/G610C) mice, an animal model of osteogenesis imperfecta.

    Science.gov (United States)

    Masci, Marco; Wang, Min; Imbert, Laurianne; Barnes, Aileen M; Spevak, Lyudmila; Lukashova, Lyudmila; Huang, Yihe; Ma, Yan; Marini, Joan C; Jacobsen, Christina M; Warman, Matthew L; Boskey, Adele L

    2016-06-01

    The Col1a2(+/G610C) knock-in mouse, models osteogenesis imperfecta in a large old order Amish family (OOA) with type IV OI, caused by a G-to-T transversion at nucleotide 2098, which alters the gly-610 codon in the triple-helical domain of the α2(I) chain of type I collagen. Mineral and matrix properties of the long bones and vertebrae of male Col1a2(+/G610C) and their wild-type controls (Col1a2(+/+)), were characterized to gain insight into the role of α2-chain collagen mutations in mineralization. Additionally, we examined the rescuability of the composition by sclerostin inhibition initiated by crossing Col1a2(+/G610C) with an LRP(+/A214V) high bone mass allele. At age 10-days, vertebrae and tibia showed few alterations by micro-CT or Fourier transform infrared imaging (FTIRI). At 2-months-of-age, Col1a2(+/G610C) tibias had 13% fewer secondary trabeculae than Col1a2(+/+), these were thinner (11%) and more widely spaced (20%) than those of Col1a2(+/+) mice. Vertebrae of Col1a2(+/G610C) mice at 2-months also had lower bone volume fraction (38%), trabecular number (13%), thickness (13%) and connectivity density (32%) compared to Col1(a2+/+). The cortical bone of Col1a2(+/G610C) tibias at 2-months had 3% higher tissue mineral density compared to Col1a2(+/+); Col1a2(+/G610C) vertebrae had lower cortical thickness (29%), bone area (37%) and polar moment of inertia (38%) relative to Col1a2(+/+). FTIRI analysis, which provides information on bone chemical composition at ~7μm-spatial resolution, showed tibias at 10-days did not differ between genotypes. Comparing identical bone types in Col1a2(+/G610C) to Col1a2(+/+) at 2-months-of-age, tibias showed higher mineral-to-matrix ratio in trabeculae (17%) and cortices (31%). and in vertebral cortices (28%). Collagen maturity was 42% higher at 10-days-of-age in Col1a2(+/G610C) vertebral trabeculae and in 2-month tibial cortices (12%), vertebral trabeculae (42%) and vertebral cortices (12%). Higher acid-phosphate substitution

  15. Initial assessment of a model relating intratumoral genetic heterogeneity to radiological morphology

    Science.gov (United States)

    Noterdaeme, O; Kelly, M; Friend, P; Soonowalla, Z; Steers, G; Brady, M

    2010-01-01

    Tumour heterogeneity has major implications for tumour development and response to therapy. Tumour heterogeneity results from mutations in the genes responsible for mismatch repair or maintenance of chromosomal stability. Cells with different genetic properties may grow at different rates and exhibit different resistance to therapeutic interventions. To date, there exists no approach to non-invasively assess tumour heterogeneity. Here we present a biologically inspired model of tumour growth, which relates intratumoral genetic heterogeneity to gross morphology visible on radiological images. The model represents the development of a tumour as a set of expanding spheres, each sphere representing a distinct clonal centre, with the sprouting of new spheres corresponding to new clonal centres. Each clonal centre may possess different characteristics relating to genetic composition, growth rate and response to treatment. We present a clinical example for which the model accurately tracks tumour growth and shows the correspondence to genetic variation (as determined by array comparative genomic hybridisation). One clinical implication of our work is that the assessment of heterogeneous tumours using Response Evaluation Criteria In Solid Tumours (RECIST) or volume measurements may not accurately reflect tumour growth, stability or the response to treatment. We believe that this is the first model linking the macro-scale appearance of tumours to their genetic composition. We anticipate that our model will provide a more informative way to assess the response of heterogeneous tumours to treatment, which is of increasing importance with the development of novel targeted anti-cancer treatments. PMID:19690073

  16. Enhancement of the glass corrosion in the presence of clay minerals: testing experimental results with an integrated glass dissolution model

    International Nuclear Information System (INIS)

    Godon, N.; Vernaz, E.Y.

    1992-01-01

    Recent glass dissolution experiments, conducted at 90 deg C in the presence of potential backfill materials, indicate remarkably faster glass corrosion in the presence of clay, compared to tests where the glass is leached either alone or with alternative backfill materials. This effect correlates with the clay content in the backfill, and may be attributed to the removal of silica from solution. Scorpion, or dissolution with reprecipitation of a silica-rich clay, have been proposed as possible mechanisms for the silica consumption. The results of some experiments have been tested against a glass dissolution model, in which a widely used kinetic equation for glass corrosion is coupled with diffusive silica transport through a single porosity, linearly sorbing medium, which represents the backfilling. Because the glass corrosion rates imposed by the kinetic equation are inversely proportional to the silicic acid concentration of the leachant contacting the glass, the model predicts enhanced glass dissolution if silica is sorbed by the porous medium. The experimental data proved to be consistent with the predicted enhancement of the glass dissolution. Moreover, the model-estimated distribution coefficients for silica sorption (K d ) fall within the range of values extracted from available literature data, thus supporting the hypothesis that the observed high corrosion rates are due to sorption of silica on the clay mineral surfaces. (author)

  17. 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.

  18. 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.

  19. Genetic Analysis of Somatic Cell Score in Danish Holsteins Using a Liability-Normal Mixture Model

    DEFF Research Database (Denmark)

    Madsen, P; Shariati, M M; Ødegård, J

    2008-01-01

    Mixture models are appealing for identifying hidden structures affecting somatic cell score (SCS) data, such as unrecorded cases of subclinical mastitis. Thus, liability-normal mixture (LNM) models were used for genetic analysis of SCS data, with the aim of predicting breeding values for such cas...

  20. Recent developments in computer modeling add ecological realism to landscape genetics

    Science.gov (United States)

    Background / Question / Methods A factor limiting the rate of progress in landscape genetics has been the shortage of spatial models capable of linking life history attributes such as dispersal behavior to complex dynamic landscape features. The recent development of new models...

  1. A model based on soil structural aspects describing the fate of genetically modified bacteria in soil

    NARCIS (Netherlands)

    Hoeven, van der N.; Elsas, van J.D.; Heijnen, C.E.

    1996-01-01

    A computer simulation model was developed which describes growth and competition of bacteria in the soil environment. In the model, soil was assumed to contain millions of pores of a few different size classes. An introduced bacterial strain, e.g. a genetically modified micro-organism (GEMMO), was

  2. Reframed Genome-Scale Metabolic Model to Facilitate Genetic Design and Integration with Expression Data.

    Science.gov (United States)

    Gu, Deqing; Jian, Xingxing; Zhang, Cheng; Hua, Qiang

    2017-01-01

    Genome-scale metabolic network models (GEMs) have played important roles in the design of genetically engineered strains and helped biologists to decipher metabolism. However, due to the complex gene-reaction relationships that exist in model systems, most algorithms have limited capabilities with respect to directly predicting accurate genetic design for metabolic engineering. In particular, methods that predict reaction knockout strategies leading to overproduction are often impractical in terms of gene manipulations. Recently, we proposed a method named logical transformation of model (LTM) to simplify the gene-reaction associations by introducing intermediate pseudo reactions, which makes it possible to generate genetic design. Here, we propose an alternative method to relieve researchers from deciphering complex gene-reactions by adding pseudo gene controlling reactions. In comparison to LTM, this new method introduces fewer pseudo reactions and generates a much smaller model system named as gModel. We showed that gModel allows two seldom reported applications: identification of minimal genomes and design of minimal cell factories within a modified OptKnock framework. In addition, gModel could be used to integrate expression data directly and improve the performance of the E-Fmin method for predicting fluxes. In conclusion, the model transformation procedure will facilitate genetic research based on GEMs, extending their applications.

  3. Bayesian network model for identification of pathways by integrating protein interaction with genetic interaction data.

    Science.gov (United States)

    Fu, Changhe; Deng, Su; Jin, Guangxu; Wang, Xinxin; Yu, Zu-Guo

    2017-09-21

    Molecular interaction data at proteomic and genetic levels provide physical and functional insights into a molecular biosystem and are helpful for the construction of pathway structures complementarily. Despite advances in inferring biological pathways using genetic interaction data, there still exists weakness in developed models, such as, activity pathway networks (APN), when integrating the data from proteomic and genetic levels. It is necessary to develop new methods to infer pathway structure by both of interaction data. We utilized probabilistic graphical model to develop a new method that integrates genetic interaction and protein interaction data and infers exquisitely detailed pathway structure. We modeled the pathway network as Bayesian network and applied this model to infer pathways for the coherent subsets of the global genetic interaction profiles, and the available data set of endoplasmic reticulum genes. The protein interaction data were derived from the BioGRID database. Our method can accurately reconstruct known cellular pathway structures, including SWR complex, ER-Associated Degradation (ERAD) pathway, N-Glycan biosynthesis pathway, Elongator complex, Retromer complex, and Urmylation pathway. By comparing N-Glycan biosynthesis pathway and Urmylation pathway identified from our approach with that from APN, we found that our method is able to overcome its weakness (certain edges are inexplicable). According to underlying protein interaction network, we defined a simple scoring function that only adopts genetic interaction information to avoid the balance difficulty in the APN. Using the effective stochastic simulation algorithm, the performance of our proposed method is significantly high. We developed a new method based on Bayesian network to infer detailed pathway structures from interaction data at proteomic and genetic levels. The results indicate that the developed method performs better in predicting signaling pathways than previously

  4. The Mouse Lemur, a Genetic Model Organism for Primate Biology, Behavior, and Health.

    Science.gov (United States)

    Ezran, Camille; Karanewsky, Caitlin J; Pendleton, Jozeph L; Sholtz, Alex; Krasnow, Maya R; Willick, Jason; Razafindrakoto, Andriamahery; Zohdy, Sarah; Albertelli, Megan A; Krasnow, Mark A

    2017-06-01

    Systematic genetic studies of a handful of diverse organisms over the past 50 years have transformed our understanding of biology. However, many aspects of primate biology, behavior, and disease are absent or poorly modeled in any of the current genetic model organisms including mice. We surveyed the animal kingdom to find other animals with advantages similar to mice that might better exemplify primate biology, and identified mouse lemurs ( Microcebus spp.) as the outstanding candidate. Mouse lemurs are prosimian primates, roughly half the genetic distance between mice and humans. They are the smallest, fastest developing, and among the most prolific and abundant primates in the world, distributed throughout the island of Madagascar, many in separate breeding populations due to habitat destruction. Their physiology, behavior, and phylogeny have been studied for decades in laboratory colonies in Europe and in field studies in Malagasy rainforests, and a high quality reference genome sequence has recently been completed. To initiate a classical genetic approach, we developed a deep phenotyping protocol and have screened hundreds of laboratory and wild mouse lemurs for interesting phenotypes and begun mapping the underlying mutations, in collaboration with leading mouse lemur biologists. We also seek to establish a mouse lemur gene "knockout" library by sequencing the genomes of thousands of mouse lemurs to identify null alleles in most genes from the large pool of natural genetic variants. As part of this effort, we have begun a citizen science project in which students across Madagascar explore the remarkable biology around their schools, including longitudinal studies of the local mouse lemurs. We hope this work spawns a new model organism and cultivates a deep genetic understanding of primate biology and health. We also hope it establishes a new and ethical method of genetics that bridges biological, behavioral, medical, and conservation disciplines, while

  5. Forecasting Shaharchay River Flow in Lake Urmia Basin using Genetic Programming and M5 Model Tree

    Directory of Open Access Journals (Sweden)

    S. Samadianfard

    2017-01-01

    Full Text Available Introduction: Precise prediction of river flows is the key factor for proper planning and management of water resources. Thus, obtaining the reliable methods for predicting river flows has great importance in water resource engineering. In the recent years, applications of intelligent methods such as artificial neural networks, fuzzy systems and genetic programming in water science and engineering have been grown extensively. These mentioned methods are able to model nonlinear process of river flows without any need to geometric properties. A huge number of studies have been reported in the field of using intelligent methods in water resource engineering. For example, Noorani and Salehi (23 presented a model for predicting runoff in Lighvan basin using adaptive neuro-fuzzy network and compared the performance of it with neural network and fuzzy inference methods in east Azerbaijan, Iran. Nabizadeh et al. (21 used fuzzy inference system and adaptive neuro-fuzzy inference system in order to predict river flow in Lighvan river. Khalili et al. (13 proposed a BL-ARCH method for prediction of flows in Shaharchay River in Urmia. Khu et al. (16 used genetic programming for runoff prediction in Orgeval catchment in France. Firat and Gungor (11 evaluated the fuzzy-neural model for predicting Mendes river flow in Turkey. The goal of present study is comparing the performance of genetic programming and M5 model trees for prediction of Shaharchay river flow in the basin of Lake Urmia and obtaining a comprehensive insight of their abilities. Materials and Methods: Shaharchay river as a main source of providing drinking water of Urmia city and agricultural needs of surrounding lands and finally one of the main input sources of Lake Urmia is quite important in the region. For obtaining the predetermined goals of present study, average monthly flows of Shaharchay River in Band hydrometric station has been gathered from 1951 to 2011. Then, two third of mentioned

  6. Minerals in deserts

    International Nuclear Information System (INIS)

    Smith, G.I.

    1982-01-01

    Almost any kind of mineral deposit can occur in desert areas, and the lack of vegetation and soil cover makes finding them easier. Some kinds of deposits, though, are more likely to occur in deserts than elsewhere. Some of these result from processes genetically related to the present desert climate that improved lower grade deposits of ore. One such process, termed secondary enrichment, is most effective in areas with deep water tables, and many low-grade copper, silver, and uranium deposits have been converted into mineable ore by the downward migration and redeposition of soluble metals. In a desert terrane, placer processes are effective whenever running water flowing over steep slopes erodes outcropping ore bodies and transports and concentrates the heavier ore minerals at lower levels, thus converting low-grade or hard-to-mine bedrock deposits into economically workable concentrations. Other kinds of deposits are better preserved in deserts because the lower rainfall at the surface, and the lower volume of flow and the greater depths to groundwater, result in less destruction of soluble ores; deposits of salines and phosphates are the most notable ores affected by these factors. Still other ore deposits are created as a consequence of the arid climate, mostly because the high evaporation rates operating on standing bodies of water produce brines that can lead directly to concentrations of salts and indirectly to secondary minerals, such as zeolites, that are produced by reaction of silicate minerals with saline waters

  7. Accounting for change of support in spatial accuracy assessment of modelled soil mineral phosphorous concentration

    NARCIS (Netherlands)

    Leopold, U.; Heuvelink, G.B.M.; Tiktak, A.; Finke, P.A.; Schoumans, O.F.

    2006-01-01

    Agricultural activities in the Netherlands cause high nitrogen and phosphorous fluxes from soil to ground- and surface water. A model chain (STONE) has been developed to study and predict the magnitude of the resulting ground- and surface water pollution under different environmental conditions.

  8. Simulated evolution applied to study the genetic code optimality using a model of codon reassignments.

    Science.gov (United States)

    Santos, José; Monteagudo, Angel

    2011-02-21

    As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino acid for another. There are two basic theories to measure the level of optimization: the statistical approach, which compares the canonical genetic code with many randomly generated alternative ones, and the engineering approach, which compares the canonical code with the best possible alternative. Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code. Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the fact that the best possible codes show the patterns of the

  9. Simulated evolution applied to study the genetic code optimality using a model of codon reassignments

    Directory of Open Access Journals (Sweden)

    Monteagudo Ángel

    2011-02-01

    Full Text Available Abstract Background As the canonical code is not universal, different theories about its origin and organization have appeared. The optimization or level of adaptation of the canonical genetic code was measured taking into account the harmful consequences resulting from point mutations leading to the replacement of one amino acid for another. There are two basic theories to measure the level of optimization: the statistical approach, which compares the canonical genetic code with many randomly generated alternative ones, and the engineering approach, which compares the canonical code with the best possible alternative. Results Here we used a genetic algorithm to search for better adapted hypothetical codes and as a method to guess the difficulty in finding such alternative codes, allowing to clearly situate the canonical code in the fitness landscape. This novel proposal of the use of evolutionary computing provides a new perspective in the open debate between the use of the statistical approach, which postulates that the genetic code conserves amino acid properties far better than expected from a random code, and the engineering approach, which tends to indicate that the canonical genetic code is still far from optimal. We used two models of hypothetical codes: one that reflects the known examples of codon reassignment and the model most used in the two approaches which reflects the current genetic code translation table. Although the standard code is far from a possible optimum considering both models, when the more realistic model of the codon reassignments was used, the evolutionary algorithm had more difficulty to overcome the efficiency of the canonical genetic code. Conclusions Simulated evolution clearly reveals that the canonical genetic code is far from optimal regarding its optimization. Nevertheless, the efficiency of the canonical code increases when mistranslations are taken into account with the two models, as indicated by the

  10. Trans gene regulation in adaptive evolution: a genetic algorithm model.

    Science.gov (United States)

    Behera, N; Nanjundiah, V

    1997-09-21

    This is a continuation of earlier studies on the evolution of infinite populations of haploid genotypes within a genetic algorithm framework. We had previously explored the evolutionary consequences of the existence of indeterminate-"plastic"-loci, where a plastic locus had a finite probability in each generation of functioning (being switched "on") or not functioning (being switched "off"). The relative probabilities of the two outcomes were assigned on a stochastic basis. The present paper examines what happens when the transition probabilities are biased by the presence of regulatory genes. We find that under certain conditions regulatory genes can improve the adaptation of the population and speed up the rate of evolution (on occasion at the cost of lowering the degree of adaptation). Also, the existence of regulatory loci potentiates selection in favour of plasticity. There is a synergistic effect of regulatory genes on plastic alleles: the frequency of such alleles increases when regulatory loci are present. Thus, phenotypic selection alone can be a potentiating factor in a favour of better adaptation. Copyright 1997 Academic Press Limited.

  11. Optimal Inference of Modelling Parameters to Simulate Complex Trends across Soft Boundaries : A Case Study in Heavy Mineral Sands

    NARCIS (Netherlands)

    Wambeke, T.; Benndorf, J.

    2014-01-01

    A risk-robust development of a heavy mineral resource requires an assessment of the geological uncertainty and spatial variability of the key factors impacting the mining and processing operation. Attributes of interest are the total heavy mineral grade, the slime content and the amount of oversized

  12. System Response Analysis and Model Order Reduction, Using Conventional Method, Bond Graph Technique and Genetic Programming

    Directory of Open Access Journals (Sweden)

    Lubna Moin

    2009-04-01

    Full Text Available This research paper basically explores and compares the different modeling and analysis techniques and than it also explores the model order reduction approach and significance. The traditional modeling and simulation techniques for dynamic systems are generally adequate for single-domain systems only, but the Bond Graph technique provides new strategies for reliable solutions of multi-domain system. They are also used for analyzing linear and non linear dynamic production system, artificial intelligence, image processing, robotics and industrial automation. This paper describes a unique technique of generating the Genetic design from the tree structured transfer function obtained from Bond Graph. This research work combines bond graphs for model representation with Genetic programming for exploring different ideas on design space tree structured transfer function result from replacing typical bond graph element with their impedance equivalent specifying impedance lows for Bond Graph multiport. This tree structured form thus obtained from Bond Graph is applied for generating the Genetic Tree. Application studies will identify key issues and importance for advancing this approach towards becoming on effective and efficient design tool for synthesizing design for Electrical system. In the first phase, the system is modeled using Bond Graph technique. Its system response and transfer function with conventional and Bond Graph method is analyzed and then a approach towards model order reduction is observed. The suggested algorithm and other known modern model order reduction techniques are applied to a 11th order high pass filter [1], with different approach. The model order reduction technique developed in this paper has least reduction errors and secondly the final model retains structural information. The system response and the stability analysis of the system transfer function taken by conventional and by Bond Graph method is compared and

  13. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation.

    Science.gov (United States)

    Yang, Ye; Christensen, Ole F; Sorensen, Daniel

    2011-02-01

    Over recent years, statistical support for the presence of genetic factors operating at the level of the environmental variance has come from fitting a genetically structured heterogeneous variance model to field or experimental data in various species. Misleading results may arise due to skewness of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box-Cox transformations. Litter size data in rabbits and pigs that had previously been analysed in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box-Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected by the presence of asymmetry in the distribution of data. We recommend that to avoid one important source of spurious inferences, future work seeking support for a genetic component acting on environmental variation using a parametric approach based on normality assumptions confirms that these are met.

  14. Modeling of Paleo Heat-and-Mass Trasport for Prognosys of Mineral Deposits Using GIS

    International Nuclear Information System (INIS)

    Cherkasov, Sergei; Vishnevskaya, Natalia; Cassard, Daniel; Sterligov, Boris; Arbuzova, Ekaterina

    2008-01-01

    The heat-and-mass flow from the mantle to the surface can be characterized by the three basic models. The first one represents just a convective heating of the crust by the hot mantle. Two other kinds of the heat-and-mass flow system are rather anomalous and sometimes serve as an engine for launching ore-forming processes. The second model describes a pipe-like conductive heat-and-flow system reasoning appearance of mafic-ultramafic intrusions coming to the surface directly from the upper mantle. The third model corresponds with a complicated convective-conductive process involving melting of crustal rocks, and forming magmatic chambers inside the crust. Analysis of gravimetric and seismic data using geographic informational systems allows us to locate elements of the anomalous heat-and-flow systems. Some of the elements (their projection on the surface) correlate with position of the known deposits of gold, silver, tungsten, tin, sometimes--molybdenum and base metals. The results of studies conducted by the Russian-French Metallogenic Laboratory in the frames of crystalline shields of Russia demonstrate location of 87% of the known gold-bearing deposits inside the zones defined by such analysis

  15. A Geochemical Model of Fluids and Mineral Interactions for Deep Hydrocarbon Reservoirs

    Directory of Open Access Journals (Sweden)

    Jun Li

    2017-01-01

    Full Text Available A mutual solubility model for CO2-CH4-brine systems is constructed in this work as a fundamental research for applications of deep hydrocarbon exploration and production. The model is validated to be accurate for wide ranges of temperature (0–250°C, pressure (1–1500 bar, and salinity (NaCl molality from 0 to more than 6 mole/KgW. Combining this model with PHREEQC functionalities, CO2-CH4-brine-carbonate-sulfate equilibrium is calculated. From the calculations, we conclude that, for CO2-CH4-brine-carbonate systems, at deeper positions, magnesium is more likely to be dissolved in aqueous phase and calcite can be more stable than dolomite and, for CO2-CH4-brine-sulfate systems, with a presence of CH4, sulfate ions are likely to be reduced to S2− and H2S in gas phase could be released after S2− saturated in the solution. The hydrocarbon “souring” process could be reproduced from geochemical calculations in this work.

  16. Probabilistic-Stochastic Model of Distribution of Physical and Mechanical Properties of Soft Mineral Rocks

    Directory of Open Access Journals (Sweden)

    O.O. Sdvizhkova

    2017-12-01

    Full Text Available The physical and mechanical characteristics of soils and soft rocks obtained as a result of laboratory tests are important initial parameters for assessing the stability of natural and artificial slopes. Such properties of rocks as adhesion and the angle of internal friction are due to the influence of a number of natural and technogenic factors. At the same time, from the set of factors influencing the stability of the slope, the most significant ones are singled out, which to a greater extent determine the properties of the rocks. The more factors are taken into account in the geotechnical model, the more closely the properties of the rocks are studied, which increases the accuracy of the scientific forecast of the landslide danger of the slope. On the other hand, an increase in the number of factors involved in the model complicates it and causes a decrease in the reliability of geotechnical calculations. The aim of the work is to construct a statistical distribution of the studied physical and mechanical properties of soft rocks and to substantiate a probabilistic statistical model. Based on the results of laboratory tests of rocks, the statistical distributions of the quantitative traits studied, the angle of internal friction φ and the cohesion, were constructed. It was established that the statistical distribution of physical mechanical properties of rocks is close to a uniform law.

  17. A Genetic Animal Model of Alcoholism for Screening Medications to Treat Addiction

    Science.gov (United States)

    Bell, Richard L.; Hauser, Sheketha; Rodd, Zachary A.; Liang, Tiebing; Sari, Youssef; McClintick, Jeanette; Rahman, Shafiqur; Engleman, Eric A.

    2016-01-01

    The purpose of this review is to present up-to-date pharmacological, genetic and behavioral findings from the alcohol-preferring P rat and summarize similar past work. Behaviorally, the focus will be on how the P rat meets criteria put forth for a valid animal model of alcoholism with a highlight on its use as an animal model of polysubstance abuse, including alcohol, nicotine and psychostimulants. Pharmacologically and genetically, the focus will be on the neurotransmitter and neuropeptide systems that have received the most attention: cholinergic, dopaminergic, GABAergic, glutamatergic, serotonergic, noradrenergic, corticotrophin releasing hormone, opioid, and neuropeptide Y. Herein we sought to place the P rat’s behavioral and neurochemical phenotypes, and to some extent its genotype, in the context of the clinical literature. After reviewing the findings thus far, this paper discusses future directions for expanding the use of this genetic animal model of alcoholism to identify molecular targets for treating drug addiction in general. PMID:27055615

  18. Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models

    Directory of Open Access Journals (Sweden)

    Paula Moran

    2016-01-01

    Full Text Available The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia.

  19. Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models.

    Science.gov (United States)

    Moran, Paula; Stokes, Jennifer; Marr, Julia; Bock, Gavin; Desbonnet, Lieve; Waddington, John; O'Tuathaigh, Colm

    2016-01-01

    The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia.

  20. Gene × Environment Interactions in Schizophrenia: Evidence from Genetic Mouse Models

    Science.gov (United States)

    Marr, Julia; Bock, Gavin; Desbonnet, Lieve; Waddington, John

    2016-01-01

    The study of gene × environment, as well as epistatic interactions in schizophrenia, has provided important insight into the complex etiopathologic basis of schizophrenia. It has also increased our understanding of the role of susceptibility genes in the disorder and is an important consideration as we seek to translate genetic advances into novel antipsychotic treatment targets. This review summarises data arising from research involving the modelling of gene × environment interactions in schizophrenia using preclinical genetic models. Evidence for synergistic effects on the expression of schizophrenia-relevant endophenotypes will be discussed. It is proposed that valid and multifactorial preclinical models are important tools for identifying critical areas, as well as underlying mechanisms, of convergence of genetic and environmental risk factors, and their interaction in schizophrenia. PMID:27725886

  1. Genetic correlations between body condition scores and fertility in dairy cattle using bivariate random regression models.

    Science.gov (United States)

    De Haas, Y; Janss, L L G; Kadarmideen, H N

    2007-10-01

    Genetic correlations between body condition score (BCS) and fertility traits in dairy cattle were estimated using bivariate random regression models. BCS was recorded by the Swiss Holstein Association on 22,075 lactating heifers (primiparous cows) from 856 sires. Fertility data during first lactation were extracted for 40,736 cows. The fertility traits were days to first service (DFS), days between first and last insemination (DFLI), calving interval (CI), number of services per conception (NSPC) and conception rate to first insemination (CRFI). A bivariate model was used to estimate genetic correlations between BCS as a longitudinal trait by random regression components, and daughter's fertility at the sire level as a single lactation measurement. Heritability of BCS was 0.17, and heritabilities for fertility traits were low (0.01-0.08). Genetic correlations between BCS and fertility over the lactation varied from: -0.45 to -0.14 for DFS; -0.75 to 0.03 for DFLI; from -0.59 to -0.02 for CI; from -0.47 to 0.33 for NSPC and from 0.08 to 0.82 for CRFI. These results show (genetic) interactions between fat reserves and reproduction along the lactation trajectory of modern dairy cows, which can be useful in genetic selection as well as in management. Maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in mid lactation when the genetic variance for BCS is largest, and the genetic correlations between BCS and fertility is strongest.

  2. Prediction of mineral scale formation in geothermal and oilfield operations using the Extended UNIQUAC model - Part II. Carbonate-scaling minerals

    DEFF Research Database (Denmark)

    Villafafila, Ada; Thomsen, Kaj; Stenby, Erling Halfdan

    2006-01-01

    Two additional parameters to account for the pressure dependency of solubility are added to the Extended UNIQUAC model presented by Thomsen and Rasmussen (1999). The improved model has been used for correlation and prediction of vapor-liquid-solid equilibrium for different carbonate systems (CaCO...

  3. [Analysis of genetic models and gene effects on main agronomy characters in rapeseed].

    Science.gov (United States)

    Li, J; Qiu, J; Tang, Z; Shen, L

    1992-01-01

    According to four different genetic models, the genetic patterns of 8 agronomy traits were analysed by using the data of 24 generations which included positive and negative cross of 81008 x Tower, both of the varieties are of good quality. The results showed that none of 8 characters could fit in with additive-dominance models. Epistasis was found in all of these characters, and it has significant effect on generation means. Seed weight/plant and some other main yield characters are controlled by duplicate interaction genes. The interaction between triple genes or multiple genes needs to be utilized in yield heterosis.

  4. Fixed Points in Discrete Models for Regulatory Genetic Networks

    Directory of Open Access Journals (Sweden)

    Orozco Edusmildo

    2007-01-01

    Full Text Available It is desirable to have efficient mathematical methods to extract information about regulatory iterations between genes from repeated measurements of gene transcript concentrations. One piece of information is of interest when the dynamics reaches a steady state. In this paper we develop tools that enable the detection of steady states that are modeled by fixed points in discrete finite dynamical systems. We discuss two algebraic models, a univariate model and a multivariate model. We show that these two models are equivalent and that one can be converted to the other by means of a discrete Fourier transform. We give a new, more general definition of a linear finite dynamical system and we give a necessary and sufficient condition for such a system to be a fixed point system, that is, all cycles are of length one. We show how this result for generalized linear systems can be used to determine when certain nonlinear systems (monomial dynamical systems over finite fields are fixed point systems. We also show how it is possible to determine in polynomial time when an ordinary linear system (defined over a finite field is a fixed point system. We conclude with a necessary condition for a univariate finite dynamical system to be a fixed point system.

  5. Emerging technologies to create inducible and genetically defined porcine cancer models

    Directory of Open Access Journals (Sweden)

    Lawrence B Schook

    2016-02-01

    Full Text Available There is an emerging need for new animal models that address unmet translational cancer research requirements. Transgenic porcine models provide an exceptional opportunity due to their genetic, anatomic and physiological similarities with humans. Due to recent advances in the sequencing of domestic animal genomes and the development of new organism cloning technologies, it is now very feasible to utilize pigs as a malleable species, with similar anatomic and physiological features with humans, in which to develop cancer models. In this review, we discuss genetic modification technologies successfully used to produce porcine biomedical models, in particular the Cre-loxP System as well as major advances and perspectives the CRISPR/Cas9 System. Recent advancements in porcine tumor modeling and genome editing will bring porcine models to the forefront of translational cancer research.

  6. Emerging Technologies to Create Inducible and Genetically Defined Porcine Cancer Models.

    Science.gov (United States)

    Schook, Lawrence B; Rund, Laurie; Begnini, Karine R; Remião, Mariana H; Seixas, Fabiana K; Collares, Tiago

    2016-01-01

    There is an emerging need for new animal models that address unmet translational cancer research requirements. Transgenic porcine models provide an exceptional opportunity due to their genetic, anatomic, and physiological similarities with humans. Due to recent advances in the sequencing of domestic animal genomes and the development of new organism cloning technologies, it is now very feasible to utilize pigs as a malleable species, with similar anatomic and physiological features with humans, in which to develop cancer models. In this review, we discuss genetic modification technologies successfully used to produce porcine biomedical models, in particular the Cre-loxP System as well as major advances and perspectives the CRISPR/Cas9 System. Recent advancements in porcine tumor modeling and genome editing will bring porcine models to the forefront of translational cancer research.

  7. A parametric model for analyzing anticipation in genetically predisposed families

    DEFF Research Database (Denmark)

    Larsen, Klaus; Petersen, Janne; Bernstein, Inge

    2009-01-01

    and are sensitive to right truncation of the data. We propose a normal random effects model that allows for right-censored observations and includes covariates, and draw statistical inference based on the likelihood function. We applied the model to the hereditary nonpolyposis colorectal cancer (HNPCC)/Lynch...... syndrome family cohort from the national Danish HNPCC register. Age-at-onset was analyzed in 824 individuals from 2-4 generations in 125 families with proved disease-predisposing mutations. A significant effect from anticipation was identified with a mean of 3 years earlier age-at-onset per generation...

  8. Chemical Force Spectroscopy Evidence Supporting the Layer-by-Layer Model of Organic Matter Binding to Iron (oxy)Hydroxide Mineral Surfaces

    KAUST Repository

    Chassé , Alexander W.; Ohno, Tsutomu; Higgins, Steven R.; Amirbahman, Aria; Yildirim, Nadir; Parr, Thomas B.

    2015-01-01

    © 2015 American Chemical Society. The adsorption of dissolved organic matter (DOM) to metal (oxy)hydroxide mineral surfaces is a critical step for C sequestration in soils. Although equilibrium studies have described some of the factors controlling this process, the molecular-scale description of the adsorption process has been more limited. Chemical force spectroscopy revealed differing adhesion strengths of DOM extracted from three soils and a reference peat soil material to an iron (oxy)hydroxide mineral surface. The DOM was characterized using ultrahigh-resolution negative ion mode electrospray ionization Fourier Transform ion cyclotron resonance mass spectrometry. The results indicate that carboxyl-rich aromatic and N-containing aliphatic molecules of DOM are correlated with high adhesion forces. Increasing molecular mass was shown to decrease the adhesion force between the mineral surface and the DOM. Kendrick mass defect analysis suggests that mechanisms involving two carboxyl groups result in the most stable bond to the mineral surface. We conceptualize these results using a layer-by-layer "onion" model of organic matter stabilization on soil mineral surfaces.

  9. Bone Tissue Collagen Maturity and Mineral Content Increase With Sustained Hyperglycemia in the KK-Ay Murine Model of Type 2 Diabetes.

    Science.gov (United States)

    Hunt, Heather B; Pearl, Jared C; Diaz, David R; King, Karen B; Donnelly, Eve

    2018-05-01

    Type 2 diabetes mellitus (T2DM) increases fracture risk for a given bone mineral density (BMD), which suggests that T2DM changes bone tissue properties independently of bone mass. In this study, we assessed the effects of hyperglycemia on bone tissue compositional properties, enzymatic collagen crosslinks, and advanced glycation end-products (AGEs) in the KK-Ay murine model of T2DM using Fourier transform infrared (FTIR) imaging and high-performance liquid chromatography (HPLC). Compared to KK-aa littermate controls (n = 8), proximal femoral bone tissue of KK-Ay mice (n = 14) exhibited increased collagen maturity, increased mineral content, and less heterogeneous mineral properties. AGE accumulation assessed by the concentration of pentosidine, as well as the concentrations of the nonenzymatic crosslinks hydroxylysylpyridinoline (HP) and lysyl pyridinoline (LP), did not differ in the proximal femurs of KK-Ay mice compared to controls. The observed differences in tissue-level compositional properties in the KK-Ay mice are consistent with bone that is older and echo observations of reduced remodeling in T2DM. © 2017 American Society for Bone and Mineral Research. © 2017 American Society for Bone and Mineral Research.

  10. Chemical Force Spectroscopy Evidence Supporting the Layer-by-Layer Model of Organic Matter Binding to Iron (oxy)Hydroxide Mineral Surfaces

    KAUST Repository

    Chassé, Alexander W.

    2015-08-18

    © 2015 American Chemical Society. The adsorption of dissolved organic matter (DOM) to metal (oxy)hydroxide mineral surfaces is a critical step for C sequestration in soils. Although equilibrium studies have described some of the factors controlling this process, the molecular-scale description of the adsorption process has been more limited. Chemical force spectroscopy revealed differing adhesion strengths of DOM extracted from three soils and a reference peat soil material to an iron (oxy)hydroxide mineral surface. The DOM was characterized using ultrahigh-resolution negative ion mode electrospray ionization Fourier Transform ion cyclotron resonance mass spectrometry. The results indicate that carboxyl-rich aromatic and N-containing aliphatic molecules of DOM are correlated with high adhesion forces. Increasing molecular mass was shown to decrease the adhesion force between the mineral surface and the DOM. Kendrick mass defect analysis suggests that mechanisms involving two carboxyl groups result in the most stable bond to the mineral surface. We conceptualize these results using a layer-by-layer "onion" model of organic matter stabilization on soil mineral surfaces.

  11. Toward an integrated genetic model for vent-distal SEDEX deposits

    Science.gov (United States)

    Sangster, D. F.

    2018-04-01

    Although genetic models have been proposed for vent-proximal SEDEX deposits, an equivalent model for vent-distal deposits has not yet appeared. In view of this, it is the object of this paper to present a preliminary integrated vent-distal genetic model through exploration of four major components: (i) nature of the ore-forming fluid, (ii) role of density of the unconsolidated host sediments, (iii) dynamics of sulfate reduction and (iv) depositional environment. Two sub-groups of SEDEX Pb-Zn deposits, vent-proximal and vent-distal, are widely recognized today. Of the two, the latter is by far the largest in terms of metal content with each of the 13 largest containing in excess of 7.5 M (Zn+Pb) metal. In contrast, only one vent-proximal deposit (Sullivan) falls within this size range. Vent-proximal deposits are characteristically underlain by local networks of sulfide-filled veins (commonly regarded as feeder veins) surrounded by a discordant complex of host rock alteration. These attributes are missing in vent-distal deposits, which has led to the widespread view that vent-distal ore-forming fluids have migrated unknown distances away from their vent sites. Because of the characteristic fine grain size of ore minerals, critical fluid inclusion data are lacking for vent-distal ore-stage sulfides. Consequently, hypothetical fluids such as those which formed MVT deposits (120 °C, 20% NaCl equiv.) are considered to represent vent-distal fluids as well. Such high-salinity fluids are capable of carrying significant concentrations of Pb and Zn as chloride complexes while the relatively low temperatures preclude high Cu contents. Densities of such metalliferous brines result in bottom-hugging fluids that collect in shallow saucer-shaped depressions (collector basins). Lateral metal zoning in several deposits reveals the direction from which the brines came. Relative densities of the ore-forming fluid and sediment determine whether the ore-forming fluid stabilizes on top

  12. First attempts of linking modelling, Postharvest behaviour and Melon Genetics

    NARCIS (Netherlands)

    Tijskens, L.M.M.; Santos, Don N.; Obando-Ulloa, J.M.; Moreno, E.; Schouten, R.E.

    2008-01-01

    The onset of climacteric is associated with the end of melon fruit shelf-life. The aim of this research was to develop practical and applicable models of fruit ripening changes (hardness, moisture loss) also able to discriminate between climacteric and non-climacteric behaviour. The decrease in

  13. Review Genetic prediction models and heritability estimates for ...

    African Journals Online (AJOL)

    edward

    2015-05-09

    May 9, 2015 ... Heritability estimates for functional longevity have been expressed on an original or a logarithmic scale with PH models. Ducrocq & Casella (1996) defined heritability on a logarithmic scale and modified under simulation to incorporate the tri-gamma function (γ) as used by Sasaki et al. (2012) and Terawaki ...

  14. Stable cycling in discrete-time genetic models.

    OpenAIRE

    Hastings, A

    1981-01-01

    Examples of stable cycling are discussed for two-locus, two-allele, deterministic, discrete-time models with constant fitnesses. The cases that cycle were found by using numerical techniques to search for stable Hopf bifurcations. One consequence of the results is that apparent cases of directional selection may be due to stable cycling.

  15. Stable cycling in discrete-time genetic models.

    Science.gov (United States)

    Hastings, A

    1981-11-01

    Examples of stable cycling are discussed for two-locus, two-allele, deterministic, discrete-time models with constant fitnesses. The cases that cycle were found by using numerical techniques to search for stable Hopf bifurcations. One consequence of the results is that apparent cases of directional selection may be due to stable cycling.

  16. Mineral accumulation in vegetative and reproductive tissues during seed development in Medicago truncatula

    Directory of Open Access Journals (Sweden)

    Christina B. Garcia

    2015-08-01

    Full Text Available Enhancing nutrient density in legume seeds is one of several strategies being explored to improve the nutritional quality of the food supply. In order to develop crop varieties with increased seed mineral concentration, a more detailed understanding of mineral translocation within the plant is required. By studying mineral accumulation in different organs within genetically diverse members of the same species, it may be possible to identify variable traits that modulate seed mineral concentration. We utilized two ecotypes (A17 and DZA315.16 of the model legume, Medicago truncatula, to study dry mass and mineral accumulation in the leaves, pod walls, and seeds during reproductive development. The pod wall dry mass was significantly different between the two ecotypes beginning at 12 days after pollination, whereas there was no significant difference in the average dry mass of individual seeds between the two ecotypes at any time point. There were also no significant differences in leaf dry mass between ecotypes; however, we observed expansion of A17 leaves during the first 21 days of pod development, while DZA315.16 leaves did not display a significant increase in leaf area. Mineral profiling of the leaves, pod walls, and seeds highlighted differences in accumulation patterns among minerals within each tissue as well as genotypic differences with respect to individual minerals. Because there were differences in the average seed number per pod, the total seed mineral content per pod was generally higher in A17 than DZA315.16. In addition, mineral partitioning to the seeds tended to be higher in A17 pods. These data revealed that mineral retention within leaves and/or pod walls might attenuate mineral accumulation within the seeds. As a result, strategies to increase seed mineral content should include approaches that will enhance export from these tissues.

  17. Bone toughness at the molecular scale: A model for fracture toughness using crosslinked osteopontin on synthetic and biogenic mineral substrates.

    Science.gov (United States)

    Cavelier, S; Dastjerdi, A K; McKee, M D; Barthelat, F

    2018-05-01

    The most prominent structural components in bone are collagen and mineral. However, bone additionally contains a substantial amount of noncollagenous proteins (most notably of the SIBLING protein family), some of which may act as cohesive/adhesive "binders" for the composite hybrid collagen/mineral scaffolding, whether in the bulk phase of bone, or at its interfaces. One such noncollagenous protein - osteopontin (OPN) - appears to be critical to the deformability and fracture toughness of bone. In the present study, we used a reconstructed synthetic mineral-OPN-mineral interface, and a biogenic (natural tooth dentin) mineral/collagen-OPN-mineral/collagen interface, to measure the fracture toughness of OPN on mineralized substrates. We used this system to test the hypothesis that OPN crosslinking by the enzyme tissue transglutaminase 2 (TG2) that is found in bone enhances interfacial adhesion to increase the fracture toughness of bone. For this, we prepared double-cantilever beam substrates of synthetic pure hydroxyapatite mineral, and of narwhal dentin, and directly apposed them to one another under different intervening OPN/crosslinking conditions, and fracture toughness was tested using a miniaturized loading stage. The work-of-fracture of the OPN interface was measured for different OPN formulations (monomer vs. polymer), crosslinking states, and substrate composition. Noncrosslinked OPN provided negligible adhesion on pure hydroxyapatite, whereas OPN crosslinking (by the chemical crosslinker glutaraldehyde, and TG2 enzyme) provided strong interfacial adhesion for both hydroxyapatite and dentin using monomeric and polymeric OPN. Pre-coating of the substrate beams with monomeric OPN further improved the adhesive performance of the samples, likely by allowing effective binding of this nascent OPN form to mineral/matrix components, with this pre-attachment providing a protein layer for additional crosslinking between the substrates. Copyright © 2018 Elsevier Inc

  18. Hydrothermal minerals

    Digital Repository Service at National Institute of Oceanography (India)

    Nath, B.N.

    flux. Circulation of seawater through the oceanic crust and upper mantle gives rise to a complex series of physical and chemical reactions that lead to the 1) formation of seafloor mineral deposits; 2) alteration of oceanic crust; 3) control... temperature in the high-temperature reaction zone near the heat source. Important parameters in determining the high- temperature fluid composition are • pressure, • temperature, • water/rock ratio, • rock composition, • recharge fluid...

  19. Application of hierarchical genetic models to Raven and WAIS subtests: a Dutch twin study.

    Science.gov (United States)

    Rijsdijk, Frühling V; Vernon, P A; Boomsma, Dorret I

    2002-05-01

    Hierarchical models of intelligence are highly informative and widely accepted. Application of these models to twin data, however, is sparse. This paper addresses the question of how a genetic hierarchical model fits the Wechsler Adult Intelligence Scale (WAIS) subtests and the Raven Standard Progressive test score, collected in 194 18-year-old Dutch twin pairs. We investigated whether first-order group factors possess genetic and environmental variance independent of the higher-order general factor and whether the hierarchical structure is significant for all sources of variance. A hierarchical model with the 3 Cohen group-factors (verbal comprehension, perceptual organisation and freedom-from-distractibility) and a higher-order g factor showed the best fit to the phenotypic data and to additive genetic influences (A), whereas the unique environmental source of variance (E) could be modeled by a single general factor and specifics. There was no evidence for common environmental influences. The covariation among the WAIS group factors and the covariation between the group factors and the Raven is predominantly influenced by a second-order genetic factor and strongly support the notion of a biological basis of g.

  20. Genetic aspects of barite mineralization related to rocks of the teschenite association in the Silesian Unit, Outer Western Carpathians, Czech Republic

    Directory of Open Access Journals (Sweden)

    Jirásek Jakub

    2017-04-01

    Full Text Available Barite is a relatively uncommon phase in vein and amygdule mineralizations hosted by igneous rocks of the teschenite association in the Silesian Unit (Western Carpathians. In macroscopically observable sizes, it has been reported from 10 sites situated only in the Czech part of the Silesian Unit. Microscopic barite produced by the hydrothermal alteration of rock matrix and also by the supergene processes is more abundant. We examined four samples of barite by mineralogical and geochemical methods. Electron microprobe analyses proved pure barites with up to 0.038 apfu Sr and without remarkable internal zonation. Fluid inclusion and sulphur isotope data suggests that multiple sources of fluid components have been involved during barite crystallization. Barite contains primary and secondary aqueous all-liquid (L or less frequent two-phase (L+V aqueous fluid inclusions with variable salinity (0.4-2.9 wt. % NaCl eq. and homogenization temperatures between 77 and 152 °C. The higher-salinity fluid endmember was probably Cretaceous seawater and the lower-salinity one was probably diagenetic water derived from surrounding flysch sediments during compaction and thermal alteration of clay minerals. The δ34S values of barite samples range between -1.0 ‰ and +16.4 ‰ CDT suggesting participation of two sources of sulphate, one with a near-zero δ34S values probably derived from wall rocks and another with high δ34S values being most probably sulphate from the Cretaceous seawater. All results underline the role of externally derived fluids during post-magmatic alteration of bodies of rock of the teschenite association.

  1. Genetics on the Fly: A Primer on the Drosophila Model System

    Science.gov (United States)

    Hales, Karen G.; Korey, Christopher A.; Larracuente, Amanda M.; Roberts, David M.

    2015-01-01

    Fruit flies of the genus Drosophila have been an attractive and effective genetic model organism since Thomas Hunt Morgan and colleagues made seminal discoveries with them a century ago. Work with Drosophila has enabled dramatic advances in cell and developmental biology, neurobiology and behavior, molecular biology, evolutionary and population genetics, and other fields. With more tissue types and observable behaviors than in other short-generation model organisms, and with vast genome data available for many species within the genus, the fly’s tractable complexity will continue to enable exciting opportunities to explore mechanisms of complex developmental programs, behaviors, and broader evolutionary questions. This primer describes the organism’s natural history, the features of sequenced genomes within the genus, the wide range of available genetic tools and online resources, the types of biological questions Drosophila can help address, and historical milestones. PMID:26564900

  2. Application of the genetic algorithm to blume-emery-griffiths model: Test Cases

    International Nuclear Information System (INIS)

    Erdinc, A.

    2004-01-01

    The equilibrium properties of the Blume-Emery-Griffiths (BEO) model Hamiltonian with the arbitrary bilinear (1), biquadratic (K) and crystal field interaction (D) are studied using the genetic algorithm technique. Results are compared with lowest approximation of the cluster variation method (CVM), which is identical to the mean field approximation. We found that the genetic algorithm to be very efficient for fast search at the average fraction of the spins, especially in the early stages as the system is far from the equilibrium state. A combination of the genetic algorithm followed by one of the well-tested simulation techniques seems to be an optimal approach. The curvature of the inverse magnetic susceptibility is also presented for the stable state of the BEG model

  3. Bayesian Modeling for Genetic Anticipation in Presence of Mutational Heterogeneity: A Case Study in Lynch Syndrome

    DEFF Research Database (Denmark)

    Boonstra, Philip S; Mukherjee, Bhramar; Taylor, Jeremy M G

    2011-01-01

    Summary Genetic anticipation, described by earlier age of onset (AOO) and more aggressive symptoms in successive generations, is a phenomenon noted in certain hereditary diseases. Its extent may vary between families and/or between mutation subtypes known to be associated with the disease phenotype....... In this article, we posit a Bayesian approach to infer genetic anticipation under flexible random effects models for censored data that capture the effect of successive generations on AOO. Primary interest lies in the random effects. Misspecifying the distribution of random effects may result in incorrect...... to cause hereditary nonpolyposis colorectal cancer, also called Lynch syndrome (LS). We find evidence for a decrease in AOO between generations in this article. Our model predicts family-level anticipation effects that are potentially useful in genetic counseling clinics for high-risk families....

  4. Selecting the Best Forecasting-Implied Volatility Model Using Genetic Programming

    Directory of Open Access Journals (Sweden)

    Wafa Abdelmalek

    2009-01-01

    Full Text Available The volatility is a crucial variable in option pricing and hedging strategies. The aim of this paper is to provide some initial evidence of the empirical relevance of genetic programming to volatility's forecasting. By using real data from S&P500 index options, the genetic programming's ability to forecast Black and Scholes-implied volatility is compared between time series samples and moneyness-time to maturity classes. Total and out-of-sample mean squared errors are used as forecasting's performance measures. Comparisons reveal that the time series model seems to be more accurate in forecasting-implied volatility than moneyness time to maturity models. Overall, results are strongly encouraging and suggest that the genetic programming approach works well in solving financial problems.

  5. A Unifying Model for the Analysis of Phenotypic, Genetic and Geographic Data

    DEFF Research Database (Denmark)

    Guillot, Gilles; Rena, Sabrina; Ledevin, Ronan

    2012-01-01

    Recognition of evolutionary units (species, populations) requires integrating several kinds of data such as genetic or phenotypic markers or spatial information, in order to get a comprehensive view concerning the dierentiation of the units. We propose a statistical model with a double original...... advantage: (i) it incorporates information about the spatial distribution of the samples, with the aim to increase inference power and to relate more explicitly observed patterns to geography; and (ii) it allows one to analyze genetic and phenotypic data within a unied model and inference framework, thus...... an intricate case of inter- and intra-species dierentiation based on an original data-set of georeferenced genetic and morphometric markers obtained on Myodes voles from Sweden. A computer program is made available as an extension of the R package Geneland....

  6. Teaching genetics using hands-on models, problem solving, and inquiry-based methods

    Science.gov (United States)

    Hoppe, Stephanie Ann

    Teaching genetics can be challenging because of the difficulty of the content and misconceptions students might hold. This thesis focused on using hands-on model activities, problem solving, and inquiry-based teaching/learning methods in order to increase student understanding in an introductory biology class in the area of genetics. Various activities using these three methods were implemented into the classes to address any misconceptions and increase student learning of the difficult concepts. The activities that were implemented were shown to be successful based on pre-post assessment score comparison. The students were assessed on the subjects of inheritance patterns, meiosis, and protein synthesis and demonstrated growth in all of the areas. It was found that hands-on models, problem solving, and inquiry-based activities were more successful in learning concepts in genetics and the students were more engaged than tradition styles of lecture.

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

    DEFF Research Database (Denmark)

    Cheng, Jade Yu

    2016-01-01

    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...... geneticists strive to establish working solutions to extract information from massive volumes of biological data. The steep increase in the quantity and quality of genomic data during the past decades provides a unique opportunity but also calls for new and improved algorithms and software to cope...... including population splits, effective population sizes, gene flow, etc. Since joining the CoalHMM development team in 2014, I have mainly contributed in two directions: 1) improving optimizations through heuristic-based evolutionary algorithms and 2) modeling of historical admixture events. Ohana, meaning...

  8. Mechanistic modelling of genetic and epigenetic events in radiation carcinogenesis

    International Nuclear Information System (INIS)

    Andreev, S. G.; Eidelman, Y. A.; Salnikov, I. V.; Khvostunov, I. K.

    2006-01-01

    Methodological problems arise on the way of radiation carcinogenesis modelling with the incorporation of radiobiological and cancer biology mechanistic data. The results of biophysical modelling of different endpoints [DNA DSB induction, repair, chromosome aberrations (CA) and cell proliferation] are presented and applied to the analysis of RBE-LET relationships for radiation-induced neoplastic transformation (RINT) of C3H/10T1/2 cells in culture. Predicted values for some endpoints correlate well with the data. It is concluded that slowly repaired DSB clusters, as well as some kind of CA, may be initiating events for RINT. As an alternative interpretation, it is possible that DNA damage can induce RINT indirectly via epigenetic process. A hypothetical epigenetic pathway for RINT is discussed. (authors)

  9. Prediction model for prevalence and incidence of advanced age-related macular degeneration based on genetic, demographic, and environmental variables.

    Science.gov (United States)

    Seddon, Johanna M; Reynolds, Robyn; Maller, Julian; Fagerness, Jesen A; Daly, Mark J; Rosner, Bernard

    2009-05-01

    The joint effects of genetic, ocular, and environmental variables were evaluated and predictive models for prevalence and incidence of AMD were assessed. Participants in the multicenter Age-Related Eye Disease Study (AREDS) were included in a prospective evaluation of 1446 individuals, of which 279 progressed to advanced AMD (geographic atrophy or neovascular disease) and 1167 did not progress during 6.3 years of follow-up. For prevalent AMD, 509 advanced cases were compared with 222 controls. Covariates for the incidence analysis included age, sex, education, smoking, body mass index (BMI), baseline AMD grade, and the AREDS vitamin-mineral treatment assignment. DNA specimens were evaluated for six variants in five genes related to AMD. Unconditional logistic regression analyses were performed for prevalent and incident advanced AMD. An algorithm was developed and receiver operating characteristic curves and C statistics were calculated to assess the predictive ability of risk scores to discriminate progressors from nonprogressors. All genetic polymorphisms were independently related to prevalence of advanced AMD, controlling for genetic factors, smoking, BMI, and AREDS treatment. Multivariate odds ratios (ORs) were 3.5 (95% confidence interval [CI], 1.7-7.1) for CFH Y402H; 3.7 (95% CI, 1.6-8.4) for CFH rs1410996; 25.4 (95% CI, 8.6-75.1) for LOC387715 A69S (ARMS2); 0.3 (95% CI, 0.1-0.7) for C2 E318D; 0.3 (95% CI, 0.1-0.5) for CFB; and 3.6 (95% CI, 1.4-9.4) for C3 R102G, comparing the homozygous risk/protective genotypes to the referent genotypes. For incident AMD, all these variants except CFB were significantly related to progression to advanced AMD, after controlling for baseline AMD grade and other factors, with ORs from 1.8 to 4.0 for presence of two risk alleles and 0.4 for the protective allele. An interaction was seen between CFH402H and treatment, after controlling for all genotypes. Smoking was independently related to AMD, with a multiplicative joint

  10. Bone mineral density changes after ovariectomy in rats as an osteopenic model : stepwise description of double dorso-lateral approach.

    Science.gov (United States)

    Park, Sung Bae; Lee, Yoon Jin; Chung, Chun Kee

    2010-10-01

    This study describes a method for inducing osteopenia using bilateral ovariectomy (OVX), which causes significant changes in bone mineral density (BMD) in rats. Twenty-five 10-week-old female Sprague Dawley rats were used. Five rats were euthanized after two weeks, and BMD was measured in their femora. The other 20 rats were assigned to one of two groups : a sham group (n = 10), which underwent a sham operation, and an OVX group (n = 10), which underwent bilateral OVX at 12 weeks of age. After six weeks, five rats from each group were euthanized, and BMD was measured in their femora. The same procedures were performed in the remaining rats form each group eight weeks later. The femur BMD was significantly lower in the six-week OVX group than in the six-week sham group, and in the eight-week OVX group than in the eight-week sham group. Bilateral OVX is a safe method for creating an osteopenic rat model. The significant decrease in BMD appears six weeks after bilateral OVX.

  11. Hydrometalurgical processes for mineral complexes

    International Nuclear Information System (INIS)

    Barskij, L.A.; Danil'chenko, L.M.

    1977-01-01

    Requirements for the technology of the processing of ores including uranium ores and principal stages of the working out of technological schemes are described in brief. There are reference data on commercial minerals and ores including uranium-thorium ores, their classification with due regard for physical, chemical and superficial properties which form the basis for ore-concentrating processes. There are also presented the classification of minerals including uranium minerals by their flotation ability, flotation regimes of minerals, structural-textural characteristics of ores, genetic types of ore formations and their concentrating ability, algorithmization of the apriori evaluation of the concentration and technological diagnostics of the processing of ores. The classification of ore concentration technique is suggested

  12. Evaluation of a regional mineral dust model over Northern Africa, Southern Europe and Middle East with AERONET data

    Science.gov (United States)

    Basart, S.; Pérez, C.; Cuevas, E.; Baldasano, J. M.

    2009-04-01

    the model to reproduce AOD (at 550nm) associated to mineral dust 24, 48 and 72h ahead. A suit of discrete statistics as Mean Normalized Bias Error (MNBE), Mean Normalized Gross Error (MNGE) and Root Mean Square Error (RMSE) has been used in order to evaluate the model behaviour. Categorical statistics or skill scores, as model accuracy, bias, probability of detection, false alarm rate and critical success index have been implemented to test the capability of the model to simulate AOD exceeding thresholds defined by the quartiles of each AERONET site. A previous aerosol characterization of AERONET data has been performed for our study region in order to discriminate desert dust contributions (Basart et al., 2008). The first results of the comparison reveal that the modelled dust field agrees in general reasonably well with sun photometer data. Since dust long-range transport is mainly driven by smaller dust particles, the results of this new 8-bins version (with increased number of dust size bins) is considerably better, since the small particle size range (<10µm effective radius) is well described. The best scores are found in North Africa and Middle East. In the Sahel region, an important sub-estimation is observed in wintertime, when the Atlantic outflow transport is important. This is partially due to the more complex processes associated to dust generation in this region (Warren et al., 2007), not well parameterized in dust models yet. Other causes, such as the correct simulation of regional winds or the threshold friction velocity are under research. Moreover, the interaction of mineral dust and biomass burning aerosols from Savannah fires is at its maximum over the region in this season. In southern Europe, the relative errors are higher than in the rest of our study domain mainly due to the presence of different types of aerosols (such as fine pollution aerosols) which appear well-mixed with desert dust. References: Basart, S., C. Pérez, E. Cuevas and J

  13. Genetic Algorithms for a Parameter Estimation of a Fermentation Process Model: A Comparison

    Directory of Open Access Journals (Sweden)

    Olympia Roeva

    2005-12-01

    Full Text Available In this paper the problem of a parameter estimation using genetic algorithms is examined. A case study considering the estimation of 6 parameters of a nonlinear dynamic model of E. coli fermentation is presented as a test problem. The parameter estimation problem is stated as a nonlinear programming problem subject to nonlinear differential-algebraic constraints. This problem is known to be frequently ill-conditioned and multimodal. Thus, traditional (gradient-based local optimization methods fail to arrive satisfied solutions. To overcome their limitations, the use of different genetic algorithms as stochastic global optimization methods is explored. These algorithms are proved to be very suitable for the optimization of highly non-linear problems with many variables. Genetic algorithms can guarantee global optimality and robustness. These facts make them advantageous in use for parameter identification of fermentation models. A comparison between simple, modified and multi-population genetic algorithms is presented. The best result is obtained using the modified genetic algorithm. The considered algorithms converged very closely to the cost value but the modified algorithm is in times faster than other two.

  14. The five-factor model of personality and borderline personality disorder: a genetic analysis of comorbidity.

    Science.gov (United States)

    Distel, Marijn A; Trull, Timothy J; Willemsen, Gonneke; Vink, Jacqueline M; Derom, Catherine A; Lynskey, Michael; Martin, Nicholas G; Boomsma, Dorret I

    2009-12-15

    Recently, the nature of personality disorders and their relationship with normal personality traits has received extensive attention. The five-factor model (FFM) of personality, consisting of the personality traits neuroticism, extraversion, openness to experience, agreeableness, and conscientiousness, is one of the proposed models to conceptualize personality disorders as maladaptive variants of continuously distributed personality traits. The present study examined the phenotypic and genetic association between borderline personality and FFM personality traits. Data were available for 4403 monozygotic twins, 4425 dizygotic twins, and 1661 siblings from 6140 Dutch, Belgian, and Australian families. Broad-sense heritability estimates for neuroticism, agreeableness, conscientiousness, extraversion, openness to experience, and borderline personality were 43%, 36%, 43%, 47%, 54%, and 45%, respectively. Phenotypic correlations between borderline personality and the FFM personality traits ranged from .06 for openness to experience to .68 for neuroticism. Multiple regression analyses showed that a combination of high neuroticism and low agreeableness best predicted borderline personality. Multivariate genetic analyses showed the genetic factors that influence individual differences in neuroticism, agreeableness, conscientiousness, and extraversion account for all genetic liability to borderline personality. Unique environmental effects on borderline personality, however, were not completely shared with those for the FFM traits (33% is unique to borderline personality). Borderline personality shares all genetic variation with neuroticism, agreeableness, conscientiousness, and extraversion. The unique environmental influences specific to borderline personality may cause individuals with a specific pattern of personality traits to cross a threshold and develop borderline personality.

  15. Estimation of genetic parameters related to eggshell strength using random regression models.

    Science.gov (United States)

    Guo, J; Ma, M; Qu, L; Shen, M; Dou, T; Wang, K

    2015-01-01

    This study examined the changes in eggshell strength and the genetic parameters related to this trait throughout a hen's laying life using random regression. The data were collected from a crossbred population between 2011 and 2014, where the eggshell strength was determined repeatedly for 2260 hens. Using random regression models (RRMs), several Legendre polynomials were employed to estimate the fixed, direct genetic and permanent environment effects. The residual effects were treated as independently distributed with heterogeneous variance for each test week. The direct genetic variance was included with second-order Legendre polynomials and the permanent environment with third-order Legendre polynomials. The heritability of eggshell strength ranged from 0.26 to 0.43, the repeatability ranged between 0.47 and 0.69, and the estimated genetic correlations between test weeks was high at > 0.67. The first eigenvalue of the genetic covariance matrix accounted for about 97% of the sum of all the eigenvalues. The flexibility and statistical power of RRM suggest that this model could be an effective method to improve eggshell quality and to reduce losses due to cracked eggs in a breeding plan.

  16. Advanced technologies for genetically manipulating the silkworm Bombyx mori, a model Lepidopteran insect

    Science.gov (United States)

    Xu, Hanfu; O'Brochta, David A.

    2015-01-01

    Genetic technologies based on transposon-mediated transgenesis along with several recently developed genome-editing technologies have become the preferred methods of choice for genetically manipulating many organisms. The silkworm, Bombyx mori, is a Lepidopteran insect of great economic importance because of its use in silk production and because it is a valuable model insect that has greatly enhanced our understanding of the biology of insects, including many agricultural pests. In the past 10 years, great advances have been achieved in the development of genetic technologies in B. mori, including transposon-based technologies that rely on piggyBac-mediated transgenesis and genome-editing technologies that rely on protein- or RNA-guided modification of chromosomes. The successful development and application of these technologies has not only facilitated a better understanding of B. mori and its use as a silk production system, but also provided valuable experiences that have contributed to the development of similar technologies in non-model insects. This review summarizes the technologies currently available for use in B. mori, their application to the study of gene function and their use in genetically modifying B. mori for biotechnology applications. The challenges, solutions and future prospects associated with the development and application of genetic technologies in B. mori are also discussed. PMID:26108630

  17. Mouse genetic model for clinical and immunological heterogeneity of leishmaniasis

    Czech Academy of Sciences Publication Activity Database

    Lipoldová, Marie; Svobodová, M.; Havelková, Helena; Krulová, Magdalena; Badalová, Jana; Nohýnková, E.; Hart, A. A. M.; Schlegel, David; Volf, P.; Demant, P.

    2002-01-01

    Roč. 54, č. 3 (2002), s. 174-183 ISSN 0093-7711 R&D Projects: GA MZd NM28; GA ČR GA310/00/0760; GA MŠk OK 394 Grant - others:Howard Hughes Medical Institute(US) HHMI55000323; WHO(XX) TDR I.D. 970772; EC(XE) ERBI-C15-CT98-0317; EC(XE) BIO-4-CT98-0445 Institutional research plan: CEZ:AV0Z5052915 Keywords : Leishmaniasis * mouse model * complex disease Subject RIV: EC - Immunology Impact factor: 2.475, year: 2002

  18. Genetic analyses of partial egg production in Japanese quail using multi-trait random regression models.

    Science.gov (United States)

    Karami, K; Zerehdaran, S; Barzanooni, B; Lotfi, E

    2017-12-01

    1. The aim of the present study was to estimate genetic parameters for average egg weight (EW) and egg number (EN) at different ages in Japanese quail using multi-trait random regression (MTRR) models. 2. A total of 8534 records from 900 quail, hatched between 2014 and 2015, were used in the study. Average weekly egg weights and egg numbers were measured from second until sixth week of egg production. 3. Nine random regression models were compared to identify the best order of the Legendre polynomials (LP). The most optimal model was identified by the Bayesian Information Criterion. A model with second order of LP for fixed effects, second order of LP for additive genetic effects and third order of LP for permanent environmental effects (MTRR23) was found to be the best. 4. According to the MTRR23 model, direct heritability for EW increased from 0.26 in the second week to 0.53 in the sixth week of egg production, whereas the ratio of permanent environment to phenotypic variance decreased from 0.48 to 0.1. Direct heritability for EN was low, whereas the ratio of permanent environment to phenotypic variance decreased from 0.57 to 0.15 during the production period. 5. For each trait, estimated genetic correlations among weeks of egg production were high (from 0.85 to 0.98). Genetic correlations between EW and EN were low and negative for the first two weeks, but they were low and positive for the rest of the egg production period. 6. In conclusion, random regression models can be used effectively for analysing egg production traits in Japanese quail. Response to selection for increased egg weight would be higher at older ages because of its higher heritability and such a breeding program would have no negative genetic impact on egg production.

  19. A general framework for the evaluation of genetic association studies using multiple marginal models

    DEFF Research Database (Denmark)

    Kitsche, Andreas; Ritz, Christian; Hothorn, Ludwig A.

    2016-01-01

    OBJECTIVE: In this study, we present a simultaneous inference procedure as a unified analysis framework for genetic association studies. METHODS: The method is based on the formulation of multiple marginal models that reflect different modes of inheritance. The basic advantage of this methodology...

  20. Automated Test Assembly for Cognitive Diagnosis Models Using a Genetic Algorithm

    Science.gov (United States)

    Finkelman, Matthew; Kim, Wonsuk; Roussos, Louis A.

    2009-01-01

    Much recent psychometric literature has focused on cognitive diagnosis models (CDMs), a promising class of instruments used to measure the strengths and weaknesses of examinees. This article introduces a genetic algorithm to perform automated test assembly alongside CDMs. The algorithm is flexible in that it can be applied whether the goal is to…

  1. Amniotic Fluid Stem Cells: A Novel Source for Modeling of Human Genetic Diseases

    Directory of Open Access Journals (Sweden)

    Ivana Antonucci

    2016-04-01

    Full Text Available In recent years, great interest has been devoted to the use of Induced Pluripotent Stem cells (iPS for modeling of human genetic diseases, due to the possibility of reprogramming somatic cells of affected patients into pluripotent cells, enabling differentiation into several cell types, and allowing investigations into the molecular mechanisms of the disease. However, the protocol of iPS generation still suffers from technical limitations, showing low efficiency, being expensive and time consuming. Amniotic Fluid Stem cells (AFS represent a potential alternative novel source of stem cells for modeling of human genetic diseases. In fact, by means of prenatal diagnosis, a number of fetuses affected by chromosomal or Mendelian diseases can be identified, and the amniotic fluid collected for genetic testing can be used, after diagnosis, for the isolation, culture and differentiation of AFS cells. This can provide a useful stem cell model for the investigation of the molecular basis of the diagnosed disease without the necessity of producing iPS, since AFS cells show some features of pluripotency and are able to differentiate in cells derived from all three germ layers “in vitro”. In this article, we describe the potential benefits provided by using AFS cells in the modeling of human genetic diseases.

  2. Bayesian Modeling for Genetic Anticipation in Presence of Mutational Heterogeneity: A Case Study in Lynch Syndrome

    DEFF Research Database (Denmark)

    Boonstra, Philip S; Mukherjee, Bhramar; Taylor, Jeremy M G

    2011-01-01

    to cause hereditary nonpolyposis colorectal cancer, also called Lynch syndrome (LS). We find evidence for a decrease in AOO between generations in this article. Our model predicts family-level anticipation effects that are potentially useful in genetic counseling clinics for high-risk families....

  3. Photocatalytic mineralization of commercial herbicides in a pilot-scale solar CPC reactor: photoreactor modeling and reaction kinetics constants independent of radiation field.

    Science.gov (United States)

    Colina-Márquez, Jose; Machuca-Martínez, Fiderman; Li Puma, Gianluca

    2009-12-01

    The six-flux absorption-scattering model (SFM) of the radiation field in the photoreactor, combined with reaction kinetics and fluid-dynamic models, has proved to be suitable to describe the degradation of water pollutants in heterogeneous photocatalytic reactors, combining simplicity and accuracy. In this study, the above approach was extended to model the photocatalytic mineralization of a commercial herbicides mixture (2,4-D, diuron, and ametryne used in Colombian sugar cane crops) in a solar, pilot-scale, compound parabolic collector (CPC) photoreactor using a slurry suspension of TiO(2). The ray-tracing technique was used jointly with the SFM to determine the direction of both the direct and diffuse solar photon fluxes and the spatial profile of the local volumetric rate of photon absorption (LVRPA) in the CPC reactor. Herbicides mineralization kinetics with explicit photon absorption effects were utilized to remove the dependence of the observed rate constants from the reactor geometry and radiation field in the photoreactor. The results showed that the overall model fitted the experimental data of herbicides mineralization in the solar CPC reactor satisfactorily for both cloudy and sunny days. Using the above approach kinetic parameters independent of the radiation field in the reactor can be estimated directly from the results of experiments carried out in a solar CPC reactor. The SFM combined with reaction kinetics and fluid-dynamic models proved to be a simple, but reliable model, for solar photocatalytic applications.

  4. Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

    Science.gov (United States)

    Chao, Lin; Rang, Camilla Ulla; Proenca, Audrey Menegaz; Chao, Jasper Ubirajara

    2016-01-01

    Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington's genetic assimilation

  5. Asymmetrical Damage Partitioning in Bacteria: A Model for the Evolution of Stochasticity, Determinism, and Genetic Assimilation.

    Directory of Open Access Journals (Sweden)

    Lin Chao

    2016-01-01

    Full Text Available Non-genetic phenotypic variation is common in biological organisms. The variation is potentially beneficial if the environment is changing. If the benefit is large, selection can favor the evolution of genetic assimilation, the process by which the expression of a trait is transferred from environmental to genetic control. Genetic assimilation is an important evolutionary transition, but it is poorly understood because the fitness costs and benefits of variation are often unknown. Here we show that the partitioning of damage by a mother bacterium to its two daughters can evolve through genetic assimilation. Bacterial phenotypes are also highly variable. Because gene-regulating elements can have low copy numbers, the variation is attributed to stochastic sampling. Extant Escherichia coli partition asymmetrically and deterministically more damage to the old daughter, the one receiving the mother's old pole. By modeling in silico damage partitioning in a population, we show that deterministic asymmetry is advantageous because it increases fitness variance and hence the efficiency of natural selection. However, we find that symmetrical but stochastic partitioning can be similarly beneficial. To examine why bacteria evolved deterministic asymmetry, we modeled the effect of damage anchored to the mother's old pole. While anchored damage strengthens selection for asymmetry by creating additional fitness variance, it has the opposite effect on symmetry. The difference results because anchored damage reinforces the polarization of partitioning in asymmetric bacteria. In symmetric bacteria, it dilutes the polarization. Thus, stochasticity alone may have protected early bacteria from damage, but deterministic asymmetry has evolved to be equally important in extant bacteria. We estimate that 47% of damage partitioning is deterministic in E. coli. We suggest that the evolution of deterministic asymmetry from stochasticity offers an example of Waddington

  6. Cox proportional hazards models have more statistical power than logistic regression models in cross-sectional genetic association studies

    NARCIS (Netherlands)

    van der Net, Jeroen B.; Janssens, A. Cecile J. W.; Eijkemans, Marinus J. C.; Kastelein, John J. P.; Sijbrands, Eric J. G.; Steyerberg, Ewout W.

    2008-01-01

    Cross-sectional genetic association studies can be analyzed using Cox proportional hazards models with age as time scale, if age at onset of disease is known for the cases and age at data collection is known for the controls. We assessed to what degree and under what conditions Cox proportional

  7. Hypothesis of Lithocoding: Origin of the Genetic Code as a "Double Jigsaw Puzzle" of Nucleobase-Containing Molecules and Amino Acids Assembled by Sequential Filling of Apatite Mineral Cellules.

    Science.gov (United States)

    Skoblikow, Nikolai E; Zimin, Andrei A

    2016-05-01

    The hypothesis of direct coding, assuming the direct contact of pairs of coding molecules with amino acid side chains in hollow unit cells (cellules) of a regular crystal-structure mineral is proposed. The coding nucleobase-containing molecules in each cellule (named "lithocodon") partially shield each other; the remaining free space determines the stereochemical character of the filling side chain. Apatite-group minerals are considered as the most preferable for this type of coding (named "lithocoding"). A scheme of the cellule with certain stereometric parameters, providing for the isomeric selection of contacting molecules is proposed. We modelled the filling of cellules with molecules involved in direct coding, with the possibility of coding by their single combination for a group of stereochemically similar amino acids. The regular ordered arrangement of cellules enables the polymerization of amino acids and nucleobase-containing molecules in the same direction (named "lithotranslation") preventing the shift of coding. A table of the presumed "LithoCode" (possible and optimal lithocodon assignments for abiogenically synthesized α-amino acids involved in lithocoding and lithotranslation) is proposed. The magmatic nature of the mineral, abiogenic synthesis of organic molecules and polymerization events are considered within the framework of the proposed "volcanic scenario".

  8. Panel 4: Recent Advances in Otitis Media in Molecular Biology, Biochemistry, Genetics, and Animal Models

    Science.gov (United States)

    Li, Jian-Dong; Hermansson, Ann; Ryan, Allen F.; Bakaletz, Lauren O.; Brown, Steve D.; Cheeseman, Michael T.; Juhn, Steven K.; Jung, Timothy T. K.; Lim, David J.; Lim, Jae Hyang; Lin, Jizhen; Moon, Sung-Kyun; Post, J. Christopher

    2014-01-01

    Background Otitis media (OM) is the most common childhood bacterial infection and also the leading cause of conductive hearing loss in children. Currently, there is an urgent need for developing novel therapeutic agents for treating OM based on full understanding of molecular pathogenesis in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Objective To provide a state-of-the-art review concerning recent advances in OM in the areas of molecular biology, biochemistry, genetics, and animal model studies and to discuss the future directions of OM studies in these areas. Data Sources and Review Methods A structured search of the current literature (since June 2007). The authors searched PubMed for published literature in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. Results Over the past 4 years, significant progress has been made in the areas of molecular biology, biochemistry, genetics, and animal model studies in OM. These studies brought new insights into our understanding of the molecular and biochemical mechanisms underlying the molecular pathogenesis of OM and helped identify novel therapeutic targets for OM. Conclusions and Implications for Practice Our understanding of the molecular pathogenesis of OM has been significantly advanced, particularly in the areas of inflammation, innate immunity, mucus overproduction, mucosal hyperplasia, middle ear and inner ear interaction, genetics, genome sequencing, and animal model studies. Although these studies are still in their experimental stages, they help identify new potential therapeutic targets. Future preclinical and clinical studies will help to translate these exciting experimental research findings into clinical applications. PMID:23536532

  9. Genetic parameters for racing records in trotters using linear and generalized linear models.

    Science.gov (United States)

    Suontama, M; van der Werf, J H J; Juga, J; Ojala, M

    2012-09-01

    Heritability and repeatability and genetic and phenotypic correlations were estimated for trotting race records with linear and generalized linear models using 510,519 records on 17,792 Finnhorses and 513,161 records on 25,536 Standardbred trotters. Heritability and repeatability were estimated for single racing time and earnings traits with linear models, and logarithmic scale was used for racing time and fourth-root scale for earnings to correct for nonnormality. Generalized linear models with a gamma distribution were applied for single racing time and with a multinomial distribution for single earnings traits. In addition, genetic parameters for annual earnings were estimated with linear models on the observed and fourth-root scales. Racing success traits of single placings, winnings, breaking stride, and disqualifications were analyzed using generalized linear models with a binomial distribution. Estimates of heritability were greatest for racing time, which ranged from 0.32 to 0.34. Estimates of heritability were low for single earnings with all distributions, ranging from 0.01 to 0.09. Annual earnings were closer to normal distribution than single earnings. Heritability estimates were moderate for annual earnings on the fourth-root scale, 0.19 for Finnhorses and 0.27 for Standardbred trotters. Heritability estimates for binomial racing success variables ranged from 0.04 to 0.12, being greatest for winnings and least for breaking stride. Genetic correlations among racing traits were high, whereas phenotypic correlations were mainly low to moderate, except correlations between racing time and earnings were high. On the basis of a moderate heritability and moderate to high repeatability for racing time and annual earnings, selection of horses for these traits is effective when based on a few repeated records. Because of high genetic correlations, direct selection for racing time and annual earnings would also result in good genetic response in racing success.

  10. Mathematical programming models for solving in equal-sized facilities layout problems. A genetic search method

    International Nuclear Information System (INIS)

    Tavakkoli-Moghaddam, R.

    1999-01-01

    This paper present unequal-sized facilities layout solutions generated by a genetic search program. named Layout Design using a Genetic Algorithm) 9. The generalized quadratic assignment problem requiring pre-determined distance and material flow matrices as the input data and the continuous plane model employing a dynamic distance measure and a material flow matrix are discussed. Computational results on test problems are reported as compared with layout solutions generated by the branch - and bound algorithm a hybrid method merging simulated annealing and local search techniques, and an optimization process of an enveloped block

  11. Genetic design of pigs as experimental models in the combat between chronic diseases and healthy aging

    DEFF Research Database (Denmark)

    Bolund, Lars

    2012-01-01

    with and without intervention. The genome of different pig breeds have been sequenced, revealing that the pig is genetically more similar to man than conventional laboratory animals - in agreement with the similarities in organ development, physiology and metabolism. Genetically designed minipigs (Göttingen...... pigs. We can also produce clones of pigs, some disease prone and some fluorescing, to perform experiments in regenerative medicine where the fate of healthy fluorescent cells can be followed in the, basically identical, disease prone animals. It is also our hope that our pig models can contribute...

  12. Models for genetic evaluations of claw health traits in Spanish dairy cattle.

    Science.gov (United States)

    Pérez-Cabal, M A; Charfeddine, N

    2015-11-01

    Genetic parameters of 7 claw health traits from Spanish dairy cattle were estimated and the predictive ability of linear and ordinal threshold models were compared and assessed. This study included data on interdigital and digital dermatitis (DE), sole ulcer (SU), white line disease (WL), interdigital hyperplasia (IH), interdigital phlegmon (IP), and chronic laminitis (CL) collected between July 2012 and June 2013 from 834 dairy herds visited by 21 trained trimmers. An overall claw disorder (OCD) was also considered an indicator the absence or the presence of at least 1 of the 6 disorders. Claw health traits were scored as categorical traits with 3 degrees of severity (nonaffected, mild, and severe disorder). Genetic parameters were estimated by fitting both a standard linear model and an ordinal threshold animal model. Around 21% of cows had at least 1 claw disorder, and the most frequent disorders were SU, DE, WL, and CL. Heritabilities of claw disorders estimated with a linear model ranged from 0.01 (IP) to 0.05 (OCD), whereas estimates from the ordinal threshold models ranged from 0.06 to 0.39 (for IP and IH, respectively). Repeatabilities of claw health estimated with the linear model varied from 0.03 to 0.18 and estimates with the ordinal threshold model ranged from 0.33 to 0.69. The global trait OCD was correlated with all disorders, except for IH and IP when the linear model was fitted. Two different genetic backgrounds of claw disorders were found. Digital dermatitis showed positive correlations with IH and IP, whereas SU was positively correlated with WL and CL. The predictive ability of the models was assessed using mean squared error and Pearson correlation between the real observation and the corresponding prediction using cross-validation. Regardless of the claw health status, the linear model led to smaller mean squared error. However, differences in predictive ability were found when predicting nonaffected and affected animals. For most traits

  13. Parameters Calculation of ZnO Surge Arrester Models by Genetic Algorithms

    Directory of Open Access Journals (Sweden)

    A. Bayadi

    2006-09-01

    Full Text Available This paper proposes to provide a new technique based on the genetic algorithm to obtain the best possible series of values of the parameters of the ZnO surge arresters models. The validity of the predicted parameters is then checked by comparing the results predicted with the experimental results available in the literature. Using the ATP-EMTP package an application of the arrester model on network system studies is presented and discussed.

  14. Comparing ESC and iPSC?Based Models for Human Genetic Disorders

    OpenAIRE

    Halevy, Tomer; Urbach, Achia

    2014-01-01

    Traditionally, human disorders were studied using animal models or somatic cells taken from patients. Such studies enabled the analysis of the molecular mechanisms of numerous disorders, and led to the discovery of new treatments. Yet, these systems are limited or even irrelevant in modeling multiple genetic diseases. The isolation of human embryonic stem cells (ESCs) from diseased blastocysts, the derivation of induced pluripotent stem cells (iPSCs) from patients’ somatic cells, and the ne...

  15. Nature and nurture: environmental influences on a genetic rat model of depression.

    Science.gov (United States)

    Mehta-Raghavan, N S; Wert, S L; Morley, C; Graf, E N; Redei, E E

    2016-03-29

    In this study, we sought to learn whether adverse events such as chronic restraint stress (CRS), or 'nurture' in the form of environmental enrichment (EE), could modify depression-like behavior and blood biomarker transcript levels in a genetic rat model of depression. The Wistar Kyoto More Immobile (WMI) is a genetic model of depression that aided in the identification of blood transcriptomic markers, which successfully distinguished adolescent and adult subjects with major depressive disorders from their matched no-disorder controls. Here, we followed the effects of CRS and EE in adult male WMIs and their genetically similar control strain, the Wistar Kyoto Less Immobile (WLI), that does not show depression-like behavior, by measuring the levels of these transcripts in the blood and hippocampus. In WLIs, increased depression-like behavior and transcriptomic changes were present in response to CRS, but in WMIs no behavioral or additive transcriptomic changes occurred. Environmental enrichment decreased both the inherent depression-like behavior in the WMIs and the behavioral difference between WMIs and WLIs, but did not reverse basal transcript level differences between the strains. The inverse behavioral change induced by CRS and EE in the WLIs did not result in parallel inverse expression changes of the transcriptomic markers, suggesting that these behavioral responses to the environment work via separate molecular pathways. In contrast, 'trait' transcriptomic markers with expression differences inherent and unchanging between the strains regardless of the environment suggest that in our model, environmental and genetic etiologies of depression work through independent molecular mechanisms.

  16. Thoracic and lumbar vertebral bone mineral density changes in a natural occurring dog model of diffuse idiopathic skeletal hyperostosis.

    Directory of Open Access Journals (Sweden)

    Steven De Decker

    Full Text Available Ankylosing spinal disorders can be associated with alterations in vertebral bone mineral density (BMD. There is however controversy about vertebral BMD in patients wuse idiopathic skeletal hyperostosis (DISH. DISH in Boxer dogs has been considered a natural occurring disease model for DISH in people. The purpose of this study was to compare vertebral BMD between Boxers with and without DISH. Fifty-nine Boxers with (n=30 or without (n=29 DISH that underwent computed tomography were included. Vertebral BMD was calculated for each thoracic and lumbar vertebra by using an earlier reported and validated protocol. For each vertebral body, a region of interest was drawn on the axial computed tomographic images at three separate locations: immediately inferior to the superior end plate, in the middle of the vertebral body, and superior to the inferior end plate. Values from the three axial slices were averaged to give a mean Hounsfield Unit value for each vertebral body. Univariate statistical analysis was performed to identify factors to be included in a multivariate model. The multivariate model including all dogs demonstrated that vertebral DISH status (Coefficient 24.63; 95% CI 16.07 to 33.19; p <0.001, lumbar vertebrae (Coefficient -17.25; 95% CI -23.42 to -11.09; p < 0.01, and to a lesser extent higher age (Coefficient -0.56; 95% CI -1.07 to -0.05; p = 0.03 were significant predictors for vertebral BMD. When the multivariate model was repeated using only dogs with DISH, vertebral DISH status (Coefficient 20.67; 95% CI, 10.98 to 30.37; p < 0.001 and lumbar anatomical region (Coefficient -38.24; 95% CI, -47.75 to -28.73; p < 0.001 were again predictors for vertebral BMD but age was not. The results of this study indicate that DISH can be associated with decreased vertebral BMD. Further studies are necessary to evaluate the clinical importance and pathophysiology of this finding.

  17. Integrating plant-microbe interactions to understand soil C stabilization with the MIcrobial-MIneral Carbon Stabilization model (MIMICS)

    Science.gov (United States)

    Grandy, Stuart; Wieder, Will; Kallenbach, Cynthia; Tiemann, Lisa

    2014-05-01

    If soil organic matter is predominantly microbial biomass, plant inputs that build biomass should also increase SOM. This seems obvious, but the implications fundamentally change how we think about the relationships between plants, microbes and SOM. Plant residues that build microbial biomass are typically characterized by low C/N ratios and high lignin contents. However, plants with high lignin contents and high C/N ratios are believed to increase SOM, an entrenched idea that still strongly motivates agricultural soil management practices. Here we use a combination of meta-analysis with a new microbial-explicit soil biogeochemistry model to explore the relationships between plant litter chemistry, microbial communities, and SOM stabilization in different soil types. We use the MIcrobial-MIneral Carbon Stabilization (MIMICS) model, newly built upon the Community Land Model (CLM) platform, to enhance our understanding of biology in earth system processes. The turnover of litter and SOM in MIMICS are governed by the activity of r- and k-selected microbial groups and temperature sensitive Michaelis-Menten kinetics. Plant and microbial residues are stabilized short-term by chemical recalcitrance or long-term by physical protection. Fast-turnover litter inputs increase SOM by >10% depending on temperature in clay soils, and it's only in sandy soils devoid of physical protection mechanisms that recalcitrant inputs build SOM. These results challenge centuries of lay knowledge as well as conventional ideas of SOM formation, but are they realistic? To test this, we conducted a meta-analysis of the relationships between the chemistry of plant liter inputs and SOM concentrations. We find globally that the highest SOM concentrations are associated with plant inputs containing low C/N ratios. These results are confirmed by individual tracer studies pointing to greater stabilization of low C/N ratio inputs, particularly in clay soils. Our model and meta-analysis results suggest

  18. A genetic algorithm for optimizing multi-pole Debye models of tissue dielectric properties

    International Nuclear Information System (INIS)

    Clegg, J; Robinson, M P

    2012-01-01

    Models of tissue dielectric properties (permittivity and conductivity) enable the interactions of tissues and electromagnetic fields to be simulated, which has many useful applications in microwave imaging, radio propagation, and non-ionizing radiation dosimetry. Parametric formulae are available, based on a multi-pole model of tissue dispersions, but although they give the dielectric properties over a wide frequency range, they do not convert easily to the time domain. An alternative is the multi-pole Debye model which works well in both time and frequency domains. Genetic algorithms are an evolutionary approach to optimization, and we found that this technique was effective at finding the best values of the multi-Debye parameters. Our genetic algorithm optimized these parameters to fit to either a Cole–Cole model or to measured data, and worked well over wide or narrow frequency ranges. Over 10 Hz–10 GHz the best fits for muscle, fat or bone were each found for ten dispersions or poles in the multi-Debye model. The genetic algorithm is a fast and effective method of developing tissue models that compares favourably with alternatives such as the rational polynomial fit. (paper)

  19. Analysis of a genetically structured variance heterogeneity model using the Box-Cox transformation

    DEFF Research Database (Denmark)

    Yang, Ye; Christensen, Ole Fredslund; Sorensen, Daniel

    2011-01-01

    of the marginal distribution of the data. To investigate how the scale of measurement affects inferences, the genetically structured heterogeneous variance model is extended to accommodate the family of Box–Cox transformations. Litter size data in rabbits and pigs that had previously been analysed...... in the untransformed scale were reanalysed in a scale equal to the mode of the marginal posterior distribution of the Box–Cox parameter. In the rabbit data, the statistical evidence for a genetic component at the level of the environmental variance is considerably weaker than that resulting from an analysis...... in the original metric. In the pig data, the statistical evidence is stronger, but the coefficient of correlation between additive genetic effects affecting mean and variance changes sign, compared to the results in the untransformed scale. The study confirms that inferences on variances can be strongly affected...

  20. Genetic evaluation of calf and heifer survival in Iranian Holstein cattle using linear and threshold models.

    Science.gov (United States)

    Forutan, M; Ansari Mahyari, S; Sargolzaei, M

    2015-02-01

    Calf and heifer survival are important traits in dairy cattle affecting profitability. This study was carried out to estimate genetic parameters of survival traits in female calves at different age periods, until nearly the first calving. Records of 49,583 female calves born during 1998 and 2009 were considered in five age periods as days 1-30, 31-180, 181-365, 366-760 and full period (day 1-760). Genetic components were estimated based on linear and threshold sire models and linear animal models. The models included both fixed effects (month of birth, dam's parity number, calving ease and twin/single) and random effects (herd-year, genetic effect of sire or animal and residual). Rates of death were 2.21, 3.37, 1.97, 4.14 and 12.4% for the above periods, respectively. Heritability estimates were very low ranging from 0.48 to 3.04, 0.62 to 3.51 and 0.50 to 4.24% for linear sire model, animal model and threshold sire model, respectively. Rank correlations between random effects of sires obtained with linear and threshold sire models and with linear animal and sire models were 0.82-0.95 and 0.61-0.83, respectively. The estimated genetic correlations between the five different periods were moderate and only significant for 31-180 and 181-365 (r(g) = 0.59), 31-180 and 366-760 (r(g) = 0.52), and 181-365 and 366-760 (r(g) = 0.42). The low genetic correlations in current study would suggest that survival at different periods may be affected by the same genes with different expression or by different genes. Even though the additive genetic variations of survival traits were small, it might be possible to improve these traits by traditional or genomic selection. © 2014 Blackwell Verlag GmbH.

  1. Cross-validation analysis for genetic evaluation models for ranking in endurance horses.

    Science.gov (United States)

    García-Ballesteros, S; Varona, L; Valera, M; Gutiérrez, J P; Cervantes, I

    2018-01-01

    Ranking trait was used as a selection criterion for competition horses to estimate racing performance. In the literature the most common approaches to estimate breeding values are the linear or threshold statistical models. However, recent studies have shown that a Thurstonian approach was able to fix the race effect (competitive level of the horses that participate in the same race), thus suggesting a better prediction accuracy of breeding values for ranking trait. The aim of this study was to compare the predictability of linear, threshold and Thurstonian approaches for genetic evaluation of ranking in endurance horses. For this purpose, eight genetic models were used for each approach with different combinations of random effects: rider, rider-horse interaction and environmental permanent effect. All genetic models included gender, age and race as systematic effects. The database that was used contained 4065 ranking records from 966 horses and that for the pedigree contained 8733 animals (47% Arabian horses), with an estimated heritability around 0.10 for the ranking trait. The prediction ability of the models for racing performance was evaluated using a cross-validation approach. The average correlation between real and predicted performances across genetic models was around 0.25 for threshold, 0.58 for linear and 0.60 for Thurstonian approaches. Although no significant differences were found between models within approaches, the best genetic model included: the rider and rider-horse random effects for threshold, only rider and environmental permanent effects for linear approach and all random effects for Thurstonian approach. The absolute correlations of predicted breeding values among models were higher between threshold and Thurstonian: 0.90, 0.91 and 0.88 for all animals, top 20% and top 5% best animals. For rank correlations these figures were 0.85, 0.84 and 0.86. The lower values were those between linear and threshold approaches (0.65, 0.62 and 0.51). In

  2. Consequences of the genetic threshold model for observing partial migration under climate change scenarios.

    Science.gov (United States)

    Cobben, Marleen M P; van Noordwijk, Arie J

    2017-10-01

    Migration is a widespread phenomenon across the animal kingdom as a response to seasonality in environmental conditions. Partially migratory populations are populations that consist of both migratory and residential individuals. Such populations are very common, yet their stability has long been debated. The inheritance of migratory activity is currently best described by the threshold model of quantitative genetics. The inclusion of such a genetic threshold model for migratory behavior leads to a stable zone in time and space of partially migratory populations under a wide range of demographic parameter values, when assuming stable environmental conditions and unlimited genetic diversity. Migratory species are expected to be particularly sensitive to global warming, as arrival at the breeding grounds might be increasingly mistimed as a result of the uncoupling of long-used cues and actual environmental conditions, with decreasing reproduction as a consequence. Here, we investigate the consequences for migratory behavior and the stability of partially migratory populations under five climate change scenarios and the assumption of a genetic threshold value for migratory behavior in an individual-based model. The results show a spatially and temporally stable zone of partially migratory populations after different lengths of time in all scenarios. In the scenarios in which the species expands its range from a particular set of starting populations, the genetic diversity and location at initialization determine the species' colonization speed across the zone of partial migration and therefore across the entire landscape. Abruptly changing environmental conditions after model initialization never caused a qualitative change in phenotype distributions, or complete extinction. This suggests that climate change-induced shifts in species' ranges as well as changes in survival probabilities and reproductive success can be met with flexibility in migratory behavior at the

  3. Microbially mediated mineral carbonation

    Science.gov (United States)

    Power, I. M.; Wilson, S. A.; Dipple, G. M.; Southam, G.

    2010-12-01

    Mineral carbonation involves silicate dissolution and carbonate precipitation, which are both natural processes that microorganisms are able to mediate in near surface environments (Ferris et al., 1994; Eq. 1). (Ca,Mg)SiO3 + 2H2CO3 + H2O → (Ca,Mg)CO3 + H2O + H4SiO4 + O2 (1) Cyanobacteria are photoautotrophs with cell surface characteristics and metabolic processes involving inorganic carbon that can induce carbonate precipitation. This occurs partly by concentrating cations within their net-negative cell envelope and through the alkalinization of their microenvironment (Thompson & Ferris, 1990). Regions with mafic and ultramafic bedrock, such as near Atlin, British Columbia, Canada, represent the best potential sources of feedstocks for mineral carbonation. The hydromagnesite playas near Atlin are a natural biogeochemical model for the carbonation of magnesium silicate minerals (Power et al., 2009). Field-based studies at Atlin and corroborating laboratory experiments demonstrate the ability of a microbial consortium dominated by filamentous cyanobacteria to induce the precipitation of carbonate minerals. Phototrophic microbes, such as cyanobacteria, have been proposed as a means for producing biodiesel and other value added products because of their efficiency as solar collectors and low requirement for valuable, cultivable land in comparison to crops (Dismukes et al., 2008). Carbonate precipitation and biomass production could be facilitated using specifically designed ponds to collect waters rich in dissolved cations (e.g., Mg2+ and Ca2+), which would allow for evapoconcentration and provide an appropriate environment for growth of cyanobacteria. Microbially mediated carbonate precipitation does not require large quantities of energy or chemicals needed for industrial systems that have been proposed for rapid carbon capture and storage via mineral carbonation (e.g., Lackner et al., 1995). Therefore, this biogeochemical approach may represent a readily

  4. Genetic mouse models relevant to schizophrenia: taking stock and looking forward.

    Science.gov (United States)

    Harrison, Paul J; Pritchett, David; Stumpenhorst, Katharina; Betts, Jill F; Nissen, Wiebke; Schweimer, Judith; Lane, Tracy; Burnet, Philip W J; Lamsa, Karri P; Sharp, Trevor; Bannerman, David M; Tunbridge, Elizabeth M

    2012-03-01

    Genetic mouse models relevant to schizophrenia complement, and have to a large extent supplanted, pharmacological and lesion-based rat models. The main attraction is that they potentially have greater construct validity; however, they share the fundamental limitations of all animal models of psychiatric disorder, and must also be viewed in the context of the uncertain and complex genetic architecture of psychosis. Some of the key issues, including the choice of gene to target, the manner of its manipulation, gene-gene and gene-environment interactions, and phenotypic characterization, are briefly considered in this commentary, illustrated by the relevant papers reported in this special issue. Copyright © 2011 Elsevier Ltd. All rights reserved.

  5. A genetic model of progressively partial melting for uranium-bearing granites in south China

    International Nuclear Information System (INIS)

    Zhai Jianping.

    1989-01-01

    A genetic model of progressively partial and enrichment mechanism of uranium during partial melting of the sources of material studied and the significance of the genetic model in search of uranium deposits is elaborated. This model accounts better for some geological and geochemical features of uranium-bearing granties and suspects the traditional idea that igneous uranium-bearing granites were formed by fusion of U-rich strata surrounding these granites. Finally this paper points out that the infuence of U-rich strata of wall rocks of granites over uranium-bearing granites depends on variation of water solubility in the magma and assimilation of magma to wall rocks during its ascending and crystallization

  6. MOESHA: A genetic algorithm for automatic calibration and estimation of parameter uncertainty and sensitivity of hydrologic models

    Science.gov (United States)

    Characterization of uncertainty and sensitivity of model parameters is an essential and often overlooked facet of hydrological modeling. This paper introduces an algorithm called MOESHA that combines input parameter sensitivity analyses with a genetic algorithm calibration routin...

  7. Estimation in a multiplicative mixed model involving a genetic relationship matrix

    Directory of Open Access Journals (Sweden)

    Eccleston John A

    2009-04-01

    Full Text Available Abstract Genetic models partitioning additive and non-additive genetic effects for populations tested in replicated multi-environment trials (METs in a plant breeding program have recently been presented in the literature. For these data, the variance model involves the direct product of a large numerator relationship matrix A, and a complex structure for the genotype by environment interaction effects, generally of a factor analytic (FA form. With MET data, we expect a high correlation in genotype rankings between environments, leading to non-positive definite covariance matrices. Estimation methods for reduced rank models have been derived for the FA formulation with independent genotypes, and we employ these estimation methods for the more complex case involving the numerator relationship matrix. We examine the performance of differing genetic models for MET data with an embedded pedigree structure, and consider the magnitude of the non-additive variance. The capacity of existing software packages to fit these complex models is largely due to the use of the sparse matrix methodology and the average information algorithm. Here, we present an extension to the standard formulation necessary for estimation with a factor analytic structure across multiple environments.

  8. Research on prediction of agricultural machinery total power based on grey model optimized by genetic algorithm

    Science.gov (United States)

    Xie, Yan; Li, Mu; Zhou, Jin; Zheng, Chang-zheng

    2009-07-01

    Agricultural machinery total power is an important index to reflex and evaluate the level of agricultural mechanization. It is the power source of agricultural production, and is the main factors to enhance the comprehensive agricultural production capacity expand production scale and increase the income of the farmers. Its demand is affected by natural, economic, technological and social and other "grey" factors. Therefore, grey system theory can be used to analyze the development of agricultural machinery total power. A method based on genetic algorithm optimizing grey modeling process is introduced in this paper. This method makes full use of the advantages of the grey prediction model and characteristics of genetic algorithm to find global optimization. So the prediction model is more accurate. According to data from a province, the GM (1, 1) model for predicting agricultural machinery total power was given based on the grey system theories and genetic algorithm. The result indicates that the model can be used as agricultural machinery total power an effective tool for prediction.

  9. Glycogen storage disease type Ia in canines: a model for human metabolic and genetic liver disease.

    Science.gov (United States)

    Specht, Andrew; Fiske, Laurie; Erger, Kirsten; Cossette, Travis; Verstegen, John; Campbell-Thompson, Martha; Struck, Maggie B; Lee, Young Mok; Chou, Janice Y; Byrne, Barry J; Correia, Catherine E; Mah, Cathryn S; Weinstein, David A; Conlon, Thomas J

    2011-01-01

    A canine model of Glycogen storage disease type Ia (GSDIa) is described. Affected dogs are homozygous for a previously described M121I mutation resulting in a deficiency of glucose-6-phosphatase-α. Metabolic, clinicopathologic, pathologic, and clinical manifestations of GSDIa observed in this model are described and compared to those observed in humans. The canine model shows more complete recapitulation of the clinical manifestations seen in humans including "lactic acidosis", larger size, and longer lifespan compared to other animal models. Use of this model in preclinical trials of gene therapy is described and briefly compared to the murine model. Although the canine model offers a number of advantages for evaluating potential therapies for GSDIa, there are also some significant challenges involved in its use. Despite these challenges, the canine model of GSDIa should continue to provide valuable information about the potential for generating curative therapies for GSDIa as well as other genetic hepatic diseases.

  10. Glycogen Storage Disease Type Ia in Canines: A Model for Human Metabolic and Genetic Liver Disease

    Directory of Open Access Journals (Sweden)

    Andrew Specht

    2011-01-01

    Full Text Available A canine model of Glycogen storage disease type Ia (GSDIa is described. Affected dogs are homozygous for a previously described M121I mutation resulting in a deficiency of glucose-6-phosphatase-α. Metabolic, clinicopathologic, pathologic, and clinical manifestations of GSDIa observed in this model are described and compared to those observed in humans. The canine model shows more complete recapitulation of the clinical manifestations seen in humans including “lactic acidosis”, larger size, and longer lifespan compared to other animal models. Use of this model in preclinical trials of gene therapy is described and briefly compared to the murine model. Although the canine model offers a number of advantages for evaluating potential therapies for GSDIa, there are also some significant challenges involved in its use. Despite these challenges, the canine model of GSDIa should continue to provide valuable information about the potential for generating curative therapies for GSDIa as well as other genetic hepatic diseases.

  11. Risk adjustment model of credit life insurance using a genetic algorithm

    Science.gov (United States)

    Saputra, A.; Sukono; Rusyaman, E.

    2018-03-01

    In managing the risk of credit life insurance, insurance company should acknowledge the character of the risks to predict future losses. Risk characteristics can be learned in a claim distribution model. There are two standard approaches in designing the distribution model of claims over the insurance period i.e, collective risk model and individual risk model. In the collective risk model, the claim arises when risk occurs is called individual claim, accumulation of individual claim during a period of insurance is called an aggregate claim. The aggregate claim model may be formed by large model and a number of individual claims. How the measurement of insurance risk with the premium model approach and whether this approach is appropriate for estimating the potential losses occur in the future. In order to solve the problem Genetic Algorithm with Roulette Wheel Selection is used.

  12. Identifying genetic signatures of selection in a non-model species, alpine gentian (Gentiana nivalis L.), using a landscape genetic approach

    DEFF Research Database (Denmark)

    Bothwell, H.; Bisbing, S.; Therkildsen, Nina Overgaard

    2013-01-01

    It is generally accepted that most plant populations are locally adapted. Yet, understanding how environmental forces give rise to adaptive genetic variation is a challenge in conservation genetics and crucial to the preservation of species under rapidly changing climatic conditions. Environmental...... loci, we compared outlier locus detection methods with a recently-developed landscape genetic approach. We analyzed 157 loci from samples of the alpine herb Gentiana nivalis collected across the European Alps. Principle coordinates of neighbor matrices (PCNM), eigenvectors that quantify multi...... variables identified eight more potentially adaptive loci than models run without spatial variables. 3) When compared to outlier detection methods, the landscape genetic approach detected four of the same loci plus 11 additional loci. 4) Temperature, precipitation, and solar radiation were the three major...

  13. A Multi-Marker Genetic Association Test Based on the Rasch Model Applied to Alzheimer's Disease.

    Directory of Open Access Journals (Sweden)

    Wenjia Wang

    Full Text Available Results from Genome-Wide Association Studies (GWAS have shown that the genetic basis of complex traits often include many genetic variants with small to moderate effects whose identification remains a challenging problem. In this context multi-marker analysis at the gene and pathway level can complement traditional point-wise approaches that treat the genetic markers individually. In this paper we propose a novel statistical approach for multi-marker analysis based on the Rasch model. The method summarizes the categorical genotypes of SNPs by a generalized logistic function into a genetic score that can be used for association analysis. Through different sets of simulations, the false-positive rate and power of the proposed approach are compared to a set of existing methods, and shows good performances. The application of the Rasch model on Alzheimer's Disease (AD ADNI GWAS dataset also allows a coherent interpretation of the results. Our analysis supports the idea that APOE is a major susceptibility gene for AD. In the top genes selected by proposed method, several could be functionally linked to AD. In particular, a pathway analysis of these genes also highlights the metabolism of cholesterol, that is known to play a key role in AD pathogenesis. Interestingly, many of these top genes can be integrated in a hypothetic signalling network.

  14. Native South American genetic structure and prehistory inferred from hierarchical modeling of mtDNA.

    Science.gov (United States)

    Lewis, Cecil M; Long, Jeffrey C

    2008-03-01

    Genetic diversity in Native South Americans forms a complex pattern at both the continental and local levels. In comparing the West to the East, there is more variation within groups and smaller genetic distances between groups. From this pattern, researchers have proposed that there is more variation in the West and that a larger, more genetically diverse, founding population entered the West than the East. Here, we question this characterization of South American genetic variation and its interpretation. Our concern arises because others have inferred regional variation from the mean variation within local populations without taking into account the variation among local populations within the same region. This failure produces a biased view of the actual variation in the East. In this study, we analyze the mitochondrial DNA sequence between positions 16040 and 16322 of the Cambridge reference sequence. Our sample represents a total of 886 people from 27 indigenous populations from South (22), Central (3), and North America (2). The basic unit of our analyses is nucleotide identity by descent, which is easily modeled and proportional to nucleotide diversity. We use a forward modeling strategy to fit a series of nested models to identity by descent within and between all pairs of local populations. This method provides estimates of identity by descent at different levels of population hierarchy without assuming homogeneity within populations, regions, or continents. Our main discovery is that Eastern South America harbors more genetic variation than has been recognized. We find no evidence that there is increased identity by descent in the East relative to the total for South America. By contrast, we discovered that populations in the Western region, as a group, harbor more identity by descent than has been previously recognized, despite the fact that average identity by descent within groups is lower. In this light, there is no need to postulate separate founding

  15. Ectopic Mineralization and Conductive Hearing Loss in Enpp1asj Mutant Mice, a New Model for Otitis Media and Tympanosclerosis.

    Science.gov (United States)

    Tian, Cong; Harris, Belinda S; Johnson, Kenneth R

    2016-01-01

    Otitis media (OM), inflammation of the middle ear, is a common cause of hearing loss in children and in patients with many different syndromic diseases. Studies of the human population and mouse models have revealed that OM is a multifactorial disease with many environmental and genetic contributing factors. Here, we report on otitis media-related hearing loss in asj (ages with stiffened joints) mutant mice, which bear a point mutation in the Enpp1 gene. Auditory-evoked brainstem response (ABR) measurements revealed that around 90% of the mutant mice (Enpp1asj/asj) tested had moderate to severe hearing impairment in at least one ear. The ABR thresholds were variable and generally elevated with age. We found otitis media with effusion (OME) in all of the hearing-impaired Enpp1asj/asj mice by anatomic and histological examinations. The volume and inflammatory cell content of the effusion varied among the asj mutant mice, but all mutants exhibited a thickened middle ear epithelium with fibrous polyps and more mucin-secreting goblet cells than controls. Other abnormalities observed in the Enpp1 mutant mice include over-ossification at the round window ridge, thickened and over-calcified stapedial artery, fusion of malleus and incus, and white patches on the inside of tympanic membrane, some of which are typical symptoms of tympanosclerosis. An excessive yellow discharge was detected in the outer ear canal of older asj mutant mice, with 100% penetrance by 5 months of age, and contributes to the progressive nature of the hearing loss. This is the first report of hearing loss and ear pathology associated with an Enpp1 mutation in mice. The Enpp1asj mutant mouse provides a new animal model for studying tympanosclerotic otitis and otitis media with effusion, and also provides a specific model for the hearing loss recently reported to be associated with human ENPP1 mutations causing generalized arterial calcification of infancy and hypophosphatemic rickets.

  16. Indicator minerals as guides to base metal sulphide mineralisation ...

    Indian Academy of Sciences (India)

    Zn-bearing minerals that act as indicator minerals for base metal sulphide mineralization from the Proterozoic Betul Belt,central India with special emphasis on their genetic significance have been discussed.Sulphide mineralisation is hosted by the felsic volcanic rocks and has similarities with volcanic-hosted massive ...

  17. Association Analysis between g.18873C>T and g.27522G>A Genetic Polymorphisms of OPG and Bone Mineral Density in Chinese Postmenopausal Women

    Directory of Open Access Journals (Sweden)

    Fei Wang

    2014-01-01

    Full Text Available Several studies report that the OPG is an important candidate gene in the pathogenesis of osteoporosis. This study aimed to detect the potential association of OPG gene polymorphisms with osteoporosis in postmenopausal women. We recruited 928 subjects containing 463 with primary postmenopausal osteoporosis and 465 healthy volunteers as controls. The BMD of neck hip, lumbar spine (L2–4, and total hip were assessed by dual-energy X-ray absorptiometry (DEXA. Through the created restriction site-polymerase chain reaction (CRS-PCR, PCR-restriction fragment length polymorphism (PCR-RFLP, and DNA sequencing methods, the g.18873C>T and g.27522G>A have been investigated. As for g.18873C>T, our data indicated that subjects with CC genotype have significantly higher BMD value than those of CT and TT genotypes (all P values A, the BMD values of subjects with GG genotype were significantly higher than those of GA and AA genotypes (all P values T and g.27522G>A genetic polymorphisms are associated with the decreased risk for osteoporosis in Chinese postmenopausal women.

  18. Modeling solar radiation of Mediterranean region in Turkey by using fuzzy genetic approach

    International Nuclear Information System (INIS)

    Kisi, Ozgur

    2014-01-01

    The study investigates the ability of FG (fuzzy genetic) approach in modeling solar radiation of seven cities from Mediterranean region of Anatolia, Turkey. Latitude, longitude, altitude and month of the year data from the Adana, K. Maras, Mersin, Antalya, Isparta, Burdur and Antakya cities are used as inputs to the FG model to estimate one month ahead solar radiation. FG model is compared with ANNs (artificial neural networks) and ANFIS (adaptive neruro fuzzzy inference system) models with respect to RMSE (root mean square errors), MAE (mean absolute errors) and determination coefficient (R 2 ) statistics. Comparison results indicate that the FG model performs better than the ANN and ANFIS models. It is found that the FG model can be successfully used for estimating solar radiation by using latitude, longitude, altitude and month of the year information. FG model with RMSE = 6.29 MJ/m 2 , MAE = 4.69 MJ/m 2 and R 2 = 0.905 in the test stage was found to be superior to the optimal ANN model with RMSE = 7.17 MJ/m 2 , MAE = 5.29 MJ/m 2 and R 2 = 0.876 and ANFIS model with RMSE = 6.75 MJ/m 2 , MAE = 5.10 MJ/m 2 and R 2 = 0.892 in estimating solar radiation. - Highlights: • SR (Solar radiation) of seven cities from Mediterranean region of Turkey is predicted. • FG (Fuzzy genetic) models are developed for accurately estimation of SR. • The ability of the FG models used in the study is found to be satisfactory. • FG models are compared with commonly used ANNs (artificial neural networks). • FG models are found to perform better than the ANNs models

  19. Genetic analysis of partial egg production records in Japanese quail using random regression models.

    Science.gov (United States)

    Abou Khadiga, G; Mahmoud, B Y F; Farahat, G S; Emam, A M; El-Full, E A

    2017-08-01

    The main objectives of this study were to detect the most appropriate random regression model (RRM) to fit the data of monthly egg production in 2 lines (selected and control) of Japanese quail and to test the consistency of different criteria of model choice. Data from 1,200 female Japanese quails for the first 5 months of egg production from 4 consecutive generations of an egg line selected for egg production in the first month (EP1) was analyzed. Eight RRMs with different orders of Legendre polynomials were compared to determine the proper model for analysis. All criteria of model choice suggested that the adequate model included the second-order Legendre polynomials for fixed effects, and the third-order for additive genetic effects and permanent environmental effects. Predictive ability of the best model was the highest among all models (ρ = 0.987). According to the best model fitted to the data, estimates of heritability were relatively low to moderate (0.10 to 0.17) showed a descending pattern from the first to the fifth month of production. A similar pattern was observed for permanent environmental effects with greater estimates in the first (0.36) and second (0.23) months of production than heritability estimates. Genetic correlations between separate production periods were higher (0.18 to 0.93) than their phenotypic counterparts (0.15 to 0.87). The superiority of the selected line over the control was observed through significant (P egg production in earlier ages (first and second months) than later ones. A methodology based on random regression animal models can be recommended for genetic evaluation of egg production in Japanese quail. © 2017 Poultry Science Association Inc.

  20. Multi-gene genetic programming based predictive models for municipal solid waste gasification in a fluidized bed gasifier.

    Science.gov (United States)

    Pandey, Daya Shankar; Pan, Indranil; Das, Saptarshi; Leahy, James J; Kwapinski, Witold

    2015-03-01

    A multi-gene genetic programming technique is proposed as a new method to predict syngas yield production and the lower heating value for municipal solid waste gasification in a fluidized bed gasifier. The study shows that the predicted outputs of the municipal solid waste gasification process are in good agreement with the experimental dataset and also generalise well to validation (untrained) data. Published experimental datasets are used for model training and validation purposes. The results show the effectiveness of the genetic programming technique for solving complex nonlinear regression problems. The multi-gene genetic programming are also compared with a single-gene genetic programming model to show the relative merits and demerits of the technique. This study demonstrates that the genetic programming based data-driven modelling strategy can be a good candidate for developing models for other types of fuels as well. Copyright © 2014 Elsevier Ltd. All rights reserved.

  1. Multi-omics reveal the lifestyle of the acidophilic, mineral-oxidizing model species Leptospirillum ferriphilumT.

    Science.gov (United States)

    Christel, Stephan; Herold, Malte; Bellenberg, Sören; El Hajjami, Mohamed; Buetti-Dinh, Antoine; Pivkin, Igor V; Sand, Wolfgang; Wilmes, Paul; Poetsch, Ansgar; Dopson, Mark

    2017-11-17

    novel identification of genes for atmospheric nitrogen fixation, and represents an essential step for further accurate proteomic and transcriptomic investigation of this acidophile model species in the future. Additionally, light is shed on Leptospirillum ferriphilum T adaptation strategies to growth on the copper mineral chalcopyrite. This data can be applied to deepen our understanding and optimization of bioleaching and biooxidation, techniques that present sustainable and environmentally friendly alternatives to many traditional methods for metal extraction. Copyright © 2017 Christel et al.

  2. Integrating the landscape epidemiology and genetics of RNA viruses: rabies in domestic dogs as a model.

    Science.gov (United States)

    Brunker, K; Hampson, K; Horton, D L; Biek, R

    2012-12-01

    Landscape epidemiology and landscape genetics combine advances in molecular techniques, spatial analyses and epidemiological models to generate a more real-world understanding of infectious disease dynamics and provide powerful new tools for the study of RNA viruses. Using dog rabies as a model we have identified how key questions regarding viral spread and persistence can be addressed using a combination of these techniques. In contrast to wildlife rabies, investigations into the landscape epidemiology of domestic dog rabies requires more detailed assessment of the role of humans in disease spread, including the incorporation of anthropogenic landscape features, human movements and socio-cultural factors into spatial models. In particular, identifying and quantifying the influence of anthropogenic features on pathogen spread and measuring the permeability of dispersal barriers are important considerations for planning control strategies, and may differ according to cultural, social and geographical variation across countries or continents. Challenges for dog rabies research include the development of metapopulation models and transmission networks using genetic information to uncover potential source/sink dynamics and identify the main routes of viral dissemination. Information generated from a landscape genetics approach will facilitate spatially strategic control programmes that accommodate for heterogeneities in the landscape and therefore utilise resources in the most cost-effective way. This can include the efficient placement of vaccine barriers, surveillance points and adaptive management for large-scale control programmes.

  3. Modeling the Isentropic Head Value of Centrifugal Gas Compressor using Genetic Programming

    Directory of Open Access Journals (Sweden)

    Safiyullah Ferozkhan

    2016-01-01

    Full Text Available Gas compressor performance is vital in oil and gas industry because of the equipment criticality which requires continuous operations. Plant operators often face difficulties in predicting appropriate time for maintenance and would usually rely on time based predictive maintenance intervals as recommended by original equipment manufacturer (OEM. The objective of this work is to develop the computational model to find the isentropic head value using genetic programming. The isentropic head value is calculated from the OEM performance chart. Inlet mass flow rate and speed of the compressor are taken as the input value. The obtained results from the GP computational models show good agreement with experimental and target data with the average prediction error of 1.318%. The genetic programming computational model will assist machinery engineers to quantify performance deterioration of gas compressor and the results from this study will be then utilized to estimate future maintenance requirements based on the historical data. In general, this genetic programming modelling provides a powerful solution for gas compressor operators to realize predictive maintenance approach in their operations.

  4. Wavelet-linear genetic programming: A new approach for modeling monthly streamflow

    Science.gov (United States)

    Ravansalar, Masoud; Rajaee, Taher; Kisi, Ozgur

    2017-06-01

    The streamflows are important and effective factors in stream ecosystems and its accurate prediction is an essential and important issue in water resources and environmental engineering systems. A hybrid wavelet-linear genetic programming (WLGP) model, which includes a discrete wavelet transform (DWT) and a linear genetic programming (LGP) to predict the monthly streamflow (Q) in two gauging stations, Pataveh and Shahmokhtar, on the Beshar River at the Yasuj, Iran were used in this study. In the proposed WLGP model, the wavelet analysis was linked to the LGP model where the original time series of streamflow were decomposed into the sub-time series comprising wavelet coefficients. The results were compared with the single LGP, artificial neural network (ANN), a hybrid wavelet-ANN (WANN) and Multi Linear Regression (MLR) models. The comparisons were done by some of the commonly utilized relevant physical statistics. The Nash coefficients (E) were found as 0.877 and 0.817 for the WLGP model, for the Pataveh and Shahmokhtar stations, respectively. The comparison of the results showed that the WLGP model could significantly increase the streamflow prediction accuracy in both stations. Since, the results demonstrate a closer approximation of the peak streamflow values by the WLGP model, this model could be utilized for the simulation of cumulative streamflow data prediction in one month ahead.

  5. Near infrared spectrometric technique for testing fruit quality: optimisation of regression models using genetic algorithms

    Science.gov (United States)

    Isingizwe Nturambirwe, J. Frédéric; Perold, Willem J.; Opara, Umezuruike L.

    2016-02-01

    Near infrared (NIR) spectroscopy has gained extensive use in quality evaluation. It is arguably one of the most advanced spectroscopic tools in non-destructive quality testing of food stuff, from measurement to data analysis and interpretation. NIR spectral data are interpreted through means often involving multivariate statistical analysis, sometimes associated with optimisation techniques for model improvement. The objective of this research was to explore the extent to which genetic algorithms (GA) can be used to enhance model development, for predicting fruit quality. Apple fruits were used, and NIR spectra in the range from 12000 to 4000 cm-1 were acquired on both bruised and healthy tissues, with different degrees of mechanical damage. GAs were used in combination with partial least squares regression methods to develop bruise severity prediction models, and compared to PLS models developed using the full NIR spectrum. A classification model was developed, which clearly separated bruised from unbruised apple tissue. GAs helped improve prediction models by over 10%, in comparison with full spectrum-based models, as evaluated in terms of error of prediction (Root Mean Square Error of Cross-validation). PLS models to predict internal quality, such as sugar content and acidity were developed and compared to the versions optimized by genetic algorithm. Overall, the results highlighted the potential use of GA method to improve speed and accuracy of fruit quality prediction.

  6. A service-oriented architecture for integrating the modeling and formal verification of genetic regulatory networks

    Directory of Open Access Journals (Sweden)

    Page Michel

    2009-12-01

    Full Text Available Abstract Background The study of biological networks has led to the development of increasingly large and detailed models. Computer tools are essential for the simulation of the dynamical behavior of the networks from the model. However, as the size of the models grows, it becomes infeasible to manually verify the predictions against experimental data or identify interesting features in a large number of simulation traces. Formal verification based on temporal logic and model checking provides promising methods to automate and scale the analysis of the models. However, a framework that tightly integrates modeling and simulation tools with model checkers is currently missing, on both the conceptual and the implementational level. Results We have developed a generic and modular web service, based on a service-oriented architecture, for integrating the modeling and formal verification of genetic regulatory networks. The architecture has been implemented in the context of the qualitative modeling and simulation tool GNA and the model checkers NUSMV and CADP. GNA has been extended with a verification module for the specification and checking of biological properties. The verification module also allows the display and visual inspection of the verification results. Conclusions The practical use of the proposed web service is illustrated by means of a scenario involving the analysis of a qualitative model of the carbon starvation response in E. coli. The service-oriented architecture allows modelers to define the model and proceed with the specification and formal verification of the biological properties by means of a unified graphical user interface. This guarantees a transparent access to formal verification technology for modelers of genetic regulatory networks.

  7. Mineralization model for Chahar Gonbad copper-gold deposit (Sirjan, using mineralogical, alteration and geochemical data and multivariate statistical methods

    Directory of Open Access Journals (Sweden)

    Seayed Jaber Yousefi

    2012-04-01

    Full Text Available The study area is located in southeastern Iran, about 110 km southwest of Kerman. Geologically, the area is composed of ophiolitic rocks, volcanic rocks, intrusive bodies and sedimentary rocks. Vein mineralization within andesite, andesitic basalt, andesitic tuffs occurred along the Chahar Gonbad fault. Sulfide mineralization in the ore deposit has taken place as dissemination, veins and veinlets in which pyrite and chalcopyrite are the most important ores. In this area, argillic, phyllic and propylitic alteration types are observed. Such elements as Au, Bi, Cu, S and Se are more enriched than others and the enrichment factors for these elements in comparison with background concentration are 321, 503, 393, 703 and 208, and with respect to Clark concentration are 401, 222, 532, 101 and 156, respectively. According to multivariate analysis, three major mineralization phases are recognized in the deposit. During the first phase, hydrothermal calcite veins are enriched in As, Cd, Pb, Zn and Ca, the second phase is manifested by the enrichment of sulfide veins in Cu, Au, Ag, Bi, Fe and S and the third phase mineralization includes Ni, Mn, Se and Sb as an intermediate level between the two previous phases.

  8. Systems genetics of obesity in an F2 pig model by genome-wide association, genetic network and pathway analyses

    DEFF Research Database (Denmark)

    Kogelman, Lisette; Pant, Sameer Dinkar; Fredholm, Merete

    2014-01-01

    .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...... 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...

  9. Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient

    Directory of Open Access Journals (Sweden)

    Rossetto Maurizio

    2012-08-01

    Full Text Available Abstract Background Four of the five species of Telopea (Proteaceae are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation. Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Results Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR and six chloroplast microsatellites (cpSSR were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM. The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed

  10. Genetic structure and bio-climatic modeling support allopatric over parapatric speciation along a latitudinal gradient.

    Science.gov (United States)

    Rossetto, Maurizio; Allen, Chris B; Thurlby, Katie A G; Weston, Peter H; Milner, Melita L

    2012-08-20

    Four of the five species of Telopea (Proteaceae) are distributed in a latitudinal replacement pattern on the south-eastern Australian mainland. In similar circumstances, a simple allopatric speciation model that identifies the origins of genetic isolation within temporal geographic separation is considered as the default model. However, secondary contact between differentiated lineages can result in similar distributional patterns to those arising from a process of parapatric speciation (where gene flow between lineages remains uninterrupted during differentiation). Our aim was to use the characteristic distributional patterns in Telopea to test whether it reflected the evolutionary models of allopatric or parapatric speciation. Using a combination of genetic evidence and environmental niche modelling, we focused on three main questions: do currently described geographic borders coincide with genetic and environmental boundaries; are there hybrid zones in areas of secondary contact between closely related species; did species distributions contract during the last glacial maximum resulting in distributional gaps even where overlap and hybridisation currently occur? Total genomic DNA was extracted from 619 individuals sampled from 36 populations representing the four species. Seven nuclear microsatellites (nSSR) and six chloroplast microsatellites (cpSSR) were amplified across all populations. Genetic structure and the signature of admixture in overlap zones was described using the Bayesian clustering methods implemented in STUCTURE and NewHybrids respectively. Relationships between chlorotypes were reconstructed as a median-joining network. Environmental niche models were produced for all species using environmental parameters from both the present day and the last glacial maximum (LGM).The nSSR loci amplified a total of 154 alleles, while data for the cpSSR loci produced a network of six chlorotypes. STRUCTURE revealed an optimum number of five clusters

  11. Poisson versus threshold models for genetic analysis of clinical mastitis in US Holsteins.

    Science.gov (United States)

    Vazquez, A I; Weigel, K A; Gianola, D; Bates, D M; Perez-Cabal, M A; Rosa, G J M; Chang, Y M

    2009-10-01

    Typically, clinical mastitis is coded as the presence or absence of disease in a given lactation, and records are analyzed with either linear models or binary threshold models. Because the presence of mastitis may include cows with multiple episodes, there is a loss of information when counts are treated as binary responses. Poisson models are appropriated for random variables measured as the number of events, and although these models are used extensively in studying the epidemiology of mastitis, they have rarely been used for studying the genetic aspects of mastitis. Ordinal threshold models are pertinent for ordered categorical responses; although one can hypothesize that the number of clinical mastitis episodes per animal reflects a continuous underlying increase in mastitis susceptibility, these models have rarely been used in genetic analysis of mastitis. The objective of this study was to compare probit, Poisson, and ordinal threshold models for the genetic evaluation of US Holstein sires for clinical mastitis. Mastitis was measured as a binary trait or as the number of mastitis cases. Data from 44,908 first-parity cows recorded in on-farm herd management software were gathered, edited, and processed for the present study. The cows were daughters of 1,861 sires, distributed over 94 herds. Predictive ability was assessed via a 5-fold cross-validation using 2 loss functions: mean squared error of prediction (MSEP) as the end point and a cost difference function. The heritability estimates were 0.061 for mastitis measured as a binary trait in the probit model and 0.085 and 0.132 for the number of mastitis cases in the ordinal threshold and Poisson models, respectively; because of scale differences, only the probit and ordinal threshold models are directly comparable. Among healthy animals, MSEP was smallest for the probit model, and the cost function was smallest for the ordinal threshold model. Among diseased animals, MSEP and the cost function were smallest

  12. An enhanced dynamic model of battery using genetic algorithm suitable for photovoltaic applications

    International Nuclear Information System (INIS)

    Blaifi, S.; Moulahoum, S.; Colak, I.; Merrouche, W.

    2016-01-01

    Highlights: • We proposed a developed dynamic battery model suitable for photovoltaic systems. • We used genetic algorithm optimization method to find parameters that gives minimized error. • The validation was carried out with real measurements from stand-alone photovoltaic string. - Abstract: Modeling of batteries in photovoltaic systems has been a major issue related to the random dynamic regime imposed by the changes of solar irradiation and ambient temperature added to the complexity of battery electrochemical and electrical behaviors. However, various approaches have been proposed to model the battery behavior by predicting from detailed electrochemical, electrical or analytical models to high-level stochastic models. In this paper, an improvement of dynamic electrical battery model is proposed by automatic parameter extraction using genetic algorithm in order to give usefulness and future implementation for practical application. It is highlighted that the enhancement of 21 values of the parameters of CEIMAT model presents a good agreement with real measurements for different modes like charge or discharge and various conditions.

  13. Behavioral phenotypes in schizophrenic animal models with multiple combinations of genetic and environmental factors.

    Science.gov (United States)

    Hida, Hirotake; Mouri, Akihiro; Noda, Yukihiro

    2013-01-01

    Schizophrenia is a multifactorial psychiatric disorder in which both genetic and environmental factors play a role. Genetic [e.g., Disrupted-in-schizophrenia 1 (DISC1), Neuregulin-1 (NRG1)] and environmental factors (e.g., maternal viral infection, obstetric complications, social stress) may act during the developmental period to increase the incidence of schizophrenia. In animal models, interactions between susceptibility genes and the environment can be controlled in ways not possible in humans; therefore, such models are useful for investigating interactions between or within factors in the pathogenesis and pathophysiology of schizophrenia. We provide an overview of schizophrenic animal models investigating interactions between or within factors. First, we reviewed gene-environment interaction animal models, in which schizophrenic candidate gene mutant mice were subjected to perinatal immune activation or adolescent stress. Next, environment-environment interaction animal models, in which mice were subjected to a combination of perinatal immune activation and adolescent administration of drugs, were described. These animal models showed interaction between or within factors; behavioral changes, which were obscured by each factor, were marked by interaction of factors and vice versa. Appropriate behavioral approaches with such models will be invaluable for translational research on novel compounds, and also for providing insight into the pathogenesis and pathophysiology of schizophrenia.

  14. Modelling the effect of structural QSAR parameters on skin penetration using genetic programming

    International Nuclear Information System (INIS)

    Chung, K K; Do, D Q

    2010-01-01

    In order to model relationships between chemical structures and biological effects in quantitative structure–activity relationship (QSAR) data, an alternative technique of artificial intelligence computing—genetic programming (GP)—was investigated and compared to the traditional method—statistical. GP, with the primary advantage of generating mathematical equations, was employed to model QSAR data and to define the most important molecular descriptions in QSAR data. The models predicted by GP agreed with the statistical results, and the most predictive models of GP were significantly improved when compared to the statistical models using ANOVA. Recently, artificial intelligence techniques have been applied widely to analyse QSAR data. With the capability of generating mathematical equations, GP can be considered as an effective and efficient method for modelling QSAR data

  15. Environmental Noise, Genetic Diversity and the Evolution of Evolvability and Robustness in Model Gene Networks

    Science.gov (United States)

    Steiner, Christopher F.

    2012-01-01

    The ability of organisms to adapt and persist in the face of environmental change is accepted as a fundamental feature of natural systems. More contentious is whether the capacity of organisms to adapt (or “evolvability”) can itself evolve and the mechanisms underlying such responses. Using model gene networks, I provide evidence that evolvability emerges more readily when populations experience positively autocorrelated environmental noise (red noise) compared to populations in stable or randomly varying (white noise) environments. Evolvability was correlated with increasing genetic robustness to effects on network viability and decreasing robustness to effects on phenotypic expression; populations whose networks displayed greater viability robustness and lower phenotypic robustness produced more additive genetic variation and adapted more rapidly in novel environments. Patterns of selection for robustness varied antagonistically with epistatic effects of mutations on viability and phenotypic expression, suggesting that trade-offs between these properties may constrain their evolutionary responses. Evolution of evolvability and robustness was stronger in sexual populations compared to asexual populations indicating that enhanced genetic variation under fluctuating selection combined with recombination load is a primary driver of the emergence of evolvability. These results provide insight into the mechanisms potentially underlying rapid adaptation as well as the environmental conditions that drive the evolution of genetic interactions. PMID:23284934

  16. Genetic Determinants of Cardio-Metabolic Risk: A Proposed Model for Phenotype Association and Interaction

    Science.gov (United States)

    Blackett, Piers R; Sanghera, Dharambir K

    2012-01-01

    This review provides a translational and unifying summary of metabolic syndrome genetics and highlights evidence that genetic studies are starting to unravel and untangle origins of the complex and challenging cluster of disease phenotypes. The associated genes effectively express in the brain, liver, kidney, arterial endothelium, adipocytes, myocytes and β cells. Progression of syndrome traits has been associated with ectopic lipid accumulation in the arterial wall, visceral adipocytes, myocytes, and liver. Thus it follows that the genetics of dyslipidemia, obesity, and non-alcoholic fatty liver (NAFLD) disease are central in triggering progression of the syndrome to overt expression of disease traits, and have become a key focus of interest for early detection and for designing prevention and treatments. To support the “birds’ eye view” approach we provide a road-map depicting commonality and interrelationships between the traits and their genetic and environmental determinants based on known risk factors, metabolic pathways, pharmacological targets, treatment responses, gene networks, pleiotropy, and association with circadian rhythm. Although only a small portion of the known heritability is accounted for and there is insufficient support for clinical application of gene-based prediction models, there is direction and encouraging progress in a rapidly moving field that is beginning to show clinical relevance. PMID:23351585

  17. Genetic determinants of cardiometabolic risk: a proposed model for phenotype association and interaction.

    Science.gov (United States)

    Blackett, Piers R; Sanghera, Dharambir K

    2013-01-01

    This review provides a translational and unifying summary of metabolic syndrome genetics and highlights evidence that genetic studies are starting to unravel and untangle origins of the complex and challenging cluster of disease phenotypes. The associated genes effectively express in the brain, liver, kidney, arterial endothelium, adipocytes, myocytes, and β cells. Progression of syndrome traits has been associated with ectopic lipid accumulation in the arterial wall, visceral adipocytes, myocytes, and liver. Thus, it follows that the genetics of dyslipidemia, obesity, and nonalcoholic fatty liver disease are central in triggering progression of the syndrome to overt expression of disease traits and have become a key focus of interest for early detection and for designing prevention and treatments. To support the "birds' eye view" approach, we provide a road-map depicting commonality and interrelationships between the traits and their genetic and environmental determinants based on known risk factors, metabolic pathways, pharmacologic targets, treatment responses, gene networks, pleiotropy, and association with circadian rhythm. Although only a small portion of the known heritability is accounted for and there is insufficient support for clinical application of gene-based prediction models, there is direction and encouraging progress in a rapidly moving field that is beginning to show clinical relevance. Copyright © 2013 National Lipid Association. Published by Elsevier Inc. All rights reserved.

  18. Pattern Discovery in Brain Imaging Genetics via SCCA Modeling with a Generic Non-convex Penalty.

    Science.gov (United States)

    Du, Lei; Liu, Kefei; Yao, Xiaohui; Yan, Jingwen; Risacher, Shannon L; Han, Junwei; Guo, Lei; Saykin, Andrew J; Shen, Li

    2017-10-25

    Brain imaging genetics intends to uncover associations between genetic markers and neuroimaging quantitative traits. Sparse canonical correlation analysis (SCCA) can discover bi-multivariate associations and select relevant features, and is becoming popular in imaging genetic studies. The L1-norm function is not only convex, but also singular at the origin, which is a necessary condition for sparsity. Thus most SCCA methods impose [Formula: see text]-norm onto the individual feature or the structure level of features to pursuit corresponding sparsity. However, the [Formula: see text]-norm penalty over-penalizes large coefficients and may incurs estimation bias. A number of non-convex penalties are proposed to reduce the estimation bias in regression tasks. But using them in SCCA remains largely unexplored. In this paper, we design a unified non-convex SCCA model, based on seven non-convex functions, for unbiased estimation and stable feature selection simultaneously. We also propose an efficient optimization algorithm. The proposed method obtains both higher correlation coefficients and better canonical loading patterns. Specifically, these SCCA methods with non-convex penalties discover a strong association between the APOE e4 rs429358 SNP and the hippocampus region of the brain. They both are Alzheimer's disease related biomarkers, indicating the potential and power of the non-convex methods in brain imaging genetics.

  19. Networking in autism: leveraging genetic, biomarker and model system findings in the search for new treatments.

    Science.gov (United States)

    Veenstra-VanderWeele, Jeremy; Blakely, Randy D

    2012-01-01

    Autism Spectrum Disorder (ASD) is a common neurodevelopmental disorder affecting approximately 1% of children. ASD is defined by core symptoms in two domains: negative symptoms of impairment in social and communication function, and positive symptoms of restricted and repetitive behaviors. Available treatments are inadequate for treating both core symptoms and associated conditions. Twin studies indicate that ASD susceptibility has a large heritable component. Genetic studies have identified promising leads, with converging insights emerging from single-gene disorders that bear ASD features, with particular interest in mammalian target of rapamycin (mTOR)-linked synaptic plasticity mechanisms. Mouse models of these disorders are revealing not only opportunities to model behavioral perturbations across species, but also evidence of postnatal rescue of brain and behavioral phenotypes. An intense search for ASD biomarkers has consistently pointed to elevated platelet serotonin (5-HT) levels and a surge in brain growth in the first 2 years of life. Following a review of the diversity of ASD phenotypes and its genetic origins and biomarkers, we discuss opportunities for translation of these findings into novel ASD treatments, focusing on mTor- and 5-HT-signaling pathways, and their possible intersection. Paralleling the progress made in understanding the root causes of rare genetic syndromes that affect cognitive development, we anticipate progress in models systems using bona fide ASD-associated molecular changes that have the potential to accelerate the development of ASD diagnostics and therapeutics.

  20. The Potential of Zebrafish as a Model Organism for Improving the Translation of Genetic Anticancer Nanomedicines

    Directory of Open Access Journals (Sweden)

    C Gutiérrez-Lovera

    2017-11-01

    Full Text Available In the last few decades, the field of nanomedicine applied to cancer has revolutionized cancer treatment: several nanoformulations have already reached the market and are routinely being used in the clinical practice. In the case of genetic nanomedicines, i.e., designed to deliver gene therapies to cancer cells for therapeutic purposes, advances have been less impressive. This is because of the many barriers that limit the access of the therapeutic nucleic acids to their target site, and the lack of models that would allow for an improvement in the understanding of how nanocarriers can be tailored to overcome them. Zebrafish has important advantages as a model species for the study of anticancer therapies, and have a lot to offer regarding the rational development of efficient delivery of genetic nanomedicines, and hence increasing the chances of their successful translation. This review aims to provide an overview of the recent advances in the development of genetic anticancer nanomedicines, and of the zebrafish models that stand as promising tools to shed light on their mechanisms of action and overall potential in oncology.

  1. An Adaptive Agent-Based Model of Homing Pigeons: A Genetic Algorithm Approach

    Directory of Open Access Journals (Sweden)

    Francis Oloo

    2017-01-01

    Full Text Available Conventionally, agent-based modelling approaches start from a conceptual model capturing the theoretical understanding of the systems of interest. Simulation outcomes are then used “at the end” to validate the conceptual understanding. In today’s data rich era, there are suggestions that models should be data-driven. Data-driven workflows are common in mathematical models. However, their application to agent-based models is still in its infancy. Integration of real-time sensor data into modelling workflows opens up the possibility of comparing simulations against real data during the model run. Calibration and validation procedures thus become automated processes that are iteratively executed during the simulation. We hypothesize that incorporation of real-time sensor data into agent-based models improves the predictive ability of such models. In particular, that such integration results in increasingly well calibrated model parameters and rule sets. In this contribution, we explore this question by implementing a flocking model that evolves in real-time. Specifically, we use genetic algorithms approach to simulate representative parameters to describe flight routes of homing pigeons. The navigation parameters of pigeons are simulated and dynamically evaluated against emulated GPS sensor data streams and optimised based on the fitness of candidate parameters. As a result, the model was able to accurately simulate the relative-turn angles and step-distance of homing pigeons. Further, the optimised parameters could replicate loops, which are common patterns in flight tracks of homing pigeons. Finally, the use of genetic algorithms in this study allowed for a simultaneous data-driven optimization and sensitivity analysis.

  2. Models for Estimating Genetic Parameters of Milk Production Traits Using Random Regression Models in Korean Holstein Cattle

    Directory of Open Access Journals (Sweden)

    C. I. Cho

    2016-05-01

    Full Text Available The objectives of the study were to estimate genetic parameters for milk production traits of Holstein cattle using random regression models (RRMs, and to compare the goodness of fit of various RRMs with homogeneous and heterogeneous residual variances. A total of 126,980 test-day milk production records of the first parity Holstein cows between 2007 and 2014 from the Dairy Cattle Improvement Center of National Agricultural Cooperative Federation in South Korea were used. These records included milk yield (MILK, fat yield (FAT, protein yield (PROT, and solids-not-fat yield (SNF. The statistical models included random effects of genetic and permanent environments using Legendre polynomials (LP of the third to fifth order (L3–L5, fixed effects of herd-test day, year-season at calving, and a fixed regression for the test-day record (third to fifth order. The residual variances in the models were either homogeneous (HOM or heterogeneous (15 classes, HET15; 60 classes, HET60. A total of nine models (3 orders of polynomials×3 types of residual variance including L3-HOM, L3-HET15, L3-HET60, L4-HOM, L4-HET15, L4-HET60, L5-HOM, L5-HET15, and L5-HET60 were compared using Akaike information criteria (AIC and/or Schwarz Bayesian information criteria (BIC statistics to identify the model(s of best fit for their respective traits. The lowest BIC value was observed for the models L5-HET15 (MILK; PROT; SNF and L4-HET15 (FAT, which fit the best. In general, the BIC values of HET15 models for a particular polynomial order was lower than that of the HET60 model in most cases. This implies that the orders of LP and types of residual variances affect the goodness of models. Also, the heterogeneity of residual variances should be considered for the test-day analysis. The heritability estimates of from the best fitted models ranged from 0.08 to 0.15 for MILK, 0.06 to 0.14 for FAT, 0.08 to 0.12 for PROT, and 0.07 to 0.13 for SNF according to days in milk of first

  3. Optimization of Catalytic Ozonation Process for Formaldehyde Mineralization from Synthetic Wastewater by Fe/MgO Nanoparticles Synthesis by Sol-Gel Method by Response Surface Model

    Directory of Open Access Journals (Sweden)

    Ghorban Asgari

    2014-09-01

    Full Text Available Background: Design experiment stages of formalin mineralization process by center composition design (CCD cause ease of work, reducing the number of samples, increasing the accuracy of optimized conditions and the interaction parameters determined during the process. The aim of this study was optimization of catalytic ozonation process for formaldehyde mineralization from synthetic wastewater by Fe/MgO nanoparticles synthesis by sol-gel method by response surface model. Methods: This experimental study was conducted in a semi-batch reactor, using a RSM by taking 3 factors in the final stage of pH (7-9, reaction time (10-20 min and catalyst dose (1.1-1.3 g/L was investigated. Synthesis of nanoparticles was done by sol-gel method. The results were analyzed by Design Expert 7.0.1 software. Results: The results showed that the process was dependent on the parameters studied and changing each parameter, affected the process efficiency and other parameters. The optimum conditions predicted for the process was 86.51% of mineralization efficiency. Optimum condition included pH=8.82, reaction time of 20 minute and catalyst dose of 1.3 g/L. The correlation coefficient for the process was determined 0.91. Conclusion: Using a statistical model could reduce the number of experiments, the accuracy and the prediction process. The catalytic ozonation process has the ability to remove formaldehyde with high efficiency and the process was environmental friendly.

  4. The Analysis of Pricing Power of Preponderant Metal Mineral Resources under the Perspective of Intergenerational Equity and Social Preferences: An Analytical Framework Based on Cournot Equilibrium Model

    Directory of Open Access Journals (Sweden)

    Meirui Zhong

    2014-01-01

    Full Text Available This paper combines intergenerational equity equilibrium and social preferences equilibrium with Cournot equilibrium solving the technological problem of intergenerational equity and strategic value compensation confirmation, achieving the effective combination between sustainable development concept and value evaluation, thinking and expanding the theoretical framework for the lack of pricing power of mineral resources. The conclusion of the theoretical model and the numerical simulation shows that intergenerational equity equilibrium and social preferences equilibrium enhance international trade market power of preponderant metal mineral resources owing to the production of intergenerational equity compensation value and strategic value. However, the impact exerted on Cournot market power by social preferences is inconsistent: that is, changes of altruistic Cournot equilibrium and reciprocal inequity Cournot equilibrium are consistent, while inequity aversion Cournot equilibrium has the characteristic of loss aversion, namely, under the consideration of inequity aversion Cournot competition, Counot-Nash equilibrium transforms monotonically with sympathy and jealousy of inequity aversion.

  5. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma.

    Science.gov (United States)

    McFadden, David G; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K; Song, Xiaoling; Pirun, Mono; Santiago, Philip M; Kim-Kiselak, Caroline; Platt, James T; Lee, Emily; Hodges, Emily; Rosebrock, Adam P; Bronson, Roderick T; Socci, Nicholas D; Hannon, Gregory J; Jacks, Tyler; Varmus, Harold

    2016-10-18

    Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity.

  6. Mutational landscape of EGFR-, MYC-, and Kras-driven genetically engineered mouse models of lung adenocarcinoma

    Science.gov (United States)

    McFadden, David G.; Politi, Katerina; Bhutkar, Arjun; Chen, Frances K.; Song, Xiaoling; Pirun, Mono; Santiago, Philip M.; Kim-Kiselak, Caroline; Platt, James T.; Lee, Emily; Hodges, Emily; Rosebrock, Adam P.; Bronson, Roderick T.; Socci, Nicholas D.; Hannon, Gregory J.; Jacks, Tyler; Varmus, Harold

    2016-01-01

    Genetically engineered mouse models (GEMMs) of cancer are increasingly being used to assess putative driver mutations identified by large-scale sequencing of human cancer genomes. To accurately interpret experiments that introduce additional mutations, an understanding of the somatic genetic profile and evolution of GEMM tumors is necessary. Here, we performed whole-exome sequencing of tumors from three GEMMs of lung adenocarcinoma driven by mutant epidermal growth factor receptor (EGFR), mutant Kirsten rat sarcoma viral oncogene homolog (Kras), or overexpression of MYC proto-oncogene. Tumors from EGFR- and Kras-driven models exhibited, respectively, 0.02 and 0.07 nonsynonymous mutations per megabase, a dramatically lower average mutational frequency than observed in human lung adenocarcinomas. Tumors from models driven by strong cancer drivers (mutant EGFR and Kras) harbored few mutations in known cancer genes, whereas tumors driven by MYC, a weaker initiating oncogene in the murine lung, acquired recurrent clonal oncogenic Kras mutations. In addition, although EGFR- and Kras-driven models both exhibited recurrent whole-chromosome DNA copy number alterations, the specific chromosomes altered by gain or loss were different in each model. These data demonstrate that GEMM tumors exhibit relatively simple somatic genotypes compared with human cancers of a similar type, making these autochthonous model systems useful for additive engineering approaches to assess the potential of novel mutations on tumorigenesis, cancer progression, and drug sensitivity. PMID:27702896

  7. Accounting for particle non-sphericity in modeling of mineral dust radiative properties in the thermal infrared

    International Nuclear Information System (INIS)

    Legrand, M.; Dubovik, O.; Lapyonok, T.; Derimian, Y.

    2014-01-01

    Spectral radiative parameters (extinction optical depth, single scattering albedo, asymmetry factor) of spheroids of mineral dust composed of quartz and clays have been simulated at wavelengths between 7.0 and 10.2 µm using a T-matrix code. In spectral intervals with high values of complex index of refraction and for large particles, the parameters cannot be fully calculated with the code. Practically, the calculations are stopped at a truncation radius over which the particles contribution cannot thus be taken into account. To deal with this issue, we have developed and applied an accurate corrective technique of T-matrix Size Truncation Compensation (TSTC). For a mineral dust described by its AERONET standard aspect ratio (AR) distribution, the full error margin when applying the TSTC is within 0.3% (or ±0.15%), whatever the radiative parameter and the wavelength considered, for quartz (the most difficult case). Large AR values limit also the possibilities of calculation with the code. The TSTC has been able to complete the calculations of the T-matrix code for a modified AERONET AR distribution with a maximum AR of 4.7 instead of 3 for the standard distribution. Comparison between the simulated properties of spheroids and of spheres of same volume confirms, in agreement with the literature, that significant differences are observed in the vicinity of the mineral resonant peaks (λ ca. 8.3–8.7 µm for quartz, ca. 9.3–9.5 µm for clays) and that they are due to absorption by the small particles. This is a favorable circumstance for the TSTC, which is concerned with the contribution of the largest particles. This technique of numerical calculation improves the accuracy of the simulated radiative parameters of mineral dust, which must lead to a progress in view of applications such as remote sensing or determination of energy balance of dust in the thermal infrared (TIR), incompletely investigated so far. - Highlights: • Completion of computation of mineral

  8. Human Urine-Derived Renal Progenitors for Personalized Modeling of Genetic Kidney Disorders.

    Science.gov (United States)

    Lazzeri, Elena; Ronconi, Elisa; Angelotti, Maria Lucia; Peired, Anna; Mazzinghi, Benedetta; Becherucci, Francesca; Conti, Sara; Sansavini, Giulia; Sisti, Alessandro; Ravaglia, Fiammetta; Lombardi, Duccio; Provenzano, Aldesia; Manonelles, Anna; Cruzado, Josep M; Giglio, Sabrina; Roperto, Rosa Maria; Materassi, Marco; Lasagni, Laura; Romagnani, Paola

    2015-08-01

    The critical role of genetic and epigenetic factors in the pathogenesis of kidney disorders is gradually becoming clear, and the need for disease models that recapitulate human kidney disorders in a personalized manner is paramount. In this study, we describe a method to select and amplify renal progenitor cultures from the urine of patients with kidney disorders. Urine-derived human renal progenitors exhibited phenotype and functional properties identical to those purified from kidney tissue, including the capacity to differentiate into tubular cells and podocytes, as demonstrated by confocal microscopy, Western blot analysis of podocyte-specific proteins, and scanning electron microscopy. Lineage tracing studies performed with conditional transgenic mice, in which podocytes are irreversibly tagged upon tamoxifen treatment (NPHS2.iCreER;mT/mG), that were subjected to doxorubicin nephropathy demonstrated that renal progenitors are the only urinary cell population that can be amplified in long-term culture. To validate the use of these cells for personalized modeling of kidney disorders, renal progenitors were obtained from (1) the urine of children with nephrotic syndrome and carrying potentially pathogenic mutations in genes encoding for podocyte proteins and (2) the urine of children without genetic alterations, as validated by next-generation sequencing. Renal progenitors obtained from patients carrying pathogenic mutations generated podocytes that exhibited an abnormal cytoskeleton structure and functional abnormalities compared with those obtained from patients with proteinuria but without genetic mutations. The results of this study demonstrate that urine-derived patient-specific renal progenitor cultures may be an innovative research tool for modeling of genetic kidney disorders. Copyright © 2015 by the American Society of Nephrology.

  9. Fatal Prion Disease in a Mouse Model of Genetic E200K Creutzfeldt-Jakob Disease

    Science.gov (United States)

    Friedman-Levi, Yael; Meiner, Zeev; Canello, Tamar; Frid, Kati; Kovacs, Gabor G.; Budka, Herbert; Avrahami, Dana; Gabizon, Ruth

    2011-01-01

    Genetic prion diseases are late onset fatal neurodegenerative disorders linked to pathogenic mutations in the prion protein-encoding gene, PRNP. The most prevalent of these is the substitution of Glutamate for Lysine at codon 200 (E200K), causing genetic Creutzfeldt-Jakob disease (gCJD) in several clusters, including Jews of Libyan origin. Investigating the pathogenesis of genetic CJD, as well as developing prophylactic treatments for young asymptomatic carriers of this and other PrP mutations, may well depend upon the availability of appropriate animal models in which long term treatments can be evaluated for efficacy and toxicity. Here we present the first effective mouse model for E200KCJD, which expresses chimeric mouse/human (TgMHu2M) E199KPrP on both a null and a wt PrP background, as is the case for heterozygous patients and carriers. Mice from both lines suffered from distinct neurological symptoms as early as 5–6 month of age and deteriorated to death several months thereafter. Histopathological examination of the brain and spinal cord revealed early gliosis and age-related intraneuronal deposition of disease-associated PrP similarly to human E200K gCJD. Concomitantly we detected aggregated, proteinase K resistant, truncated and oxidized PrP forms on immunoblots. Inoculation of brain extracts from TgMHu2ME199K mice readily induced, the first time for any mutant prion transgenic model, a distinct fatal prion disease in wt mice. We believe that these mice may serve as an ideal platform for the investigation of the pathogenesis of genetic prion disease and thus for the monitoring of anti-prion treatments. PMID:22072968

  10. Fatal prion disease in a mouse model of genetic E200K Creutzfeldt-Jakob disease.

    Directory of Open Access Journals (Sweden)

    Yael Friedman-Levi

    2011-11-01

    Full Text Available Genetic prion diseases are late onset fatal neurodegenerative disorders linked to pathogenic mutations in the prion protein-encoding gene, PRNP. The most prevalent of these is the substitution of Glutamate for Lysine at codon 200 (E200K, causing genetic Creutzfeldt-Jakob disease (gCJD in several clusters, including Jews of Libyan origin. Investigating the pathogenesis of genetic CJD, as well as developing prophylactic treatments for young asymptomatic carriers of this and other PrP mutations, may well depend upon the availability of appropriate animal models in which long term treatments can be evaluated for efficacy and toxicity. Here we present the first effective mouse model for E200KCJD, which expresses chimeric mouse/human (TgMHu2M E199KPrP on both a null and a wt PrP background, as is the case for heterozygous patients and carriers. Mice from both lines suffered from distinct neurological symptoms as early as 5-6 month of age and deteriorated to death several months thereafter. Histopathological examination of the brain and spinal cord revealed early gliosis and age-related intraneuronal deposition of disease-associated PrP similarly to human E200K gCJD. Concomitantly we detected aggregated, proteinase K resistant, truncated and oxidized PrP forms on immunoblots. Inoculation of brain extracts from TgMHu2ME199K mice readily induced, the first time for any mutant prion transgenic model, a distinct fatal prion disease in wt mice. We believe that these mice may serve as an ideal platform for the investigation of the pathogenesis of genetic prion disease and thus for the monitoring of anti-prion treatments.

  11. lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals.

    Science.gov (United States)

    Ziyatdinov, Andrey; Vázquez-Santiago, Miquel; Brunel, Helena; Martinez-Perez, Angel; Aschard, Hugues; Soria, Jose Manuel

    2018-02-27

    Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by modeling such correlations as random effects in linear mixed models (LMMs). The R package lme4 is a well-established tool that implements major LMM features using sparse matrix methods; however, it is not fully adapted for QTL mapping association and linkage studies. In particular, two LMM features are lacking in the base version of lme4: the definition of random effects by custom covariance matrices; and parameter constraints, which are essential in advanced QTL models. Apart from applications in linkage studies of related individuals, such functionalities are of high interest for association studies in situations where multiple covariance matrices need to be modeled, a scenario not covered by many genome-wide association study (GWAS) software. To address the aforementioned limitations, we developed a new R package lme4qtl as an extension of lme4. First, lme4qtl contributes new models for genetic studies within a single tool integrated with lme4 and its companion packages. Second, lme4qtl offers a flexible framework for scenarios with multiple levels of relatedness and becomes efficient when covariance matrices are sparse. We showed the value of our package using real family-based data in the Genetic Analysis of Idiopathic Thrombophilia 2 (GAIT2) project. Our software lme4qtl enables QTL mapping models with a versatile structure of random effects and efficient computation for sparse covariances. lme4qtl is available at https://github.com/variani/lme4qtl .

  12. Genetic parameters for body condition score, body weight, milk yield, and fertility estimated using random regression models.

    Science.gov (United States)

    Berry, D P; Buckley, F; Dillon, P; Evans, R D; Rath, M; Veerkamp, R F

    2003-11-01

    Genetic (co)variances between body condition score (BCS), body weight (BW), milk yield, and fertility were estimated using a random regression animal model extended to multivariate analysis. The data analyzed included 81,313 BCS observations, 91,937 BW observations, and 100,458 milk test-day yields from 8725 multiparous Holstein-Friesian cows. A cubic random regression was sufficient to model the changing genetic variances for BCS, BW, and milk across different days in milk. The genetic correlations between BCS and fertility changed little over the lactation; genetic correlations between BCS and interval to first service and between BCS and pregnancy rate to first service varied from -0.47 to -0.31, and from 0.15 to 0.38, respectively. This suggests that maximum genetic gain in fertility from indirect selection on BCS should be based on measurements taken in midlactation when the genetic variance for BCS is largest. Selection for increased BW resulted in shorter intervals to first service, but more services and poorer pregnancy rates; genetic correlations between BW and pregnancy rate to first service varied from -0.52 to -0.45. Genetic selection for higher lactation milk yield alone through selection on increased milk yield in early lactation is likely to have a more deleterious effect on genetic merit for fertility than selection on higher milk yield in late lactation.

  13. Distinct virulence of Rift Valley fever phlebovirus strains from different genetic lineages in a mouse model.

    Directory of Open Access Journals (Sweden)

    Tetsuro Ikegami

    Full Text Available Rift Valley fever phlebovirus (RVFV causes high rates of abortions and fetal malformations in ruminants, and hemorrhagic fever, encephalitis, or blindness in humans. Viral transmission occurs via mosquito vectors in endemic areas, which necessitates regular vaccination of susceptible livestock animals to prevent the RVF outbreaks. Although ZH501 strain has been used as a challenge strain for past vaccine efficacy studies, further characterization of other RVFV strains is important to optimize ruminant and nonhuman primate RVFV challenge models. This study aimed to characterize the virulence of wild-type RVFV strains belonging to different genetic lineages in outbred CD1 mice. Mice were intraperitoneally infected with 1x103 PFU of wild-type ZH501, Kenya 9800523, Kenya 90058, Saudi Arabia 200010911, OS1, OS7, SA75, Entebbe, or SA51 strains. Among them, mice infected with SA51, Entebbe, or OS7 strain showed rapid dissemination of virus in livers and peracute necrotic hepatitis at 2-3 dpi. Recombinant SA51 (rSA51 and Zinga (rZinga strains were recovered by reverse genetics, and their virulence was also tested in CD1 mice. The rSA51 strain reproduced peracute RVF disease in mice, whereas the rZinga strain showed a similar virulence with that of rZH501 strain. This study showed that RVFV strains in different genetic lineages display distinct virulence in outbred mice. Importantly, since wild-type RVFV strains contain defective-interfering RNA or various genetic subpopulations during passage from original viral isolations, recombinant RVFV strains generated by reverse genetics will be better suitable for reproducible challenge studies for vaccine development as well as pathological studies.

  14. Energy sorghum--a genetic model for the design of C4 grass bioenergy crops.

    Science.gov (United States)

    Mullet, John; Morishige, Daryl; McCormick, Ryan; Truong, Sandra; Hilley, Josie; McKinley, Brian; Anderson, Robert; Olson, Sara N; Rooney, William

    2014-07-01

    Sorghum is emerging as an excellent genetic model for the design of C4 grass bioenergy crops. Annual energy Sorghum hybrids also serve as a source of biomass for bioenergy production. Elucidation of Sorghum's flowering time gene regulatory network, and identification of complementary alleles for photoperiod sensitivity, enabled large-scale generation of energy Sorghum hybrids for testing and commercial use. Energy Sorghum hybrids with long vegetative growth phases were found to accumulate more than twice as much biomass as grain Sorghum, owing to extended growing seasons, greater light interception, and higher radiation use efficiency. High biomass yield, efficient nitrogen recycling, and preferential accumulation of stem biomass with low nitrogen content contributed to energy Sorghum's elevated nitrogen use efficiency. Sorghum's integrated genetics-genomics-breeding platform, diverse germplasm, and the opportunity for annual testing of new genetic designs in controlled environments and in multiple field locations is aiding fundamental discovery, and accelerating the improvement of biomass yield and optimization of composition for biofuels production. Recent advances in wide hybridization between Sorghum and other C4 grasses could allow the deployment of improved genetic designs of annual energy Sorghums in the form of wide-hybrid perennial crops. The current trajectory of energy Sorghum genetic improvement indicates that it will be possible to sustainably produce biofuels from C4 grass bioenergy crops that are cost competitive with petroleum-based transportation fuels. © The Author 2014. Published by Oxford University Press on behalf of the Society for Experimental Biology. All rights reserved. For permissions, please email: journals.permissions@oup.com.

  15. GSEVM v.2: MCMC software to analyse genetically structured environmental variance models

    DEFF Research Database (Denmark)

    Ibáñez-Escriche, N; Garcia, M; Sorensen, D

    2010-01-01

    This note provides a description of software that allows to fit Bayesian genetically structured variance models using Markov chain Monte Carlo (MCMC). The gsevm v.2 program was written in Fortran 90. The DOS and Unix executable programs, the user's guide, and some example files are freely available...... for research purposes at http://www.bdporc.irta.es/estudis.jsp. The main feature of the program is to compute Monte Carlo estimates of marginal posterior distributions of parameters of interest. The program is quite flexible, allowing the user to fit a variety of linear models at the level of the mean...

  16. Genetic Algorithms for Agent-Based Infrastructure Interdependency Modeling and Analysis

    Energy Technology Data Exchange (ETDEWEB)

    May Permann

    2007-03-01

    Today’s society relies greatly upon an array of complex national and international infrastructure networks such as transportation, electric power, telecommunication, and financial networks. This paper describes initial research combining agent-based infrastructure modeling software and genetic algorithms (GAs) to help optimize infrastructure protection and restoration decisions. This research proposes to apply GAs to the problem of infrastructure modeling and analysis in order to determine the optimum assets to restore or protect from attack or other disaster. This research is just commencing and therefore the focus of this paper is the integration of a GA optimization method with a simulation through the simulation’s agents.

  17. Using genetic algorithms for calibrating simplified models of nuclear reactor dynamics

    International Nuclear Information System (INIS)

    Marseguerra, Marzio; Zio, Enrico; Canetta, Raffaele

    2004-01-01

    In this paper the use of genetic algorithms for the estimation of the effective parameters of a model of nuclear reactor dynamics is investigated. The calibration of the effective parameters is achieved by best fitting the model responses of the quantities of interest (e.g., reactor power, average fuel and coolant temperatures) to the actual evolution profiles, here simulated by the Quandry based reactor kinetics (Quark) code available from the Nuclear Energy Agency. Alternative schemes of single- and multi-objective optimization are investigated. The efficiency of convergence of the algorithm with respect to the different effective parameters to be calibrated is studied with reference to the physical relationships involved