WorldWideScience

Sample records for background modifies phenotypes

  1. Destabilizing protein polymorphisms in the genetic background direct phenotypic expression of mutant SOD1 toxicity.

    Directory of Open Access Journals (Sweden)

    Tali Gidalevitz

    2009-03-01

    Full Text Available Genetic background exerts a strong modulatory effect on the toxicity of aggregation-prone proteins in conformational diseases. In addition to influencing the misfolding and aggregation behavior of the mutant proteins, polymorphisms in putative modifier genes may affect the molecular processes leading to the disease phenotype. Mutations in SOD1 in a subset of familial amyotrophic lateral sclerosis (ALS cases confer dominant but clinically variable toxicity, thought to be mediated by misfolding and aggregation of mutant SOD1 protein. While the mechanism of toxicity remains unknown, both the nature of the SOD1 mutation and the genetic background in which it is expressed appear important. To address this, we established a Caenorhabditis elegans model to systematically examine the aggregation behavior and genetic interactions of mutant forms of SOD1. Expression of three structurally distinct SOD1 mutants in C. elegans muscle cells resulted in the appearance of heterogeneous populations of aggregates and was associated with only mild cellular dysfunction. However, introduction of destabilizing temperature-sensitive mutations into the genetic background strongly enhanced the toxicity of SOD1 mutants, resulting in exposure of several deleterious phenotypes at permissive conditions in a manner dependent on the specific SOD1 mutation. The nature of the observed phenotype was dependent on the temperature-sensitive mutation present, while its penetrance reflected the specific combination of temperature-sensitive and SOD1 mutations. Thus, the specific toxic phenotypes of conformational disease may not be simply due to misfolding/aggregation toxicity of the causative mutant proteins, but may be defined by their genetic interactions with cellular pathways harboring mildly destabilizing missense alleles.

  2. Hand Gesture Recognition Using Modified 1$ and Background Subtraction Algorithms

    Directory of Open Access Journals (Sweden)

    Hazem Khaled

    2015-01-01

    Full Text Available Computers and computerized machines have tremendously penetrated all aspects of our lives. This raises the importance of Human-Computer Interface (HCI. The common HCI techniques still rely on simple devices such as keyboard, mice, and joysticks, which are not enough to convoy the latest technology. Hand gesture has become one of the most important attractive alternatives to existing traditional HCI techniques. This paper proposes a new hand gesture detection system for Human-Computer Interaction using real-time video streaming. This is achieved by removing the background using average background algorithm and the 1$ algorithm for hand’s template matching. Then every hand gesture is translated to commands that can be used to control robot movements. The simulation results show that the proposed algorithm can achieve high detection rate and small recognition time under different light changes, scales, rotation, and background.

  3. The NMBU Phenotyping Robot; A Modified Version of Thorvald

    OpenAIRE

    Skattum, Kristine

    2017-01-01

    Soil compaction is a big problem in farming industry. This is why Pål Johan From in 2014, along with four master students, designed and built the agricultural robot Thorvald I. A light weighted robot that avoids soil compaction. Two years later, a new team of master students designed and built Thorvald II, where the goal was to make the robot module based. The modularity formed the basis of this thesis, where the goal was to design a modified version of Thorvald. The modified robot is ord...

  4. Genetic background of nonmutant Piebald-Virol-Glaxo rats does not influence nephronophthisis phenotypes

    Directory of Open Access Journals (Sweden)

    Yengkopiong JP

    2013-02-01

    Full Text Available Jada Pasquale Yengkopiong, Joseph Daniel Wani LakoJohn Garang Memorial University of Science and Technology, Faculty of Science and Technology, Bor, Jonglei State, Republic of South SudanBackground: Nephronophthisis (NPHP, which affects multiple organs, is a hereditary cystic kidney disease (CKD, characterized by interstitial fibrosis and numerous fluid-filled cysts in the kidneys. It is caused by mutations in NPHP genes, which encode for ciliary proteins known as nephrocystins. The disorder affects many people across the world and leads to end-stage renal disease. The aim of this study was to determine if the genetic background of the nonmutant female Piebald-Virol-Glaxo (PVG/Seac-/- rat influences phenotypic inheritance of NPHP from mutant male Lewis polycystic kidney rats.Methods: Mating experiments were performed between mutant Lewis polycystic kidney male rats with CKD and nonmutant PVG and Wistar Kyoto female rats without cystic kidney disease to raise second filial and backcross 1 progeny, respectively. Rats that developed cystic kidneys were identified. Systolic blood pressure was determined in each rat at 12 weeks of age using the tail and cuff method. After euthanasia, blood samples were collected and chemistry was determined. Histological examination of the kidneys, pancreas, and liver of rats with and without cystic kidney disease was performed.Results: It was established that the genetic background of nonmutant female PVG rats did not influence the phenotypic inheritance of the CKD from mutant male Lewis polycystic kidney rats. The disease arose as a result of a recessive mutation in a single gene (second filial generation, CKD = 13, non-CKD = 39, Χ2 = 0.00, P ≥ 0.97; backcross 1 generation, CKD = 67, non-CKD = 72, Χ2 = 0.18, P > 0.05 and inherited as NPHP. The rats with CKD developed larger fluid-filled cystic kidneys, higher systolic blood pressure, and anemia, but there were no extrarenal cysts and disease did not lead to

  5. The expression of HSP in human skeletal muscle. Effects of muscle fiber phenotype and training background

    DEFF Research Database (Denmark)

    Folkesson, Mattias; Mackey, Abigail L; Langberg, Henning

    2013-01-01

    AIM: Exercise-induced adaptations of skeletal muscle are related to training mode and can be muscle fibre type specific. This study aimed to investigate heat shock protein expression in type I and type II muscle fibres in resting skeletal muscle of subjects with different training backgrounds...... myosin heavy chain I and IIA, αB-crystallin, HSP27, HSP60 and HSP70. RESULTS: In ACT and RES, but not in END, a fibre type specific expression with higher staining intensity in type I than type II fibres was seen for αB-crystallin. The opposite (II>I) was found for HSP27 in subjects from ACT (6 of 12...... HSPs in human skeletal muscle is influenced by muscle fibre phenotype. The fibre type specific expression of HSP70 is influenced by resistance and endurance training whereas those of αB-crystallin and HSP27 are influenced only by endurance training suggesting the existence of a training...

  6. MutLα Heterodimers Modify the Molecular Phenotype of Friedreich Ataxia

    Science.gov (United States)

    Ezzatizadeh, Vahid; Sandi, Chiranjeevi; Sandi, Madhavi; Anjomani-Virmouni, Sara; Al-Mahdawi, Sahar; Pook, Mark A.

    2014-01-01

    Background Friedreich ataxia (FRDA), the most common autosomal recessive ataxia disorder, is caused by a dynamic GAA repeat expansion mutation within intron 1 of FXN gene, resulting in down-regulation of frataxin expression. Studies of cell and mouse models have revealed a role for the mismatch repair (MMR) MutS-heterodimer complexes and the PMS2 component of the MutLα complex in the dynamics of intergenerational and somatic GAA repeat expansions: MSH2, MSH3 and MSH6 promote GAA repeat expansions, while PMS2 inhibits GAA repeat expansions. Methodology/Principal Findings To determine the potential role of the other component of the MutLα complex, MLH1, in GAA repeat instability in FRDA, we have analyzed intergenerational and somatic GAA repeat expansions from FXN transgenic mice that have been crossed with Mlh1 deficient mice. We find that loss of Mlh1 activity reduces both intergenerational and somatic GAA repeat expansions. However, we also find that loss of either Mlh1 or Pms2 reduces FXN transcription, suggesting different mechanisms of action for Mlh1 and Pms2 on GAA repeat expansion dynamics and regulation of FXN transcription. Conclusions/Significance Both MutLα components, PMS2 and MLH1, have now been shown to modify the molecular phenotype of FRDA. We propose that upregulation of MLH1 or PMS2 could be potential FRDA therapeutic approaches to increase FXN transcription. PMID:24971578

  7. Color Mixing Correction for Post-printed Patterns on Colored Background Using Modified Particle Density Model

    OpenAIRE

    Suwa , Misako; Fujimoto , Katsuhito

    2006-01-01

    http://www.suvisoft.com; Color mixing occurs between background and foreground colors when a pattern is post-printed on a colored area because ink is not completely opaque. This paper proposes a new method for the correction of color mixing in line pattern such as characters and stamps, by using a modified particle density model. Parameters of the color correction can be calculated from two sets of foreground and background colors. By employing this method, the colors of foreground patterns o...

  8. Determinants and modifiers of bleeding phenotypes in haemophilia-A: General and tropical perspectives

    Directory of Open Access Journals (Sweden)

    Umma A. Ibrahim

    2018-07-01

    Full Text Available Haemophilia-A is an X-linked recessive bleeding disorder characterized by deficiency of FVIII. Although severity of haemophilia is largely determined by the extent to which different mutations abolish FVIII production, the overall phenotypic variations among haemophiliacs is determined by a combination of several other factors, which range from general to tropical factors on the one hand, and from genetic to immunologic and infective factors on the other hand. Determinants and modifiers of haemophilic bleeding phenotypes are important predictors of prognosis. However, tropical determinants of haemophilic bleeding phenotypes are virtually ignored because majority of haemophilia research originated from developed non-tropical countries. The aim of this paper is to present a balanced review of the haemophilic bleeding phenotypes from general and tropical perspectives. Hence, we present a concisely updated comprehensive review of the pathophysiologic and clinical significance of general vis-à-vis tropical determinants and modifiers of haemophilic bleeding phenotypes from genetic, immunologic and infective perspectives. Understanding of general phenotypic determinants such as FVIII gene mutations, immunological (inhibitors and infective (e.g. hepatitis and HIV complications, classical thrombophilias (e.g. FV-Leiden and non-classical thrombophilias (e.g. non-O blood groups will throw more light into the mechanisms by which some tropical prothrombotic gene mutations (such as sickle β-globin gene and certain chronic tropical pro-haemorrhagic parasitic infections (such as urinary and gastrointestinal helminthiasis may modify frequency, intensity and pattern of bleeding among haemophiliacs in the tropics. The clinical significance of iron deficiency within the context of helminthiasis and haemophilia is also reviewed. More research is needed to determine the precise effect of non-classical thrombophilias such as sickling disorders and ABO blood groups

  9. Quantitative analysis of planar technetium-99m-sestamibi myocardial perfusion images using modified background subtraction

    International Nuclear Information System (INIS)

    Koster, K.; Wackers, F.J.; Mattera, J.A.; Fetterman, R.C.

    1990-01-01

    Standard interpolative background subtraction, as used for thallium-201 ( 201 Tl), may create artifacts when applied to planar technetium-99m-Sestamibi ( 99m Tc-Sestamibi) images, apparently because of the oversubtraction of relatively high extra-cardiac activity. A modified background subtraction algorithm was developed and compared to standard background subtraction in 16 patients who had both exercise-delayed 201 Tl and exercise-rest 99m Tc-Sestamibi imaging. Furthermore, a new normal data base was generated. Normal 99m Tc-Sestamibi distribution was slightly different compared to 201 Tl. Using standard background subtraction, mean defect reversibility was significantly underestimated by 99m Tc-Sestamibi compared to 201 Tl (2.8 +/- 4.9 versus -1.8 +/- 8.4, p less than 0.05). Using the modified background subtraction, mean defect reversibility on 201 Tl and 99m Tc-Sestamibi images was comparable (2.8 +/- 4.9 versus 1.7 +/- 5.2, p = NS). We conclude, that for quantification of 99m Tc-Sestamibi images a new normal data base, as well as a modification of the interpolative background subtraction method should be employed to obtain quantitative results comparable to those with 201 Tl

  10. Phenotype-Based Screening of Small Molecules to Modify Plant Cell Walls Using BY-2 Cells.

    Science.gov (United States)

    Okubo-Kurihara, Emiko; Matsui, Minami

    2018-01-01

    The plant cell wall is an important and abundant biomass with great potential for use as a modern recyclable resource. For effective utilization of this cellulosic biomass, its ability to degrade efficiently is key point. With the aim of modifying the cell wall to allow easy decomposition, we used chemical biological technology to alter its structure. As a first step toward evaluating the chemicals in the cell wall we employed a phenotype-based approach using high-throughput screening. As the plant cell wall is essential in determining cell morphology, phenotype-based screening is particularly effective in identifying compounds that bring about alterations in the cell wall. For rapid and reproducible screening, tobacco BY-2 cell is an excellent system in which to observe cell morphology. In this chapter, we provide a detailed chemical biological methodology for studying cell morphology using tobacco BY-2 cells.

  11. Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats

    NARCIS (Netherlands)

    Homberg, J.R.; Nijman, I.J.; Kuijpers, S.; Cuppen, E.

    2010-01-01

    BACKGROUND: Genetic variation in the regulatory region of the human serotonin transporter gene (SLC6A4) has been shown to affect brain functionality and personality. However, large heterogeneity in its biological effects is observed, which is at least partially due to genetic modifiers. To gain

  12. The Pleiotropic Phenotype of Apc Mutations in the Mouse: Allele Specificity and Effects of the Genetic Background

    Science.gov (United States)

    Halberg, Richard B.; Chen, Xiaodi; Amos-Landgraf, James M.; White, Alanna; Rasmussen, Kristin; Clipson, Linda; Pasch, Cheri; Sullivan, Ruth; Pitot, Henry C.; Dove, William F.

    2008-01-01

    Familial adenomatous polyposis (FAP) is a human cancer syndrome characterized by the development of hundreds to thousands of colonic polyps and extracolonic lesions including desmoid fibromas, osteomas, epidermoid cysts, and congenital hypertrophy of the pigmented retinal epithelium. Afflicted individuals are heterozygous for mutations in the APC gene. Detailed investigations of mice heterozygous for mutations in the ortholog Apc have shown that other genetic factors strongly influence the phenotype. Here we report qualitative and quantitative modifications of the phenotype of Apc mutants as a function of three genetic variables: Apc allele, p53 allele, and genetic background. We have found major differences between the Apc alleles Min and 1638N in multiplicity and regionality of intestinal tumors, as well as in incidence of extracolonic lesions. By contrast, Min mice homozygous for either of two different knockout alleles of p53 show similar phenotypic effects. These studies illustrate the classic principle that functional genetics is enriched by assessing penetrance and expressivity with allelic series. The mouse permits study of an allelic gene series on multiple genetic backgrounds, thereby leading to a better understanding of gene action in a range of biological processes. PMID:18723878

  13. A new mouse model for marfan syndrome presents phenotypic variability associated with the genetic background and overall levels of Fbn1 expression.

    Directory of Open Access Journals (Sweden)

    Bruno L Lima

    2010-11-01

    Full Text Available Marfan syndrome is an autosomal dominant disease of connective tissue caused by mutations in the fibrillin-1 encoding gene FBN1. Patients present cardiovascular, ocular and skeletal manifestations, and although being fully penetrant, MFS is characterized by a wide clinical variability both within and between families. Here we describe a new mouse model of MFS that recapitulates the clinical heterogeneity of the syndrome in humans. Heterozygotes for the mutant Fbn1 allele mgΔloxPneo, carrying the same internal deletion of exons 19-24 as the mgΔ mouse model, present defective microfibrillar deposition, emphysema, deterioration of aortic wall and kyphosis. However, the onset of a clinical phenotypes is earlier in the 129/Sv than in C57BL/6 background, indicating the existence of genetic modifiers of MFS between these two mouse strains. In addition, we characterized a wide clinical variability within the 129/Sv congenic heterozygotes, suggesting involvement of epigenetic factors in disease severity. Finally, we show a strong negative correlation between overall levels of Fbn1 expression and the severity of the phenotypes, corroborating the suggested protective role of normal fibrillin-1 in MFS pathogenesis, and supporting the development of therapies based on increasing Fbn1 expression.

  14. Identification of genetic modifiers of behavioral phenotypes in serotonin transporter knockout rats

    Directory of Open Access Journals (Sweden)

    Nijman Isaäc J

    2010-05-01

    Full Text Available Abstract Background Genetic variation in the regulatory region of the human serotonin transporter gene (SLC6A4 has been shown to affect brain functionality and personality. However, large heterogeneity in its biological effects is observed, which is at least partially due to genetic modifiers. To gain insight into serotonin transporter (SERT-specific genetic modifiers, we studied an intercross between the Wistar SERT-/- rat and the behaviorally and genetically divergent Brown Norway rat, and performed a QTL analysis. Results In a cohort of >150 intercross SERT-/- and control (SERT+/+ rats we characterized 12 traits that were previously associated with SERT deficiency, including activity, exploratory pattern, cocaine-induced locomotor activity, and abdominal and subcutaneous fat. Using 325 genetic markers, 10 SERT-/--specific quantitative trait loci (QTLs for parameters related to activity and exploratory pattern (Chr.1,9,11,14, and cocaine-induced anxiety and locomotor activity (Chr.5,8 were identified. No significant QTLs were found for fat parameters. Using in silico approaches we explored potential causal genes within modifier QTL regions and found interesting candidates, amongst others, the 5-HT1D receptor (Chr. 5, dopamine D2 receptor (Chr. 8, cannabinoid receptor 2 (Chr. 5, and genes involved in fetal development and plasticity (across chromosomes. Conclusions We anticipate that the SERT-/--specific QTLs may lead to the identification of new modulators of serotonergic signaling, which may be targets for pharmacogenetic and therapeutic approaches.

  15. Mediterranean Dietary Pattern Adherence Modify the Association between FTO Genetic Variations and Obesity Phenotypes

    Directory of Open Access Journals (Sweden)

    Firoozeh Hosseini-Esfahani

    2017-09-01

    Full Text Available There is increasing interest of which dietary patterns can modify the association of fat mass and obesity associated (FTO variants with obesity. This study was aimed at investigating the interaction of the Mediterranean dietary pattern (Med Diet with FTO polymorphisms in relation to obesity phenotypes. Subjects of this nested case-control study were selected from the Tehran Lipid and Glucose Study participants. Each case was individually matched with a normal weight control (n = 1254. Selected polymorphisms (rs1421085, rs1121980, rs17817449, rs8050136, rs9939973, and rs3751812 were genotyped. Genetic risk score (GRS were calculated using the weighted method. The Mediterranean dietary score (MDS was computed. Individuals with minor allele carriers of rs9939973, rs8050136, rs1781749, and rs3751812 had lower risk of obesity when they had higher MDS, compared to wild-type homozygote genotype carriers. The obesity risk was decreased across quartiles of MDS in participants with high GRS (OR: 1, 0.8, 0.79, 0.67 compared to individuals with low GRS (OR: 1.33, 1.06, 0.97, 1.12 (Pinteraction < 0.05. No significant interaction between the GRS and MDS on abdominal obesity was found. A higher Med Diet adherence was associated with lower obesity risk in subjects with more genetic predisposition to obesity, compared to those with lower adherence to the Med Diet and lower GRS.

  16. MutLα heterodimers modify the molecular phenotype of Friedreich ataxia.

    Directory of Open Access Journals (Sweden)

    Vahid Ezzatizadeh

    Full Text Available Friedreich ataxia (FRDA, the most common autosomal recessive ataxia disorder, is caused by a dynamic GAA repeat expansion mutation within intron 1 of FXN gene, resulting in down-regulation of frataxin expression. Studies of cell and mouse models have revealed a role for the mismatch repair (MMR MutS-heterodimer complexes and the PMS2 component of the MutLα complex in the dynamics of intergenerational and somatic GAA repeat expansions: MSH2, MSH3 and MSH6 promote GAA repeat expansions, while PMS2 inhibits GAA repeat expansions.To determine the potential role of the other component of the MutLα complex, MLH1, in GAA repeat instability in FRDA, we have analyzed intergenerational and somatic GAA repeat expansions from FXN transgenic mice that have been crossed with Mlh1 deficient mice. We find that loss of Mlh1 activity reduces both intergenerational and somatic GAA repeat expansions. However, we also find that loss of either Mlh1 or Pms2 reduces FXN transcription, suggesting different mechanisms of action for Mlh1 and Pms2 on GAA repeat expansion dynamics and regulation of FXN transcription.Both MutLα components, PMS2 and MLH1, have now been shown to modify the molecular phenotype of FRDA. We propose that upregulation of MLH1 or PMS2 could be potential FRDA therapeutic approaches to increase FXN transcription.

  17. Modified Carbapenem Inactivation Method for Phenotypic Detection of Carbapenemase Production among Enterobacteriaceae.

    Science.gov (United States)

    Pierce, Virginia M; Simner, Patricia J; Lonsway, David R; Roe-Carpenter, Darcie E; Johnson, J Kristie; Brasso, William B; Bobenchik, April M; Lockett, Zabrina C; Charnot-Katsikas, Angella; Ferraro, Mary Jane; Thomson, Richard B; Jenkins, Stephen G; Limbago, Brandi M; Das, Sanchita

    2017-08-01

    The ability of clinical microbiology laboratories to reliably detect carbapenemase-producing carbapenem-resistant Enterobacteriaceae (CP-CRE) is an important element of the effort to prevent and contain the spread of these pathogens and an integral part of antimicrobial stewardship. All existing methods have limitations. A new, straightforward, inexpensive, and specific phenotypic method for the detection of carbapenemase production, the carbapenem inactivation method (CIM), was recently described. Here we describe a two-stage evaluation of a modified carbapenem inactivation method (mCIM), in which tryptic soy broth was substituted for water during the inactivation step and the length of this incubation was extended. A validation study was performed in a single clinical laboratory to determine the accuracy of the mCIM, followed by a nine-laboratory study to verify the reproducibility of these results and define the zone size cutoff that best discriminated between CP-CRE and members of the family Enterobacteriaceae that do not produce carbapenemases. Bacterial isolates previously characterized through whole-genome sequencing or targeted PCR as to the presence or absence of carbapenemase genes were tested for carbapenemase production using the mCIM; isolates with Ambler class A, B, and D carbapenemases, non-CP-CRE isolates, and carbapenem-susceptible isolates were included. The sensitivity of the mCIM observed in the validation study was 99% (95% confidence interval [95% CI], 93% to 100%), and the specificity was 100% (95% CI, 82% to 100%). In the second stage of the study, the range of sensitivities observed across nine laboratories was 93% to 100%, with a mean of 97%; the range of specificities was 97% to 100%, with a mean of 99%. The mCIM was easy to perform and interpret for Enterobacteriaceae , with results in less than 24 h and excellent reproducibility across laboratories. Copyright © 2017 American Society for Microbiology.

  18. Identification of 16q21 as a modifier of nonsyndromic orofacial cleft phenotypes

    DEFF Research Database (Denmark)

    Carlson, Jenna C; Standley, Jennifer; Petrin, Aline

    2017-01-01

    Orofacial clefts (OFCs) are common, complex birth defects with extremely heterogeneous phenotypic presentations. Two common subtypes-cleft lip alone (CL) and CL plus cleft palate (CLP)-are typically grouped into a single phenotype for genetic analysis (i.e., CL with or without cleft palate, CL/P)...

  19. The effect of chemically modified alginates on macrophage phenotype and biomolecule transport.

    Science.gov (United States)

    Bygd, Hannah C; Bratlie, Kaitlin M

    2016-07-01

    Macrophage (MΦ) reprogramming has received significant attention in applications such as cancer therapeutics and tissue engineering where the host immune response to biomaterials is crucial in determining the success or failure of an implanted device. Polymeric systems can potentially be used to redirect infiltrating M1 MΦs toward a proangiogenic phenotype. This work exploits the concept of MΦ reprogramming in the engineering of materials for improving the longevity of tissue engineering scaffolds. We have investigated the effect of 13 different chemical modifications of alginate on MΦ phenotype. Markers of the M1 response-tumor necrosis factor-α (TNF-α) and inducible nitric oxide synthase-and the M2 response-arginase-were measured and used to determine the ability of the materials to alter MΦ phenotype. It was found that some modifications were able to reduce the pro-inflammatory response of M1 MΦs, others appeared to amplify the M2 phenotype, and the results for two materials suggested they were able to reprogram a MΦ population from M1 to M2. These findings were supplemented by studies done to examine the permselectivity of the materials. Diffusion of TNF-α was completely prevented through some of these materials, while up to 84% was found to diffuse through others. The diffusion of insulin through the materials was statistically consistent. These results suggest that the modification of these materials might alter mass transport in beneficial ways. The ability to control polarization of MΦ phenotypes with immunoprotective materials has the potential to augment the success of tissue engineering scaffolds. © 2016 Wiley Periodicals, Inc. J Biomed Mater Res Part A: 104A: 1707-1719, 2016. © 2016 Wiley Periodicals, Inc.

  20. Isotropic background for interacting two fluid scenario coupled with zero mass scalar field in modified gravity

    International Nuclear Information System (INIS)

    Chirde, V.R.; Shekh, S.H.

    2016-01-01

    The modified theories of gravity have engrossed much attention in the last decade, especially f(R) gravity. In this contextual exploration, we investigate interaction between barotropic fluid and dark energy with zero-mass scalar field for the spatially homogeneous and isotropic flat FRW universe. In this universe, the field equations correspond to the particular choice of f(R) = R+bR m . The exact solutions of the field equations are obtained by applying volumetric power law and exponential law of expansion. In power and exponential law of expansion, the universe shows both matter dominated and DE era for b ≤ 0 and b ≥ 0 and remain present in dark era respectively, but power law model is fully occupying with real matter for b > 0 and for b < 0 exponential model expands with negative pressure and remain present in matter dominated phase respectively. The physical behavior of the universe has been discussed by using some physical quantities

  1. CYBRD1 as a modifier gene that modulates iron phenotype in HFE p.C282Y homozygous patients.

    Science.gov (United States)

    Pelucchi, Sara; Mariani, Raffaella; Calza, Stefano; Fracanzani, Anna Ludovica; Modignani, Giulia Litta; Bertola, Francesca; Busti, Fabiana; Trombini, Paola; Fraquelli, Mirella; Forni, Gian Luca; Girelli, Domenico; Fargion, Silvia; Specchia, Claudia; Piperno, Alberto

    2012-12-01

    Most patients with hereditary hemochromatosis in the Caucasian population are homozygous for the p.C282Y mutation in the HFE gene. The penetrance and expression of hereditary hemochromatosis differ largely among cases of homozygous p.C282Y. Genetic factors might be involved in addition to environmental factors. In the present study, we analyzed 50 candidate genes involved in iron metabolism and evaluated the association between 214 single nucleotide polymorphisms in these genes and three phenotypic outcomes of iron overload (serum ferritin, iron removed and transferrin saturation) in a large group of 296 p.C282Y homozygous Italians. Polymorphisms were tested for genetic association with each single outcome using linear regression models adjusted for age, sex and alcohol consumption. We found a series of 17 genetic variants located in different genes with possible additive effects on the studied outcomes. In order to evaluate whether the selected polymorphisms could provide a predictive signature for adverse phenotype, we re-evaluated data by dividing patients in two extreme phenotype classes based on the three phenotypic outcomes. We found that only a small improvement in prediction could be achieved by adding genetic information to clinical data. Among the selected polymorphisms, a significant association was observed between rs3806562, located in the 5'UTR of CYBRD1, and transferrin saturation. This variant belongs to the same haplotype block that contains the CYBRD1 polymorphism rs884409, found to be associated with serum ferritin in another population of p.C282Y homozygotes, and able to modulate promoter activity. A luciferase assay indicated that rs3806562 does not have a significant functional role, suggesting that it is a genetic marker linked to the putative genetic modifier rs884409. While our results support the hypothesis that polymorphisms in genes regulating iron metabolism may modulate penetrance of HFE-hereditary hemochromatosis, with emphasis on

  2. Existence of stable wormholes on a non-commutative-geometric background in modified gravity

    Energy Technology Data Exchange (ETDEWEB)

    Zubair, M.; Mustafa, G. [COMSATS, Institute of Information Technology, Department of Mathematics, Lahore (Pakistan); Waheed, Saira [Prince Mohammad Bin Fahd University, Al Khobar (Saudi Arabia); Abbas, G. [The Islamia University of Bahawalpur, Department of Mathematics, Bahawalpur (Pakistan)

    2017-10-15

    In this paper, we discuss spherically symmetric wormhole solutions in f(R, T) modified theory of gravity by introducing well-known non-commutative geometry in terms of Gaussian and Lorentzian distributions of string theory. For analytic discussion, we consider an interesting model of f(R, T) gravity defined by f(R, T) = f{sub 1}(R) + λT. By taking two different choices for the function f{sub 1}(R), that is, f{sub 1}(R) = R and f{sub 1}(R) = R + αR{sup 2} + γR{sup n}, we discuss the possible existence of wormhole solutions. In the presence of non-commutative Gaussian and Lorentzian distributions, we get exact and numerical solutions for both these models. By taking appropriate values of the free parameters, we discuss different properties of these wormhole models analytically and graphically. Further, using an equilibrium condition, it is found that these solutions are stable. Also, we discuss the phenomenon of gravitational lensing for the exact wormhole model and it is found that the deflection angle diverges at the wormhole throat. (orig.)

  3. Modified intracellular-associated phenotypes in a recombinant Salmonella Typhi expressing S. Typhimurium SPI-3 sequences.

    Directory of Open Access Journals (Sweden)

    Patricio Retamal

    Full Text Available A bioinformatics comparison of Salmonella Pathogenicity Island 3 sequences from S. Typhi and S. Typhimurium serovars showed that ten genes are highly conserved. However three of them are pseudogenes in S. Typhi. Our aim was to understand what functions are lost in S. Typhi due to pseudogenes by constructing a S. Typhi genetic hybrid carrying the SPI-3 region of S. Typhimurium instead of its own SPI-3. We observed that under stressful conditions the hybrid strain showed a clear impairment in resistance to hydrogen peroxide and decreased survival within U937 culture monocytes. We hypothesized that the marT-fidL operon, encoded in SPI-3, was responsible for the new phenotypes because marT is a pseudogen in S. Typhi and has a demonstrated role as a transcriptional regulator in S. Typhimurium. Therefore we cloned and transferred the S. Typhimurium marT-fidL operon into S. Typhi and confirmed that invasion of monocytes was dramatically decreased. Finally, our findings suggest that the genomic and functional differences between SPI-3 sequences have implications in the host specificity of Typhi and Typhimurium serovars.

  4. Genetic Modifiers of Cardiovascular Phenotype Caused by Elastin Haploinsufficiency Act by Extrinsic Noncomplementation*

    Science.gov (United States)

    Kozel, Beth A.; Knutsen, Russell H.; Ye, Li; Ciliberto, Christopher H.; Broekelmann, Thomas J.; Mecham, Robert P.

    2011-01-01

    Elastin haploinsufficiency causes the cardiovascular complications associated with Williams-Beuren syndrome and isolated supravalvular aortic stenosis. Significant variability exists in the vascular pathology in these individuals. Using the Eln+/− mouse, we sought to identify the source of this variability. Following outcrossing of C57Bl/6J Eln+/−, two backgrounds were identified whose cardiovascular parameters deviated significantly from the parental strain. F1 progeny of the C57Bl/6J; Eln+/−x129X1/SvJ were more hypertensive and their arteries less compliant. In contrast, Eln+/− animals crossed to DBA/2J were protected from the pathologic changes associated with elastin insufficiency. Among the crosses, aortic elastin and collagen content did not correlate with quantitative vasculopathy traits. Quantitative trait locus analysis performed on F2 C57; Eln+/−x129 intercrosses identified highly significant peaks on chromosome 1 (LOD 9.7) for systolic blood pressure and on chromosome 9 (LOD 8.7) for aortic diameter. Additional peaks were identified that affect only Eln+/−, including a region upstream of Eln on chromosome 5 (LOD 4.5). Bioinformatic analysis of the quantitative trait locus peaks revealed several interesting candidates, including Ren1, Ncf1, and Nos1; genes whose functions are unrelated to elastic fiber assembly, but whose effects may synergize with elastin insufficiency to predispose to hypertension and stiffer blood vessels. Real time RT-PCR studies show background-specific increased expression of Ncf1 (a subunit of the NOX2 NAPDH oxidase) that parallel the presence of increased oxidative stress in Eln+/− aortas. This finding raises the possibility that polymorphisms in genes affecting the generation of reactive oxygen species alter cardiovascular function in individuals with elastin haploinsufficiency through extrinsic noncomplementation. PMID:22049077

  5. Tmprss6 is a genetic modifier of the Hfe-hemochromatosis phenotype in mice

    Science.gov (United States)

    Whittlesey, Rebecca L.; Andrews, Nancy C.

    2011-01-01

    The hereditary hemochromatosis protein HFE promotes the expression of hepcidin, a circulating hormone produced by the liver that inhibits dietary iron absorption and macrophage iron release. HFE mutations are associated with impaired hepatic bone morphogenetic protein (BMP)/SMAD signaling for hepcidin production. TMPRSS6, a transmembrane serine protease mutated in iron-refractory iron deficiency anemia, inhibits hepcidin expression by dampening BMP/SMAD signaling. In the present study, we used genetic approaches in mice to examine the relationship between Hfe and Tmprss6 in the regulation of systemic iron homeostasis. Heterozygous loss of Tmprss6 in Hfe−/− mice reduced systemic iron overload, whereas homozygous loss caused systemic iron deficiency and elevated hepatic expression of hepcidin and other Bmp/Smad target genes. In contrast, neither genetic loss of Hfe nor hepatic Hfe overexpression modulated the hepcidin elevation and systemic iron deficiency of Tmprss6−/− mice. These results indicate that genetic loss of Tmprss6 increases Bmp/Smad signaling in an Hfe-independent manner that can restore Bmp/Smad signaling in Hfe−/− mice. Furthermore, these results suggest that natural genetic variation in the human ortholog TMPRSS6 might modify the clinical penetrance of HFE-associated hereditary hemochromatosis, raising the possibility that pharmacologic inhibition of TMPRSS6 could attenuate iron loading in this disorder. PMID:21355094

  6. Staphylococcal phenotypes induced by naturally occurring and synthetic membrane-interactive polyphenolic β-lactam resistance modifiers.

    Directory of Open Access Journals (Sweden)

    Lucia Palacios

    Full Text Available Galloyl catechins, in particular (--epicatechin gallate (ECg, have the capacity to abrogate β-lactam resistance in methicillin-resistant strains of Staphylococcus aureus (MRSA; they also prevent biofilm formation, reduce the secretion of a large proportion of the exoproteome and induce profound changes to cell morphology. Current evidence suggests that these reversible phenotypic traits result from their intercalation into the bacterial cytoplasmic membrane. We have endeavoured to potentiate the capacity of ECg to modify the MRSA phenotype by stepwise removal of hydroxyl groups from the B-ring pharmacophore and the A:C fused ring system of the naturally occurring molecule. ECg binds rapidly to the membrane, inducing up-regulation of genes responsible for protection against cell wall stress and maintenance of membrane integrity and function. Studies with artificial membranes modelled on the lipid composition of the staphylococcal bilayer indicated that ECg adopts a position deep within the lipid palisade, eliciting major alterations in the thermotropic behaviour of the bilayer. The non-galloylated homolog (--epicatechin enhanced ECg-mediated effects by facilitating entry of ECg molecules into the membrane. ECg analogs with unnatural B-ring hydroxylation patterns induced higher levels of gene expression and more profound changes to MRSA membrane fluidity than ECg but adopted a more superficial location within the bilayer. ECg possessed a high affinity for the positively charged staphylococcal membrane and induced changes to the biophysical properties of the bilayer that are likely to account for its capacity to disperse the cell wall biosynthetic machinery responsible for β-lactam resistance. The ability to enhance these properties by chemical modification of ECg raises the possibility that more potent analogs could be developed for clinical evaluation.

  7. Evaluation of the XRCC1 gene as a phenotypic modifier in BRCA1/2 mutation carriers. Results from the consortium of investigators of modifiers of BRCA1/BRCA2

    NARCIS (Netherlands)

    Osorio, A.; Milne, R. L.; Alonso, R.; Pita, G.; Peterlongo, P.; Teulé, A.; Nathanson, K. L.; Domchek, S. M.; Rebbeck, T.; Lasa, A.; Konstantopoulou, I.; Hogervorst, F. B.; Verhoef, S.; van Dooren, M. F.; Jager, A.; Ausems, M. G. E. M.; Aalfs, C. M.; van Asperen, C. J.; Vreeswijk, M.; Waisfisz, Q.; van Roozendaal, C. E.; Ligtenberg, M. J.; Easton, D. F.; Peock, S.; Cook, M.; Oliver, C. T.; Frost, D.; Curzon, B.; Evans, D. G.; Lalloo, F.; Eeles, R.; Izatt, L.; Davidson, R.; Adlard, J.; Eccles, D.; Ong, K.-r; Douglas, F.; Downing, S.; Brewer, C.; Walker, L.; Nevanlinna, H.; Aittomäki, K.; Couch, F. J.; Fredericksen, Z.; Lindor, N. M.; Godwin, A.; Isaacs, C.; Caligo, M. A.; Loman, N.; Jernström, H.; Barbany-Bustinza, G.; Liljegren, A.; Ehrencrona, H.; Stenmark-Askmalm, M.; Feliubadaló, L.; Manoukian, S.; Peissel, B.; Zaffaroni, D.; Bonanni, B.; Fortuzzi, S.; Johannsson, O. T.; Chenevix-Trench, G.; Chen, X.-C.; Beesley, J.; Spurdle, A. B.; Sinilnikova, O. M.; Healey, S.; McGuffog, L.; Antoniou, A. C.; Brunet, J.; Radice, P.; Benítez, J.; Hogervorst, F. B. L.; Verheus, M.; van 't Veer, L. J.; van Leeuwen, F. E.; Rookus, M. A.; Collée, M.; van den Ouweland, A. M. W.; Hooning, M. J.; Tilanus-Linthorst, M. M. A.; Seynaeve, C.; Wijnen, J. T.; Vreeswijk, M. P.; Tollenaar, R. A.; Devilee, P.; Hoogerbrugge, N.; Ausems, M. G.; van der Luijt, R. B.; van Os, T. A.; Gille, J. J. P.; Meijers-Heijboer, H. E. J.; Gomez-Garcia, E. B.; Blok, Marinus J.; Caanen, B.; Oosterwijk, J. C.; van der Hout, A. H.; Mourits, M. J.; Vasen, H. F.; Peock, Susan; Cook, Margaret; Oliver, Clare; Frost, Debra; Miedzybrodzka, Zosia; Gregory, Helen; Morrison, Patrick; Jeffers, Lisa; Cole, Trevor; McKeown, Carole; Ong, Kai-Ren; Hoffman, Jonathan; Donaldson, Alan; Paterson, Joan; Downing, Sarah; Taylor, Amy; Murray, Alexandra; Rogers, Mark T.; McCann, Emma; Kennedy, M. John; Barton, David; East, South; Porteous, Mary; Drummond, Sarah; Brewer, Carole; Kivuva, Emma; Searle, Anne; Goodman, Selina; Hill, Kathryn; Davidson, Rosemarie; Bradshaw, Nicola; Snadden, Lesley; Longmuir, Mark; Watt, Catherine; Gibson, Sarah; Izatt, Louise; Jacobs, Chris; Langman, Caroline; Whaite, Anna; Dorkins, Huw; Barwell, Julian; Adlard, Julian; Chu, Carol; Miller, Julie; Ellis, Ian; Evans, D. Gareth; Lalloo, Fiona; Taylor, Jane; Side, Lucy; Male, Alison; Berlin, Cheryl; Eason, Jacqueline; Collier, Rebecca; Douglas, Fiona; Claber, Oonagh; Walker, Lisa; McLeod, Diane; Halliday, Dorothy; Durell, Sarah; Stayner, Barbara; Eeles, Ros; Shanley, Susan; Rahman, Nazneen; Houlston, Richard; Bancroft, Elizabeth; D'Mello, Lucia; Page, Elizabeth; Ardern-Jones, Audrey; Kohut, Kelly; Wiggins, Jennifer; Castro, Elena; Mitra, Anitra; Robertson, Lisa; Cook, Jackie; Quarrell, Oliver; Bardsley, Cathryn; Hodgson, Shirley; Goff, Sheila; Brice, Glen; Winchester, Lizzie; Eddy, Charlotte; Tripathi, Vishakha; Attard, Virginia; Eccles, Diana; Lucassen, Anneke; Crawford, Gillian; McBride, Donna; Smalley, Sarah; Godwin, A. K.; Karlsson, Per; Nordling, Margareta; Bergman, Annika; Einbeigi, Zakaria; Stenmark- Askmalm, Marie; Liedgren, Sigrun; Borg, Ake; Loman, Niklas; Olsson, Håkan; Kristoffersson, Ulf; Jernström, Helena; Harbst, Katja; Henriksson, Karin; Lindblom, Annika; Arver, Brita; Wachenfeldt, Anna von; Liljegren, Annelie; Barbany-Bustinza, Gisela; Rantala, Johanna; Melin, Beatrice; Grönberg, Henrik; Stattin, Eva-Lena; Emanuelsson, Monica; Ehrencrona, Hans; Rosenquist Brandell, Richard; Dahl, Niklas

    2011-01-01

    Single-nucleotide polymorphisms (SNPs) in genes involved in DNA repair are good candidates to be tested as phenotypic modifiers for carriers of mutations in the high-risk susceptibility genes BRCA1 and BRCA2. The base excision repair (BER) pathway could be particularly interesting given the relation

  8. Positional dependence of scale size and shape in butterfly wings: wing-wide phenotypic coordination of color-pattern elements and background.

    Science.gov (United States)

    Kusaba, Kiseki; Otaki, Joji M

    2009-02-01

    Butterfly wing color-patterns are a phenotypically coordinated array of scales whose color is determined as cellular interpretation outputs for morphogenic signals. Here we investigated distribution patterns of scale shape and size in relation to position and coloration on the hindwings of a nymphalid butterfly Junonia orithya. Most scales had a smooth edge but scales at and near the natural and ectopic eyespot foci and in the postbasal area were jagged. Scale size decreased regularly from the postbasal to distal areas, and eyespots occasionally had larger scales than the background. Reasonable correlations were obtained between the eyespot size and focal scale size in females. Histological and real-time individual observations of the color-pattern developmental sequence showed that the background brown and blue colors expanded from the postbasal to distal areas independently from the color-pattern elements such as eyespots. These data suggest that morphogenic signals for coloration directly or indirectly influence the scale shape and size and that the blue "background" is organized by a long-range signal from an unidentified organizing center in J. orithya.

  9. Biomarker-driven phenotyping in Parkinson disease: a translational missing link in disease-modifying clinical trials

    Science.gov (United States)

    Espay, Alberto J.; Schwarzschild, Michael A.; Tanner, Caroline M.; Fernandez, Hubert H; Simon, David K.; Leverenz, James B.; Merola, Aristide; Chen-Plotkin, Alice; Brundin, Patrik; Kauffman, Marcelo A.; Erro, Roberto; Kieburtz, Karl; Woo, Daniel; Macklin, Eric A.; Standaert, David G.; Lang, Anthony E.

    2016-01-01

    Past clinical trials of putative neuroprotective therapies have targeted Parkinson disease (PD) as a single pathogenic disease entity. From an Oslerian clinico-pathologic perspective, the wide complexity of PD converges into Lewy bodies and justifies a reductionist approach to PD: a single-mechanism therapy can affect most of those sharing the classic pathologic hallmark. From a systems-biology perspective, PD is a group of disorders that, while related by sharing the feature of nigral dopamine-neuron degeneration, exhibit unique genetic, biological and molecular abnormalities, which probably respond differentially to a given therapeutic approach, particularly for strategies aimed at neuroprotection. Under this model, only biomarker-defined, homogenous subtypes of PD are likely to respond optimally to therapies proven to affect the biological processes within each subtype. Therefore, we suggest that precision medicine applied to PD requires a reevaluation of the biomarker-discovery effort. This effort is currently centered on correlating biological measures to clinical features of PD and on identifying factors that predict whether various prodromal states will convert into the classical movement disorder. We suggest, instead, that subtyping of PD requires the reverse view, where abnormal biological signals (i.e., biomarkers) rather than clinical definitions are used to define disease phenotypes. Successful development of disease-modifying strategies will depend on how relevant the specific biological processes addressed by an intervention are to the pathogenetic mechanisms in the subgroup of targeted patients. This precision-medicine approach will likely yield smaller but well-defined subsets of PD amenable to successful neuroprotection. PMID:28233927

  10. Production of a Marfan cellular phenotype by expressing a mutant human fibrillin allele on a normal human or murine genetic background

    Energy Technology Data Exchange (ETDEWEB)

    Eldadah, Z.A.; Dietz, H.C. [Johns Hopkins Univ. School of Medicine, Baltimore, MD (United States); Brenn, T. [Stanford Univ. Medical Center, CA (United States)] [and others

    1994-09-01

    The Marfan Syndrome (MFS) is a heritable disorder of connective tissue caused by defects in fibrillin (FBN1), a 350 kD glycoprotein and principal component of the extracellular microfibril. Previous correlations of mutant transcript level and disease severity suggested a dominant negative model of MFS pathogenesis. To address this hypothesis we assembled an expression construct containing the mutant allele from a patient with severe MFS. This mutation causes skipping of FBN1 exon 2 and a frame shift, leading to a premature termination codon in exon 4. The predicted peptide would thus consist of 55 wild type and 45 missense amino acids. The construct was stably transfected into cultured human and mouse fibroblasts, and several clonal cell populations were established. Human and mouse cells expressing the truncated peptide exhibited markedly diminished fibrillin deposition and disorganized microfibrillar architecture by immunofluorescence. Pulse-chase analysis of these cells demonstrated normal levels of fibrillin synthesis but substantially decreased fibrillin deposition into the extracellular matrix. These data illustrate that expression of a mutant FBN1 allele, on a background of two normal alleles, is sufficient to disrupt normal fibrillin aggregation and reproduce the MFS cellular phenotype. This provides confirmation of a dominant negative model of MFS pathogenesis and may offer mutant allele knockout as a strategy for gene therapy. In addition, these data underscore the importance of the FBN1 amino-terminus in normal multimer formation and suggest that expression of the human extreme 5{prime} FBN1 coding sequence may be sufficient, in isolation, to produce an animal model of MFS. Indeed, transgenic mice harboring this mutant allele have been produced, and phenotype analysis is currently in progress.

  11. Direct determination of Cd and Pb in human urine by GFAAS with deuterium-lamp background correction using different chemical modifiers

    International Nuclear Information System (INIS)

    Husakova, L.; Baoinova, M.; Sramkova, J.; Cernohorsky, T.

    2007-01-01

    Several authors have contributed to the elaboration of methodology for direct determination of Cd and Pb in urine by graphite furnace atomic absorption spectrometry (GFAAS). In the proposed approaches, Zeeman background correction systems were predominantly used, without paying much attention to the selection of an appropriate chemical modifier. However, systematic studies on eleven recommended and less commonly used modifiers have resulted in optimization of atomization conditions, so that accurate analysis also with the use of D 2 -lamp background correction became possible. This was confirmed by comparative measurements using both background correction systems. For determination of Cd in urine, NH 4 F has been selected resulting in the lowest limit of detection (LOD): 0.07 μg L -1 . NH 4 F promotes efficient atomization at low temperatures and suppresses chloride interference effect. Pd + Sr (nitrate) has been selected as the most adequate modifier for determination of Pb. Its presence raised the maximum tolerable pyrolysis temperature up to 1200 o C, which resulted in the maximum reduction of the background signal and the lowest LOD of 1.5 mg L -1 for Pb (10 μL aliquots of dispensed urine). Applying the above modifiers to the analysis of standards and samples, direct aqueous calibration for accurate analysis of diluted and acidified urine samples became possible. Accuracy of the analysis was verified by the use of commercially available quality control reference materials. (authors)

  12. Recovery of native genetic background in admixed populations using haplotypes, phenotypes, and pedigree information--using Cika cattle as a case breed.

    Directory of Open Access Journals (Sweden)

    Mojca Simčič

    Full Text Available The aim of this study was to obtain unbiased estimates of the diversity parameters, the population history, and the degree of admixture in Cika cattle which represents the local admixed breeds at risk of extinction undergoing challenging conservation programs. Genetic analyses were performed on the genome-wide Single Nucleotide Polymorphism (SNP Illumina Bovine SNP50 array data of 76 Cika animals and 531 animals from 14 reference populations. To obtain unbiased estimates we used short haplotypes spanning four markers instead of single SNPs to avoid an ascertainment bias of the BovineSNP50 array. Genome-wide haplotypes combined with partial pedigree and type trait classification show the potential to improve identification of purebred animals with a low degree of admixture. Phylogenetic analyses demonstrated unique genetic identity of Cika animals. Genetic distance matrix presented by rooted Neighbour-Net suggested long and broad phylogenetic connection between Cika and Pinzgauer. Unsupervised clustering performed by the admixture analysis and two-dimensional presentation of the genetic distances between individuals also suggest Cika is a distinct breed despite being similar in appearance to Pinzgauer. Animals identified as the most purebred could be used as a nucleus for a recovery of the native genetic background in the current admixed population. The results show that local well-adapted strains, which have never been intensively managed and differentiated into specific breeds, exhibit large haplotype diversity. They suggest a conservation and recovery approach that does not rely exclusively on the search for the original native genetic background but rather on the identification and removal of common introgressed haplotypes would be more powerful. Successful implementation of such an approach should be based on combining phenotype, pedigree, and genome-wide haplotype data of the breed of interest and a spectrum of reference breeds which

  13. Humans, Fish, and Whales: How Right Whales Modify Calling Behavior in Response to Shifting Background Noise Conditions.

    Science.gov (United States)

    Parks, Susan E; Groch, Karina; Flores, Paulo; Sousa-Lima, Renata; Urazghildiiev, Ildar R

    2016-01-01

    This study investigates the role of behavioral plasticity in the variation of sound production of southern right whales (Eubalaena australis) in response to changes in the ambient background noise conditions. Data were collected from southern right whales in Brazilian waters in October and November 2011. The goal of this study was to quantify differences in right whale vocalizations recorded in low background noise as a control, fish chorus noise, and vessel noise. Variation in call parameters were detected among the three background noise conditions and have implications for future studies of noise effects on whale sound production.

  14. Identification of Atg2 and ArfGAP1 as Candidate Genetic Modifiers of the Eye Pigmentation Phenotype of Adaptor Protein-3 (AP-3) Mutants in Drosophila melanogaster.

    Science.gov (United States)

    Rodriguez-Fernandez, Imilce A; Dell'Angelica, Esteban C

    2015-01-01

    The Adaptor Protein (AP)-3 complex is an evolutionary conserved, molecular sorting device that mediates the intracellular trafficking of proteins to lysosomes and related organelles. Genetic defects in AP-3 subunits lead to impaired biogenesis of lysosome-related organelles (LROs) such as mammalian melanosomes and insect eye pigment granules. In this work, we have performed a forward screening for genetic modifiers of AP-3 function in the fruit fly, Drosophila melanogaster. Specifically, we have tested collections of large multi-gene deletions--which together covered most of the autosomal chromosomes-to identify chromosomal regions that, when deleted in single copy, enhanced or ameliorated the eye pigmentation phenotype of two independent AP-3 subunit mutants. Fine-mapping led us to define two non-overlapping, relatively small critical regions within fly chromosome 3. The first critical region included the Atg2 gene, which encodes a conserved protein involved in autophagy. Loss of one functional copy of Atg2 ameliorated the pigmentation defects of mutants in AP-3 subunits as well as in two other genes previously implicated in LRO biogenesis, namely Blos1 and lightoid, and even increased the eye pigment content of wild-type flies. The second critical region included the ArfGAP1 gene, which encodes a conserved GTPase-activating protein with specificity towards GTPases of the Arf family. Loss of a single functional copy of the ArfGAP1 gene ameliorated the pigmentation phenotype of AP-3 mutants but did not to modify the eye pigmentation of wild-type flies or mutants in Blos1 or lightoid. Strikingly, loss of the second functional copy of the gene did not modify the phenotype of AP-3 mutants any further but elicited early lethality in males and abnormal eye morphology when combined with mutations in Blos1 and lightoid, respectively. These results provide genetic evidence for new functional links connecting the machinery for biogenesis of LROs with molecules implicated in

  15. Identification of Atg2 and ArfGAP1 as Candidate Genetic Modifiers of the Eye Pigmentation Phenotype of Adaptor Protein-3 (AP-3 Mutants in Drosophila melanogaster.

    Directory of Open Access Journals (Sweden)

    Imilce A Rodriguez-Fernandez

    Full Text Available The Adaptor Protein (AP-3 complex is an evolutionary conserved, molecular sorting device that mediates the intracellular trafficking of proteins to lysosomes and related organelles. Genetic defects in AP-3 subunits lead to impaired biogenesis of lysosome-related organelles (LROs such as mammalian melanosomes and insect eye pigment granules. In this work, we have performed a forward screening for genetic modifiers of AP-3 function in the fruit fly, Drosophila melanogaster. Specifically, we have tested collections of large multi-gene deletions--which together covered most of the autosomal chromosomes-to identify chromosomal regions that, when deleted in single copy, enhanced or ameliorated the eye pigmentation phenotype of two independent AP-3 subunit mutants. Fine-mapping led us to define two non-overlapping, relatively small critical regions within fly chromosome 3. The first critical region included the Atg2 gene, which encodes a conserved protein involved in autophagy. Loss of one functional copy of Atg2 ameliorated the pigmentation defects of mutants in AP-3 subunits as well as in two other genes previously implicated in LRO biogenesis, namely Blos1 and lightoid, and even increased the eye pigment content of wild-type flies. The second critical region included the ArfGAP1 gene, which encodes a conserved GTPase-activating protein with specificity towards GTPases of the Arf family. Loss of a single functional copy of the ArfGAP1 gene ameliorated the pigmentation phenotype of AP-3 mutants but did not to modify the eye pigmentation of wild-type flies or mutants in Blos1 or lightoid. Strikingly, loss of the second functional copy of the gene did not modify the phenotype of AP-3 mutants any further but elicited early lethality in males and abnormal eye morphology when combined with mutations in Blos1 and lightoid, respectively. These results provide genetic evidence for new functional links connecting the machinery for biogenesis of LROs with

  16. Genetic polymorphisms in one-carbon metabolism: associations with CpG island methylator phenotype (CIMP) in colon cancer and the modifying effects of diet.

    Science.gov (United States)

    Curtin, Karen; Slattery, Martha L; Ulrich, Cornelia M; Bigler, Jeannette; Levin, Theodore R; Wolff, Roger K; Albertsen, Hans; Potter, John D; Samowitz, Wade S

    2007-08-01

    This study investigated associations between CpG island methylator phenotype (CIMP) colon cancer and genetic polymorphisms relevant to one-carbon metabolism and thus, potentially the provision of methyl groups and risk of colon cancer. Data from a large, population-based case-control study (916 incident colon cancer cases and 1,972 matched controls) were used. Candidate polymorphisms in methylenetetrahydrofolate reductase (MTHFR), thymidylate synthase (TS), transcobalamin II (TCNII), methionine synthase (MTR), reduced folate carrier (RFC), methylenetetrahydrofolate dehydrogenase 1 (MTHFD1), dihydrofolate reductase (DHFR) and alcohol dehydrogenase 3 (ADH3) were evaluated. CIMP- or CIMP+ phenotype was based on five CpG island markers: MINT1, MINT2, MINT31, p16 and MLH1. The influence of specific dietary factors (folate, methionine, vitamin B(12) and alcohol) on these associations was also analyzed. We hypothesized that polymorphisms involved in the provision of methyl groups would be associated with CIMP+ tumors (two or more of five markers methylated), potentially modified by diet. Few associations specific to CIMP+ tumors were observed overall, which does not support the hypothesis that the provision of methyl groups is important in defining a methylator phenotype. However, our data suggest that genetic polymorphisms in MTHFR 1,298A > C, interacting with diet, may be involved in the development of highly CpG-methylated colon cancers. AC and CC genotypes in conjunction with a high-risk dietary pattern (low folate and methionine intake and high alcohol use) were associated with CIMP+ (OR = 2.1, 95% CI = 1.3-3.4 versus AA/high risk; P-interaction = 0.03). These results provide only limited support for a role of polymorphisms in one-carbon metabolism in the etiology of CIMP colon cancer.

  17. Investigation of chemical modifiers for the determination of lead in fertilizers and limestone using graphite furnace atomic absorption spectrometry with Zeeman-effect background correction and slurry sampling

    Energy Technology Data Exchange (ETDEWEB)

    Borges, Aline R. [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq–INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Becker, Emilene M.; Dessuy, Morgana B. [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Vale, Maria Goreti R., E-mail: mgrvale@ufrgs.br [Instituto de Química, Universidade Federal do Rio Grande do Sul, Av. Bento Gonçalves 9500, 91501-970 Porto Alegre, RS (Brazil); Instituto Nacional de Ciência e Tecnologia do CNPq–INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Welz, Bernhard [Instituto Nacional de Ciência e Tecnologia do CNPq–INCT de Energia e Ambiente, Universidade Federal da Bahia, Salvador, BA (Brazil); Departamento de Química, Universidade Federal de Santa Catarina, 88040-900 Florianópolis, SC (Brazil)

    2014-02-01

    In this work, chemical modifiers in solution (Pd/Mg, NH{sub 4}H{sub 2}PO{sub 4} and NH{sub 4}NO{sub 3}/Pd) were compared with permanent modifiers (Ir and Ru) for the determination of lead in fertilizer and limestone samples using slurry sampling and graphite furnace atomic absorption spectrometry with Zeeman-effect background correction. The analytical line at 283.3 nm was used due to some spectral interference observed at 217.0 nm. The NH{sub 4}H{sub 2}PO{sub 4} was abandoned due to severe spectral interference even at the 283.3-nm line. For Pd/Mg and NH{sub 4}NO{sub 3}/Pd the optimum pyrolysis and atomization temperatures were 900 °C and 1900 °C, respectively. For Ru and Ir, the integrated absorbance signal was stable up to pyrolysis temperatures of 700 °C and 900 °C, respectively, and up to atomization temperature of 1700 °C. The limit of detection (LOD) was 17 ng g{sup −1} using Pd/Mg and 29 ng g{sup −1} using NH{sub 4}NO{sub 3}/Pd. Among the permanent modifiers investigated, the LOD was 22 ng g{sup −1} Pb for Ir and 10 ng g{sup −1} Pb for Ru. The accuracy of the method was evaluated using the certified reference material NIST SRM 695. Although Ru provided lower LOD, which can be attributed to a lower blank signal, only the modifiers in solution showed concordant values of Pb concentration for the NIST SRM 695 and the most of analyzed samples. Moreover, the Pd/Mg modifier provided the highest sensitivity and for this reason it is more suitable for the determination of Pb in fertilizers samples in slurry; besides this it presented a better signal-to-noise ratio than NH{sub 4}NO{sub 3}/Pd. - Highlights: • Lead has been determined in fertilizers using slurry sampling GF AAS. • The mixture of palladium and magnesium nitrates was found to be the ideal chemical modifier. • Calibration could be carried out against aqueous standard solutions. • The proposed method is much faster than the EPA method, which includes sample digestion.

  18. Genetic background strongly modifies the severity of symptoms of Hirschsprung disease, but not hearing loss in rats carrying Ednrb(sl mutations.

    Directory of Open Access Journals (Sweden)

    Ruihua Dang

    Full Text Available Hirschsprung disease (HSCR is thought to result as a consequence of multiple gene interactions that modulate the ability of enteric neural crest cells to populate the developing gut. However, it remains unknown whether the single complete deletion of important HSCR-associated genes is sufficient to result in HSCR disease. In this study, we found that the null mutation of the Ednrb gene, thought indispensable for enteric neuron development, is insufficient to result in HSCR disease when bred onto a different genetic background in rats carrying Ednrb(sl mutations. Moreover, we found that this mutation results in serious congenital sensorineural deafness, and these strains may be used as ideal models of Waardenburg Syndrome Type 4 (WS4. Furthermore, we evaluated how the same changed genetic background modifies three features of WS4 syndrome, aganglionosis, hearing loss, and pigment disorder in these congenic strains. We found that the same genetic background markedly changed the aganglionosis, but resulted in only slight changes to hearing loss and pigment disorder. This provided the important evidence, in support of previous studies, that different lineages of neural crest-derived cells migrating along with various pathways are regulated by different signal molecules. This study will help us to better understand complicated diseases such as HSCR and WS4 syndrome.

  19. Randomly detected genetically modified (GM maize (Zea mays L. near a transport route revealed a fragile 45S rDNA phenotype.

    Directory of Open Access Journals (Sweden)

    Nomar Espinosa Waminal

    Full Text Available Monitoring of genetically modified (GM crops has been emphasized to prevent their potential effects on the environment and human health. Monitoring of the inadvertent dispersal of transgenic maize in several fields and transport routes in Korea was carried out by qualitative multiplex PCR, and molecular analyses were conducted to identify the events of the collected GM maize. Cytogenetic investigations through fluorescence in situ hybridization (FISH of the GM maize were performed to check for possible changes in the 45S rDNA cluster because this cluster was reported to be sensitive to replication and transcription stress. Three GM maize kernels were collected from a transport route near Incheon port, Korea, and each was found to contain NK603, stacked MON863 x NK603, and stacked NK603 x MON810 inserts, respectively. Cytogenetic analysis of the GM maize containing the stacked NK603 x MON810 insert revealed two normal compact 5S rDNA signals, but the 45S rDNA showed a fragile phenotype, demonstrating a "beads-on-a-string" fragmentation pattern, which seems to be a consequence of genetic modification. Implications of the 45S rDNA cluster fragility in GM maize are also discussed.

  20. Policy-Led Comparative Environmental Risk Assessment of Genetically Modified Crops: Testing for Increased Risk Rather Than Profiling Phenotypes Leads to Predictable and Transparent Decision-Making

    Directory of Open Access Journals (Sweden)

    Alan Raybould

    2018-04-01

    Full Text Available We describe two contrasting methods of comparative environmental risk assessment for genetically modified (GM crops. Both are science-based, in the sense that they use science to help make decisions, but they differ in the relationship between science and policy. Policy-led comparative risk assessment begins by defining what would be regarded as unacceptable changes when the use a particular GM crop replaces an accepted use of another crop. Hypotheses that these changes will not occur are tested using existing or new data, and corroboration or falsification of the hypotheses is used to inform decision-making. Science-led comparative risk assessment, on the other hand, tends to test null hypotheses of no difference between a GM crop and a comparator. The variables that are compared may have little or no relevance to any previously stated policy objective and hence decision-making tends to be ad hoc in response to possibly spurious statistical significance. We argue that policy-led comparative risk assessment is the far more effective method. With this in mind, we caution that phenotypic profiling of GM crops, particularly with omics methods, is potentially detrimental to risk assessment.

  1. The Protective Effect of Minocycline in a Paraquat-Induced Parkinson's Disease Model in Drosophila is Modified in Altered Genetic Backgrounds

    Directory of Open Access Journals (Sweden)

    Arati A. Inamdar

    2012-01-01

    Full Text Available Epidemiological studies link the herbicide paraquat to increased incidence of Parkinson's disease (PD. We previously reported that Drosophila exposed to paraquat recapitulate PD symptoms, including region-specific degeneration of dopaminergic neurons. Minocycline, a tetracycline derivative, exerts ameliorative effects in neurodegenerative disease models, including Drosophila. We investigated whether our environmental toxin-based PD model could contribute to an understanding of cellular and genetic mechanisms of minocycline action and whether we could assess potential interference with these drug effects in altered genetic backgrounds. Cofeeding of minocycline with paraquat prolonged survival, rescued mobility defects, blocked generation of reactive oxygen species, and extended dopaminergic neuron survival, as has been reported previously for a genetic model of PD in Drosophila. We then extended this study to identify potential interactions of minocycline with genes regulating dopamine homeostasis that might modify protection against paraquat and found that deficits in GTP cyclohydrolase adversely affect minocycline rescue. We further performed genetic studies to identify signaling pathways that are necessary for minocycline protection against paraquat toxicity and found that mutations in the Drosophila genes that encode c-Jun N-terminal kinase (JNK and Akt/Protein kinase B block minocycline rescue.

  2. Antibacterial and antibiotic resistance modifying activity of the extracts from Allanblackia gabonensis, Combretum molle and Gladiolus quartinianus against Gram-negative bacteria including multi-drug resistant phenotypes.

    Science.gov (United States)

    Fankam, Aimé G; Kuiate, Jules R; Kuete, Victor

    2015-06-30

    Bacterial resistance to antibiotics is becoming a serious problem worldwide. The discovery of new and effective antimicrobials and/or resistance modulators is necessary to tackle the spread of resistance or to reverse the multi-drug resistance. We investigated the antibacterial and antibiotic-resistance modifying activities of the methanol extracts from Allanblackia gabonensis, Gladiolus quartinianus and Combretum molle against 29 Gram-negative bacteria including multi-drug resistant (MDR) phenotypes. The broth microdilution method was used to determine the minimal inhibitory concentrations (MIC) and minimal bactericidal concentrations (MBC) of the samples meanwhile the standard phytochemical methods were used for the preliminary phytochemical screening of the plant extracts. Phytochemical analysis showed the presence of alkaloids, flavonoids, phenols and tannins in all studied extracts. Other chemical classes of secondary metabolites were selectively presents. Extracts from A. gabonensis and C. molle displayed a broad spectrum of activity with MICs varying from 16 to 1024 μg/mL against about 72.41% of the tested bacteria. The extract from the fruits of A. gabonensis had the best activity, with MIC values below 100 μg/mL on 37.9% of tested bacteria. Percentages of antibiotic-modulating effects ranging from 67 to 100% were observed against tested MDR bacteria when combining the leaves extract from C. molle (at MIC/2 and MIC/4) with chloramphenicol, kanamycin, streptomycin and tetracycline. The overall results of the present study provide information for the possible use of the studied plant, especially Allanblackia gabonensis and Combretum molle in the control of Gram-negative bacterial infections including MDR species as antibacterials as well as resistance modulators.

  3. Comparison of palladium chemical modifiers for the determination of selenium in plasma by Zeeman-effect background corrected electrothermal atomic absorption spectrometry

    DEFF Research Database (Denmark)

    Gammelgaard, Bente; Jons, O.

    1997-01-01

    , It was not possible to stabilize trimethylselenonium to the same extent with this modifier, Peak shapes and appearance times of the atomization signals were equal for the four selenium species with this modifier, The addition of 20 mu g of palladium was used for the analysis of the serum reference material Seronorm...

  4. Estimating rice yield related traits and quantitative trait loci analysis under different nitrogen treatments using a simple tower-based field phenotyping system with modified single-lens reflex cameras

    Science.gov (United States)

    Naito, Hiroki; Ogawa, Satoshi; Valencia, Milton Orlando; Mohri, Hiroki; Urano, Yutaka; Hosoi, Fumiki; Shimizu, Yo; Chavez, Alba Lucia; Ishitani, Manabu; Selvaraj, Michael Gomez; Omasa, Kenji

    2017-03-01

    Application of field based high-throughput phenotyping (FB-HTP) methods for monitoring plant performance in real field conditions has a high potential to accelerate the breeding process. In this paper, we discuss the use of a simple tower based remote sensing platform using modified single-lens reflex cameras for phenotyping yield traits in rice under different nitrogen (N) treatments over three years. This tower based phenotyping platform has the advantages of simplicity, ease and stability in terms of introduction, maintenance and continual operation under field conditions. Out of six phenological stages of rice analyzed, the flowering stage was the most useful in the estimation of yield performance under field conditions. We found a high correlation between several vegetation indices (simple ratio (SR), normalized difference vegetation index (NDVI), transformed vegetation index (TVI), corrected transformed vegetation index (CTVI), soil-adjusted vegetation index (SAVI) and modified soil-adjusted vegetation index (MSAVI)) and multiple yield traits (panicle number, grain weight and shoot biomass) across a three trials. Among all of the indices studied, SR exhibited the best performance in regards to the estimation of grain weight (R2 = 0.80). Under our tower-based field phenotyping system (TBFPS), we identified quantitative trait loci (QTL) for yield related traits using a mapping population of chromosome segment substitution lines (CSSLs) and a single nucleotide polymorphism data set. Our findings suggest the TBFPS can be useful for the estimation of yield performance during early crop development. This can be a major opportunity for rice breeders whom desire high throughput phenotypic selection for yield performance traits.

  5. Human TRMU encoding the mitochondrial 5-methylaminomethyl-2-thiouridylate-methyltransferase is a putative nuclear modifier gene for the phenotypic expression of the deafness-associated 12S rRNA mutations

    International Nuclear Information System (INIS)

    Yan Qingfeng; Bykhovskaya, Yelena; Li Ronghua; Mengesha, Emebet; Shohat, Mordechai; Estivill, Xavier; Fischel-Ghodsian, Nathan; Guan Minxin

    2006-01-01

    Nuclear modifier genes have been proposed to modulate the phenotypic manifestation of human mitochondrial 12S rRNA A1491G mutation associated with deafness in many families world-wide. Here we identified and characterized the putative nuclear modifier gene TRMU encoding a highly conserved mitochondrial protein related to tRNA modification. A 1937 bp TRMU cDNA has been isolated and the genomic organization of TRMU has been elucidated. The human TRMU gene containing 11 exons encodes a 421 residue protein with a strong homology to the TRMU-like proteins of bacteria and other homologs. TRMU is ubiquitously expressed in various tissues, but abundantly in tissues with high metabolic rates including heart, liver, kidney, and brain. Immunofluorescence analysis of human 143B cells expressing TRMU-GFP fusion protein demonstrated that the human Trmu localizes and functions in mitochondrion. Furthermore, we show that in families with the deafness-associated 12S rRNA A1491G mutation there is highly suggestive linkage and linkage disequilibrium between microsatellite markers adjacent to TRMU and the presence of deafness. These observations suggest that human TRMU may modulate the phenotypic manifestation of the deafness-associated mitochondrial 12S rRNA mutations

  6. The impact of metabolic syndrome and CRP on vascular phenotype in type 2 diabetes mellitus

    NARCIS (Netherlands)

    Alizadeh Dehnavi, R.; Beishuizen, E.D.; Ree, M.A. van de; Le Cessie, S.; Huisman, M.V.; Kluft, C.; Princen, H.M.G.; Tamsma, J.T.

    2008-01-01

    Background: The burden of cardiovascular disease in diabetes mellitus type 2 (DM2) patients is variable. We hypothesize that metabolic syndrome (MS) and low-grade systemic inflammation modify the extent of atherosclerosis in DM2. Methods: Vascular phenotype was determined using the following

  7. Cowpea mosaic virus-based chimaeras Effects of inserted peptides on the phenotype, host range, and transmissibility of the modified viruses

    International Nuclear Information System (INIS)

    Porta, Claudine; Spall, Valerie E.; Findlay, Kim C.; Gergerich, Rose C.; Farrance, Christine E.; Lomonossoff, George P.

    2003-01-01

    Expression of foreign peptides on the surface of cowpea mosaic virus particles leads to the creation of chimaeras with a variety of phenotypes and yields. Two factors were shown to be particularly significant in determining the properties of a given chimaera: the length of the inserted sequence and its isoelectric point. The deleterious effect of high isoelectric point on the ability of chimeras to produce a systemic infection occurs irrespective of the site of insertion of the peptide. Ultrastructural analysis of tissue infected with chimaeras with different phenotypes showed that all produced particles with a tendency to aggregate, irrespective of the size or isoelectric point of the insert. Host range and transmission studies revealed that the expression of a foreign peptide did not (1) alter the virus host range, (2) increase the rate of transmission by beetles or through seed, or (3) change the insect vector specificity. These findings have implications for both the utility and the biosafety of Cowpea mosaic virus-based chimaeras

  8. Gender as a Modifying Factor Influencing Myotonic Dystrophy Type 1 Phenotype Severity and Mortality: A Nationwide Multiple Databases Cross-Sectional Observational Study.

    Directory of Open Access Journals (Sweden)

    Celine Dogan

    Full Text Available Myotonic Dystrophy type 1 (DM1 is one of the most heterogeneous hereditary disease in terms of age of onset, clinical manifestations, and severity, challenging both medical management and clinical trials. The CTG expansion size is the main factor determining the age of onset although no factor can finely predict phenotype and prognosis. Differences between males and females have not been specifically reported. Our aim is to study gender impact on DM1 phenotype and severity.We first performed cross-sectional analysis of main multiorgan clinical parameters in 1409 adult DM1 patients (>18 y from the DM-Scope nationwide registry and observed different patterns in males and females. Then, we assessed gender impact on social and economic domains using the AFM-Téléthon DM1 survey (n = 970, and morbidity and mortality using the French National Health Service Database (n = 3301.Men more frequently had (1 severe muscular disability with marked myotonia, muscle weakness, cardiac, and respiratory involvement; (2 developmental abnormalities with facial dysmorphism and cognitive impairment inferred from low educational levels and work in specialized environments; and (3 lonely life. Alternatively, women more frequently had cataracts, dysphagia, digestive tract dysfunction, incontinence, thyroid disorder and obesity. Most differences were out of proportion to those observed in the general population. Compared to women, males were more affected in their social and economic life. In addition, they were more frequently hospitalized for cardiac problems, and had a higher mortality rate.Gender is a previously unrecognized factor influencing DM1 clinical profile and severity of the disease, with worse socio-economic consequences of the disease and higher morbidity and mortality in males. Gender should be considered in the design of both stratified medical management and clinical trials.

  9. Deep Learning for Plant Phenotyping

    OpenAIRE

    Mori, Matteo

    2016-01-01

    Plant Phenotyping is an emerging science which provides us the knowledge to better understand plants. Indeed, the study of the link between genetic background and environment in which plants develop can help us to determine cures for plants’ sicknesses and new ways to improve yields using limited resources. In this regard, one of the main aspects of Plant Phenotyping that were studied in the past, was Root Phenotyping, which is based on the study of the root architectures. In particular, toda...

  10. Background Material

    DEFF Research Database (Denmark)

    Zandersen, Marianne; Hyytiäinen, Kari; Saraiva, Sofia

    This document serves as a background material to the BONUS Pilot Scenario Workshop, which aims to develop harmonised regional storylines of socio-ecological futures in the Baltic Sea region in a collaborative effort together with other BONUS projects and stakeholders.......This document serves as a background material to the BONUS Pilot Scenario Workshop, which aims to develop harmonised regional storylines of socio-ecological futures in the Baltic Sea region in a collaborative effort together with other BONUS projects and stakeholders....

  11. Frequent phosphodiesterase 11A gene (PDE11A) defects in patients with Carney complex (CNC) caused by PRKAR1A mutations: PDE11A may contribute to adrenal and testicular tumors in CNC as a modifier of the phenotype.

    Science.gov (United States)

    Libé, Rossella; Horvath, Anelia; Vezzosi, Delphine; Fratticci, Amato; Coste, Joel; Perlemoine, Karine; Ragazzon, Bruno; Guillaud-Bataille, Marine; Groussin, Lionel; Clauser, Eric; Raffin-Sanson, Marie-Laure; Siegel, Jennifer; Moran, Jason; Drori-Herishanu, Limor; Faucz, Fabio Rueda; Lodish, Maya; Nesterova, Maria; Bertagna, Xavier; Bertherat, Jerome; Stratakis, Constantine A

    2011-01-01

    Carney complex (CNC) is an autosomal dominant multiple neoplasia, caused mostly by inactivating mutations of the regulatory subunit 1A of the protein kinase A (PRKAR1A). Primary pigmented nodular adrenocortical disease (PPNAD) is the most frequent endocrine manifestation of CNC with a great inter-individual variability. Germline, protein-truncating mutations of phosphodiesterase type 11A (PDE11A) have been described to predispose to a variety of endocrine tumors, including adrenal and testicular tumors. Our objective was to investigate the role of PDE11A as a possible gene modifier of the phenotype in a series of 150 patients with CNC. A higher frequency of PDE11A variants in patients with CNC compared with healthy controls was found (25.3 vs. 6.8%, P CNC patients, those with PPNAD were significantly more frequently carriers of PDE11A variants compared with patients without PPNAD (30.8 vs. 13%, P = 0.025). Furthermore, men with PPNAD were significantly more frequently carriers of PDE11A sequence variants (40.7%) than women with PPNAD (27.3%) (P CNC patients, a high frequency of PDE11A variants, suggesting that PDE11A is a genetic modifying factor for the development of testicular and adrenal tumors in patients with germline PRKAR1A mutation.

  12. Lack of CCR5 modifies glial phenotypes and population of the nigral dopaminergic neurons, but not MPTP-induced dopaminergic neurodegeneration.

    Science.gov (United States)

    Choi, Dong-Young; Lee, Myung Koo; Hong, Jin Tae

    2013-01-01

    Constitutive expression of C-C chemokine receptor (CCR) 5 has been detected in astrocytes, microglia and neurons, but its physiological roles in the central nervous system are obscure. The bidirectional interactions between neuron and glial cells through CCR5 and its ligands were thought to be crucial for maintaining normal neuronal activities. No study has described function of CCR5 in the dopaminergic neurodegeneration in Parkinson's disease. In order to examine effects of CCR5 on 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine (MPTP)-induced dopaminergic neurodegeneration, we employed CCR5 wild type (WT) and knockout (KO) mice. Immunostainings for tyrosine hydroxylase (TH) exhibited that CCR5 KO mice had lower number of TH-positive neurons even in the absence of MPTP. Difference in MPTP (15mg/kg×4 times, 2hr interval)-mediated loss of TH-positive neurons was subtle between CCR5 WT and KO mice, but there was larger dopamine depletion, behavioral impairments and microglial activation in CCR5 deficient mice. Intriguingly, CCR5 KO brains contained higher immunoreactivity for monoamine oxidase (MAO) B which was mainly localized within astrocytes. In agreement with upregulation of MAO B, concentration of MPP+ was higher in the substantia nigra and striatum of CCR5 KO mice after MPTP injection. We found remarkable activation of p38 MAPK in CCR5 deficient mice, which positively regulates MAO B expression. These results indicate that CCR5 deficiency modifies the nigrostriatal dopaminergic neuronal system and bidirectional interaction between neurons and glial cells via CCR5 might be important for dopaminergic neuronal survival. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Background radiation

    International Nuclear Information System (INIS)

    Arnott, D.

    1985-01-01

    The effects of background radiation, whether natural or caused by man's activities, are discussed. The known biological effects of radiation in causing cancers or genetic mutations are explained. The statement that there is a threshold below which there is no risk is examined critically. (U.K.)

  14. Chemicalome and metabolome profiling of polymethoxylated flavonoids in Citri Reticulatae Pericarpium based on an integrated strategy combining background subtraction and modified mass defect filter in a Microsoft Excel Platform.

    Science.gov (United States)

    Zeng, Su-Ling; Duan, Li; Chen, Bai-Zhong; Li, Ping; Liu, E-Hu

    2017-07-28

    Detection of metabolites in complex biological matrixes is a great challenge because of the background noise and endogenous components. Herein, we proposed an integrated strategy that combined background subtraction program and modified mass defect filter (MMDF) data mining in a Microsoft Excel platform for chemicalome and metabolome profiling of the polymethoxylated flavonoids (PMFs) in Citri Reticulatae Pericarpium (CRP). The exogenously-sourced ions were firstly filtered out by the developed Visual Basic for Applications (VBA) program incorporated in the Microsoft Office. The novel MMDF strategy was proposed for detecting both target and untarget constituents and metabolites based on narrow, well-defined mass defect ranges. The approach was validated to be powerful, and potentially useful for the metabolite identification of both single compound and homologous compound mixture. We successfully identified 30 and 31 metabolites from rat biosamples after oral administration of nobiletin and tangeretin, respectively. A total of 56 PMFs compounds were chemically characterized and 125 metabolites were captured. This work demonstrated the feasibility of the integrated approach for reliable characterization of the constituents and metabolites in herbal medicines. Copyright © 2017 Elsevier B.V. All rights reserved.

  15. The natural radiation background

    International Nuclear Information System (INIS)

    Duggleby, J.C.

    1982-01-01

    The components of the natural background radiation and their variations are described. Cosmic radiation is a major contributor to the external dose to the human body whilst naturally-occurring radionuclides of primordial and cosmogenic origin contribute to both the external and internal doses, with the primordial radionuclides being the major contributor in both cases. Man has continually modified the radiation dose to which he has been subjected. The two traditional methods of measuring background radiation, ionisation chamber measurements and scintillation counting, are looked at and the prospect of using thermoluminescent dosimetry is considered

  16. Genetic modification of glaucoma associated phenotypes between AKXD-28/Ty and DBA/2J mice

    Directory of Open Access Journals (Sweden)

    Zabaleta Adriana

    2001-01-01

    Full Text Available Abstract Background Glaucoma is a common disease but its molecular etiology is poorly understood. It involves retinal ganglion cell death and optic nerve damage that is often associated with elevated intraocular pressure. Identifying genes that modify glaucoma associated phenotypes is likely to provide insights to mechanisms of glaucoma. We previously reported glaucoma in DBA/2J mice caused by recessive alleles at two loci, isa and ipd, that cause iris stromal atrophy and iris pigment dispersion, respectively. A approach for identifying modifier genes is to study the effects of specific mutations in different mouse strains. When the phenotypic effect of a mutation is modified upon its introduction into a new strain, crosses between the parental strains can be used to identify modifier genes. The purpose of this study was to determine if the effects of the DBA/2J derived isa and ipd loci are modified in strain AKXD-28/Ty. Results AKXD-28/Ty mice develop glaucoma characterized by intraocular pressure elevation, retinal ganglion loss, and optic nerve excavation. In AKXD-28/Ty, isa causes an iris stromal atrophy phenotype as in DBA/2J. However, the iris pigment dispersion phenotype associated with ipd in DBA/2J does not occur in AKXD-28/Ty. Additionally, a greater severity and speed of retinal and optic nerve damage following intraocular pressure elevation in AKXD-28/Ty compared to DBA/2J mice suggests that AKXD-28/Ty is more susceptible to pressure-induced cell death. Conclusions The consequences of the ipd and isa mutations are modified in the AKXD-28/Ty background. These strains provide a resource for the identification of modifier genes that modulate pigment dispersion and susceptibility to pressure-induced cell death.

  17. REVIEW ARTICLE One gene, many phenotypes

    African Journals Online (AJOL)

    salah

    Phenotype descriptions are valuable information right at the interface of medi- cine and biology. ... the interaction of alleles at different loci. Modifier genes. 5. ... the amount of normal protein is called ..... Institute, using computer simulations,.

  18. Study of modifiers factors associated to mitochondrial mutations in individuals with hearing impairment

    International Nuclear Information System (INIS)

    Sousa de Moraes, Vanessa Cristine; Alexandrino, Fabiana; Andrade, Paula Baloni; Camara, Marilia Fontenele; Sartorato, Edi Lucia

    2009-01-01

    Hearing impairment is the most prevalent sensorial deficit in the general population. Congenital deafness occurs in about 1 in 1000 live births, of which approximately 50% has hereditary cause in development countries. Non-syndromic deafness can be caused by mutations in both nuclear and mitochondrial genes. Mutations in mtDNA have been associated with aminoglycoside-induced and non-syndromic deafness in many families worldwide. However, the nuclear background influences the phenotypic expression of these pathogenic mutations. Indeed, it has been proposed that nuclear modifier genes modulate the phenotypic manifestation of the mitochondrial A1555G mutation in the MTRNR1 gene. The both putative nuclear modifiers genes TRMU and MTO1 encoding a highly conserved mitochondrial related to tRNA modification. It has been hypothesizes that human TRMU and also MTO1 nuclear genes may modulate the phenotypic manifestation of deafness-associated mitochondrial mutations. The aim of this work was to elucidate the contribution of mitochondrial mutations, nuclear modifier genes mutations and aminoglycoside exposure in the deafness phenotype. Our findings suggest that the genetic background of individuals may play an important role in the pathogenesis of deafness-associated with mitochondrial mutation and aminoglycoside-induced.

  19. Phenotypic plasticity in the range-margin population of the lycaenid butterfly Zizeeria maha

    Directory of Open Access Journals (Sweden)

    Otaki Joji M

    2010-08-01

    Full Text Available Abstract Background Many butterfly species have been experiencing the northward range expansion and physiological adaptation, probably due to climate warming. Here, we document an extraordinary field case of a species of lycaenid butterfly, Zizeeria maha, for which plastic phenotypes of wing color-patterns were revealed at the population level in the course of range expansion. Furthermore, we examined whether this outbreak of phenotypic changes was able to be reproduced in a laboratory. Results In the recently expanded northern range margins of this species, more than 10% of the Z. maha population exhibited characteristic color-pattern modifications on the ventral wings for three years. We physiologically reproduced similar phenotypes by an artificial cold-shock treatment of a normal southern population, and furthermore, we genetically reproduced a similar phenotype after selective breeding of a normal population for ten generations, demonstrating that the cold-shock-induced phenotype was heritable and partially assimilated genetically in the breeding line. Similar genetic process might have occurred in the previous and recent range-margin populations as well. Relatively minor modifications expressed in the tenth generation of the breeding line together with other data suggest a role of founder effect in this field case. Conclusions Our results support the notion that the outbreak of the modified phenotypes in the recent range-margin population was primed by the revelation of plastic phenotypes in response to temperature stress and by the subsequent genetic process in the previous range-margin population, followed by migration and temporal establishment of genetically unstable founders in the recent range margins. This case presents not only an evolutionary role of phenotypic plasticity in the field but also a novel evolutionary aspect of range expansion at the species level.

  20. Note on bouncing backgrounds

    Science.gov (United States)

    de Haro, Jaume; Pan, Supriya

    2018-05-01

    The theory of inflation is one of the fundamental and revolutionary developments of modern cosmology that became able to explain many issues of the early Universe in the context of the standard cosmological model (SCM). However, the initial singularity of the Universe, where physics is indefinite, is still obscure in the combined SCM +inflation scenario. An alternative to SCM +inflation without the initial singularity is thus always welcome, and bouncing cosmology is an attempt at that. The current work is thus motivated to investigate the bouncing solutions in modified gravity theories when the background universe is described by the spatially flat Friedmann-Lemaître-Robertson-Walker (FLRW) geometry. We show that the simplest way to obtain the bouncing cosmologies in such spacetime is to consider some kind of Lagrangian whose gravitational sector depends only on the square of the Hubble parameter of the FLRW universe. For these modified Lagrangians, the corresponding Friedmann equation, a constraint in the dynamics of the Universe, depicts a curve in the phase space (H ,ρ ), where H is the Hubble parameter and ρ is the energy density of the Universe. As a consequence, a bouncing cosmology is obtained when this curve is closed and crosses the axis H =0 at least twice, and whose simplest particular example is the ellipse depicting the well-known holonomy corrected Friedmann equation in loop quantum cosmology (LQC). Sometimes, a crucial point in such theories is the appearance of the Ostrogradski instability at the perturbative level; however, fortunately enough, in the present work, as long as the linear level of perturbations is concerned, this instability does not appear, although it may appear at the higher order of perturbations.

  1. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

    KAUST Repository

    AlShahrani, Mona; Hoehndorf, Robert

    2018-01-01

    In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease's (or patient's) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

  2. Semantic Disease Gene Embeddings (SmuDGE): phenotype-based disease gene prioritization without phenotypes

    KAUST Repository

    Alshahrani, Mona

    2018-04-30

    In the past years, several methods have been developed to incorporate information about phenotypes into computational disease gene prioritization methods. These methods commonly compute the similarity between a disease\\'s (or patient\\'s) phenotypes and a database of gene-to-phenotype associations to find the phenotypically most similar match. A key limitation of these methods is their reliance on knowledge about phenotypes associated with particular genes which is highly incomplete in humans as well as in many model organisms such as the mouse. Results: We developed SmuDGE, a method that uses feature learning to generate vector-based representations of phenotypes associated with an entity. SmuDGE can be used as a trainable semantic similarity measure to compare two sets of phenotypes (such as between a disease and gene, or a disease and patient). More importantly, SmuDGE can generate phenotype representations for entities that are only indirectly associated with phenotypes through an interaction network; for this purpose, SmuDGE exploits background knowledge in interaction networks comprising of multiple types of interactions. We demonstrate that SmuDGE can match or outperform semantic similarity in phenotype-based disease gene prioritization, and furthermore significantly extends the coverage of phenotype-based methods to all genes in a connected interaction network.

  3. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

    KAUST Repository

    Boudellioua, Imene

    2018-05-02

    Purpose: An increasing number of Mendelian disorders have been identified for which two or more variants in one or more genes are required to cause the disease, or significantly modify its severity or phenotype. It is difficult to discover such interactions using existing approaches. The purpose of our work is to develop and evaluate a system that can identify combinations of variants underlying oligogenic diseases in individual whole exome or whole genome sequences. Methods: Information that links patient phenotypes to databases of gene-phenotype associations observed in clinical research can provide useful information and improve variant prioritization for Mendelian diseases. Additionally, background knowledge about interactions between genes can be utilized to guide and restrict the selection of candidate disease modules. Results: We developed OligoPVP, an algorithm that can be used to identify variants in oligogenic diseases and their interactions, using whole exome or whole genome sequences together with patient phenotypes as input. We demonstrate that OligoPVP has significantly improved performance when compared to state of the art pathogenicity detection methods. Conclusions: Our results show that OligoPVP can efficiently detect oligogenic interactions using a phenotype-driven approach and identify etiologically important variants in whole genomes.

  4. A Regulatory RNA Inducing Transgenerationally Inherited Phenotypes

    DEFF Research Database (Denmark)

    Jensen, Lea Møller

    . The variation in Arabidopsis enables different regulatory networks and mechanisms to shape the phenotypic characteristics. The thesis describes the identification of regulatory RNA encoded by an enzyme encoding gene. The RNA regulates by inducing transgenerationally inherited phenotypes. The function of the RNA...... is dependent on the genetic background illustrating that polymorphisms are found in either interactors or target genes of the RNA. Furthermore, the RNA provides a mechanistic link between accumulation of glucosinolate and onset of flowering....

  5. Color change, phenotypic plasticity, and camouflage

    Directory of Open Access Journals (Sweden)

    Martin eStevens

    2016-05-01

    Full Text Available The ability to change appearance over a range of timescales is widespread in nature, existing in many invertebrate and vertebrate groups. This can include color change occurring in seconds, minutes, and hours, to longer term changes associated with phenotypic plasticity and development. A major function is for camouflage against predators because color change and plasticity enables animals to match their surroundings and potentially reduce the risk of predation. Recently, we published findings (Stevens et al. 2014a showing how shore crabs can change their appearance and better match the background to predator vision in the short term. This, coupled with a number of past studies, emphasizes the potential that animals have to modify their appearance for camouflage. However, the majority of studies on camouflage and color plasticity have focused on a small number of species capable of unusually rapid changes. There are many broad questions that remain about the nature, mechanisms, evolution, and adaptive value of color change and plasticity for concealment. Here, I discuss past work and outline six questions relating to color change and plasticity, as well as major avenues for future work.

  6. Gtl2lacZ, an insertional mutation on mouse chromosome 12 with parental origin-dependent phenotype.

    Science.gov (United States)

    Schuster-Gossler, K; Simon-Chazottes, D; Guenet, J L; Zachgo, J; Gossler, A

    1996-01-01

    We have produced a transgenic mouse line, Gtl2lacZ (Gene trap locus 2), that carries an insertional mutation with a dominant modified pattern of inheritance:heterozygous Gtl2lacZ mice that inherited the transgene from the father show a proportionate dwarfism phenotype, whereas the penetrance and expressivity of the phenotype is strongly reduced in Gtl2lacZ mice that inherited the transgene from the mother. On a mixed genetic background this pattern of inheritance was reversible upon transmission of the transgene through the germ line of the opposite sex. On a predominantly 129/Sv genetic background, however, transgene passage through the female germ line modified the transgene effect, such that the penetrance of the mutation was drastically reduced and the phenotype was no longer obvious after subsequent male germ line transmission. Expression of the transgene, however, was neither affected by genetic background nor by parental legacy. Gtl2lacZ maps to mouse Chromosome 12 in a region that displays imprinting effects associated with maternal and paternal disomy. Our results suggest that the transgene insertion in Gtl2lacZ mice affects an endogenous gene(s) required for fetal and postnatal growth and that this gene(s) is predominantly paternally expressed.

  7. Asthma phenotypes in childhood.

    Science.gov (United States)

    Reddy, Monica B; Covar, Ronina A

    2016-04-01

    This review describes the literature over the past 18 months that evaluated childhood asthma phenotypes, highlighting the key aspects of these studies, and comparing these studies to previous ones in this area. Recent studies on asthma phenotypes have identified new phenotypes on the basis of statistical analyses (using cluster analysis and latent class analysis methodology) and have evaluated the outcomes and associated risk factors of previously established early childhood asthma phenotypes that are based on asthma onset and patterns of wheezing illness. There have also been investigations focusing on immunologic, physiologic, and genetic correlates of various phenotypes, as well as identification of subphenotypes of severe childhood asthma. Childhood asthma remains a heterogeneous condition, and investigations into these various presentations, risk factors, and outcomes are important since they can offer therapeutic and prognostic relevance. Further investigation into the immunopathology and genetic basis underlying childhood phenotypes is important so therapy can be tailored accordingly.

  8. Background sources at PEP

    International Nuclear Information System (INIS)

    Lynch, H.; Schwitters, R.F.; Toner, W.T.

    1988-01-01

    Important sources of background for PEP experiments are studied. Background particles originate from high-energy electrons and positrons which have been lost from stable orbits, γ-rays emitted by the primary beams through bremsstrahlung in the residual gas, and synchrotron radiation x-rays. The effect of these processes on the beam lifetime are calculated and estimates of background rates at the interaction region are given. Recommendations for the PEP design, aimed at minimizing background are presented. 7 figs., 4 tabs

  9. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel

    2017-12-19

    Background Integration and analysis of phenotype data from humans and model organisms is a key challenge in building our understanding of normal biology and pathophysiology. However, the range of phenotypes and anatomical details being captured in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization that includes as one of its components an ontology designed to integrate phenotype ontologies. While not applicable to matching arbitrary ontologies, PhenomeNET can be used to identify related phenotypes in different species, including human, mouse, zebrafish, nematode worm, fruit fly, and yeast. Results Here, we apply the PhenomeNET to identify related classes from two phenotype and two disease ontologies using automated reasoning. We demonstrate that we can identify a large number of mappings, some of which require automated reasoning and cannot easily be identified through lexical approaches alone. Combining automated reasoning with lexical matching further improves results in aligning ontologies. Conclusions PhenomeNET can be used to align and integrate phenotype ontologies. The results can be utilized for biomedical analyses in which phenomena observed in model organisms are used to identify causative genes and mutations underlying human disease.

  10. Cosmic Microwave Background Timeline

    Science.gov (United States)

    Cosmic Microwave Background Timeline 1934 : Richard Tolman shows that blackbody radiation in an will have a blackbody cosmic microwave background with temperature about 5 K 1955: Tigran Shmaonov anisotropy in the cosmic microwave background, this strongly supports the big bang model with gravitational

  11. Similarity-based search of model organism, disease and drug effect phenotypes

    KAUST Repository

    Hoehndorf, Robert; Gruenberger, Michael; Gkoutos, Georgios V; Schofield, Paul N

    2015-01-01

    Background: Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions

  12. OligoPVP: Phenotype-driven analysis of individual genomic information to prioritize oligogenic disease variants

    KAUST Repository

    Boudellioua, Imene; Kulmanov, Maxat; Schofield, Paul N; Gkoutos, Georgios V; Hoehndorf, Robert

    2018-01-01

    patient phenotypes to databases of gene-phenotype associations observed in clinical research can provide useful information and improve variant prioritization for Mendelian diseases. Additionally, background knowledge about interactions between genes can

  13. Modified cyanobacteria

    Science.gov (United States)

    Vermaas, Willem F J.

    2014-06-17

    Disclosed is a modified photoautotrophic bacterium comprising genes of interest that are modified in terms of their expression and/or coding region sequence, wherein modification of the genes of interest increases production of a desired product in the bacterium relative to the amount of the desired product production in a photoautotrophic bacterium that is not modified with respect to the genes of interest.

  14. Clinical phenotypes of asthma

    NARCIS (Netherlands)

    Bel, Elisabeth H.

    2004-01-01

    PURPOSE OF REVIEW: Asthma is a phenotypically heterogeneous disorder and, over the years, many different clinical subtypes of asthma have been described. A precise definition of asthma phenotypes is now becoming more and more important, not only for a better understanding of pathophysiologic

  15. Autism beyond diagnostic categories : characterization of autistic phenotypes in schizophrenia :

    OpenAIRE

    Kästner, A.; Begemann, M.; Michel, T.; Everts, S.; Stepniak, B.; Bach, C.; Poustka, L.; Becker, J.; Banaschewski, T.; Dose, M.; Ehrenreich, H.

    2015-01-01

    Abstract Background Behavioral phenotypical continua from health to disease suggest common underlying mechanisms with quantitative rather than qualitative differences. Until recently, autism spectrum disorders and schizophrenia were considered distinct nosologic entities. However, emerging evidence contributes to the blurring of symptomatic and genetic boundaries between these conditions. The present study aimed at quantifying behavioral phenotypes shared by autism spectrum disorders and schi...

  16. Genotype-Phenotype Aspects of Type 2 Long QT Syndrome

    NARCIS (Netherlands)

    Shimizu, Wataru; Moss, Arthur J.; Wilde, Arthur A. M.; Towbin, Jeffrey A.; Ackerman, Michael J.; January, Craig T.; Tester, David J.; Zareba, Wojciech; Robinson, Jennifer L.; Qi, Ming; Vincent, G. Michael; Kaufman, Elizabeth S.; Hofman, Nynke; Noda, Takashi; Kamakura, Shiro; Miyamoto, Yoshihiro; Shah, Samit; Amin, Vinit; Goldenberg, Ilan; Andrews, Mark L.; McNitt, Scott

    2009-01-01

    Objectives The purpose of this study was to investigate the effect of location, coding type, and topology of KCNH2(hERG) mutations on clinical phenotype in type 2 long QT syndrome (LQTS). Background Previous studies were limited by population size in their ability to examine phenotypic effect of

  17. Differential Impact of Lactose/Lactase Phenotype on Colonic Microflora

    Directory of Open Access Journals (Sweden)

    Andrew Szilagyi

    2010-01-01

    Full Text Available BACKGROUND: The ability to digest lactose divides the world’s population into two phenotypes that may be risk variability markers for several diseases. Prebiotic effects likely favour lactose maldigesters who experience lactose spilling into their colon.

  18. Optimal background matching camouflage.

    Science.gov (United States)

    Michalis, Constantine; Scott-Samuel, Nicholas E; Gibson, David P; Cuthill, Innes C

    2017-07-12

    Background matching is the most familiar and widespread camouflage strategy: avoiding detection by having a similar colour and pattern to the background. Optimizing background matching is straightforward in a homogeneous environment, or when the habitat has very distinct sub-types and there is divergent selection leading to polymorphism. However, most backgrounds have continuous variation in colour and texture, so what is the best solution? Not all samples of the background are likely to be equally inconspicuous, and laboratory experiments on birds and humans support this view. Theory suggests that the most probable background sample (in the statistical sense), at the size of the prey, would, on average, be the most cryptic. We present an analysis, based on realistic assumptions about low-level vision, that estimates the distribution of background colours and visual textures, and predicts the best camouflage. We present data from a field experiment that tests and supports our predictions, using artificial moth-like targets under bird predation. Additionally, we present analogous data for humans, under tightly controlled viewing conditions, searching for targets on a computer screen. These data show that, in the absence of predator learning, the best single camouflage pattern for heterogeneous backgrounds is the most probable sample. © 2017 The Authors.

  19. Phenotypic Approaches to Drought in Cassava: Review

    Directory of Open Access Journals (Sweden)

    Emmanuel eOkogbenin

    2013-05-01

    Full Text Available Cassava is an important crop in Africa, Asia, Latin America and the Caribbean. Cassava can be produced adequately in drought conditions making it the ideal food security crop in marginal environments. Although cassava can tolerate drought stress, it can be genetically improved to enhance productivity in such environments. Drought adaptation studies in over three decades in cassava have identified relevant mechanisms which have been explored in conventional breeding. Drought is a quantitative trait and its multigenic nature makes it very challenging to effectively manipulate and combine genes in breeding for rapid genetic gain and selection process. Cassava has a long growth cycle of 12 - 18 months which invariably contributes to a long breeding scheme for the crop. Modern breeding using advances in genomics and improved genotyping, is facilitating the dissection and genetic analysis of complex traits including drought tolerance, thus helping to better elucidate and understand the genetic basis of such traits. A beneficial goal of new innovative breeding strategies is to shorten the breeding cycle using minimized, efficient or fast phenotyping protocols. While high throughput genotyping have been achieved, this is rarely the case for phenotyping for drought adaptation. Some of the storage root phenotyping in cassava are often done very late in the evaluation cycle making selection process very slow. This paper highlights some modified traits suitable for early-growth phase phenotyping that may be used to reduce drought phenotyping cycle in cassava. Such modified traits can significantly complement the high throughput genotyping procedures to fast track breeding of improved drought tolerant varieties. The need for metabolite profiling, improved phenomics to take advantage of next generation sequencing technologies and high throughput phenotyping are basic steps for future direction to improve genetic gain and maximize speed for drought tolerance

  20. NF1 Neuronal Genotype Phenotype Relationships

    Science.gov (United States)

    2017-06-01

    interesting results from the Drosophila functional assays, at present we have decided to focus our attention on selected NF1 patient missense mutations...complexity of NF1 disease phenotypes in different tissues, age and sex dependency of symptoms, impact of environmental factors and genetic heterogeneity...suggesting the role of modifier genes [12]. This work aims to shed light on this issue by studying the functional consequences of selected NF1

  1. Maxwell-Chern-Simons theory for curved spacetime backgrounds

    International Nuclear Information System (INIS)

    Kant, E.; Klinkhamer, F.R.

    2005-01-01

    We consider a modified version of four-dimensional electrodynamics, which has a photonic Chern-Simons-like term with spacelike background vector in the action. Light propagation in curved spacetime backgrounds is discussed using the geometrical-optics approximation. The corresponding light path is modified, which allows for new effects. In a Schwarzschild background, for example, there now exist stable bounded orbits of light rays and the two polarization modes of light rays in unbounded orbits can have different gravitational redshifts

  2. Cosmic microwave background radiation

    International Nuclear Information System (INIS)

    Wilson, R.W.

    1979-01-01

    The 20-ft horn-reflector antenna at Bell Laboratories is discussed in detail with emphasis on the 7.35 cm radiometer. The circumstances leading to the detection of the cosmic microwave background radiation are explored

  3. Zambia Country Background Report

    DEFF Research Database (Denmark)

    Hampwaye, Godfrey; Jeppesen, Søren; Kragelund, Peter

    This paper provides background data and general information for the Zambia studies focusing on local food processing sub­‐sector; and the local suppliers to the mines as part of the SAFIC project (Successful African Firms and Institutional Change).......This paper provides background data and general information for the Zambia studies focusing on local food processing sub­‐sector; and the local suppliers to the mines as part of the SAFIC project (Successful African Firms and Institutional Change)....

  4. Invasion strategies in clonal aquatic plants: Are phenotypic differences caused by phenotypic plasticity or local adaptation?

    DEFF Research Database (Denmark)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit

    2010-01-01

    conditions and plant morphological characteristics. Conclusions: The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between......Background and Aims: The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important....... Methods: Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity...

  5. The phenotypic spectrum of organic acidurias and urea cycle disorders Part 2: the evolving clinical phenotype

    NARCIS (Netherlands)

    Kölker, Stefan; Valayannopoulos, Vassili; Burlina, Alberto B.; Sykut-Cegielska, Jolanta; Wijburg, Frits A.; Teles, Elisa Leão; Zeman, Jiri; Dionisi-Vici, Carlo; Barić, Ivo; Karall, Daniela; Arnoux, Jean-Baptiste; Avram, Paula; Baumgartner, Matthias R.; Blasco-Alonso, Javier; Boy, S. P. Nikolas; Rasmussen, Marlene Bøgehus; Burgard, Peter; Chabrol, Brigitte; Chakrapani, Anupam; Chapman, Kimberly; Cortès I Saladelafont, Elisenda; Couce, Maria L.; de Meirleir, Linda; Dobbelaere, Dries; Furlan, Francesca; Gleich, Florian; González, Maria Julieta; Gradowska, Wanda; Grünewald, Stephanie; Honzik, Tomas; Hörster, Friederike; Ioannou, Hariklea; Jalan, Anil; Häberle, Johannes; Haege, Gisela; Langereis, Eveline; de Lonlay, Pascale; Martinelli, Diego; Matsumoto, Shirou; Mühlhausen, Chris; Murphy, Elaine; de Baulny, Hélène Ogier; Ortez, Carlos; Pedrón, Consuelo C.; Pintos-Morell, Guillem; Pena-Quintana, Luis; Ramadža, Danijela Petković; Rodrigues, Esmeralda; Scholl-Bürgi, Sabine; Sokal, Etienne; Summar, Marshall L.; Thompson, Nicholas; Vara, Roshni; Pinera, Inmaculada Vives; Walter, John H.; Williams, Monique; Lund, Allan M.; Garcia-Cazorla, Angeles; Garcia Cazorla, Angeles

    2015-01-01

    Background The disease course and long-term outcome of patients with organic acidurias (OAD) and urea cycle disorders (UCD) are incompletely understood. Aims To evaluate the complex clinical phenotype of OAD and UCD patients at different ages. Results Acquired microcephaly and movement disorders

  6. Core neuropathological abnormalities in progranulin-deficient mice are penetrant on multiple genetic backgrounds.

    Science.gov (United States)

    Petkau, T L; Hill, A; Leavitt, B R

    2016-02-19

    Loss-of-function mutations in the progranulin gene (GRN) are a common cause of familial frontotemporal lobar degeneration (FTLD). A high degree of heterogeneity in the age-of-onset, duration of disease, and clinical presentation of FTLD, even among families carrying the same GRN mutation, suggests that additional modifying genes may be important to pathogenesis. Progranulin-knockout mice display subtle behavioral abnormalities and progressive neuropathological changes, as well as altered dendritic morphology and synaptic deficits in the hippocampus. In this study we evaluated multiple neuropathological endpoints in aged progranulin knockout mice and their wild-type littermates on two different genetic backgrounds: C57Bl/6 and 129/SvImJ. We find that in most brain regions, both strains are susceptible to progranulin-mediated neuropathological phenotypes, including astrogliosis, microgliosis, and highly accelerated deposition of the aging pigment lipofuscin. Neuroinflammation due to progranulin deficiency is exaggerated in the B6 strain and present, but less pronounced, in the 129 strain. Differences between the strains in hippocampal neuron counts and neuronal morphology suggest a complex role for progranulin in the hippocampus. We conclude that core progranulin-mediated neurodegenerative phenotypes are penetrant on multiple inbred mouse strains, but that genetic background modulates progranulin's role in neuroinflammation and hippocampal biology. Copyright © 2015 IBRO. Published by Elsevier Ltd. All rights reserved.

  7. Effects of background radiation

    International Nuclear Information System (INIS)

    Knox, E.G.; Stewart, A.M.; Gilman, E.A.; Kneale, G.W.

    1987-01-01

    The primary objective of this investigation is to measure the relationship between exposure to different levels of background gamma radiation in different parts of the country, and different Relative Risks for leukaemias and cancers in children. The investigation is linked to an earlier analysis of the effects of prenatal medical x-rays upon leukaemia and cancer risk; the prior hypothesis on which the background-study was based, is derived from the earlier results. In a third analysis, the authors attempted to measure varying potency of medical x-rays delivered at different stages of gestation and the results supply a link between the other two estimates. (author)

  8. The cosmic microwave background

    International Nuclear Information System (INIS)

    Silk, J.

    1991-01-01

    Recent limits on spectral distortions and angular anisotropies in the cosmic microwave background are reviewed. The various backgrounds are described, and the theoretical implications are assessed. Constraints on inflationary cosmology dominated by cold dark matter (CDM) and on open cosmological models dominated by baryonic dark matter (BDM), with, respectively, primordial random phase scale-invariant curvature fluctuations or non-gaussian isocurvature fluctuations are described. More exotic theories are addressed, and I conclude with the 'bottom line': what theories expect experimentalists to be measuring within the next two to three years without having to abandon their most cherished theorists. (orig.)

  9. The Cosmic Background Explorer

    Science.gov (United States)

    Gulkis, Samuel; Lubin, Philip M.; Meyer, Stephan S.; Silverberg, Robert F.

    1990-01-01

    The Cosmic Background Explorer (CBE), NASA's cosmological satellite which will observe a radiative relic of the big bang, is discussed. The major questions connected to the big bang theory which may be clarified using the CBE are reviewed. The satellite instruments and experiments are described, including the Differential Microwave Radiometer, which measures the difference between microwave radiation emitted from two points on the sky, the Far-Infrared Absolute Spectrophotometer, which compares the spectrum of radiation from the sky at wavelengths from 100 microns to one cm with that from an internal blackbody, and the Diffuse Infrared Background Experiment, which searches for the radiation from the earliest generation of stars.

  10. COPD: Definition and Phenotypes

    DEFF Research Database (Denmark)

    Vestbo, J.

    2014-01-01

    particles or gases. Exacerbations and comorbidities contribute to the overall severity in individual patients. The evolution of this definition and the diagnostic criteria currently in use are discussed. COPD is increasingly divided in subgroups or phenotypes based on specific features and association...

  11. Phenotypic Resistance to Antibiotics

    Directory of Open Access Journals (Sweden)

    Jose L. Martinez

    2013-04-01

    Full Text Available The development of antibiotic resistance is usually associated with genetic changes, either to the acquisition of resistance genes, or to mutations in elements relevant for the activity of the antibiotic. However, in some situations resistance can be achieved without any genetic alteration; this is called phenotypic resistance. Non-inherited resistance is associated to specific processes such as growth in biofilms, a stationary growth phase or persistence. These situations might occur during infection but they are not usually considered in classical susceptibility tests at the clinical microbiology laboratories. Recent work has also shown that the susceptibility to antibiotics is highly dependent on the bacterial metabolism and that global metabolic regulators can modulate this phenotype. This modulation includes situations in which bacteria can be more resistant or more susceptible to antibiotics. Understanding these processes will thus help in establishing novel therapeutic approaches based on the actual susceptibility shown by bacteria during infection, which might differ from that determined in the laboratory. In this review, we discuss different examples of phenotypic resistance and the mechanisms that regulate the crosstalk between bacterial metabolism and the susceptibility to antibiotics. Finally, information on strategies currently under development for diminishing the phenotypic resistance to antibiotics of bacterial pathogens is presented.

  12. Thermal background noise limitations

    Science.gov (United States)

    Gulkis, S.

    1982-01-01

    Modern detection systems are increasingly limited in sensitivity by the background thermal photons which enter the receiving system. Expressions for the fluctuations of detected thermal radiation are derived. Incoherent and heterodyne detection processes are considered. References to the subject of photon detection statistics are given.

  13. Berkeley Low Background Facility

    International Nuclear Information System (INIS)

    Thomas, K. J.; Norman, E. B.; Smith, A. R.; Poon, A. W. P.; Chan, Y. D.; Lesko, K. T.

    2015-01-01

    The Berkeley Low Background Facility (BLBF) at Lawrence Berkeley National Laboratory (LBNL) in Berkeley, California provides low background gamma spectroscopy services to a wide array of experiments and projects. The analysis of samples takes place within two unique facilities; locally within a carefully-constructed, low background laboratory on the surface at LBNL and at the Sanford Underground Research Facility (SURF) in Lead, SD. These facilities provide a variety of gamma spectroscopy services to low background experiments primarily in the form of passive material screening for primordial radioisotopes (U, Th, K) or common cosmogenic/anthropogenic products; active screening via neutron activation analysis for U,Th, and K as well as a variety of stable isotopes; and neutron flux/beam characterization measurements through the use of monitors. A general overview of the facilities, services, and sensitivities will be presented. Recent activities and upgrades will also be described including an overview of the recently installed counting system at SURF (recently relocated from Oroville, CA in 2014), the installation of a second underground counting station at SURF in 2015, and future plans. The BLBF is open to any users for counting services or collaboration on a wide variety of experiments and projects

  14. Gene-environment and protein degradation signatures characterize genomic and phenotypic diversity in wild Caenorhabditis elegans populations

    NARCIS (Netherlands)

    Volkers, J.M.; Snoek, L.B.; Hellenberg Hubar, van C.J.; Coopman, R.; Chen, W.; Yang, Wentao; Sterken, M.G.; Schulenburg, H.; Braeckman, B.; Kammenga, J.E.

    2013-01-01

    Background: Analyzing and understanding the relationship between genotypes and phenotypes is at the heart of genetics. Research on the nematode Caenorhabditis elegans has been instrumental for unraveling genotype-phenotype relations, and has important implications for understanding the biology of

  15. Reciprocal Effects on Neurocognitive and Metabolic Phenotypes in Mouse Models of 16p11.2 Deletion and Duplication Syndromes.

    Directory of Open Access Journals (Sweden)

    Thomas Arbogast

    2016-02-01

    Full Text Available The 16p11.2 600 kb BP4-BP5 deletion and duplication syndromes have been associated with developmental delay; autism spectrum disorders; and reciprocal effects on the body mass index, head circumference and brain volumes. Here, we explored these relationships using novel engineered mouse models carrying a deletion (Del/+ or a duplication (Dup/+ of the Sult1a1-Spn region homologous to the human 16p11.2 BP4-BP5 locus. On a C57BL/6N inbred genetic background, Del/+ mice exhibited reduced weight and impaired adipogenesis, hyperactivity, repetitive behaviors, and recognition memory deficits. In contrast, Dup/+ mice showed largely opposite phenotypes. On a F1 C57BL/6N × C3B hybrid genetic background, we also observed alterations in social interaction in the Del/+ and the Dup/+ animals, with other robust phenotypes affecting recognition memory and weight. To explore the dosage effect of the 16p11.2 genes on metabolism, Del/+ and Dup/+ models were challenged with high fat and high sugar diet, which revealed opposite energy imbalance. Transcriptomic analysis revealed that the majority of the genes located in the Sult1a1-Spn region were sensitive to dosage with a major effect on several pathways associated with neurocognitive and metabolic phenotypes. Whereas the behavioral consequence of the 16p11 region genetic dosage was similar in mice and humans with activity and memory alterations, the metabolic defects were opposite: adult Del/+ mice are lean in comparison to the human obese phenotype and the Dup/+ mice are overweight in comparison to the human underweight phenotype. Together, these data indicate that the dosage imbalance at the 16p11.2 locus perturbs the expression of modifiers outside the CNV that can modulate the penetrance, expressivity and direction of effects in both humans and mice.

  16. Modified SEAGULL

    Science.gov (United States)

    Salas, M. D.; Kuehn, M. S.

    1994-01-01

    Original version of program incorporated into program SRGULL (LEW-15093) for use on National Aero-Space Plane project, its duty being to model forebody, inlet, and nozzle portions of vehicle. However, real-gas chemistry effects in hypersonic flow fields limited accuracy of that version, because it assumed perfect-gas properties. As a result, SEAGULL modified according to real-gas equilibrium-chemistry methodology. This program analyzes two-dimensional, hypersonic flows of real gases. Modified version of SEAGULL maintains as much of original program as possible, and retains ability to execute original perfect-gas version.

  17. Elucidating the genotype–phenotype map by automatic enumeration and analysis of the phenotypic repertoire

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2015-01-01

    Background: The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. Methods: The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Results: Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Conclusions: Starting with a system’s relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy. PMID:26998346

  18. Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

    Directory of Open Access Journals (Sweden)

    Yook Karen

    2011-01-01

    Full Text Available Abstract Background Caenorhabditis elegans gene-based phenotype information dates back to the 1970's, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. Results We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO. The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. Conclusions We provide a phenotype ontology (WPO that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and

  19. The Cosmic Microwave Background

    Directory of Open Access Journals (Sweden)

    Jones Aled

    1998-01-01

    Full Text Available We present a brief review of current theory and observations of the cosmic microwave background (CMB. New predictions for cosmological defect theories and an overview of the inflationary theory are discussed. Recent results from various observations of the anisotropies of the microwave background are described and a summary of the proposed experiments is presented. A new analysis technique based on Bayesian statistics that can be used to reconstruct the underlying sky fluctuations is summarised. Current CMB data is used to set some preliminary constraints on the values of fundamental cosmological parameters $Omega$ and $H_circ$ using the maximum likelihood technique. In addition, secondary anisotropies due to the Sunyaev-Zel'dovich effect are described.

  20. Genetic Modifiers of Sickle Cell Disease

    Science.gov (United States)

    Steinberg, Martin H.; Sebastiani, Paola

    2015-01-01

    Sickle cell anemia is associated with unusual clinical heterogeneity for a Mendelian disorder. Fetal hemoglobin concentration and coincident ∝ thalassemia, both which directly affect the sickle erythrocyte, are the major modulators of the phenotype of disease. Understanding the genetics underlying the heritable subphenotypes of sickle cell anemia would be prognostically useful, could inform personalized therapeutics, and might help the discovery of new “druggable” pathophysiologic targets. Genotype-phenotype association studies have been used to identify novel genetic modifiers. In the future, whole genome sequencing with its promise of discovering hitherto unsuspected variants could add to our understanding of the genetic modifiers of this disease. PMID:22641398

  1. Relationship between endophenotype and phenotype in ADHD

    Directory of Open Access Journals (Sweden)

    Buitelaar Jan K

    2008-01-01

    Full Text Available Abstract Background It has been hypothesized that genetic and environmental factors relate to psychiatric disorders through the effect of intermediating, vulnerability traits called endophenotypes. The study had a threefold aim: to examine the predictive validity of an endophenotypic construct for the ADHD diagnosis, to test whether the magnitude of group differences at the endophenotypic and phenotypic level is comparable, and to investigate whether four factors (gender, age, IQ, rater bias have an effect (moderation or mediation on the relation between endophenotype and phenotype. Methods Ten neurocognitive tasks were administered to 143 children with ADHD, 68 non-affected siblings, and 120 control children (first-borns and 132 children with ADHD, 78 non-affected siblings, and 113 controls (second-borns (5 – 19 years. The task measures have been investigated previously for their endophenotypic viability and were combined to one component which was labeled 'the endophenotypic construct': one measure representative of endophenotypic functioning across several domains of functioning. Results The endophenotypic construct classified children with moderate accuracy (about 50% for each of the three groups. Non-affected children differed as much from controls at the endophenotypic as at the phenotypic level, but affected children displayed a more severe phenotype than endophenotype. Although a potentially moderating effect (age and several mediating effects (gender, age, IQ were found affecting the relation between endophenotypic construct and phenotype, none of the effects studied could account for the finding that affected children had a more severe phenotype than endophenotype. Conclusion Endophenotypic functioning is moderately predictive of the ADHD diagnosis, though findings suggest substantial overlap exists between endophenotypic functioning in the groups of affected children, non-affected siblings, and controls. Results suggest other

  2. Family Background and Entrepreneurship

    DEFF Research Database (Denmark)

    Lindquist, Matthew J.; Sol, Joeri; Van Praag, Mirjam

    Vast amounts of money are currently being spent on policies aimed at promoting entrepreneurship. The success of such policies, however, rests in part on the assumption that individuals are not ‘born entrepreneurs’. In this paper, we assess the importance of family background and neighborhood...... effects as determinants of entrepreneurship. We start by estimating sibling correlations in entrepreneurship. We find that between 20 and 50 percent of the variance in different entrepreneurial outcomes is explained by factors that siblings share. The average is 28 percent. Allowing for differential...... entrepreneurship does play a large role, as do shared genes....

  3. Malaysia; Background Paper

    OpenAIRE

    International Monetary Fund

    1996-01-01

    This Background Paper on Malaysia examines developments and trends in the labor market since the mid-1980s. The paper describes the changes in the employment structure and the labor force. It reviews wages and productivity trends and their effects on unit labor cost. The paper highlights that Malaysia’s rapid growth, sustained since 1987, has had a major impact on the labor market. The paper outlines the major policy measures to address the labor constraints. It also analyzes Malaysia’s recen...

  4. Natural genetic variation in transcriptome reflects network structure inferred with major effect mutations: insulin/TOR and associated phenotypes in Drosophila melanogaster

    Directory of Open Access Journals (Sweden)

    Harshman Lawrence G

    2009-03-01

    Full Text Available Abstract Background A molecular process based genotype-to-phenotype map will ultimately enable us to predict how genetic variation among individuals results in phenotypic alterations. Building such a map is, however, far from straightforward. It requires understanding how molecular variation re-shapes developmental and metabolic networks, and how the functional state of these networks modifies phenotypes in genotype specific way. We focus on the latter problem by describing genetic variation in transcript levels of genes in the InR/TOR pathway among 72 Drosophila melanogaster genotypes. Results We observe tight co-variance in transcript levels of genes not known to influence each other through direct transcriptional control. We summarize transcriptome variation with factor analyses, and observe strong co-variance of gene expression within the dFOXO-branch and within the TOR-branch of the pathway. Finally, we investigate whether major axes of transcriptome variation shape phenotypes expected to be influenced through the InR/TOR pathway. We find limited evidence that transcript levels of individual upstream genes in the InR/TOR pathway predict fly phenotypes in expected ways. However, there is no evidence that these effects are mediated through the major axes of downstream transcriptome variation. Conclusion In summary, our results question the assertion of the 'sparse' nature of genetic networks, while validating and extending candidate gene approaches in the analyses of complex traits.

  5. Anogenital distance as a phenotypic signature through infancy

    DEFF Research Database (Denmark)

    Priskorn, Lærke; Petersen, Jørgen H; Jørgensen, Niels

    2018-01-01

    BACKGROUND: Anogenital distance (AGD) has been suggested to represent a phenotypic signature reflecting in utero androgen action. However, it is not known whether an individual's AGD at birth correlates to AGD later in life. We investigate correlations of AGD between 3 and 18 months and asses rep......-up through childhood and puberty will reveal whether AGD represents a phenotypic signature throughout life.Pediatric Research accepted article preview online, 20 November 2017. doi:10.1038/pr.2017.287....

  6. Backgrounded but not peripheral

    DEFF Research Database (Denmark)

    Hovmark, Henrik

    2013-01-01

    .e. the schema enters into apparently contradictory constructions of the informants’ local home-base and, possibly, of their identity (cf. Hovmark, 2010). Second, I discuss the status and role of the specific linguistic category in question, i.e. the directional adverbs. On the one hand we claim that the DDAs......In this paper I pay a closer look at the use of the CENTRE-PERIPHERY schema in context. I address two specific issues: first, I show how the CENTRE-PERIPHERY schema, encoded in the DDAs, enters into discourses that conceptualize and characterize a local community as both CENTRE and PERIPHERY, i......; furthermore, the DDAs are backgrounded in discourse. Is it reasonable to claim, rather boldly, that “the informants express their identity in the use of the directional adverb ud ‘out’ etc.”? In the course of this article, however, I suggest that the DDAs in question do contribute to the socio...

  7. OCRWM Backgrounder, January 1987

    International Nuclear Information System (INIS)

    1987-01-01

    The Nuclear Waste Policy Act of 1982 (NWPA) assigns to the US Department of Energy (DOE) responsibility for developing a system to safely and economically transport spent nuclear fuel and high-level radioactive waste from various storage sites to geologic repositories or other facilities that constitute elements of the waste management program. This transportation system will evolve from technologies and capabilities already developed. Shipments of spent fuel to a monitored retrievable storage (MRS) facility could begin as early as 1996 if Congress authorizes its construction. Shipments of spent fuel to a geologic repository are scheduled to begin in 1998. The backgrounder provides an overview of DOE's cask development program. Transportation casks are a major element in the DOE nuclear waste transportation system because they are the primary protection against any potential radiation exposure to the public and transportation workers in the event an accident occurs

  8. Monitored background radiometer

    International Nuclear Information System (INIS)

    Ruel, C.

    1988-01-01

    A monitored background radiometer is described comprising: a thermally conductive housing; low conductivity support means mounted on the housing; a sensing plate mounted on the low conductivity support means and spaced from the housing so as to be thermally insulated from the housing and having an outwardly facing first surface; the sensing plate being disposed relative to the housing to receive direct electromagnetic radiation from sources exterior to the radiometer upon the first surface only; means for controllably heating the sensing plate; first temperature sensitive means to measure the temperature of the housing; and second temperature sensitive means to measure the temperature of the sensing plate, so that the heat flux at the sensing plate may be determined from the temperatures of the housing and sensing plate after calibration of the radiometer by measuring the temperatures of the housing and sensing plate while controllably heating the sensing plate

  9. Genetic modifiers of nutritional status in cystic fibrosis1234

    Science.gov (United States)

    Bradley, Gia M; Blackman, Scott M; Watson, Christopher P; Doshi, Vishal K; Cutting, Garry R

    2012-01-01

    Background: Improved nutrition early in life is associated with better pulmonary function for patients with cystic fibrosis (CF). However, nutritional status is poorly correlated with the CFTR genotype. Objective: We investigated the extent to which modifier genes influence nutrition in children with CF. Design: BMI data were longitudinally collected from the CF Twin-Sibling Study and Cystic Fibrosis Foundation Patient Registry for twins and siblings from 2000 to 2010. A nutritional phenotype was derived for 1124 subjects by calculating the average BMI z score from 5–10 y of age (BMI-z5to10). The genetic contribution to the variation in BMI-z5to10 (ie, heritability) was estimated by comparing the similarity of the phenotype in monozygous twins to that in dizygous twins and siblings. Linkage analysis identified potential modifier-gene loci. Results: The median BMI-z5to10 was −0.07 (range: −3.89 to 2.30), which corresponded to the 47th CDC percentile. BMI-z5to10 was negatively correlated with pancreatic insufficiency, history of meconium ileus, and female sex but positively correlated with later birth cohorts and lung function. Monozygous twins showed greater concordance for BMI-z5to10 than did dizygous twins and siblings; heritability estimates from same-sex twin-only analyses ranged from 0.54 to 0.82. For 1010 subjects with pancreatic insufficiency, genome-wide significant linkage was identified on chromosomes 1p36.1 [log of odds (LOD): 5.3] and 5q14 (LOD: 5.1). These loci explained ≥16% and ≥15%, respectively, of the BMI variance. Conclusions: The analysis of twins and siblings with CF indicates a prominent role for genes other than CFTR to BMI variation. Specifically, regions on chromosomes 1 and 5 appear to harbor genetic modifiers of substantial effect. PMID:23134884

  10. Low background infrared (LBIR) facility

    Data.gov (United States)

    Federal Laboratory Consortium — The Low background infrared (LBIR) facility was originally designed to calibrate user supplied blackbody sources and to characterize low-background IR detectors and...

  11. Hanford Site background: Part 1, Soil background for nonradioactive analytes

    International Nuclear Information System (INIS)

    1993-04-01

    Volume two contains the following appendices: Description of soil sampling sites; sampling narrative; raw data soil background; background data analysis; sitewide background soil sampling plan; and use of soil background data for the detection of contamination at waste management unit on the Hanford Site

  12. MiR-29b Downregulation Induces Phenotypic Modulation of Vascular Smooth Muscle Cells: Implication for Intracranial Aneurysm Formation and Progression to Rupture

    Directory of Open Access Journals (Sweden)

    Liqian Sun

    2017-01-01

    Full Text Available Background/Aims: Our previous microarray results identified numerous microRNAs (miRNAs, including miR-29b, that were differentially expressed in the serum of intracranial aneurysm (IA patients. The current study aimed to investigate whether miR-29b downregulation in IA could promote the phenotypic modulation of vascular smooth muscle cells (VSMCs involved in the pathogenesis of aneurysm by activating ATG14-mediated autophagy. Methods: First, the levels of miR-29b and autophagy related genes (ATGs between IA patients and normal subjects were compared. Next, we modified the level of miR-29b via lentivirus particles in the VSMCs and examined the effects of miR-29b on proliferation, migration, and phenotypic modulation of VSMCs from a contractile phenotype to a synthetic phenotype, as well as the levels of autophagy. Finally, the binding of miR-29b to the 3’UTR of ATG14 mRNA and its effects on ATG14 expression were analysed by a luciferase reporter assay and Western blot, respectively. Results: The level of miR-29b was decreased, and autophagy markers were increased in the IA patients compared to that of the normal subjects. Knockdown of miR-29b significantly promoted VSMCs proliferation and migration and, more importantly, induced the phenotypic modulation associated with autophagy activation, whereas miR-29b overexpression showed the opposite effects. The luciferase reporter assay demonstrated that ATG14 was a functional target gene of miR-29b. Notably, knockdown of ATG14 by siRNA apparently abrogated miR-29b inhibition-mediated phenotypic modulation. Conclusion: Downregulation of miR-29b induced VSMCs phenotypic modulation by directly activating ATG14-mediated autophagy, which is associated with the formation, growth and rupture of IAs.

  13. Metabolic profiles to define the genome: can we hear the phenotypes?

    OpenAIRE

    Griffin, Julian L

    2004-01-01

    There is an increased reliance on genetically modified organisms as a functional genomic tool to elucidate the role of genes and their protein products. Despite this, many models do not express the expected phenotype thought to be associated with the gene or protein. There is thus an increased need to further define the phenotype resultant from a genetic modification to understand how the transcriptional or proteomic network may conspire to alter the expected phenotype. This is best typified ...

  14. The Autism Simplex Collection : an international, expertly phenotyped autism sample for genetic and phenotypic analyses

    OpenAIRE

    Buxbaum, Joseph D.; Bolshakova, Nadia; Brownfeld, Jessica M.; Anney, Richard J. L.; Bender, Patrick; Bernier, Raphael; Cook, Edwin H.; Coon, Hilary; Cuccaro, Michael L.; Freitag, Christine M.; Hallmayer, Joachim; Geschwind, Daniel H.; Klauck, Sabine M.; Nurnberger, John I.; Oliveira, Guiomar

    2014-01-01

    Background: There is an urgent need for expanding and enhancing autism spectrum disorder (ASD) samples, in order to better understand causes of ASD. Methods: In a unique public-private partnership, 13 sites with extensive experience in both the assessment and diagnosis of ASD embarked on an ambitious, 2-year program to collect samples for genetic and phenotypic research and begin analyses on these samples. The program was called The Autism Simplex Collection (TASC). TASC sample collection ...

  15. Interfacial Modifiers

    Energy Technology Data Exchange (ETDEWEB)

    Martin, Ina; French, Roger H.

    2018-03-19

    Our project objective in the first and only Budget Period was to demonstrate the potential of nm-scale organofunctional silane coatings as a method of extending the lifetime of PV materials and devices. Specifically, the target was to double the lifetime performance of a laminated Cu(In,Ga)Se2 (CIGS) cell under real-world and accelerated aging exposure conditions. Key findings are that modification of aluminum-doped zinc oxide (AZO) films (materials used as transparent conductive oxide (TCO) top contacts) resulted in decreased degradation of optical and electrical properties under damp heat (DH) exposure compared to un-modified AZO. The most significant finding is that modification of the AZO top contact of full CIGS devices resulted in significantly improved properties under DH exposure compared to un-modified devices, by a factor of 4 after 1000 h. Results of this one-year project have demonstrated that surface functionalization is a viable pathway for extending the lifetime of state-of-the-art CIGS devices.

  16. CLC-2 single nucleotide polymorphisms (SNPs) as potential modifiers of cystic fibrosis disease severity

    Science.gov (United States)

    Blaisdell, Carol J; Howard, Timothy D; Stern, Augustus; Bamford, Penelope; Bleecker, Eugene R; Stine, O Colin

    2004-01-01

    Background Cystic fibrosis (CF) lung disease manifest by impaired chloride secretion leads to eventual respiratory failure. Candidate genes that may modify CF lung disease severity include alternative chloride channels. The objectives of this study are to identify single nucleotide polymorphisms (SNPs) in the airway epithelial chloride channel, CLC-2, and correlate these polymorphisms with CF lung disease. Methods The CLC-2 promoter, intron 1 and exon 20 were examined for SNPs in adult CF dF508/dF508 homozygotes with mild and severe lung disease (forced expiratory volume at one second (FEV1) > 70% and < 40%). Results PCR amplification of genomic CLC-2 and sequence analysis revealed 1 polymorphism in the hClC -2 promoter, 4 in intron 1, and none in exon 20. Fisher's analysis within this data set, did not demonstrate a significant relationship between the severity of lung disease and SNPs in the CLC-2 gene. Conclusions CLC-2 is not a key modifier gene of CF lung phenotype. Further studies evaluating other phenotypes associated with CF may be useful in the future to assess the ability of CLC-2 to modify CF disease severity. PMID:15507145

  17. CLC-2 single nucleotide polymorphisms (SNPs as potential modifiers of cystic fibrosis disease severity

    Directory of Open Access Journals (Sweden)

    Bleecker Eugene R

    2004-10-01

    Full Text Available Abstract Background Cystic fibrosis (CF lung disease manifest by impaired chloride secretion leads to eventual respiratory failure. Candidate genes that may modify CF lung disease severity include alternative chloride channels. The objectives of this study are to identify single nucleotide polymorphisms (SNPs in the airway epithelial chloride channel, CLC-2, and correlate these polymorphisms with CF lung disease. Methods The CLC-2 promoter, intron 1 and exon 20 were examined for SNPs in adult CF dF508/dF508 homozygotes with mild and severe lung disease (forced expiratory volume at one second (FEV1 > 70% and Results PCR amplification of genomic CLC-2 and sequence analysis revealed 1 polymorphism in the hClC -2 promoter, 4 in intron 1, and none in exon 20. Fisher's analysis within this data set, did not demonstrate a significant relationship between the severity of lung disease and SNPs in the CLC-2 gene. Conclusions CLC-2 is not a key modifier gene of CF lung phenotype. Further studies evaluating other phenotypes associated with CF may be useful in the future to assess the ability of CLC-2 to modify CF disease severity.

  18. From metabolome to phenotype

    DEFF Research Database (Denmark)

    Khakimov, Bekzod; Rasmussen, Morten Arendt; Kannangara, Rubini Maya

    2017-01-01

    for ideal vegetable protein production and for augmented β-glucan production. Seeds from three barley lines (Bomi, lys3.a and lys5.f) were sampled eight times during grain filling and analysed for metabolites using gas chromatography-mass spectrometry (GC-MS). The lys3.a mutation disrupts a regulator gene...... their successful application to link genetic and environmental factors with the seed phenotype of unique and agro-economically important barley models for optimal vegetable protein and dietary fibre production......., causing an increase in proteins rich in the essential amino acid lysine, while lys5.f carries a mutation in an ADP-glucose transporter gene leading to a significant increase in production of mixed-linkage β-glucan at the expense of α-glucan. Unique metabolic patterns associated with the tricarboxylic acid...

  19. Haploinsufficient Bmp4 ocular phenotypes include anterior segment dysgenesis with elevated intraocular pressure

    Directory of Open Access Journals (Sweden)

    Nusinowitz Steven

    2001-11-01

    Full Text Available Abstract Background Glaucoma is a blinding disease usually associated with high intraocular pressure (IOP. In some families, abnormal anterior segment development contributes to glaucoma. The genes causing anterior segment dysgenesis and glaucoma in most of these families are not identified and the affected developmental processes are poorly understood. Bone morphogenetic proteins (BMPs participate in various developmental processes. We tested the importance of Bmp4 gene dosage for ocular development and developmental glaucoma. Results Bmp4+/- mice have anterior segment abnormalities including malformed, absent or blocked trabecular meshwork and Schlemm's canal drainage structures. Mice with severe drainage structure abnormalities, over 80% or more of their angle's extent, have elevated IOP. The penetrance and severity of abnormalities is strongly influenced by genetic background, being most severe on the C57BL/6J background and absent on some other backgrounds. On the C57BL/6J background there is also persistence of the hyaloid vasculature, diminished numbers of inner retinal cells, and absence of the optic nerve. Conclusions We demonstrate that heterozygous deficiency of BMP4 results in anterior segment dysgenesis and elevated IOP. The abnormalities are similar to those in human patients with developmental glaucoma. Thus, BMP4 is a strong candidate to contribute to Axenfeld-Rieger anomaly and other developmental conditions associated with human glaucoma. BMP4 also participates in posterior segment development and wild-type levels are usually critical for optic nerve development on the C57BL/6J background. Bmp4+/- mice are useful for studying various components of ocular development, and may allow identification of strain specific modifiers affecting a variety of ocular phenotypes.

  20. Plants having modified response to ethylene

    Science.gov (United States)

    Meyerowitz, E.M.; Chang, C.; Bleecker, A.B.

    1997-11-18

    The invention includes transformed plants having at least one cell transformed with a modified ETR nucleic acid. Such plants have a phenotype characterized by a decrease in the response of at least one transformed plant cell to ethylene as compared to a plant not containing the transformed plant cell. Tissue and/or temporal specificity for expression of the modified ETR nucleic acid is controlled by selecting appropriate expression regulation sequences to target the location and/or time of expression of the transformed nucleic acid. The plants are made by transforming at least one plant cell with an appropriate modified ETR nucleic acid, regenerating plants from one or more of the transformed plant cells and selecting at least one plant having the desired phenotype. 31 figs.

  1. Invasion strategies in clonal aquatic plants: are phenotypic differences caused by phenotypic plasticity or local adaptation?

    Science.gov (United States)

    Riis, Tenna; Lambertini, Carla; Olesen, Birgit; Clayton, John S.; Brix, Hans; Sorrell, Brian K.

    2010-01-01

    Background and Aims The successful spread of invasive plants in new environments is often linked to multiple introductions and a diverse gene pool that facilitates local adaptation to variable environmental conditions. For clonal plants, however, phenotypic plasticity may be equally important. Here the primary adaptive strategy in three non-native, clonally reproducing macrophytes (Egeria densa, Elodea canadensis and Lagarosiphon major) in New Zealand freshwaters were examined and an attempt was made to link observed differences in plant morphology to local variation in habitat conditions. Methods Field populations with a large phenotypic variety were sampled in a range of lakes and streams with different chemical and physical properties. The phenotypic plasticity of the species before and after cultivation was studied in a common garden growth experiment, and the genetic diversity of these same populations was also quantified. Key Results For all three species, greater variation in plant characteristics was found before they were grown in standardized conditions. Moreover, field populations displayed remarkably little genetic variation and there was little interaction between habitat conditions and plant morphological characteristics. Conclusions The results indicate that at the current stage of spread into New Zealand, the primary adaptive strategy of these three invasive macrophytes is phenotypic plasticity. However, while limited, the possibility that genetic diversity between populations may facilitate ecotypic differentiation in the future cannot be excluded. These results thus indicate that invasive clonal aquatic plants adapt to new introduced areas by phenotypic plasticity. Inorganic carbon, nitrogen and phosphorous were important in controlling plant size of E. canadensis and L. major, but no other relationships between plant characteristics and habitat conditions were apparent. This implies that within-species differences in plant size can be explained

  2. Executive Summary - Historical background

    International Nuclear Information System (INIS)

    2005-01-01

    matter physics experiments at the High Flux Reactor of The Laue Langevin Institute and the ISIS spallation source at Rutherford-Appleton. Recently, we very actively entered the ICARUS neutrino collaboration and were invited to the PIERRE AUGER collaboration which will search for the highest energies in the Universe. Having close ties with CERN we are very actively engaged in CROSS-GRID, a large computer network project. To better understand the historical background of the INP development, it is necessary to add a few comments on financing of science in Poland. During the 70's and the 80's, research was financed through the so-called Central Research Projects for Science and Technical Development. The advantage of this system was that state-allocated research funds were divided only by a few representatives of the scientific community, which allowed realistic allocation of money to a small number of projects. After 1989 we were able to purchase commercially available equipment, which led to the closure of our large and very experienced electronic workshop. We also considerably reduced our well equipped mechanical shop. During the 90's the reduced state financing of science was accompanied by a newly established Committee of Scientific Research which led to the creation of a system of small research projects. This precluded the development of more ambitious research projects and led to the dispersion of equipment among many smaller laboratories and universities. A large research establishment, such as our Institute, could not develop properly under such conditions. In all, between 1989 and 2004 we reduced our personnel from about 800 to 470 and our infrastructure became seriously undercapitalised. However, with energetic search for research funds, from European rather than national research programs, we hope to improve and modernize our laboratories and their infrastructure in the coming years

  3. Integration of curated databases to identify genotype-phenotype associations

    Directory of Open Access Journals (Sweden)

    Li Jianrong

    2006-10-01

    Full Text Available Abstract Background The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curated biological information. Here we utilize a systematic approach to discover genotype-phenotype associations that combines phenotypic information from a biomedical informatics database, GIDEON, with the molecular information contained in National Center for Biotechnology Information's Clusters of Orthologous Groups database (NCBI COGs. Results Integrating the information in the two databases, we are able to correlate the presence or absence of a given protein in a microbe with its phenotype as measured by certain morphological characteristics or survival in a particular growth media. With a 0.8 correlation score threshold, 66% of the associations found were confirmed by the literature and at a 0.9 correlation threshold, 86% were positively verified. Conclusion Our results suggest possible phenotypic manifestations for proteins biochemically associated with sugar metabolism and electron transport. Moreover, we believe our approach can be extended to linking pathogenic phenotypes with functionally related proteins.

  4. A simple phenotypic classification for celiac disease

    Directory of Open Access Journals (Sweden)

    Ajit Sood

    2018-04-01

    Full Text Available Background/Aims : Celiac disease is a global health problem. The presentation of celiac disease has unfolded over years and it is now known that it can manifest at different ages, has varied presentations, and is prone to develop complications, if not managed properly. Although the Oslo definitions provide consensus on the various terminologies used in literature, there is no phenotypic classification providing a composite diagnosis for the disease. Methods : Various variables identified for phenotypic classification included age at diagnosis, age at onset of symptoms, clinical presentation, family history and complications. These were applied to the existing registry of 1,664 patients at Dayanand Medical College and Hospital, Ludhiana, India. In addition, age was evaluated as below 15 and below 18 years. Cross tabulations were used for the verification of the classification using the existing data. Expert opinion was sought from both international and national experts of varying fields. Results : After empirical verification, age at diagnosis was considered appropriate in between A1 (<18 and A2 (≧18. The disease presentation has been classified into 3 types–P1 (classical, P2 (non-classical and P3 (asymptomatic. Complications were considered as absent (C0 or present (C1. A single phenotypic classification based on these 3 characteristics, namely age at the diagnosis, clinical presentation, and intestinal complications (APC classification was derived. Conclusions : APC classification (age at diagnosis, presentation, complications is a simple disease explanatory classification for patients with celiac disease aimed at providing a composite diagnosis.

  5. Dissecting phenotypic variation among AIS patients

    International Nuclear Information System (INIS)

    Wang Minghua; Wang Jiucun; Zhang Zhen; Zhao Zhimin; Zhang Rongmei; Hu Xiaohua; Tan Tao; Luo Shijing; Luo Zewei

    2005-01-01

    We have created genital skin fibroblast cell lines directly from three patients in a Chinese family affected by androgen insensitivity syndrome (AIS). All patients in the family share an identical AR Arg 840 Cys mutant but show different disease phenotypes. By using the cell lines, we find that the mutation has not influenced a normal androgen-binding capacity at 37 deg C but has reduced the affinity for androgens and may cause thermolability of the androgen-receptor complex. The impaired nuclear trafficking of the androgen receptor in the cell lines is highly correlated with the severity of donors' disease phenotype. The transactivity of the mutant is substantially weakened and the extent of the reduced transactivity reflects severity of the donors' disease symptom. Our data reveal that although etiology of AIS is monogenic and the mutant may alter the major biological functions of its wild allele, the function of the mutant AR can also be influenced by the different genetic backgrounds and thus explains the divergent disease phenotypes

  6. Predictable Phenotypes of Antibiotic Resistance Mutations.

    Science.gov (United States)

    Knopp, M; Andersson, D I

    2018-05-15

    Antibiotic-resistant bacteria represent a major threat to our ability to treat bacterial infections. Two factors that determine the evolutionary success of antibiotic resistance mutations are their impact on resistance level and the fitness cost. Recent studies suggest that resistance mutations commonly show epistatic interactions, which would complicate predictions of their stability in bacterial populations. We analyzed 13 different chromosomal resistance mutations and 10 host strains of Salmonella enterica and Escherichia coli to address two main questions. (i) Are there epistatic interactions between different chromosomal resistance mutations? (ii) How does the strain background and genetic distance influence the effect of chromosomal resistance mutations on resistance and fitness? Our results show that the effects of combined resistance mutations on resistance and fitness are largely predictable and that epistasis remains rare even when up to four mutations were combined. Furthermore, a majority of the mutations, especially target alteration mutations, demonstrate strain-independent phenotypes across different species. This study extends our understanding of epistasis among resistance mutations and shows that interactions between different resistance mutations are often predictable from the characteristics of the individual mutations. IMPORTANCE The spread of antibiotic-resistant bacteria imposes an urgent threat to public health. The ability to forecast the evolutionary success of resistant mutants would help to combat dissemination of antibiotic resistance. Previous studies have shown that the phenotypic effects (fitness and resistance level) of resistance mutations can vary substantially depending on the genetic context in which they occur. We conducted a broad screen using many different resistance mutations and host strains to identify potential epistatic interactions between various types of resistance mutations and to determine the effect of strain

  7. Recurrent duplications of 17q12 associated with variable phenotypes

    DEFF Research Database (Denmark)

    Mitchell, Elyse; Douglas, Andrew; Kjaegaard, Susanne

    2015-01-01

    The ability to identify the clinical nature of the recurrent duplication of chromosome 17q12 has been limited by its rarity and the diverse range of phenotypes associated with this genomic change. In order to further define the clinical features of affected patients, detailed clinical information......, potentially contributory copy number changes in a subset of patients, including one patient each with 16p11.2 deletion and 15q13.3 deletion. Our data further define and expand the clinical spectrum associated with duplications of 17q12 and provide support for the role of genomic modifiers contributing...... to phenotypic variability....

  8. Plant Phenotype Characterization System

    Energy Technology Data Exchange (ETDEWEB)

    Daniel W McDonald; Ronald B Michaels

    2005-09-09

    This report is the final scientific report for the DOE Inventions and Innovations Project: Plant Phenotype Characterization System, DE-FG36-04GO14334. The period of performance was September 30, 2004 through July 15, 2005. The project objective is to demonstrate the viability of a new scientific instrument concept for the study of plant root systems. The root systems of plants are thought to be important in plant yield and thus important to DOE goals in renewable energy sources. The scientific study and understanding of plant root systems is hampered by the difficulty in observing root activity and the inadequacy of existing root study instrumentation options. We have demonstrated a high throughput, non-invasive, high resolution technique for visualizing plant root systems in-situ. Our approach is based upon low-energy x-ray radiography and the use of containers and substrates (artificial soil) which are virtually transparent to x-rays. The system allows us to germinate and grow plant specimens in our containers and substrates and to generate x-ray images of the developing root system over time. The same plant can be imaged at different times in its development. The system can be used for root studies in plant physiology, plant morphology, plant breeding, plant functional genomics and plant genotype screening.

  9. Sex hormone binding globulin phenotypes

    DEFF Research Database (Denmark)

    Cornelisse, M M; Bennett, Patrick; Christiansen, M

    1994-01-01

    Human sex hormone binding globulin (SHBG) is encoded by a normal and a variant allele. The resulting SHBG phenotypes (the homozygous normal SHBG, the heterozygous SHBG and the homozygous variant SHBG phenotype) can be distinguished by their electrophoretic patterns. We developed a novel detection....... This method of detection was used to determine the distribution of SHBG phenotypes in healthy controls of both sexes and in five different pathological conditions characterized by changes in the SHBG level or endocrine disturbances (malignant and benign ovarian neoplasms, hirsutism, liver cirrhosis...... on the experimental values. Differences in SHBG phenotypes do not appear to have any clinical significance and no sex difference was found in the SHBG phenotype distribution....

  10. Near-fatal asthma phenotype in the ENFUMOSA Cohort

    NARCIS (Netherlands)

    Romagnoli, M.; Caramori, G.; Braccioni, F.; Ravenna, F.; Barreiro, E.; Siafakas, N. M.; Vignola, A. M.; Chanez, P.; Fabbri, L. M.; Papi, A.; Bel, E. H.

    2007-01-01

    BACKGROUND: Near-fatal asthma (NFA) is characterized by severe asthma attacks usually requiring intensive care unit admission. This phenotype of asthma has been studied mainly in acute conditions. METHODS: The aim of our study was to compare the clinical, functional and inflammatory characteristics

  11. Sickle cell disease clinical phenotypes in children from South ...

    African Journals Online (AJOL)

    2014-07-20

    Jul 20, 2014 ... Background:The clinical phenotypes of children with sickle cell disease (SCD) are poorly described in many sub-Saharan countries ..... World Health Organization. ... apps.who.int/gb/ebwha/pdf_files/WHA59/A59_9‑en.pdf.

  12. 3. Phenotypic Characteristics of Zambian patients with Parkinson's

    African Journals Online (AJOL)

    Esem

    ABSTRACT. Objective: To describe the phenotypic characteristics of adult Zambian patients with newly diagnosed Parkinson's disease (PD) at University Teaching Hospital (UTH). Background: The genetic basis of idiopathic Parkinson's disease is remains unknown. Little information is available regarding the genotype and ...

  13. Using iterative cluster merging with improved gap statistics to perform online phenotype discovery in the context of high-throughput RNAi screens

    Directory of Open Access Journals (Sweden)

    Sun Youxian

    2008-06-01

    Full Text Available Abstract Background The recent emergence of high-throughput automated image acquisition technologies has forever changed how cell biologists collect and analyze data. Historically, the interpretation of cellular phenotypes in different experimental conditions has been dependent upon the expert opinions of well-trained biologists. Such qualitative analysis is particularly effective in detecting subtle, but important, deviations in phenotypes. However, while the rapid and continuing development of automated microscope-based technologies now facilitates the acquisition of trillions of cells in thousands of diverse experimental conditions, such as in the context of RNA interference (RNAi or small-molecule screens, the massive size of these datasets precludes human analysis. Thus, the development of automated methods which aim to identify novel and biological relevant phenotypes online is one of the major challenges in high-throughput image-based screening. Ideally, phenotype discovery methods should be designed to utilize prior/existing information and tackle three challenging tasks, i.e. restoring pre-defined biological meaningful phenotypes, differentiating novel phenotypes from known ones and clarifying novel phenotypes from each other. Arbitrarily extracted information causes biased analysis, while combining the complete existing datasets with each new image is intractable in high-throughput screens. Results Here we present the design and implementation of a novel and robust online phenotype discovery method with broad applicability that can be used in diverse experimental contexts, especially high-throughput RNAi screens. This method features phenotype modelling and iterative cluster merging using improved gap statistics. A Gaussian Mixture Model (GMM is employed to estimate the distribution of each existing phenotype, and then used as reference distribution in gap statistics. This method is broadly applicable to a number of different types of

  14. Background noise levels in Europe

    OpenAIRE

    Gjestland, Truls

    2008-01-01

    - This report gives a brief overview of typical background noise levels in Europe, and suggests a procedure for the prediction of background noise levels based on population density. A proposal for the production of background noise maps for Europe is included.

  15. Multidimensionality of behavioural phenotypes in Atlantic cod, Gadus morhua.

    Science.gov (United States)

    Meager, Justin J; Fernö, Anders; Skjæraasen, Jon Egil; Järvi, Torbjörn; Rodewald, Petra; Sverdrup, Gisle; Winberg, Svante; Mayer, Ian

    2012-06-25

    Much of the inter-individual variation observed in animal behaviour is now attributed to the existence of behavioural phenotypes or animal personalities. Such phenotypes may be fundamental to fisheries and aquaculture, yet there have been few detailed studies of this phenomenon in exploited marine animals. We investigated the behavioural and neuroendocrine responses of Atlantic cod (Gadus morhua L.), to situations reflecting critical ecological challenges: predator attacks and territorial challenges. Both hatchery-reared and wild fish were tested and behavioural profiles were compared with baseline conditions. We then used an objective, multivariate approach, rather than assigning individuals along one-dimensional behavioural axes, to examine whether distinct behavioural phenotypes were present. Our results indicate that two distinct behavioural phenotypes were evident in fish from each background. In hatchery-reared fish, phenotypes displayed divergent locomotor activity, sheltering, brain monoamine concentrations and responses to competitive challenges. In wild fish, phenotypes were distinguished primarily by locomotor activity, sheltering and responsiveness to predator stimuli. Hatcheries presumably represent a more stressful social environment, and social behaviour and neuroendocrine responses were important in discerning behavioural phenotypes in hatchery fish, whereas antipredator responses were important in discerning phenotypes in wild fish that have previously encountered predators. In both fish types, behavioural and physiological traits that classified individuals into phenotypes were not the same as those that were correlated across situations. These results highlight the multidimensionality of animal personalities, and that the processes that regulate one suite of behavioural traits may be very different to the processes that regulate other behaviours. Copyright © 2012 Elsevier Inc. All rights reserved.

  16. Differences in phenotype and disease course in adult and paediatric inflammatory bowel disease

    DEFF Research Database (Denmark)

    Jakobsen, Christian; Bartek, Jiri; Wewer, Anne Vibeke

    2011-01-01

    Background Few studies have compared phenotype and disease course in children and adults with inflammatory bowel disease (IBD). Aim To compare phenotype, treatment and disease course in children (<15 years) and adults (=18 years) with IBD. Methods Two population-based cohorts comprising paediatri...

  17. Phenotypic plasticity, costs of phenotypes, and costs of plasticity

    DEFF Research Database (Denmark)

    Callahan, Hilary S; Maughan, Heather; Steiner, Uli

    2008-01-01

    Why are some traits constitutive and others inducible? The term costs often appears in work addressing this issue but may be ambiguously defined. This review distinguishes two conceptually distinct types of costs: phenotypic costs and plasticity costs. Phenotypic costs are assessed from patterns...... of covariation, typically between a focal trait and a separate trait relevant to fitness. Plasticity costs, separable from phenotypic costs, are gauged by comparing the fitness of genotypes with equivalent phenotypes within two environments but differing in plasticity and fitness. Subtleties associated with both...... types of costs are illustrated by a body of work addressing predator-induced plasticity. Such subtleties, and potential interplay between the two types of costs, have also been addressed, often in studies involving genetic model organisms. In some instances, investigators have pinpointed the mechanistic...

  18. Phenotype Instance Verification and Evaluation Tool (PIVET): A Scaled Phenotype Evidence Generation Framework Using Web-Based Medical Literature

    Science.gov (United States)

    Ke, Junyuan; Ho, Joyce C; Ghosh, Joydeep; Wallace, Byron C

    2018-01-01

    Background Researchers are developing methods to automatically extract clinically relevant and useful patient characteristics from raw healthcare datasets. These characteristics, often capturing essential properties of patients with common medical conditions, are called computational phenotypes. Being generated by automated or semiautomated, data-driven methods, such potential phenotypes need to be validated as clinically meaningful (or not) before they are acceptable for use in decision making. Objective The objective of this study was to present Phenotype Instance Verification and Evaluation Tool (PIVET), a framework that uses co-occurrence analysis on an online corpus of publically available medical journal articles to build clinical relevance evidence sets for user-supplied phenotypes. PIVET adopts a conceptual framework similar to the pioneering prototype tool PheKnow-Cloud that was developed for the phenotype validation task. PIVET completely refactors each part of the PheKnow-Cloud pipeline to deliver vast improvements in speed without sacrificing the quality of the insights PheKnow-Cloud achieved. Methods PIVET leverages indexing in NoSQL databases to efficiently generate evidence sets. Specifically, PIVET uses a succinct representation of the phenotypes that corresponds to the index on the corpus database and an optimized co-occurrence algorithm inspired by the Aho-Corasick algorithm. We compare PIVET’s phenotype representation with PheKnow-Cloud’s by using PheKnow-Cloud’s experimental setup. In PIVET’s framework, we also introduce a statistical model trained on domain expert–verified phenotypes to automatically classify phenotypes as clinically relevant or not. Additionally, we show how the classification model can be used to examine user-supplied phenotypes in an online, rather than batch, manner. Results PIVET maintains the discriminative power of PheKnow-Cloud in terms of identifying clinically relevant phenotypes for the same corpus with

  19. Backgrounder

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC CRDI

    Center for Mountain Ecosystem Studies, Kunming Institute of Botany of the Chinese Academy of Sciences, China: $1,526,000 to inform effective water governance in the Asian highlands of China, Nepal, and Pakistan. • Ashoka Trust for Research in Ecology and the Environment (ATREE), India: $1,499,300 for research on ...

  20. BACKGROUNDER

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC CRDI

    demographic trends, socio-economic development pathways, and strong ... knowledge and experience, and encourage innovation. ... choices, and will work with stakeholders in government, business, civil society, and regional economic.

  1. Backgrounder

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC CRDI

    Safe and Inclusive Cities: ... improving urban environments and public spaces might have on reducing the city's high ... violence against women among urban youth of working class neighbourhoods of Islamabad, Rawalpindi, and Karachi,.

  2. BACKGROUNDER

    International Development Research Centre (IDRC) Digital Library (Canada)

    IDRC CRDI

    CARIAA's research agenda addresses gaps and priorities highlighted in the ... Research focuses on climate risk, institutional and regulatory frameworks, markets, and ... The researchers will identify relevant drivers and trends and use develop ...

  3. BACKGROUNDER

    International Development Research Centre (IDRC) Digital Library (Canada)

    Corey Piccioni

    achieving long‐term food security in Africa, with a focus on post‐harvest loss, ... nutrion and health, and the socio‐economic factors that affect food supply ... Water use. Agricultural producvity in sub‐Saharan Africa is the lowest in the world.

  4. Deep Phenotyping: Deep Learning For Temporal Phenotype/Genotype Classification

    OpenAIRE

    Najafi, Mohammad; Namin, Sarah; Esmaeilzadeh, Mohammad; Brown, Tim; Borevitz, Justin

    2017-01-01

    High resolution and high throughput, genotype to phenotype studies in plants are underway to accelerate breeding of climate ready crops. Complex developmental phenotypes are observed by imaging a variety of accessions in different environment conditions, however extracting the genetically heritable traits is challenging. In the recent years, deep learning techniques and in particular Convolutional Neural Networks (CNNs), Recurrent Neural Networks (RNNs) and Long-Short Term Memories (LSTMs), h...

  5. Genotypes in relation to phenotypic appearance and exposure to environmental factors in Graves' hyperthyroidism

    NARCIS (Netherlands)

    Vos, Xander G.; Endert, Erik; Tijssen, Jan G. P.; Wiersinga, Wilmar M.

    2012-01-01

    Background: Genetic polymorphisms and environmental factors are both involved in the pathogenesis of Graves' disease, but their interaction and effect on Graves' phenotypes have scarcely been investigated. Objective: To test the hypothesis that subjects with susceptibility genotypes develop more

  6. Root Traits and Phenotyping Strategies for Plant Improvement.

    Science.gov (United States)

    Paez-Garcia, Ana; Motes, Christy M; Scheible, Wolf-Rüdiger; Chen, Rujin; Blancaflor, Elison B; Monteros, Maria J

    2015-06-15

    Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics) and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.

  7. Root Traits and Phenotyping Strategies for Plant Improvement

    Directory of Open Access Journals (Sweden)

    Ana Paez-Garcia

    2015-06-01

    Full Text Available Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, water and nutrient acquisition. Available approaches for root phenotyping in laboratory, greenhouse and field encompass simple agar plates to labor-intensive root digging (i.e., shovelomics and soil boring methods, the construction of underground root observation stations and sophisticated computer-assisted root imaging. Here, we summarize root architectural traits relevant to crop productivity, survey root phenotyping strategies and describe their advantages, limitations and practical value for crop and forage breeding programs.

  8. The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    KAUST Repository

    Hoehndorf, Robert

    2016-11-14

    Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. Results We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. Conclusions The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established

  9. Diffuse Cosmic Infrared Background Radiation

    Science.gov (United States)

    Dwek, Eli

    2002-01-01

    The diffuse cosmic infrared background (CIB) consists of the cumulative radiant energy released in the processes of structure formation that have occurred since the decoupling of matter and radiation following the Big Bang. In this lecture I will review the observational data that provided the first detections and limits on the CIB, and the theoretical studies explaining the origin of this background. Finally, I will also discuss the relevance of this background to the universe as seen in high energy gamma-rays.

  10. Background current of radioisotope manometer

    International Nuclear Information System (INIS)

    Vydrik, A.A.

    1987-01-01

    The technique for calculating the main component of the background current of radioisotopic monometers, current from direct collision of ionizing particles and a collector, is described. The reasons for appearance of background photoelectron current are clarified. The most effective way of eliminating background current components is collector protection from the source by a screen made of material with a high gamma-quanta absorption coefficient, such as lead, for example

  11. PHENOTYPIC CORRELATIONS AND BODY WEIGHTS ...

    African Journals Online (AJOL)

    Dr Osondu

    Ethiopian Journal of Environmental Studies and Management Vol. 4 No.3 2011. PHENOTYPIC ... because of its high meat quality and acceptance by her populace. The meat is ... commands high price in the restaurants and markets than other ...

  12. Spice: discovery of phenotype-determining component interplays

    Directory of Open Access Journals (Sweden)

    Chen Zhengzhang

    2012-05-01

    Full Text Available Abstract Background A latent behavior of a biological cell is complex. Deriving the underlying simplicity, or the fundamental rules governing this behavior has been the Holy Grail of systems biology. Data-driven prediction of the system components and their component interplays that are responsible for the target system’s phenotype is a key and challenging step in this endeavor. Results The proposed approach, which we call System Phenotype-related Interplaying Components Enumerator (Spice, iteratively enumerates statistically significant system components that are hypothesized (1 to play an important role in defining the specificity of the target system’s phenotype(s; (2 to exhibit a functionally coherent behavior, namely, act in a coordinated manner to perform the phenotype-specific function; and (3 to improve the predictive skill of the system’s phenotype(s when used collectively in the ensemble of predictive models. Spice can be applied to both instance-based data and network-based data. When validated, Spice effectively identified system components related to three target phenotypes: biohydrogen production, motility, and cancer. Manual results curation agreed with the known phenotype-related system components reported in literature. Additionally, using the identified system components as discriminatory features improved the prediction accuracy by 10% on the phenotype-classification task when compared to a number of state-of-the-art methods applied to eight benchmark microarray data sets. Conclusion We formulate a problem—enumeration of phenotype-determining system component interplays—and propose an effective methodology (Spice to address this problem. Spice improved identification of cancer-related groups of genes from various microarray data sets and detected groups of genes associated with microbial biohydrogen production and motility, many of which were reported in literature. Spice also improved the predictive skill of the

  13. Background subtraction theory and practice

    CERN Document Server

    Elgammal, Ahmed

    2014-01-01

    Background subtraction is a widely used concept for detection of moving objects in videos. In the last two decades there has been a lot of development in designing algorithms for background subtraction, as well as wide use of these algorithms in various important applications, such as visual surveillance, sports video analysis, motion capture, etc. Various statistical approaches have been proposed to model scene backgrounds. The concept of background subtraction also has been extended to detect objects from videos captured from moving cameras. This book reviews the concept and practice of back

  14. The acute stress response of red porgy, Pagrus pagrus, kept on a red or white background

    NARCIS (Netherlands)

    Salm, A.L. van der; Pavlidis, M; Flik, G.; Wendelaar Bonga, S.E.

    2005-01-01

    The skin colour of red porgy, Pagrus pagrus, can be modified by exposure to different background colours. Red and white background colours brighten the dark skin colour that develops under common culture conditions in red porgy. To assess whether skin colour is also modified by aquaculture related

  15. Root Traits and Phenotyping Strategies for Plant Improvement

    OpenAIRE

    Ana Paez-Garcia; Christy M. Motes; Wolf-Rüdiger Scheible; Rujin Chen; Elison B. Blancaflor; Maria J. Monteros

    2015-01-01

    Roots are crucial for nutrient and water acquisition and can be targeted to enhance plant productivity under a broad range of growing conditions. A current challenge for plant breeding is the limited ability to phenotype and select for desirable root characteristics due to their underground location. Plant breeding efforts aimed at modifying root traits can result in novel, more stress-tolerant crops and increased yield by enhancing the capacity of the plant for soil exploration and, thus, wa...

  16. Hanford Site background: Part 1, Soil background for nonradioactive analytes

    International Nuclear Information System (INIS)

    1993-04-01

    The determination of soil background is one of the most important activities supporting environmental restoration and waste management on the Hanford Site. Background compositions serve as the basis for identifying soil contamination, and also as a baseline in risk assessment processes used to determine soil cleanup and treatment levels. These uses of soil background require an understanding of the extent to which analytes of concern occur naturally in the soils. This report documents the results of sampling and analysis activities designed to characterize the composition of soil background at the Hanford Site, and to evaluate the feasibility for use as Sitewide background. The compositions of naturally occurring soils in the vadose Zone have been-determined for-nonradioactive inorganic and organic analytes and related physical properties. These results confirm that a Sitewide approach to the characterization of soil background is technically sound and is a viable alternative to the determination and use of numerous local or area backgrounds that yield inconsistent definitions of contamination. Sitewide soil background consists of several types of data and is appropriate for use in identifying contamination in all soils in the vadose zone on the Hanford Site. The natural concentrations of nearly every inorganic analyte extend to levels that exceed calculated health-based cleanup limits. The levels of most inorganic analytes, however, are well below these health-based limits. The highest measured background concentrations occur in three volumetrically minor soil types, the most important of which are topsoils adjacent to the Columbia River that are rich in organic carbon. No organic analyte levels above detection were found in any of the soil samples

  17. Backgrounds and characteristics of arsonists

    NARCIS (Netherlands)

    Labree, W.; Nijman, H.L.I.; Marle, H.J.C. van; Rassin, E.

    2010-01-01

    The aim of this study was to gain more insight in the backgrounds and characteristics of arsonists. For this, the psychiatric, psychological, personal, and criminal backgrounds of all arsonists (n = 25), sentenced to forced treatment in the maximum security forensic hospital “De Kijvelanden”, were

  18. Measurement of natural background neutron

    CERN Document Server

    Li Jain, Ping; Tang Jin Hua; Tang, E S; Xie Yan Fong

    1982-01-01

    A high sensitive neutron monitor is described. It has an approximate counting rate of 20 cpm for natural background neutrons. The pulse amplitude resolution, sensitivity and direction dependence of the monitor were determined. This monitor has been used for natural background measurement in Beijing area. The yearly average dose is given and compared with the results of KEK and CERN.

  19. The background scale Ward identity in quantum gravity

    Energy Technology Data Exchange (ETDEWEB)

    Percacci, Roberto [International School for Advanced Studies, Trieste (Italy); INFN, Sezione di Trieste, Trieste (Italy); Vacca, Gian Paolo [INFN, Sezione di Bologna, Bologna (Italy)

    2017-01-15

    We show that with suitable choices of parametrization, gauge fixing and cutoff, the anomalous variation of the effective action under global rescalings of the background metric is identical to the derivative with respect to the cutoff, i.e. to the beta functional, as defined by the exact RG equation. The Ward identity and the RG equation can be combined, resulting in a modified flow equation that is manifestly invariant under global background rescalings. (orig.)

  20. Aluminum as a source of background in low background experiments

    Energy Technology Data Exchange (ETDEWEB)

    Majorovits, B., E-mail: bela@mppmu.mpg.de [MPI fuer Physik, Foehringer Ring 6, 80805 Munich (Germany); Abt, I. [MPI fuer Physik, Foehringer Ring 6, 80805 Munich (Germany); Laubenstein, M. [Laboratori Nazionali del Gran Sasso, INFN, S.S.17/bis, km 18 plus 910, I-67100 Assergi (Italy); Volynets, O. [MPI fuer Physik, Foehringer Ring 6, 80805 Munich (Germany)

    2011-08-11

    Neutrinoless double beta decay would be a key to understanding the nature of neutrino masses. The next generation of High Purity Germanium experiments will have to be operated with a background rate of better than 10{sup -5} counts/(kg y keV) in the region of interest around the Q-value of the decay. Therefore, so far irrelevant sources of background have to be considered. The metalization of the surface of germanium detectors is in general done with aluminum. The background from the decays of {sup 22}Na, {sup 26}Al, {sup 226}Ra and {sup 228}Th introduced by this metalization is discussed. It is shown that only a special selection of aluminum can keep these background contributions acceptable.

  1. Epigenetic reversion of breast carcinoma phenotype is accompaniedby DNA sequestration

    Energy Technology Data Exchange (ETDEWEB)

    Sandal, Tone; Valyi-Nagy, Klara; Spencer, Virginia A.; Folberg,Robert; Bissell, Mina J.; Maniotis, Andrew J.

    2006-07-19

    The importance of microenvironment and context in regulation of tissue-specific genes is finally well established. DNA exposure to, or sequestration from, nucleases can be used to detect differences in higher order chromatin structure in intact cells without disturbing cellular or tissue architecture. To investigate the relationship between chromatin organization and tumor phenotype, we utilized an established 3-D assay where normal and malignant human breast cells can be easily distinguished by the morphology of the structures they make (acinus-like vs tumor-like, respectively). We show that these phenotypes can be distinguished also by sensitivity to AluI digestion where the malignant cells are resistant to digestion relative to non-malignant cells. Reversion of the T4-2 breast cancer cells by either cAMP analogs, or a phospatidylinositol 3-kinase (P13K) inhibitor not only reverted the phenotype, but also the chromatin sensitivity to AluI. By using different cAMP-analogs, we show that the cAMP-induced phenotypic reversion, polarization, and shift in DNA organization act through a cAMP-dependent-protein-kinase A-coupled signaling pathway. Importantly, inhibitory antibody to fibronectin also reverted the malignant phenotype, polarized the acini, and changed chromatin sequestration. These experiments show not only that modifying the tumor microenvironment can alter the organization of tumor cells but also that architecture of the tissues and the global chromatin organization are coupled and yet highly plastic.

  2. Duality invariant class of exact string backgrounds

    CERN Document Server

    Klimcík, C

    1994-01-01

    We consider a class of $2+D$ - dimensional string backgrounds with a target space metric having a covariantly constant null Killing vector and flat `transverse' part. The corresponding sigma models are invariant under $D$ abelian isometries and are transformed by $O(D,D)$ duality into models belonging to the same class. The leading-order solutions of the conformal invariance equations (metric, antisymmetric tensor and dilaton), as well as the action of $O(D,D)$ duality transformations on them, are exact, i.e. are not modified by $\\a'$-corrections. This makes a discussion of different space-time representations of the same string solution (related by $O(D,D|Z)$ duality subgroup) rather explicit. We show that the $O(D,D)$ duality may connect curved $2+D$-dimensional backgrounds with solutions having flat metric but, in general, non-trivial antisymmetric tensor and dilaton. We discuss several particular examples including the $2+D=4$ - dimensional background that was recently interpreted in terms of a WZW model.

  3. Snowshoe hares display limited phenotypic plasticity to mismatch in seasonal camouflage

    Science.gov (United States)

    Zimova, Marketa; Mills, L. Scott; Lukacs, Paul M.; Mitchell, Michael S.

    2014-01-01

    As duration of snow cover decreases owing to climate change, species undergoing seasonal colour moults can become colour mismatched with their background. The immediate adaptive solution to this mismatch is phenotypic plasticity, either in phenology of seasonal colour moults or in behaviours that reduce mismatch or its consequences. We observed nearly 200 snowshoe hares across a wide range of snow conditions and two study sites in Montana, USA, and found minimal plasticity in response to mismatch between coat colour and background. We found that moult phenology varied between study sites, likely due to differences in photoperiod and climate, but was largely fixed within study sites with only minimal plasticity to snow conditions during the spring white-to-brown moult. We also found no evidence that hares modify their behaviour in response to colour mismatch. Hiding and fleeing behaviours and resting spot preference of hares were more affected by variables related to season, site and concealment by vegetation, than by colour mismatch. We conclude that plasticity in moult phenology and behaviours in snowshoe hares is insufficient for adaptation to camouflage mismatch, suggesting that any future adaptation to climate change will require natural selection on moult phenology or behaviour.

  4. JEM-X background models

    DEFF Research Database (Denmark)

    Huovelin, J.; Maisala, S.; Schultz, J.

    2003-01-01

    Background and determination of its components for the JEM-X X-ray telescope on INTEGRAL are discussed. A part of the first background observations by JEM-X are analysed and results are compared to predictions. The observations are based on extensive imaging of background near the Crab Nebula...... on revolution 41 of INTEGRAL. Total observing time used for the analysis was 216 502 s, with the average of 25 cps of background for each of the two JEM-X telescopes. JEM-X1 showed slightly higher average background intensity than JEM-X2. The detectors were stable during the long exposures, and weak orbital...... background was enhanced in the central area of a detector, and it decreased radially towards the edge, with a clear vignetting effect for both JEM-X units. The instrument background was weakest in the central area of a detector and showed a steep increase at the very edges of both JEM-X detectors...

  5. The phenotypic plasticity of developmental modules

    Directory of Open Access Journals (Sweden)

    Aabha I. Sharma

    2016-08-01

    Full Text Available Abstract Background Organisms develop and evolve in a modular fashion, but how individual modules interact with the environment remains poorly understood. Phenotypically plastic traits are often under selection, and studies are needed to address how traits respond to the environment in a modular fashion. In this study, tissue-specific plasticity of melanic spots was examined in the large milkweed bug, Oncopeltus fasciatus. Results Although the size of the abdominal melanic bands varied according to rearing temperatures, wing melanic bands were more robust. To explore the regulation of abdominal pigmentation plasticity, candidate genes involved in abdominal melanic spot patterning and biosynthesis of melanin were analyzed. While the knockdown of dopa decarboxylase (Ddc led to lighter pigmentation in both the wings and the abdomen, the shape of the melanic elements remained unaffected. Although the knockdown of Abdominal-B (Abd-B partially phenocopied the low-temperature phenotype, the abdominal bands were still sensitive to temperature shifts. These observations suggest that regulators downstream of Abd-B but upstream of DDC are responsible for the temperature response of the abdomen. Ablation of wings led to the regeneration of a smaller wing with reduced melanic bands that were shifted proximally. In addition, the knockdown of the Wnt signaling nuclear effector genes, armadillo 1 and armadillo 2, altered both the melanic bands and the wing shape. Thus, the pleiotropic effects of Wnt signaling may constrain the amount of plasticity in wing melanic bands. Conclusions We propose that when traits are regulated by distinct pre-patterning mechanisms, they can respond to the environment in a modular fashion, whereas when the environment impacts developmental regulators that are shared between different modules, phenotypic plasticity can manifest as a developmentally integrated system.

  6. Two Clinical Phenotypes in Polycythemia Vera

    Science.gov (United States)

    Spivak, Jerry L.; Considine, Michael; Williams, Donna M.; Talbot, Conover C.; Rogers, Ophelia; Moliterno, Alison R.; Jie, Chunfa; Ochs, Michael F.

    2014-01-01

    BACKGROUND Polycythemia vera is the ultimate phenotypic consequence of the V617F mutation in Janus kinase 2 (encoded by JAK2), but the extent to which this mutation influences the behavior of the involved CD34+ hematopoietic stem cells is unknown. METHODS We analyzed gene expression in CD34+ peripheral-blood cells from 19 patients with polycythemia vera, using oligonucleotide microarray technology after correcting for potential confounding by sex, since the phenotypic features of the disease differ between men and women. RESULTS Men with polycythemia vera had twice as many up-regulated or down-regulated genes as women with polycythemia vera, in a comparison of gene expression in the patients and in healthy persons of the same sex, but there were 102 genes with differential regulation that was concordant in men and women. When these genes were used for class discovery by means of unsupervised hierarchical clustering, the 19 patients could be divided into two groups that did not differ significantly with respect to age, neutrophil JAK2 V617F allele burden, white-cell count, platelet count, or clonal dominance. However, they did differ significantly with respect to disease duration; hemoglobin level; frequency of thromboembolic events, palpable splenomegaly, and splenectomy; chemotherapy exposure; leukemic transformation; and survival. The unsupervised clustering was confirmed by a supervised approach with the use of a top-scoring-pair classifier that segregated the 19 patients into the same two phenotypic groups with 100% accuracy. CONCLUSIONS Removing sex as a potential confounder, we identified an accurate molecular method for classifying patients with polycythemia vera according to disease behavior, independently of their JAK2 V617F allele burden, and identified previously unrecognized molecular pathways in polycythemia vera outside the canonical JAK2 pathway that may be amenable to targeted therapy. PMID:25162887

  7. Wolfram syndrome: new mutations, different phenotype.

    Directory of Open Access Journals (Sweden)

    Concetta Aloi

    Full Text Available BACKGROUND: Wolfram Syndrome (WS is an autosomal recessive neurodegenerative disorder characterized by Diabetes Insipidus, Diabetes Mellitus, Optic Atrophy, and Deafness identified by the acronym "DIDMOAD". The WS gene, WFS1, encodes a transmembrane protein called Wolframin, which recent evidence suggests may serve as a novel endoplasmic reticulum calcium channel in pancreatic β-cells and neurons. WS is a rare disease, with an estimated prevalence of 1/550.000 children, with a carrier frequency of 1/354. The aim of our study was to determine the genotype of WS patients in order to establish a genotype/phenotype correlation. METHODOLOGY/PRINCIPAL FINDINGS: We clinically evaluated 9 young patients from 9 unrelated families (6 males, 3 females. Basic criteria for WS clinical diagnosis were coexistence of insulin-treated diabetes mellitus and optic atrophy occurring before 15 years of age. Genetic analysis for WFS1 was performed by direct sequencing. Molecular sequencing revealed 5 heterozygous compound and 3 homozygous mutations. All of them were located in exon 8, except one in exon 4. In one proband only an heterozygous mutation (A684V was found. Two new variants c.2663 C>A and c.1381 A>C were detected. CONCLUSIONS/SIGNIFICANCE: Our study increases the spectrum of WFS1 mutations with two novel variants. The male patient carrying the compound mutation [c.1060_1062delTTC]+[c.2663 C>A] showed the most severe phenotype: diabetes mellitus, optic atrophy (visual acuity 5/10, deafness with deep auditory bilaterally 8000 Hz, diabetes insipidus associated to reduced volume of posterior pituitary and pons. He died in bed at the age of 13 years. The other patient carrying the compound mutation [c.409_424dup16]+[c.1381 A>C] showed a less severe phenotype (DM, OA.

  8. Novel statistical framework to identify differentially expressed genes allowing transcriptomic background differences.

    Science.gov (United States)

    Ling, Zhi-Qiang; Wang, Yi; Mukaisho, Kenichi; Hattori, Takanori; Tatsuta, Takeshi; Ge, Ming-Hua; Jin, Li; Mao, Wei-Min; Sugihara, Hiroyuki

    2010-06-01

    Tests of differentially expressed genes (DEGs) from microarray experiments are based on the null hypothesis that genes that are irrelevant to the phenotype/stimulus are expressed equally in the target and control samples. However, this strict hypothesis is not always true, as there can be several transcriptomic background differences between target and control samples, including different cell/tissue types, different cell cycle stages and different biological donors. These differences lead to increased false positives, which have little biological/medical significance. In this article, we propose a statistical framework to identify DEGs between target and control samples from expression microarray data allowing transcriptomic background differences between these samples by introducing a modified null hypothesis that the gene expression background difference is normally distributed. We use an iterative procedure to perform robust estimation of the null hypothesis and identify DEGs as outliers. We evaluated our method using our own triplicate microarray experiment, followed by validations with reverse transcription-polymerase chain reaction (RT-PCR) and on the MicroArray Quality Control dataset. The evaluations suggest that our technique (i) results in less false positive and false negative results, as measured by the degree of agreement with RT-PCR of the same samples, (ii) can be applied to different microarray platforms and results in better reproducibility as measured by the degree of DEG identification concordance both intra- and inter-platforms and (iii) can be applied efficiently with only a few microarray replicates. Based on these evaluations, we propose that this method not only identifies more reliable and biologically/medically significant DEG, but also reduces the power-cost tradeoff problem in the microarray field. Source code and binaries freely available for download at http://comonca.org.cn/fdca/resources/softwares/deg.zip.

  9. Childhood asthma-predictive phenotype.

    Science.gov (United States)

    Guilbert, Theresa W; Mauger, David T; Lemanske, Robert F

    2014-01-01

    Wheezing is a fairly common symptom in early childhood, but only some of these toddlers will experience continued wheezing symptoms in later childhood. The definition of the asthma-predictive phenotype is in children with frequent, recurrent wheezing in early life who have risk factors associated with the continuation of asthma symptoms in later life. Several asthma-predictive phenotypes were developed retrospectively based on large, longitudinal cohort studies; however, it can be difficult to differentiate these phenotypes clinically as the expression of symptoms, and risk factors can change with time. Genetic, environmental, developmental, and host factors and their interactions may contribute to the development, severity, and persistence of the asthma phenotype over time. Key characteristics that distinguish the childhood asthma-predictive phenotype include the following: male sex; a history of wheezing, with lower respiratory tract infections; history of parental asthma; history of atopic dermatitis; eosinophilia; early sensitization to food or aeroallergens; or lower lung function in early life. Copyright © 2014 American Academy of Allergy, Asthma & Immunology. Published by Elsevier Inc. All rights reserved.

  10. Stochastic backgrounds of gravitational waves

    International Nuclear Information System (INIS)

    Maggiore, M.

    2001-01-01

    We review the motivations for the search for stochastic backgrounds of gravitational waves and we compare the experimental sensitivities that can be reached in the near future with the existing bounds and with the theoretical predictions. (author)

  11. Berkeley Low Background Counting Facility

    Data.gov (United States)

    Federal Laboratory Consortium — Sensitive low background assay detectors and sample analysis are available for non-destructive direct gamma-ray assay of samples. Neutron activation analysis is also...

  12. Spectral characterization of natural backgrounds

    Science.gov (United States)

    Winkelmann, Max

    2017-10-01

    As the distribution and use of hyperspectral sensors is constantly increasing, the exploitation of spectral features is a threat for camouflaged objects. To improve camouflage materials at first the spectral behavior of backgrounds has to be known to adjust and optimize the spectral reflectance of camouflage materials. In an international effort, the NATO CSO working group SCI-295 "Development of Methods for Measurements and Evaluation of Natural Background EO Signatures" is developing a method how this characterization of backgrounds has to be done. It is obvious that the spectral characterization of a background will be quite an effort. To compare and exchange data internationally the measurements will have to be done in a similar way. To test and further improve this method an international field trial has been performed in Storkow, Germany. In the following we present first impressions and lessons learned from this field campaign and describe the data that has been measured.

  13. Confinining properties of QCD in strong magnetic backgrounds

    Directory of Open Access Journals (Sweden)

    Bonati Claudio

    2017-01-01

    Full Text Available Strong magnetic backgrounds are known to modify QCD properties at a nonperturbative level. We discuss recent lattice results, obtained for Nf = 2 + 1 QCD with physical quark masses, concerning in particular the modifications and the anisotropies induced at the level of the static quark-antiquark potential, both at zero and finite temperature.

  14. Cosmic microwave background, where next?

    CERN Multimedia

    CERN. Geneva

    2009-01-01

    Ground-based, balloon-borne and space-based experiments will observe the Cosmic Microwave Background in greater details to address open questions about the origin and the evolution of the Universe. In particular, detailed observations the polarization pattern of the Cosmic Microwave Background radiation have the potential to directly probe physics at the GUT scale and illuminate aspects of the physics of the very early Universe.

  15. Modifiable risk factors of hypertension and socio demographic ...

    African Journals Online (AJOL)

    Background: Factors associated with the development of hypertension can be categorized into modifiable and non‑modifiable risk factors. The modifiable risk factors include obesity, physical inactivity, high salt diet, smoking alcohol consumption and others. Aim: This study was aimed to determine the prevalence of ...

  16. Similarity-based search of model organism, disease and drug effect phenotypes

    KAUST Repository

    Hoehndorf, Robert

    2015-02-19

    Background: Semantic similarity measures over phenotype ontologies have been demonstrated to provide a powerful approach for the analysis of model organism phenotypes, the discovery of animal models of human disease, novel pathways, gene functions, druggable therapeutic targets, and determination of pathogenicity. Results: We have developed PhenomeNET 2, a system that enables similarity-based searches over a large repository of phenotypes in real-time. It can be used to identify strains of model organisms that are phenotypically similar to human patients, diseases that are phenotypically similar to model organism phenotypes, or drug effect profiles that are similar to the phenotypes observed in a patient or model organism. PhenomeNET 2 is available at http://aber-owl.net/phenomenet. Conclusions: Phenotype-similarity searches can provide a powerful tool for the discovery and investigation of molecular mechanisms underlying an observed phenotypic manifestation. PhenomeNET 2 facilitates user-defined similarity searches and allows researchers to analyze their data within a large repository of human, mouse and rat phenotypes.

  17. Identification and distribution of COPD phenotypes in clinical practice according to Spanish COPD Guidelines: the FENEPOC study

    Directory of Open Access Journals (Sweden)

    Calle Rubio M

    2017-08-01

    Full Text Available Myriam Calle Rubio,1,2 Ricard Casamor,3 Marc Miravitlles4 On behalf of the FENEPOC study group1Pulmonary Department, Hospital Clínico San Carlos, 2Department of Medicine, Faculty of Medicine, University Complutense of Madrid, Research Institute of Hospital Clínico San Carlos (IdISSC, Madrid, 3Medical Department, Novartis Farmaceutica, Barcelona, 4Pneumology Department, University Hospital Vall d’Hebron, CIBER de Enfermedades Respiratorias (CIBERES, Barcelona, SpainBackground: The Spanish Guidelines for COPD (GesEPOC describe four clinical phenotypes: non-exacerbator (NE, asthma-COPD overlap syndrome (ACO, frequent exacerbator with emphysema (EE, and exacerbator with chronic bronchitis (ECB. The objective of this study was to determine the frequency of COPD phenotypes, their clinical characteristics, and the availability of diagnostic tools to classify COPD phenotypes in clinical practice.Materials and methods: This study was an epidemiological, cross-sectional, and multicentered study. Patients ≥40 years old with a post-bronchodilator forced expiratory volume in 1 s (FEV1/forced vital capacity ratio of <0.7 and who were smokers or former smokers (with at least 10 pack-years were included. The availability of diagnostic tools to classify COPD phenotypes was assessed by an ad hoc questionnaire.Results: A total of 647 patients (294 primary care [PC], 353 pulmonology centers were included. Most patients were male (80.8%, with a mean age (SD of 68.2 (9.2 years, mean post-bronchodilator FEV1 was 53.2% (18.9% and they suffered a mean of 2.2 (2.1 exacerbations in the last year. NE was the most frequent phenotype (47.5% found, followed by ECB (29.1%, EE (17.0%, and ACO (6.5%. Significant differences between the four phenotypes were found regarding age; sex; body mass index; FEV1; body mass index, airflow obstruction, dyspnea, and exercise capacity (BODE/body mass index, airflow obstruction, dyspnea and exacerbations (BODEx index; modified Medical

  18. Identification of extreme motor phenotypes in Huntington's disease.

    Science.gov (United States)

    Braisch, Ulrike; Hay, Birgit; Muche, Rainer; Rothenbacher, Dietrich; Landwehrmeyer, G Bernhard; Long, Jeffrey D; Orth, Michael

    2017-04-01

    The manifestation of motor signs in Huntington's disease (HD) has a well-known inverse relationship with HTT CAG repeat length, but the prediction is far from perfect. The probability of finding disease modifiers is enhanced in individuals with extreme HD phenotypes. We aimed to identify extreme HD motor phenotypes conditional on CAG and age, such as patients with very early or very late onset of motor manifestation. Retrospective data were available from 1,218 healthy controls and 9,743 HD participants with CAG repeats ≥40, and a total of about 30,000 visits. Boundaries (2.5% and 97.5% quantiles) for extreme motor phenotypes (UHDRS total motor score (TMS) and motor age-at-onset) were estimated using quantile regression for longitudinal data. More than 15% of HD participants had an extreme TMS phenotype for at least one visit. In contrast, only about 4% of participants were consistent TMS extremes at two or more visits. Data from healthy controls revealed an upper cut-off of 13 for the TMS representing the extreme of motor ratings for a normal aging population. In HD, boundaries of motor age-at-onset based on diagnostic confidence or derived from the TMS data cut-off in controls were similar. In summary, a UHDRS TMS of more than 13 in an individual carrying the HD mutation indicates a high likelihood of motor manifestations of HD irrespective of CAG repeat length or age. The identification of motor phenotype extremes can be useful in the search for disease modifiers, for example, genetic or environmental such as medication. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. Looking for Cosmic Neutrino Background

    Directory of Open Access Journals (Sweden)

    Chiaki eYanagisawa

    2014-06-01

    Full Text Available Since the discovery of neutrino oscillation in atmospheric neutrinos by the Super-Kamiokande experiment in 1998, study of neutrinos has been one of exciting fields in high-energy physics. All the mixing angles were measured. Quests for 1 measurements of the remaining parameters, the lightest neutrino mass, the CP violating phase(s, and the sign of mass splitting between the mass eigenstates m3 and m1, and 2 better measurements to determine whether the mixing angle theta23 is less than pi/4, are in progress in a well-controlled manner. Determining the nature of neutrinos, whether they are Dirac or Majorana particles is also in progress with continuous improvement. On the other hand, although the ideas of detecting cosmic neutrino background have been discussed since 1960s, there has not been a serious concerted effort to achieve this goal. One of the reasons is that it is extremely difficult to detect such low energy neutrinos from the Big Bang. While there has been tremendous accumulation of information on Cosmic Microwave Background since its discovery in 1965, there is no direct evidence for Cosmic Neutrino Background. The importance of detecting Cosmic Neutrino Background is that, although detailed studies of Big Bang Nucleosynthesis and Cosmic Microwave Background give information of the early Universe at ~a few minutes old and ~300 k years old, respectively, observation of Cosmic Neutrino Background allows us to study the early Universe at $sim$ 1 sec old. This article reviews progress made in the past 50 years on detection methods of Cosmic Neutrino Background.

  20. A role for BELLRINGER in cell wall development is supported by loss-of-function phenotypes

    Directory of Open Access Journals (Sweden)

    Etchells J

    2012-11-01

    Full Text Available Abstract Background Homeodomain transcription factors play critical roles in metazoan development. BELLRINGER (BLR, one such transcription factor, is involved in diverse developmental processes in Arabidopsis, acting in vascular differentiation, phyllotaxy, flower and fruit development. BLR also has a redundant role in meristem maintenance. Cell wall remodelling underpins many of these processes, and BLR has recently been shown to regulate expression of PECTIN METHYL-ESTERASE 5 (PME5, a cell wall modifying enzyme in control of phyllotaxy. We have further explored the role of BLR in plant development by analysing phenotypes and gene expression in a series of plants over-expressing BLR, and generating combinatorial mutants with blr, brevipedicellus (bp, a member of the KNOX1 family of transcription factors that has previously been shown to interact with blr, and the homeodomain transcription factor revoluta (rev, required for radial patterning of the stem. Results Plants over-expressing BLR exhibited a wide range of phenotypes. Some were defective in cell size and demonstrated misregulation of genes predominantly affecting cell wall development. Other lines with more extreme phenotypes failed to generate lateral organs, consistent with BLR repressing transcription in the shoot apex. Cell wall dynamics are also affected in blr mutant plants, and BLR has previously been shown to regulate vascular development in conjunction with BP. We found that when bp and blr were combined with rev, a set of defects was observed that were distinct from those of bp blr lines. In these triple mutants xylem development was most strikingly affected, resulting in an almost complete lack of vessels and xylem parenchyma with secondary thickening. Conclusions Our data support a role for BLR in ordering the shoot apex and, in conjunction with BP and REV, playing a part in determining the composition and organisation of the vascular system. Microarray analysis strongly

  1. Natural variation of model mutant phenotypes in Ciona intestinalis.

    Directory of Open Access Journals (Sweden)

    Paolo Sordino

    Full Text Available BACKGROUND: The study of ascidians (Chordata, Tunicata has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. METHODOLOGY/PRINCIPAL FINDINGS: Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. CONCLUSIONS/SIGNIFICANCE: Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity.

  2. Natural Variation of Model Mutant Phenotypes in Ciona intestinalis

    Science.gov (United States)

    Brown, Euan R.; Leccia, Nicola I.; Squarzoni, Paola; Tarallo, Raffaella; Alfano, Christian; Caputi, Luigi; D'Ambrosio, Palmira; Daniele, Paola; D'Aniello, Enrico; D'Aniello, Salvatore; Maiella, Sylvie; Miraglia, Valentina; Russo, Monia Teresa; Sorrenti, Gerarda; Branno, Margherita; Cariello, Lucio; Cirino, Paola; Locascio, Annamaria; Spagnuolo, Antonietta; Zanetti, Laura; Ristoratore, Filomena

    2008-01-01

    Background The study of ascidians (Chordata, Tunicata) has made a considerable contribution to our understanding of the origin and evolution of basal chordates. To provide further information to support forward genetics in Ciona intestinalis, we used a combination of natural variation and neutral population genetics as an approach for the systematic identification of new mutations. In addition to the significance of developmental variation for phenotype-driven studies, this approach can encompass important implications in evolutionary and population biology. Methodology/Principal Findings Here, we report a preliminary survey for naturally occurring mutations in three geographically interconnected populations of C. intestinalis. The influence of historical, geographical and environmental factors on the distribution of abnormal phenotypes was assessed by means of 12 microsatellites. We identified 37 possible mutant loci with stereotyped defects in embryonic development that segregate in a way typical of recessive alleles. Local populations were found to differ in genetic organization and frequency distribution of phenotypic classes. Conclusions/Significance Natural genetic polymorphism of C. intestinalis constitutes a valuable source of phenotypes for studying embryonic development in ascidians. Correlating genetic structure and the occurrence of abnormal phenotypes is a crucial focus for understanding the selective forces that shape natural finite populations, and may provide insights of great importance into the evolutionary mechanisms that generate animal diversity. PMID:18523552

  3. Hypertriglyceridemic Waist Phenotype in Adolescents Aged 15 to 18 Years

    Directory of Open Access Journals (Sweden)

    Caridad Hernández Gutiérrez

    2015-09-01

    Full Text Available Background: presence of the hypertriglyceridemic waist phenotype is a predictor of cardiometabolic deterioration, increased type 2 diabetes mellitus and coronary heart disease. Objective: to determine the hypertriglyceridemic waist phenotype in adolescents aged 15 to 18 years from the Area III of Cienfuegos. Method: a case series study was conducted in a universe of 198 adolescents aged 15 to 18 years who attended a consultation created for this study at the Octavio de la Concepción y de la Pedraja University Polyclinic in Cienfuegos municipality from March to December 2013. Each patient completed a questionnaire including the following variables: age, sex, personal medical history, family medical history, weight, height, body mass index, presence of acanthosis nigricans, triglycerides and perimeter. Results: frequency of the phenotype was determined in 15.1 % of the participants with a slight predominance of the 18 age group (16.3 % and female sex (8.6 %. Twenty-one point six percent of the adolescents with a family history of obesity and 21.7 % of those with first-degree diabetic relatives presented the phenotype, being hypertriglyceridemia the most significant condition. Conclusions: a relationship between a family history of diabetes mellitus, obesity, body mass index above the 90th percentile value and presence of the phenotype was established.

  4. Phenotypic spectrum of GABRA1

    DEFF Research Database (Denmark)

    Johannesen, Katrine; Marini, Carla; Pfeffer, Siona

    2016-01-01

    OBJECTIVE: To delineate phenotypic heterogeneity, we describe the clinical features of a cohort of patients with GABRA1 gene mutations. METHODS: Patients with GABRA1 mutations were ascertained through an international collaboration. Clinical, EEG, and genetic data were collected. Functional analy...

  5. Leaf segmentation in plant phenotyping

    NARCIS (Netherlands)

    Scharr, Hanno; Minervini, Massimo; French, Andrew P.; Klukas, Christian; Kramer, David M.; Liu, Xiaoming; Luengo, Imanol; Pape, Jean Michel; Polder, Gerrit; Vukadinovic, Danijela; Yin, Xi; Tsaftaris, Sotirios A.

    2016-01-01

    Image-based plant phenotyping is a growing application area of computer vision in agriculture. A key task is the segmentation of all individual leaves in images. Here we focus on the most common rosette model plants, Arabidopsis and young tobacco. Although leaves do share appearance and shape

  6. Delineating SPTAN1 associated phenotypes

    DEFF Research Database (Denmark)

    Syrbe, Steffen; Harms, Frederike L; Parrini, Elena

    2017-01-01

    De novo in-frame deletions and duplications in the SPTAN1 gene, encoding the non-erythrocyte αII spectrin, have been associated with severe West syndrome with hypomyelination and pontocerebellar atrophy. We aimed at comprehensively delineating the phenotypic spectrum associated with SPTAN1 mutati...

  7. Neutron background estimates in GESA

    Directory of Open Access Journals (Sweden)

    Fernandes A.C.

    2014-01-01

    Full Text Available The SIMPLE project looks for nuclear recoil events generated by rare dark matter scattering interactions. Nuclear recoils are also produced by more prevalent cosmogenic neutron interactions. While the rock overburden shields against (μ,n neutrons to below 10−8 cm−2 s−1, it itself contributes via radio-impurities. Additional shielding of these is similar, both suppressing and contributing neutrons. We report on the Monte Carlo (MCNP estimation of the on-detector neutron backgrounds for the SIMPLE experiment located in the GESA facility of the Laboratoire Souterrain à Bas Bruit, and its use in defining additional shielding for measurements which have led to a reduction in the extrinsic neutron background to ∼ 5 × 10−3 evts/kgd. The calculated event rate induced by the neutron background is ∼ 0,3 evts/kgd, with a dominant contribution from the detector container.

  8. LOFT gamma densitometer background fluxes

    International Nuclear Information System (INIS)

    Grimesey, R.A.; McCracken, R.T.

    1978-01-01

    Background gamma-ray fluxes were calculated at the location of the γ densitometers without integral shielding at both the hot-leg and cold-leg primary piping locations. The principal sources for background radiation at the γ densitometers are 16 N activity from the primary piping H 2 O and γ radiation from reactor internal sources. The background radiation was calculated by the point-kernel codes QAD-BSA and QAD-P5A. Reasonable assumptions were required to convert the response functions calculated by point-kernel procedures into the gamma-ray spectrum from reactor internal sources. A brief summary of point-kernel equations and theory is included

  9. A definition of background independence

    International Nuclear Information System (INIS)

    Gryb, Sean

    2010-01-01

    We propose a definition for background (in)/dependence in dynamical theories of the evolution of configurations that have a continuous symmetry and test this definition on particle models and on gravity. Our definition draws from Barbour's best matching framework developed for the purpose of implementing spatial and temporal relationalism. Among other interesting theories, general relativity can be derived within this framework in novel ways. We study the detailed canonical structure of a wide range of best matching theories and show that their actions must have a local gauge symmetry. When gauge theory is derived in this way, we obtain at the same time a conceptual framework for distinguishing between background-dependent and -independent theories. Gauge invariant observables satisfying Kuchar's criterion are identified and, in simple cases, explicitly computed. We propose a procedure for inserting a global background time into temporally relational theories. Interestingly, using this procedure in general relativity leads to unimodular gravity.

  10. GENOTYPE-PHENOTYPE STUDY OF FAMILIAL HEMOPHAGOCYTIC LYMPHOHISTIOCYTOSIS TYPE 3

    OpenAIRE

    Sieni , Elena; Cetica , Valentina; Santoro , Alessandra; Beutel , Karin; Mastrodicasa , Elena; Meeths , Marie; Ciambotti , Benedetta; Brugnolo , Francesca; Zur Stadt , Udo; Pende , Daniela; Moretta , Lorenzo; Griffiths , Gillian M.; Henter , Jan-Inge; Janka , Gritta; Arico , Maurizio

    2011-01-01

    Abstract Background: Mutations of UNC13D are causative for FHL3 (OMIM 608898). We present a genotype-phenotype study of 845 FHL3 patients. Methods: A consortium of 3 countries planned to pool in a common database data on presenting features and mutations from individual patients with biallelic UNC13D mutations. Results: 845 FHL3 patients (median age: 4.1 months) were reported from Florence, Italy (n=54), Hamburg, Germany (n=18), Stockholm, Sweden (n=123). Their ethnic origi...

  11. Fried frailty phenotype assessment components as applied to geriatric inpatients

    OpenAIRE

    Bieniek, Joanna; Wilczy?ski, Krzysztof; Szewieczek, Jan

    2016-01-01

    Joanna Bieniek, Krzysztof Wilczynski, Jan Szewieczek Department of Geriatrics, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland Background: Management of geriatric patients would be simplified if a universally accepted definition of frailty for clinical use was defined. Among definitions of frailty, Fried frailty phenotype criteria constitute a common reference frame for many geriatric studies. However, this reference frame has been tested primarily in ...

  12. Generative electronic background music system

    Energy Technology Data Exchange (ETDEWEB)

    Mazurowski, Lukasz [Faculty of Computer Science, West Pomeranian University of Technology in Szczecin, Zolnierska Street 49, Szczecin, PL (Poland)

    2015-03-10

    In this short paper-extended abstract the new approach to generation of electronic background music has been presented. The Generative Electronic Background Music System (GEBMS) has been located between other related approaches within the musical algorithm positioning framework proposed by Woller et al. The music composition process is performed by a number of mini-models parameterized by further described properties. The mini-models generate fragments of musical patterns used in output composition. Musical pattern and output generation are controlled by container for the mini-models - a host-model. General mechanism has been presented including the example of the synthesized output compositions.

  13. Background metric in supergravity theories

    International Nuclear Information System (INIS)

    Yoneya, T.

    1978-01-01

    In supergravity theories, we investigate the conformal anomaly of the path-integral determinant and the problem of fermion zero modes in the presence of a nontrivial background metric. Except in SO(3) -invariant supergravity, there are nonvanishing conformal anomalies. As a consequence, amplitudes around the nontrivial background metric contain unpredictable arbitrariness. The fermion zero modes which are explicitly constructed for the Euclidean Schwarzschild metric are interpreted as an indication of the supersymmetric multiplet structure of a black hole. The degree of degeneracy of a black hole is 2/sup 4n/ in SO(n) supergravity

  14. Background music and cognitive performance.

    Science.gov (United States)

    Angel, Leslie A; Polzella, Donald J; Elvers, Greg C

    2010-06-01

    The present experiment employed standardized test batteries to assess the effects of fast-tempo music on cognitive performance among 56 male and female university students. A linguistic processing task and a spatial processing task were selected from the Criterion Task Set developed to assess verbal and nonverbal performance. Ten excerpts from Mozart's music matched for tempo were selected. Background music increased the speed of spatial processing and the accuracy of linguistic processing. The findings suggest that background music can have predictable effects on cognitive performance.

  15. Children of ethnic minority backgrounds

    DEFF Research Database (Denmark)

    Johansen, Stine Liv

    2010-01-01

    media products and toys just as they will have knowledge of different media texts, play genres, rhymes etc. This has consequences for their ability to access social settings, for instance in play. New research in this field will focus on how children themselves make sense of this balancing of cultures......Children of ethnic minority background balance their everyday life between a cultural background rooted in their ethnic origin and a daily life in day care, schools and with peers that is founded in a majority culture. This means, among other things, that they often will have access to different...

  16. Generative electronic background music system

    International Nuclear Information System (INIS)

    Mazurowski, Lukasz

    2015-01-01

    In this short paper-extended abstract the new approach to generation of electronic background music has been presented. The Generative Electronic Background Music System (GEBMS) has been located between other related approaches within the musical algorithm positioning framework proposed by Woller et al. The music composition process is performed by a number of mini-models parameterized by further described properties. The mini-models generate fragments of musical patterns used in output composition. Musical pattern and output generation are controlled by container for the mini-models - a host-model. General mechanism has been presented including the example of the synthesized output compositions

  17. Transgene x environment interactions in genetically modified wheat.

    Directory of Open Access Journals (Sweden)

    Simon L Zeller

    Full Text Available BACKGROUND: The introduction of transgenes into plants may cause unintended phenotypic effects which could have an impact on the plant itself and the environment. Little is published in the scientific literature about the interrelation of environmental factors and possible unintended effects in genetically modified (GM plants. METHODS AND FINDINGS: We studied transgenic bread wheat Triticum aestivum lines expressing the wheat Pm3b gene against the fungus powdery mildew Blumeria graminis f.sp. tritici. Four independent offspring pairs, each consisting of a GM line and its corresponding non-GM control line, were grown under different soil nutrient conditions and with and without fungicide treatment in the glasshouse. Furthermore, we performed a field experiment with a similar design to validate our glasshouse results. The transgene increased the resistance to powdery mildew in all environments. However, GM plants reacted sensitive to fungicide spraying in the glasshouse. Without fungicide treatment, in the glasshouse GM lines had increased vegetative biomass and seed number and a twofold yield compared with control lines. In the field these results were reversed. Fertilization generally increased GM/control differences in the glasshouse but not in the field. Two of four GM lines showed up to 56% yield reduction and a 40-fold increase of infection with ergot disease Claviceps purpurea compared with their control lines in the field experiment; one GM line was very similar to its control. CONCLUSIONS: Our results demonstrate that, depending on the insertion event, a particular transgene can have large effects on the entire phenotype of a plant and that these effects can sometimes be reversed when plants are moved from the glasshouse to the field. However, it remains unclear which mechanisms underlie these effects and how they may affect concepts in molecular plant breeding and plant evolutionary ecology.

  18. Interoperability between phenotype and anatomy ontologies.

    Science.gov (United States)

    Hoehndorf, Robert; Oellrich, Anika; Rebholz-Schuhmann, Dietrich

    2010-12-15

    Phenotypic information is important for the analysis of the molecular mechanisms underlying disease. A formal ontological representation of phenotypic information can help to identify, interpret and infer phenotypic traits based on experimental findings. The methods that are currently used to represent data and information about phenotypes fail to make the semantics of the phenotypic trait explicit and do not interoperate with ontologies of anatomy and other domains. Therefore, valuable resources for the analysis of phenotype studies remain unconnected and inaccessible to automated analysis and reasoning. We provide a framework to formalize phenotypic descriptions and make their semantics explicit. Based on this formalization, we provide the means to integrate phenotypic descriptions with ontologies of other domains, in particular anatomy and physiology. We demonstrate how our framework leads to the capability to represent disease phenotypes, perform powerful queries that were not possible before and infer additional knowledge. http://bioonto.de/pmwiki.php/Main/PheneOntology.

  19. Adaptation to an extraordinary environment by evolution of phenotypic plasticity and genetic assimilation.

    Science.gov (United States)

    Lande, Russell

    2009-07-01

    Adaptation to a sudden extreme change in environment, beyond the usual range of background environmental fluctuations, is analysed using a quantitative genetic model of phenotypic plasticity. Generations are discrete, with time lag tau between a critical period for environmental influence on individual development and natural selection on adult phenotypes. The optimum phenotype, and genotypic norms of reaction, are linear functions of the environment. Reaction norm elevation and slope (plasticity) vary among genotypes. Initially, in the average background environment, the character is canalized with minimum genetic and phenotypic variance, and no correlation between reaction norm elevation and slope. The optimal plasticity is proportional to the predictability of environmental fluctuations over time lag tau. During the first generation in the new environment the mean fitness suddenly drops and the mean phenotype jumps towards the new optimum phenotype by plasticity. Subsequent adaptation occurs in two phases. Rapid evolution of increased plasticity allows the mean phenotype to closely approach the new optimum. The new phenotype then undergoes slow genetic assimilation, with reduction in plasticity compensated by genetic evolution of reaction norm elevation in the original environment.

  20. Genetic modifiers of Duchenne and facioscapulohumeral muscular dystrophies.

    Science.gov (United States)

    Hightower, Rylie M; Alexander, Matthew S

    2018-01-01

    Muscular dystrophy is defined as the progressive wasting of skeletal muscles that is caused by inherited or spontaneous genetic mutations. Next-generation sequencing has greatly improved the accuracy and speed of diagnosis for different types of muscular dystrophy. Advancements in depth of coverage, convenience, and overall reduced cost have led to the identification of genetic modifiers that are responsible for phenotypic variability in affected patients. These genetic modifiers have been postulated to explain key differences in disease phenotypes, including age of loss of ambulation, steroid responsiveness, and the presence or absence of cardiac defects in patients with the same form of muscular dystrophy. This review highlights recent findings on genetic modifiers of Duchenne and facioscapulohumeral muscular dystrophies based on animal and clinical studies. These genetic modifiers hold great promise to be developed into novel therapeutic targets for the treatment of muscular dystrophies. Muscle Nerve 57: 6-15, 2018. © 2017 Wiley Periodicals, Inc.

  1. Modifier genes: Moving from pathogenesis to therapy.

    Science.gov (United States)

    McCabe, Edward R B

    2017-09-01

    This commentary will focus on how we can use our knowledge about the complexity of human disease and its pathogenesis to identify novel approaches to therapy. We know that even for single gene Mendelian disorders, patients with identical mutations often have different presentations and outcomes. This lack of genotype-phenotype correlation led us and others to examine the roles of modifier genes in the context of biological networks. These investigations have utilized vertebrate and invertebrate model organisms. Since one of the goals of research on modifier genes and networks is to identify novel therapeutic targets, the challenges to patient access and compliance because of the high costs of medications for rare genetic diseases must be recognized. A recent article explored protective modifiers, including plastin 3 (PLS3) and coronin 1C (CORO1C), in spinal muscular atrophy (SMA). SMA is an autosomal recessive deficit of survival motor neuron protein (SMN) caused by mutations in SMN1. However, the severity of SMA is determined primarily by the number of SMN2 copies, and this results in significant phenotypic variability. PLS3 was upregulated in siblings who were asymptomatic compared with those who had SMA2 or SMA3, but identical homozygous SMN1 deletions and equal numbers of SMN2 copies. CORO1C was identified by interrogation of the PLS3 interactome. Overexpression of these proteins rescued endocytosis in SMA models. In addition, antisense RNA for upregulation of SMN2 protein expression is being developed as another way of modifying the SMA phenotype. These investigations suggest the practical application of protective modifiers to rescue SMA phenotypes. Other examples of the potential therapeutic value of novel protective modifiers will be discussed, including in Duchenne muscular dystrophy and glycerol kinase deficiency. This work shows that while we live in an exciting era of genomic sequencing, a functional understanding of biology, the impact of its

  2. Low Background Micromegas in CAST

    DEFF Research Database (Denmark)

    Garza, J G; Aune, S.; Aznar, F.

    2014-01-01

    Solar axions could be converted into x-rays inside the strong magnetic field of an axion helioscope, triggering the detection of this elusive particle. Low background x-ray detectors are an essential component for the sensitivity of these searches. We report on the latest developments of the Micr...

  3. Teaching about Natural Background Radiation

    Science.gov (United States)

    Al-Azmi, Darwish; Karunakara, N.; Mustapha, Amidu O.

    2013-01-01

    Ambient gamma dose rates in air were measured at different locations (indoors and outdoors) to demonstrate the ubiquitous nature of natural background radiation in the environment and to show that levels vary from one location to another, depending on the underlying geology. The effect of a lead shield on a gamma radiation field was also…

  4. Educational Choice. A Background Paper.

    Science.gov (United States)

    Quality Education for Minorities Network, Washington, DC.

    This paper addresses school choice, one proposal to address parental involvement concerns, focusing on historical background, definitions, rationale for advocating choice, implementation strategies, and implications for minorities and low-income families. In the past, transfer payment programs such as tuition tax credits and vouchers were…

  5. Kerr metric in cosmological background

    Energy Technology Data Exchange (ETDEWEB)

    Vaidya, P C [Gujarat Univ., Ahmedabad (India). Dept. of Mathematics

    1977-06-01

    A metric satisfying Einstein's equation is given which in the vicinity of the source reduces to the well-known Kerr metric and which at large distances reduces to the Robertson-Walker metric of a nomogeneous cosmological model. The radius of the event horizon of the Kerr black hole in the cosmological background is found out.

  6. Low Background Micromegas in CAST

    CERN Document Server

    Garza, J.G.; Aznar, F.; Calvet, D.; Castel, J.F.; Christensen, F.E.; Dafni, T.; Davenport, M.; Decker, T.; Ferrer-Ribas, E.; Galán, J.; García, J.A.; Giomataris, I.; Hill, R.M.; Iguaz, F.J.; Irastorza, I.G.; Jakobsen, A.C.; Jourde, D.; Mirallas, H.; Ortega, I.; Papaevangelou, T.; Pivovaroff, M.J.; Ruz, J.; Tomás, A.; Vafeiadis, T.; Vogel, J.K.

    2015-11-16

    Solar axions could be converted into x-rays inside the strong magnetic field of an axion helioscope, triggering the detection of this elusive particle. Low background x-ray detectors are an essential component for the sensitivity of these searches. We report on the latest developments of the Micromegas detectors for the CERN Axion Solar Telescope (CAST), including technological pathfinder activities for the future International Axion Observatory (IAXO). The use of low background techniques and the application of discrimination algorithms based on the high granularity of the readout have led to background levels below 10$^{-6}$ counts/keV/cm$^2$/s, more than a factor 100 lower than the first generation of Micromegas detectors. The best levels achieved at the Canfranc Underground Laboratory (LSC) are as low as 10$^{-7}$ counts/keV/cm$^2$/s, showing good prospects for the application of this technology in IAXO. The current background model, based on underground and surface measurements, is presented, as well as ...

  7. Genetic background influences age-related decline in visual and nonvisual retinal responses, circadian rhythms, and sleep☆

    Science.gov (United States)

    Banks, Gareth; Heise, Ines; Starbuck, Becky; Osborne, Tamzin; Wisby, Laura; Potter, Paul; Jackson, Ian J.; Foster, Russell G.; Peirson, Stuart N.; Nolan, Patrick M.

    2015-01-01

    The circadian system is entrained to the environmental light/dark cycle via retinal photoreceptors and regulates numerous aspects of physiology and behavior, including sleep. These processes are all key factors in healthy aging showing a gradual decline with age. Despite their importance, the exact mechanisms underlying this decline are yet to be fully understood. One of the most effective tools we have to understand the genetic factors underlying these processes are genetically inbred mouse strains. The most commonly used reference mouse strain is C57BL/6J, but recently, resources such as the International Knockout Mouse Consortium have started producing large numbers of mouse mutant lines on a pure genetic background, C57BL/6N. Considering the substantial genetic diversity between mouse strains we expect there to be phenotypic differences, including differential effects of aging, in these and other strains. Such differences need to be characterized not only to establish how different mouse strains may model the aging process but also to understand how genetic background might modify age-related phenotypes. To ascertain the effects of aging on sleep/wake behavior, circadian rhythms, and light input and whether these effects are mouse strain-dependent, we have screened C57BL/6J, C57BL/6N, C3H-HeH, and C3H-Pde6b+ mouse strains at 5 ages throughout their life span. Our data show that sleep, circadian, and light input parameters are all disrupted by the aging process. Moreover, we have cataloged a number of strain-specific aging effects, including the rate of cataract development, decline in the pupillary light response, and changes in sleep fragmentation and the proportion of time spent asleep. PMID:25179226

  8. Genetic background influences age-related decline in visual and nonvisual retinal responses, circadian rhythms, and sleep.

    Science.gov (United States)

    Banks, Gareth; Heise, Ines; Starbuck, Becky; Osborne, Tamzin; Wisby, Laura; Potter, Paul; Jackson, Ian J; Foster, Russell G; Peirson, Stuart N; Nolan, Patrick M

    2015-01-01

    The circadian system is entrained to the environmental light/dark cycle via retinal photoreceptors and regulates numerous aspects of physiology and behavior, including sleep. These processes are all key factors in healthy aging showing a gradual decline with age. Despite their importance, the exact mechanisms underlying this decline are yet to be fully understood. One of the most effective tools we have to understand the genetic factors underlying these processes are genetically inbred mouse strains. The most commonly used reference mouse strain is C57BL/6J, but recently, resources such as the International Knockout Mouse Consortium have started producing large numbers of mouse mutant lines on a pure genetic background, C57BL/6N. Considering the substantial genetic diversity between mouse strains we expect there to be phenotypic differences, including differential effects of aging, in these and other strains. Such differences need to be characterized not only to establish how different mouse strains may model the aging process but also to understand how genetic background might modify age-related phenotypes. To ascertain the effects of aging on sleep/wake behavior, circadian rhythms, and light input and whether these effects are mouse strain-dependent, we have screened C57BL/6J, C57BL/6N, C3H-HeH, and C3H-Pde6b+ mouse strains at 5 ages throughout their life span. Our data show that sleep, circadian, and light input parameters are all disrupted by the aging process. Moreover, we have cataloged a number of strain-specific aging effects, including the rate of cataract development, decline in the pupillary light response, and changes in sleep fragmentation and the proportion of time spent asleep. Copyright © 2015 The Authors. Published by Elsevier Inc. All rights reserved.

  9. The Cosmic Infrared Background Experiment

    Science.gov (United States)

    Bock, James; Battle, J.; Cooray, A.; Hristov, V.; Kawada, M.; Keating, B.; Lee, D.; Matsumoto, T.; Matsuura, S.; Nam, U.; Renbarger, T.; Sullivan, I.; Tsumura, K.; Wada, T.; Zemcov, M.

    2009-01-01

    We are developing the Cosmic Infrared Background ExpeRiment (CIBER) to search for signatures of first-light galaxy emission in the extragalactic background. The first generation of stars produce characteristic signatures in the near-infrared extragalactic background, including a redshifted Ly-cutoff feature and a characteristic fluctuation power spectrum, that may be detectable with a specialized instrument. CIBER consists of two wide-field cameras to measure the fluctuation power spectrum, and a low-resolution and a narrow-band spectrometer to measure the absolute background. The cameras will search for fluctuations on angular scales from 7 arcseconds to 2 degrees, where the first-light galaxy spatial power spectrum peaks. The cameras have the necessary combination of sensitivity, wide field of view, spatial resolution, and multiple bands to make a definitive measurement. CIBER will determine if the fluctuations reported by Spitzer arise from first-light galaxies. The cameras observe in a single wide field of view, eliminating systematic errors associated with mosaicing. Two bands are chosen to maximize the first-light signal contrast, at 1.6 um near the expected spectral maximum, and at 1.0 um; the combination is a powerful discriminant against fluctuations arising from local sources. We will observe regions of the sky surveyed by Spitzer and Akari. The low-resolution spectrometer will search for the redshifted Lyman cutoff feature in the 0.7 - 1.8 um spectral region. The narrow-band spectrometer will measure the absolute Zodiacal brightness using the scattered 854.2 nm Ca II Fraunhofer line. The spectrometers will test if reports of a diffuse extragalactic background in the 1 - 2 um band continues into the optical, or is caused by an under estimation of the Zodiacal foreground. We report performance of the assembled and tested instrument as we prepare for a first sounding rocket flight in early 2009. CIBER is funded by the NASA/APRA sub-orbital program.

  10. The severity of retinal degeneration in Rp1h gene-targeted mice is dependent on genetic background.

    Science.gov (United States)

    Liu, Qin; Saveliev, Alexei; Pierce, Eric A

    2009-04-01

    The severity of disease in patients with retinitis pigmentosa (RP) can vary significantly, even among patients with the same primary mutations. It is hypothesized that modifier genes play important roles in determining the severity of RP, including the retinitis pigmentosa 1 (RP1) form of disease. To investigate the basis of variation in disease expression for RP1 disease, the authors generated congenic mice with a gene-targeted retinitis pigmentosa 1 homolog (Rp1h) allele (Rp1h(tm1Eap)) on several different genetic backgrounds and analyzed their retinal phenotypes. The Rp1h(tm1Eap) allele was placed onto the C57BL/6J, DBA1/J, and A/J backgrounds. Retinal function of the resultant congenic mice was evaluated using electroretinographic analyses. Retinal structure and ultrastructure were evaluated using light and electron microscopy. Rp1h protein location was determined with immunofluorescence microscopy. Analysis of the retinal phenotype of incipient congenic (N6) B6.129S-Rp1h(+/tm1Eap), DBA.129S(B6)-Rp1h(+/tm1Eap), and A.129S(B6)-Rp1h(+/tm1Eap) mice at 1 year of age showed retinal degeneration only in the A.129S(B6)-Rp1h(+/tm1Eap) mice. Further analyses revealed that the photoreceptors of the fully congenic A.129S(B6)-Rp1h(+/tm1Eap) mice show evidence of degeneration at 6 months of age and are almost completely lost by 18 months of age. In contrast, the photoreceptor cells in the fully congenic B6.129S-Rp1h(+/tm1Eap) mice remain healthy up to 18 months. The severity of the retinal degeneration caused by the Rp1h(tm1Eap) allele is notably dependent on genetic background. The development and characterization of the B6.129S-Rp1h(+/tm1Eap) and A.129S(B6)-Rp1h(+/tm1Eap) congenic mouse lines will facilitate identification of sequence alterations in genes that modify the severity of RP1 disease.

  11. Automated phenotyping of permanent crops

    Science.gov (United States)

    McPeek, K. Thomas; Steddom, Karl; Zamudio, Joseph; Pant, Paras; Mullenbach, Tyler

    2017-05-01

    AGERpoint is defining a new technology space for the growers' industry by introducing novel applications for sensor technology and data analysis to growers of permanent crops. Serving data to a state-of-the-art analytics engine from a cutting edge sensor platform, a new paradigm in precision agriculture is being developed that allows growers to understand the unique needs of each tree, bush or vine in their operation. Autonomous aerial and terrestrial vehicles equipped with multiple varieties of remote sensing technologies give AGERpoint the ability to measure key morphological and spectral features of permanent crops. This work demonstrates how such phenotypic measurements combined with machine learning algorithms can be used to determine the variety of crops (e.g., almond and pecan trees). This phenotypic and varietal information represents the first step in enabling growers with the ability to tailor their management practices to individual plants and maximize their economic productivity.

  12. Phenotypic deconstruction of gene circuitry.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  13. Phenotypic deconstruction of gene circuitry

    Science.gov (United States)

    Lomnitz, Jason G.; Savageau, Michael A.

    2013-06-01

    It remains a challenge to obtain a global perspective on the behavioral repertoire of complex nonlinear gene circuits. In this paper, we describe a method for deconstructing complex systems into nonlinear sub-systems, based on mathematically defined phenotypes, which are then represented within a system design space that allows the repertoire of qualitatively distinct phenotypes of the complex system to be identified, enumerated, and analyzed. This method efficiently characterizes large regions of system design space and quickly generates alternative hypotheses for experimental testing. We describe the motivation and strategy in general terms, illustrate its use with a detailed example involving a two-gene circuit with a rich repertoire of dynamic behavior, and discuss experimental means of navigating the system design space.

  14. Simultaneous Analysis of the Behavioural Phenotype, Physical Factors, and Parenting Stress in People with Cornelia De Lange Syndrome

    Science.gov (United States)

    Wulffaert, J.; van Berckelaer-Onnes, I.; Kroonenberg, P.; Scholte, E.; Bhuiyan, Z.; Hennekam, R.

    2009-01-01

    Background: Studies into the phenotype of rare genetic syndromes largely rely on bivariate analysis. The aim of this study was to describe the phenotype of Cornelia de Lange syndrome (CdLS) in depth by examining a large number of variables with varying measurement levels. Virtually the only suitable multivariate technique for this is categorical…

  15. Wine Expertise Predicts Taste Phenotype.

    Science.gov (United States)

    Hayes, John E; Pickering, Gary J

    2012-03-01

    Taste phenotypes have long been studied in relation to alcohol intake, dependence, and family history, with contradictory findings. However, on balance - with appropriate caveats about populations tested, outcomes measured and psychophysical methods used - an association between variation in taste responsiveness and some alcohol behaviors is supported. Recent work suggests super-tasting (operationalized via propylthiouracil (PROP) bitterness) not only associates with heightened response but also with more acute discrimination between stimuli. Here, we explore relationships between food and beverage adventurousness and taste phenotype. A convenience sample of wine drinkers (n=330) were recruited in Ontario and phenotyped for PROP bitterness via filter paper disk. They also filled out a short questionnaire regarding willingness to try new foods, alcoholic beverages and wines as well as level of wine involvement, which was used to classify them as a wine expert (n=110) or wine consumer (n=220). In univariate logisitic models, food adventurousness predicted trying new wines and beverages but not expertise. Likewise, wine expertise predicted willingness to try new wines and beverages but not foods. In separate multivariate logistic models, willingness to try new wines and beverages was predicted by expertise and food adventurousness but not PROP. However, mean PROP bitterness was higher among wine experts than wine consumers, and the conditional distribution functions differed between experts and consumers. In contrast, PROP means and distributions did not differ with food adventurousness. These data suggest individuals may self-select for specific professions based on sensory ability (i.e., an active gene-environment correlation) but phenotype does not explain willingness to try new stimuli.

  16. From plant genomes to phenotypes

    OpenAIRE

    Bolger, Marie; Gundlach, Heidrun; Scholz, Uwe; Mayer, Klaus; Usadel, Björn; Schwacke, Rainer; Schmutzer, Thomas; Chen, Jinbo; Arend, Daniel; Oppermann, Markus; Weise, Stephan; Lange, Matthias; Fiorani, Fabio; Spannagl, Manuel

    2017-01-01

    Recent advances in sequencing technologies have greatly accelerated the rate of plant genome and applied breeding research. Despite this advancing trend, plant genomes continue to present numerous difficulties to the standard tools and pipelines not only for genome assembly but also gene annotation and downstream analysis.Here we give a perspective on tools, resources and services necessary to assemble and analyze plant genomes and link them to plant phenotypes.

  17. Background radioactivity in environmental materials

    International Nuclear Information System (INIS)

    Maul, P.R.; O'Hara, J.P.

    1989-01-01

    This paper presents the results of a literature search to identify information on concentrations of 'background' radioactivity in foodstuffs and other commonly available environmental materials. The review has concentrated on naturally occurring radioactivity in foods and on UK data, although results from other countries have also been considered where appropriate. The data are compared with established definitions of a 'radioactive' substance and radionuclides which do not appear to be adequately covered in the literature are noted. (author)

  18. Background paper on aquaculture research

    OpenAIRE

    Wenblad, Axel; Jokumsen, Alfred; Eskelinen, Unto; Torrissen, Ole

    2013-01-01

    The Board of MISTRA established in 2012 a Working Group (WG) on Aquaculture to provide the Board with background information for its upcoming decision on whether the foundation should invest in aquaculture research. The WG included Senior Advisor Axel Wenblad, Sweden (Chairman), Professor Ole Torrissen, Norway, Senior Advisory Scientist Unto Eskelinen, Finland and Senior Advisory Scientist Alfred Jokumsen, Denmark. The WG performed an investigation of the Swedish aquaculture sector including ...

  19. Environment Changes Genetic Effects on Respiratory Conditions and Allergic Phenotypes

    DEFF Research Database (Denmark)

    Song, Yong; Schwager, Michelle J; Backer, Vibeke

    2017-01-01

    The prevalence of asthma and allergic diseases is disproportionately distributed among different populations, with an increasing trend observed in Western countries. Here we investigated how the environment affected genotype-phenotype association in a genetically homogeneous, but geographically...... separated population. We evaluated 18 single nucleotide polymorphisms (SNPs) corresponding to 8 genes (ADAM33, ALOX5, LT-α, LTC4S, NOS1, ORMDL3, TBXA2R and TNF-α), the lung function and five respiratory/allergic conditions (ever asthma, bronchitis, rhinitis, dermatitis and atopy) in two populations of Inuit......-phenotype associations relating to bronchitis and allergy susceptibility are dependent on the environment and that environmental factors/lifestyles modify genetic predisposition and change the genetic effects on diseases....

  20. Characterizing visible and invisible cell wall mutant phenotypes

    Energy Technology Data Exchange (ETDEWEB)

    Carpita, Nicholas C.; McCann, Maureen C.

    2015-04-06

    About 10% of a plant's genome is devoted to generating the protein machinery to synthesize, remodel, and deconstruct the cell wall. High-throughput genome sequencing technologies have enabled a reasonably complete inventory of wall-related genes that can be assembled into families of common evolutionary origin. Assigning function to each gene family member has been aided immensely by identification of mutants with visible phenotypes or by chemical and spectroscopic analysis of mutants with ‘invisible’ phenotypes of modified cell wall composition and architecture that do not otherwise affect plant growth or development. This review connects the inference of gene function on the basis of deviation from the wild type in genetic functional analyses to insights provided by modern analytical techniques that have brought us ever closer to elucidating the sequence structures of the major polysaccharide components of the plant cell wall.

  1. The isotropic radio background revisited

    Energy Technology Data Exchange (ETDEWEB)

    Fornengo, Nicolao; Regis, Marco [Dipartimento di Fisica Teorica, Università di Torino, via P. Giuria 1, I–10125 Torino (Italy); Lineros, Roberto A. [Instituto de Física Corpuscular – CSIC/U. Valencia, Parc Científic, calle Catedrático José Beltrán, 2, E-46980 Paterna (Spain); Taoso, Marco, E-mail: fornengo@to.infn.it, E-mail: rlineros@ific.uv.es, E-mail: regis@to.infn.it, E-mail: taoso@cea.fr [Institut de Physique Théorique, CEA/Saclay, F-91191 Gif-sur-Yvette Cédex (France)

    2014-04-01

    We present an extensive analysis on the determination of the isotropic radio background. We consider six different radio maps, ranging from 22 MHz to 2.3 GHz and covering a large fraction of the sky. The large scale emission is modeled as a linear combination of an isotropic component plus the Galactic synchrotron radiation and thermal bremsstrahlung. Point-like and extended sources are either masked or accounted for by means of a template. We find a robust estimate of the isotropic radio background, with limited scatter among different Galactic models. The level of the isotropic background lies significantly above the contribution obtained by integrating the number counts of observed extragalactic sources. Since the isotropic component dominates at high latitudes, thus making the profile of the total emission flat, a Galactic origin for such excess appears unlikely. We conclude that, unless a systematic offset is present in the maps, and provided that our current understanding of the Galactic synchrotron emission is reasonable, extragalactic sources well below the current experimental threshold seem to account for the majority of the brightness of the extragalactic radio sky.

  2. The isotropic radio background revisited

    International Nuclear Information System (INIS)

    Fornengo, Nicolao; Regis, Marco; Lineros, Roberto A.; Taoso, Marco

    2014-01-01

    We present an extensive analysis on the determination of the isotropic radio background. We consider six different radio maps, ranging from 22 MHz to 2.3 GHz and covering a large fraction of the sky. The large scale emission is modeled as a linear combination of an isotropic component plus the Galactic synchrotron radiation and thermal bremsstrahlung. Point-like and extended sources are either masked or accounted for by means of a template. We find a robust estimate of the isotropic radio background, with limited scatter among different Galactic models. The level of the isotropic background lies significantly above the contribution obtained by integrating the number counts of observed extragalactic sources. Since the isotropic component dominates at high latitudes, thus making the profile of the total emission flat, a Galactic origin for such excess appears unlikely. We conclude that, unless a systematic offset is present in the maps, and provided that our current understanding of the Galactic synchrotron emission is reasonable, extragalactic sources well below the current experimental threshold seem to account for the majority of the brightness of the extragalactic radio sky

  3. Backgrounds and characteristics of arsonists.

    Science.gov (United States)

    Labree, Wim; Nijman, Henk; van Marle, Hjalmar; Rassin, Eric

    2010-01-01

    The aim of this study was to gain more insight in the backgrounds and characteristics of arsonists. For this, the psychiatric, psychological, personal, and criminal backgrounds of all arsonists (n=25), sentenced to forced treatment in the maximum security forensic hospital "De Kijvelanden", were compared to the characteristics of a control group of patients (n=50), incarcerated at the same institution for other severe crimes. Apart from DSM-IV Axis I and Axis II disorders, family backgrounds, level of education, treatment history, intelligence (WAIS scores), and PCL-R scores were included in the comparisons. Furthermore, the apparent motives for the arson offences were explored. It was found that arsonists had more often received psychiatric treatment, prior to committing their index offence, and had a history of severe alcohol abuse more often in comparison to the controls. The arsonists turned out to be less likely to suffer from a major psychotic disorder. Both groups did not differ significantly on the other variables, among which the PCL-R total scores and factor scores. Exploratory analyses however, did suggest that arsonists may differentiate from non-arsonists on three items of the PCL-R, namely impulsivity (higher scores), superficial charm (lower scores), and juvenile delinquency (lower scores). Although the number of arsonists with a major psychotic disorder was relatively low (28%), delusional thinking of some form was judged to play a role in causing arson crimes in about half of the cases (52%).

  4. Prevalence and clinical characteristics of metabolically healthy obese individuals and other obese/non-obese metabolic phenotypes in a working population: results from the Icaria study

    Directory of Open Access Journals (Sweden)

    Albert Goday

    2016-04-01

    Full Text Available Abstract Background Metabolically healthy obese (MHO phenotype may present with distinct characteristics compared with those with a metabolically unhealthy obese phenotype. Epidemiologic data on the distribution of these conditions in the working population are lacking. We aimed to evaluate the prevalence and clinical characteristics of MHO and other obese/non-obese metabolic phenotypes in a working population. Methods Cross-sectional analysis of all subjects who had undergone a medical examination with Ibermutuamur Prevention Society from May 2004 to December 2007. Participants were classified into 5 categories according to their body mass index (BMI; within each of these categories, participants were further classified as metabolically healthy (MH or metabolically unhealthy (MUH according to the modified NCEP-ATPIII criteria. A logistic regression analysis was performed to evaluate some clinically relevant factors associated with a MH status. Results In the overall population, the prevalence of the MHO phenotype was 8.6 %. The proportions of MH individuals in the overweight and obese categories were: 87.1 % (overweight and 55.5 % (obese I-III [58.8, 40.0, and 38.7 % of the obese I, II, and III categories, respectively]. When the overweight and obese categories were considered, compared with individuals who were MUH, those who were MH tended to be younger and more likely to be female or participate in physical exercise; they were also less likely to smoke, or to be a heavy drinker. In the underweight and normal weight categories, compared with individuals who were MH, those who were MUH were more likely to be older, male, manual (blue collar workers, smokers and heavy drinkers. Among participants in the MUH, normal weight group, the proportion of individuals with a sedentary lifestyle was higher relative to those in the MH, normal weight group. The factors more strongly associated with the MUH phenotype were BMI and age, followed by the

  5. Phenotypic covariance at species' borders.

    Science.gov (United States)

    Caley, M Julian; Cripps, Edward; Game, Edward T

    2013-05-28

    Understanding the evolution of species limits is important in ecology, evolution, and conservation biology. Despite its likely importance in the evolution of these limits, little is known about phenotypic covariance in geographically marginal populations, and the degree to which it constrains, or facilitates, responses to selection. We investigated phenotypic covariance in morphological traits at species' borders by comparing phenotypic covariance matrices (P), including the degree of shared structure, the distribution of strengths of pair-wise correlations between traits, the degree of morphological integration of traits, and the ranks of matricies, between central and marginal populations of three species-pairs of coral reef fishes. Greater structural differences in P were observed between populations close to range margins and conspecific populations toward range centres, than between pairs of conspecific populations that were both more centrally located within their ranges. Approximately 80% of all pair-wise trait correlations within populations were greater in the north, but these differences were unrelated to the position of the sampled population with respect to the geographic range of the species. Neither the degree of morphological integration, nor ranks of P, indicated greater evolutionary constraint at range edges. Characteristics of P observed here provide no support for constraint contributing to the formation of these species' borders, but may instead reflect structural change in P caused by selection or drift, and their potential to evolve in the future.

  6. Adaptive evolution of molecular phenotypes

    International Nuclear Information System (INIS)

    Held, Torsten; Nourmohammad, Armita; Lässig, Michael

    2014-01-01

    Molecular phenotypes link genomic information with organismic functions, fitness, and evolution. Quantitative traits are complex phenotypes that depend on multiple genomic loci. In this paper, we study the adaptive evolution of a quantitative trait under time-dependent selection, which arises from environmental changes or through fitness interactions with other co-evolving phenotypes. We analyze a model of trait evolution under mutations and genetic drift in a single-peak fitness seascape. The fitness peak performs a constrained random walk in the trait amplitude, which determines the time-dependent trait optimum in a given population. We derive analytical expressions for the distribution of the time-dependent trait divergence between populations and of the trait diversity within populations. Based on this solution, we develop a method to infer adaptive evolution of quantitative traits. Specifically, we show that the ratio of the average trait divergence and the diversity is a universal function of evolutionary time, which predicts the stabilizing strength and the driving rate of the fitness seascape. From an information-theoretic point of view, this function measures the macro-evolutionary entropy in a population ensemble, which determines the predictability of the evolutionary process. Our solution also quantifies two key characteristics of adapting populations: the cumulative fitness flux, which measures the total amount of adaptation, and the adaptive load, which is the fitness cost due to a population's lag behind the fitness peak. (paper)

  7. Advanced Background Subtraction Applied to Aeroacoustic Wind Tunnel Testing

    Science.gov (United States)

    Bahr, Christopher J.; Horne, William C.

    2015-01-01

    An advanced form of background subtraction is presented and applied to aeroacoustic wind tunnel data. A variant of this method has seen use in other fields such as climatology and medical imaging. The technique, based on an eigenvalue decomposition of the background noise cross-spectral matrix, is robust against situations where isolated background auto-spectral levels are measured to be higher than levels of combined source and background signals. It also provides an alternate estimate of the cross-spectrum, which previously might have poor definition for low signal-to-noise ratio measurements. Simulated results indicate similar performance to conventional background subtraction when the subtracted spectra are weaker than the true contaminating background levels. Superior performance is observed when the subtracted spectra are stronger than the true contaminating background levels. Experimental results show limited success in recovering signal behavior for data where conventional background subtraction fails. They also demonstrate the new subtraction technique's ability to maintain a proper coherence relationship in the modified cross-spectral matrix. Beam-forming and de-convolution results indicate the method can successfully separate sources. Results also show a reduced need for the use of diagonal removal in phased array processing, at least for the limited data sets considered.

  8. Characterization of modified clinoptilolite

    International Nuclear Information System (INIS)

    Novosad, J.; Jandl, J.; Woollins, J.D.

    1992-01-01

    Samples of clinoptilolite were modified using insoluble hexacyanoferrate from aqueous solution. The modified samples were characterized by elemental analysis, powder X-ray diffraction, solid state NMR and vibrational spectroscopy. The sorption properties of modified clinoptilolite were studied, too. Higher affinity for 137 Cs sorption in comparison with the natural clinoptilolite has been proved. (author) 5 refs.; 3 figs.; 2 tabs

  9. Simulation of PEP-II Accelerator Backgrounds Using TURTLE

    CERN Document Server

    Barlow, Roger J; Kozanecki, Witold; Majewski, Stephanie; Roudeau, Patrick; Stocchi, Achille

    2005-01-01

    We present studies of accelerator-induced backgrounds in the BaBar detector at the SLAC B-Factory, carried out using a modified version ofthe DECAY TURTLE simulation package. Lost-particle backgrounds in PEP-II are dominated by a combination of beam-gas bremstrahlung, beam-gas Coulomb scattering, radiative-Bhabha events and beam-beam blow-up. The radiation damage and detector occupancy caused by the associated electromagnetic shower debris can limit the usable luminosity. In order to understand and mitigate such backgrounds, we have performed a full programme of beam-gas and luminosity-background simulations, that include the effects of the detector solenoidal field, detailed modelling of limiting apertures in both collider rings, and optimization of the betatron collimation scheme in the presence of large transverse tails.

  10. Low genetic and phenotypic divergence in a contact zone between freshwater and marine sticklebacks: gene flow constrains adaptation

    DEFF Research Database (Denmark)

    Pedersen, Susanne Holst; Ferchaud, Anne-Laure; Bertelsen, Mia Smedegaard

    2017-01-01

    Background: Distinct hybrid zones and phenotypic and genomic divergence is often observed between marine and freshwater threespine sticklebacks (Gasterosteus aculeatus). Nevertheless, cases also exist where marinefreshwater divergence is diffuse despite seemingly similar environmental settings...

  11. Family Background and Educational Choices

    DEFF Research Database (Denmark)

    McIntosh, James; D. Munk, Martin

    enrollments, especially for females. Not only did the educational opportunities for individuals with disadvantaged backgrounds improve absolutely, but their relative position also improved. A similarly dramatic increase in attendance at university for the period 1985-2005 was found for these cohorts when......We examine the participation in secondary and tertiary education of five cohorts of Danish males and females who were aged twenty starting in 1982 and ending in 2002. We find that the large expansion of secondary education in this period was characterized by a phenomenal increase in gymnasium...

  12. A novel 3D imaging system for strawberry phenotyping

    Directory of Open Access Journals (Sweden)

    Joe Q. He

    2017-11-01

    Full Text Available Abstract Background Accurate and quantitative phenotypic data in plant breeding programmes is vital in breeding to assess the performance of genotypes and to make selections. Traditional strawberry phenotyping relies on the human eye to assess most external fruit quality attributes, which is time-consuming and subjective. 3D imaging is a promising high-throughput technique that allows multiple external fruit quality attributes to be measured simultaneously. Results A low cost multi-view stereo (MVS imaging system was developed, which captured data from 360° around a target strawberry fruit. A 3D point cloud of the sample was derived and analysed with custom-developed software to estimate berry height, length, width, volume, calyx size, colour and achene number. Analysis of these traits in 100 fruits showed good concordance with manual assessment methods. Conclusion This study demonstrates the feasibility of an MVS based 3D imaging system for the rapid and quantitative phenotyping of seven agronomically important external strawberry traits. With further improvement, this method could be applied in strawberry breeding programmes as a cost effective phenotyping technique.

  13. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-27

    Phenotypes are the observable characteristics of an organism, and they are widely recorded in biology and medicine. To facilitate data integration, ontologies that formally describe phenotypes are being developed in several domains. I will describe a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology of phenotypes is now applied in biomedical research.

  14. Background radiation map of Thailand

    International Nuclear Information System (INIS)

    Angsuwathana, P.; Chotikanatis, P.

    1997-01-01

    The radioelement concentration in the natural environment as well as the radiation exposure to man in day-to-day life is now the most interesting topic. The natural radiation is frequently referred as a standard for comparing additional sources of man-made radiation such as atomic weapon fallout, nuclear power generation, radioactive waste disposal, etc. The Department of Mineral Resources commenced a five-year project of nationwide airborne geophysical survey by awarding to Kenting Earth Sciences International Limited in 1984. The original purpose of survey was to support mineral exploration and geological mapping. Subsequently, the data quantity has been proved to be suitable for natural radiation information. In 1993 the Department of Mineral Resources, with the assistance of IAEA, published a Background Radiation Map of Thailand at the scale of 1:1,000,000 from the existing airborne radiometric digital data. The production of Background Radiation Map of Thailand is the result of data compilation and correction procedure developed over the Canadian Shield. This end product will be used as a base map in environmental application not only for Thailand but also Southeast Asia region. (author)

  15. [Cosmic Microwave Background (CMB) Anisotropies

    Science.gov (United States)

    Silk, Joseph

    1998-01-01

    One of the main areas of research is the theory of cosmic microwave background (CMB) anisotropies and analysis of CMB data. Using the four year COBE data we were able to improve existing constraints on global shear and vorticity. We found that, in the flat case (which allows for greatest anisotropy), (omega/H)0 less than 10(exp -7), where omega is the vorticity and H is the Hubble constant. This is two orders of magnitude lower than the tightest, previous constraint. We have defined a new set of statistics which quantify the amount of non-Gaussianity in small field cosmic microwave background maps. By looking at the distribution of power around rings in Fourier space, and at the correlations between adjacent rings, one can identify non-Gaussian features which are masked by large scale Gaussian fluctuations. This may be particularly useful for identifying unresolved localized sources and line-like discontinuities. Levin and collaborators devised a method to determine the global geometry of the universe through observations of patterns in the hot and cold spots of the CMB. We have derived properties of the peaks (maxima) of the CMB anisotropies expected in flat and open CDM models. We represent results for angular resolutions ranging from 5 arcmin to 20 arcmin (antenna FWHM), scales that are relevant for the MAP and COBRA/SAMBA space missions and the ground-based interferometer. Results related to galaxy formation and evolution are also discussed.

  16. Optical polarization: background and camouflage

    Science.gov (United States)

    Škerlind, Christina; Hallberg, Tomas; Eriksson, Johan; Kariis, Hans; Bergström, David

    2017-10-01

    Polarimetric imaging sensors in the electro-optical region, already military and commercially available in both the visual and infrared, show enhanced capabilities for advanced target detection and recognition. The capabilities arise due to the ability to discriminate between man-made and natural background surfaces using the polarization information of light. In the development of materials for signature management in the visible and infrared wavelength regions, different criteria need to be met to fulfil the requirements for a good camouflage against modern sensors. In conventional camouflage design, the aimed design of the surface properties of an object is to spectrally match or adapt it to a background and thereby minimizing the contrast given by a specific threat sensor. Examples will be shown from measurements of some relevant materials and how they in different ways affect the polarimetric signature. Dimensioning properties relevant in an optical camouflage from a polarimetric perspective, such as degree of polarization, the viewing or incident angle, and amount of diffuse reflection, mainly in the infrared region, will be discussed.

  17. The Cosmic Microwave Background Anisotropy

    Science.gov (United States)

    Bennett, C. L.

    1994-12-01

    The properties of the cosmic microwave background radiation provide unique constraints on the history and evolution of the universe. The first detection of anisotropy of the microwave radiation was reported by the COBE Team in 1992, based on the first year of flight data. The latest analyses of the first two years of COBE data are reviewed in this talk, including the amplitude of the microwave anisotropy as a function of angular scale and the statistical nature of the fluctuations. The two-year results are generally consistent with the earlier first year results, but the additional data allow for a better determination of the key cosmological parameters. In this talk the COBE results are compared with other observational anisotropy results and directions for future cosmic microwave anisotropy observations will be discussed. The National Aeronautics and Space Administration/Goddard Space Flight Center (NASA/GSFC) is responsible for the design, development, and operation of the Cosmic Background Explorer (COBE). Scientific guidance is provided by the COBE Science Working Group.

  18. NIH Mouse Metabolic Phenotyping Centers: the power of centralized phenotyping.

    Science.gov (United States)

    Laughlin, Maren R; Lloyd, K C Kent; Cline, Gary W; Wasserman, David H

    2012-10-01

    The Mouse Metabolic Phenotyping Centers (MMPCs) were founded in 2001 by the National Institutes of Health (NIH) to advance biomedical research by providing the scientific community with standardized, high-quality phenotyping services for mouse models of diabetes, obesity, and their complications. The intent is to allow researchers to take optimum advantage of the many new mouse models produced in labs and in high-throughput public efforts. The six MMPCs are located at universities around the country and perform complex metabolic tests in intact mice and hormone and analyte assays in tissues on a fee-for-service basis. Testing is subsidized by the NIH in order to reduce the barriers for mouse researchers. Although data derived from these tests belong to the researcher submitting mice or tissues, these data are archived after publication in a public database run by the MMPC Coordinating and Bioinformatics Unit. It is hoped that data from experiments performed in many mouse models of metabolic diseases, using standard protocols, will be useful in understanding the nature of these complex disorders. The current areas of expertise include energy balance and body composition, insulin action and secretion, whole-body and tissue carbohydrate and lipid metabolism, cardiovascular and renal function, and metabolic pathway kinetics. In addition to providing services, the MMPC staff provides expertise and advice to researchers, and works to develop and refine test protocols to best meet the community's needs in light of current scientific developments. Test technology is disseminated by publications and through annual courses.

  19. The Human Phenotype Ontology in 2017

    International Nuclear Information System (INIS)

    Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin; McMurry, Julie

    2016-01-01

    Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human PhenotypeOntology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.

  20. Phenotypic variability in Meesmann's dystrophy

    DEFF Research Database (Denmark)

    Ehlers, Niels; Hjortdal, Jesper; Nielsen, Kim

    2008-01-01

    symptoms often include blurred vision and ocular irritation. Typical cases may be entirely free of complaints. Intermittent pain episodes, such as occur in recurrent erosion syndrome, are not the rule. Genetic sequencing indicated a familial relationship with the originally described Meesmann family......'s dystrophy occurs worldwide. The largest family described is the original German one, now supplemented with a Danish branch. Despite the presence of an identical genetic defect, the clinical phenotype varies. This suggests that non-KRT12-related mechanisms are responsible for the variation....

  1. The thrifty phenotype hypothesis revisited

    DEFF Research Database (Denmark)

    Vaag, A A; Grunnet, L G; Arora, G P

    2012-01-01

    Twenty years ago, Hales and Barker along with their co-workers published some of their pioneering papers proposing the 'thrifty phenotype hypothesis' in Diabetologia (4;35:595-601 and 3;36:62-67). Their postulate that fetal programming could represent an important player in the origin of type 2...... of the underlying molecular mechanisms. Type 2 diabetes is a multiple-organ disease, and developmental programming, with its idea of organ plasticity, is a plausible hypothesis for a common basis for the widespread organ dysfunctions in type 2 diabetes and the metabolic syndrome. Only two among the 45 known type 2...

  2. The clinical phenotype of Lynch syndrome due to germline PMS2 mutations

    Science.gov (United States)

    Senter, Leigha; Clendenning, Mark; Sotamaa, Kaisa; Hampel, Heather; Green, Jane; Potter, John D.; Lindblom, Annika; Lagerstedt, Kristina; Thibodeau, Stephen N.; Lindor, Noralane M.; Young, Joanne; Winship, Ingrid; Dowty, James G.; White, Darren M.; Hopper, John L.; Baglietto, Laura; Jenkins, Mark A.; de la Chapelle, Albert

    2009-01-01

    Background and Aims Although the clinical phenotype of Lynch syndrome (also known as Hereditary Nonpolyposis Colorectal Cancer) has been well described, little is known about disease in PMS2 mutation carriers. Now that mutation detection methods can discern mutations in PMS2 from mutations in its pseudogenes, more mutation carriers have been identified. Information about the clinical significance of PMS2 mutations is crucial for appropriate counseling. Here, we report the clinical characteristics of a large series of PMS2 mutation carriers. Methods We performed PMS2 mutation analysis using long range PCR and MLPA for 99 probands diagnosed with Lynch syndrome-associated tumors showing isolated loss of PMS2 by immunohistochemistry. Penetrance was calculated using a modified segregation analysis adjusting for ascertainment. Results Germline PMS2 mutations were detected in 62% of probands (n = 55 monoallelic; 6 biallelic). Among families with monoallelic PMS2 mutations, 65.5% met revised Bethesda guidelines. Compared with the general population, in mutation carriers, the incidence of colorectal cancer was 5.2 fold higher and the incidence of endometrial cancer was 7.5 fold higher. In North America, this translates to a cumulative cancer risk to age 70 of 15–20% for colorectal cancer, 15% for endometrial cancer, and 25–32% for any Lynch syndrome-associated cancer. No elevated risk for non-Lynch syndrome-associated cancers was observed. Conclusions PMS2 mutations contribute significantly to Lynch syndrome but the penetrance for monoallelic mutation carriers appears to be lower than that for the other mismatch repair genes. Modified counseling and cancer surveillance guidelines for PMS2 mutation carriers are proposed. PMID:18602922

  3. Low background aspects of GERDA

    International Nuclear Information System (INIS)

    Simgen, Hardy

    2011-01-01

    The GERDA experiment operates bare Germanium diodes enriched in 76 Ge in an environment of pure liquid argon to search for neutrinoless double beta decay. A very low radioactive background is essential for the success of the experiment. We present here the research done in order to remove radio-impurities coming from the liquid argon, the stainless steel cryostat and the front-end electronics. We found that liquid argon can be purified efficiently from 222 Rn. The main source of 222 Rn in GERDA is the cryostat which emanates about 55 mBq. A thin copper shroud in the center of the cryostat was implemented to prevent radon from approaching the diodes. Gamma ray screening of radio-pure components for front-end electronics resulted in the development of a pre-amplifier with a total activity of less than 1 mBq 228 Th.

  4. The cosmic microwave background radiation

    International Nuclear Information System (INIS)

    Wilson, R.W.

    1980-01-01

    The history is described of the discovery of microwave radiation of the cosmic background using the 20-foot horn antenna at the Bell Laboratories back in 1965. Ruby masers with travelling wave were used, featuring the lowest noise in the world. The measurement proceeded on 7 cm. In measuring microwave radiation from the regions outside the Milky Way continuous noise was discovered whose temperature exceeded the calculated contributions of the individual detection system elements by 3 K. A comparison with the theory showed that relict radiation from the Big Bang period was the source of the noise. The discovery was verified by measurements on the 20.1 cm wavelength and by other authors' measurements on 0.5 mm to 74 cm, and by optical measurements of the interstellar molecule spectrum. (Ha)

  5. Polarization of Cosmic Microwave Background

    International Nuclear Information System (INIS)

    Buzzelli, A; Cabella, P; De Gasperis, G; Vittorio, N

    2016-01-01

    In this work we present an extension of the ROMA map-making code for data analysis of Cosmic Microwave Background polarization, with particular attention given to the inflationary polarization B-modes. The new algorithm takes into account a possible cross- correlated noise component among the different detectors of a CMB experiment. We tested the code on the observational data of the BOOMERanG (2003) experiment and we show that we are provided with a better estimate of the power spectra, in particular the error bars of the BB spectrum are smaller up to 20% for low multipoles. We point out the general validity of the new method. A possible future application is the LSPE balloon experiment, devoted to the observation of polarization at large angular scales. (paper)

  6. ACE phenotyping in Gaucher disease.

    Science.gov (United States)

    Danilov, Sergei M; Tikhomirova, Victoria E; Metzger, Roman; Naperova, Irina A; Bukina, Tatiana M; Goker-Alpan, Ozlem; Tayebi, Nahid; Gayfullin, Nurshat M; Schwartz, David E; Samokhodskaya, Larisa M; Kost, Olga A; Sidransky, Ellen

    2018-04-01

    Gaucher disease is characterized by the activation of splenic and hepatic macrophages, accompanied by dramatically increased levels of angiotensin-converting enzyme (ACE). To evaluate the source of the elevated blood ACE, we performed complete ACE phenotyping using blood, spleen and liver samples from patients with Gaucher disease and controls. ACE phenotyping included 1) immunohistochemical staining for ACE; 2) measuring ACE activity with two substrates (HHL and ZPHL); 3) calculating the ratio of the rates of substrate hydrolysis (ZPHL/HHL ratio); 4) assessing the conformational fingerprint of ACE by evaluating the pattern of binding of monoclonal antibodies to 16 different ACE epitopes. We show that in patients with Gaucher disease, the dramatically increased levels of ACE originate from activated splenic and/or hepatic macrophages (Gaucher cells), and that both its conformational fingerprint and kinetic characteristics (ZPHL/HHL ratio) differ from controls and from patients with sarcoid granulomas. Furthermore, normal spleen was found to produce high levels of endogenous ACE inhibitors and a novel, tightly-bound 10-30 kDa ACE effector which is deficient in Gaucher spleen. The conformation of ACE is tissue-specific. In Gaucher disease, ACE produced by activated splenic macrophages differs from that in hepatic macrophages, as well as from macrophages and dendritic cells in sarcoid granulomas. The observed differences are likely due to altered ACE glycosylation or sialylation in these diseased organs. The conformational differences in ACE may serve as a specific biomarker for Gaucher disease. Copyright © 2018 Elsevier Inc. All rights reserved.

  7. Alanine aminotransferase variants conferring diverse NUE phenotypes in Arabidopsis thaliana.

    Science.gov (United States)

    McAllister, Chandra H; Good, Allen G

    2015-01-01

    Alanine aminotransferase (AlaAT, E.C. 2.6.1.2), is a pyridoxal-5'-phosphate-dependent (PLP) enzyme that catalyzes the reversible transfer of an amino group from alanine to 2-oxoglutarate to produce glutamate and pyruvate, or vice versa. It has been well documented in both greenhouse and field studies that tissue-specific over-expression of AlaAT from barley (Hordeum vulgare, HvAlaAT) results in a significant increase in plant NUE in both canola and rice. While the physical phenotypes associated with over-expression of HvAlaAT have been well characterized, the role this enzyme plays in vivo to create a more N efficient plant remains unknown. Furthermore, the importance of HvAlaAT, in contrast to other AlaAT enzyme homologues in creating this phenotype has not yet been explored. To address the role of AlaAT in NUE, AlaAT variants from diverse sources and different subcellular locations, were expressed in the wild-type Arabidopsis thaliana Col-0 background and alaat1;2 (alaat1-1;alaat2-1) knockout background in various N environments. The analysis and comparison of both the physical and physiological properties of AlaAT over-expressing transgenic plants demonstrated significant differences between plants expressing the different AlaAT enzymes under different external conditions. This analysis indicates that the over-expression of AlaAT variants other than HvAlaAT in crop plants could further increase the NUE phenotype(s) previously observed.

  8. On Modified Bar recursion

    DEFF Research Database (Denmark)

    Oliva, Paulo Borges

    2002-01-01

    Modified bar recursion is a variant of Spector's bar recursion which can be used to give a realizability interpretation of the classical axiom of dependent choice. This realizability allows for the extraction of witnesses from proofs of forall-exists-formulas in classical analysis. In this talk I...... shall report on results regarding the relationship between modified and Spector's bar recursion. I shall also show that a seemingly weak form of modified bar recursion is as strong as "full" modified bar recursion in higher types....

  9. Phenotypic and genetic characterization of a novel phenotype in pigs characterized by juvenile hairlessness and age dependent emphysema

    DEFF Research Database (Denmark)

    Bruun, Camilla S.; Jørgensen, Claus B.; Bay, Lene

    2008-01-01

    Background: A pig phenotype characterized by juvenile hairlessness, thin skin and age dependent lung emphysema has been discovered in a Danish pig herd. The trait shows autosomal co-dominant inheritance with all three genotypes distinguishable. Since the phenotype shows resemblance to the integrin...... of musculi arrectores pili, and at puberty or later localized areas of emphysema are seen in the lungs. Comparative mapping predicted that the porcine ITGB6 and ITGAV orthologs map to SSC15. In an experimentall family (n=113), showing segregation of the trait, the candidate region was confirmed by linkage...... splicing of the ITGB6 pre-mRNA was detected. For both ITGB6 and ITGAV quantitative PCR revealed no significant difference in the expression levels in normal and affected animals. In a western blot, ITGB6 was detected in lung protein samples of all three genotypes. This result was supported by flow...

  10. Early phenotypical diagnoses in Trembler-J mice model.

    Science.gov (United States)

    Rosso, Gonzalo; Cal, Karina; Canclini, Lucía; Damián, Juan Pablo; Ruiz, Paul; Rodríguez, Héctor; Sotelo, José Roberto; Vazquez, Cristina; Kun, Alejandra

    2010-06-30

    Pmp-22 mutant mice (Trembler-J: B6.D2-Pmp22/J), are used as a model to study Charcot-Marie-Tooth type 1A (CMT1A). The identification of individual genotypes is a routine in the management of the Tr(J) colony. The earliest phenotypic manifestation of the pmp-22 mutation is just about 20th postnatal days, when pups begin to tremble. In this study, a rapid and simple diagnostic method was developed by modifying the Tail Suspension Test (MTST) to determine the difference between the Tr(J) and the wild-type mice phenotype. The animal behavioral phenotypes generated during the test were consistent with the specific genotype of each animal. The MTST allowed us to infer the heterozygous genotype in early postnatal stages, at 11 days after birth. The motor impairment of Tr(J) mice was also analyzed by a Fixed Bar Test (FBT), which revealed the disease evolution according to age. The main advantages of MTST are its objectivity, simplicity, and from the viewpoint of animal welfare, it is a non-invasive technique that combined with his rapidity show its very well applicability for use from an early age in these mice. Copyright 2010 Elsevier B.V. All rights reserved.

  11. Evolution of the androgen-induced male phenotype.

    Science.gov (United States)

    Fuxjager, Matthew J; Miles, Meredith C; Schlinger, Barney A

    2018-01-01

    The masculine reproductive phenotype varies significantly across vertebrates. As a result, biologists have long recognized that many of the mechanisms that support these phenotypes-particularly the androgenic system-is evolutionarily labile, and thus susceptible to the effects of selection for different traits. However, exactly how androgenic signaling systems vary in a way which results in dramatically different functional outputs, remain largely unclear. We explore this topic here by outlining four key-but non-mutually exclusive-hypotheses that propose how the mechanisms of androgenic signaling might change over time to potentiate the emergence of phenotypical variation in masculine behavior and physiology. We anchor this framework in a review of our own studies of a tropical bird called the golden-collared manakin (Manacus vitellinus), which has evolved an exaggerated acrobatic courtship display that is heavily androgen-dependent. The result is an example of how the cellular basis of androgenic action can be modified to support a unique reproductive repertoire. We end this review by highlighting a broad pathway forward to further pursue the intricate ways by which the mechanisms of hormone action evolve to support processes of adaptation and animal design.

  12. Plenoptic background oriented schlieren imaging

    International Nuclear Information System (INIS)

    Klemkowsky, Jenna N; Fahringer, Timothy W; Clifford, Christopher J; Thurow, Brian S; Bathel, Brett F

    2017-01-01

    The combination of the background oriented schlieren (BOS) technique with the unique imaging capabilities of a plenoptic camera, termed plenoptic BOS, is introduced as a new addition to the family of schlieren techniques. Compared to conventional single camera BOS, plenoptic BOS is capable of sampling multiple lines-of-sight simultaneously. Displacements from each line-of-sight are collectively used to build a four-dimensional displacement field, which is a vector function structured similarly to the original light field captured in a raw plenoptic image. The displacement field is used to render focused BOS images, which qualitatively are narrow depth of field slices of the density gradient field. Unlike focused schlieren methods that require manually changing the focal plane during data collection, plenoptic BOS synthetically changes the focal plane position during post-processing, such that all focal planes are captured in a single snapshot. Through two different experiments, this work demonstrates that plenoptic BOS is capable of isolating narrow depth of field features, qualitatively inferring depth, and quantitatively estimating the location of disturbances in 3D space. Such results motivate future work to transition this single-camera technique towards quantitative reconstructions of 3D density fields. (paper)

  13. Concerning background from calorimeter ports

    International Nuclear Information System (INIS)

    Digiacomo, N.J.

    1985-01-01

    Any detector system viewing a port or slit in a calorimeter wall will see, in addition to the primary particles of interest, a background of charged and neutral particles and photons generated by scattering from the port walls and by leakage from incompletely contained primary particle showers in the calorimeter near the port. The signal to noise ratio attainable outside the port is a complex function of the primary source spectrum, the calorimeter and port design and, of course, the nature and acceptance of the detector system that views the port. Rather than making general statements about the overall suitability (or lack thereof) of calorimeter ports, we offer here a specific example based on the external spectrometer and slit of the NA34 experiment. This combination of slit and spectrometer is designed for fixed-target work, so that the primary particle momentum spectrum contains higher momentum particles than expected in a heavy ion colliding beam environment. The results are, nevertheless, quite relevant for the collider case

  14. Natural background radiation in Jordan

    International Nuclear Information System (INIS)

    Daoud, M.N.S.

    1997-01-01

    An Airborne Gamma Ray survey has been accomplished for Jordan since 1979. A complete report has been submitted to the Natural Resources Authority along with field and processed data ''digital and analogue''. Natural radioelements concentration is not provided with this report. From the corrected count rate data for each natural radioelement, Concentrations and exposure rates at the ground level were calculated. Contoured maps, showing the exposure rates and the dose rates were created. Both maps reflect the surface geology of Jordan, where the Phosphate areas are very well delineated by high-level contours. In southeastern Jordan the Ordovician sandstone, which contain high percentage of Th (around 2000 ppm in some places) and a moderate percentage of U (about 300 ppm), also show high gamma radiation exposures compared with the surrounding areas. Comparing the values of the exposure rates given in (μR/h) to those obtained from other countries such as United States, Canada, Germany, etc. Jordan shows higher background radiation which reach two folds and even more than those in these countries. More detailed studies should be performed in order to evaluate the radiological risk limits on people who are living in areas of high radiation such that the area of the phosphatic belt which covers a vast area of Jordan high Plateau. (author)

  15. Natural background radiation in Jordan

    Energy Technology Data Exchange (ETDEWEB)

    Daoud, M N.S. [National Resources Authority, Ministry of Energy and Mineral Resources, Amman (Jordan)

    1997-11-01

    An Airborne Gamma Ray survey has been accomplished for Jordan since 1979. A complete report has been submitted to the Natural Resources Authority along with field and processed data ``digital and analogue``. Natural radioelements concentration is not provided with this report. From the corrected count rate data for each natural radioelement, Concentrations and exposure rates at the ground level were calculated. Contoured maps, showing the exposure rates and the dose rates were created. Both maps reflect the surface geology of Jordan, where the Phosphate areas are very well delineated by high-level contours. In southeastern Jordan the Ordovician sandstone, which contain high percentage of Th (around 2000 ppm in some places) and a moderate percentage of U (about 300 ppm), also show high gamma radiation exposures compared with the surrounding areas. Comparing the values of the exposure rates given in ({mu}R/h) to those obtained from other countries such as United States, Canada, Germany, etc. Jordan shows higher background radiation which reach two folds and even more than those in these countries. More detailed studies should be performed in order to evaluate the radiological risk limits on people who are living in areas of high radiation such that the area of the phosphatic belt which covers a vast area of Jordan high Plateau. (author). 8 refs, 10 figs, 7 tabs.

  16. Supplementary Material for: The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

    KAUST Repository

    Hoehndorf, Robert

    2016-01-01

    Abstract Background The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text. Results We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities. Conclusions The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established

  17. The influence of different helminth infection phenotypes on immune responses against HIV in co-infected adults in South Africa

    Directory of Open Access Journals (Sweden)

    Mabaso Musawenkosi LH

    2011-10-01

    Full Text Available Abstract Background The convergent distribution of the Human Immunodeficiency Virus (HIV and helminth infections has led to the suggestion that infection with helminths exacerbates the HIV epidemic in developing countries. In South Africa, it is estimated that 57% of the population lives in poverty and carries the highest burden of both HIV and helmith infections, however, the disease interactions are under-researched. Methods We employed both coproscopy and Ascaris lumbricoides-specific serum IgE to increase diagnostic sensitivity and to distinguish between different helminth infection phenotypes and their effects on immune responses in HIV co-infected individuals. Coproscopy was done by formol ether and Kato Katz methods. HIV positive and negative adults were stratified according to the presence or absence of A. lumbricoides and/or Trichuris trichuria eggs with or without elevated Ascaris IgE. Lymphocyte subsets were phenotyped by flow cytometry. Viral loads, serum total IgE and eosinophils were also analysed. Lymphocyte activation markers (CCR5, HLA-DR, CD25, CD38 and CD71 were determined. Non parametric statistics were used to describe differences in the variables between the subgroups. Results Helminth prevalence ranged between 40%-60%. Four distinct subgroups of were identified, and this included egg positive/high Ascaris-specific IgE (egg+IgEhi, egg positive/low IgE (egg+IgElo, egg negative/high IgE (egg-IgEhi and egg negative/low IgE (egg-IgElo individuals. The egg+IgEhi subgroup displayed lymphocytopenia, eosinophilia, (low CD4+ counts in HIV- group, high viral load (in HIV+ group, and an activated lymphocyte profile. High Ascaris IgE subgroups (egg+IgEhi and egg-IgEhi had eosinophilia, highest viral loads, and lower CD4+ counts in the HIV- group. Egg excretion and low IgE (egg+IgElo status demonstrated a modified Th2 immune profile with a relatively competent response to HIV. Conclusions People with both helminth egg excretion and high

  18. Modified Allergens for Immunotherapy.

    Science.gov (United States)

    Satitsuksanoa, Pattraporn; Głobińska, Anna; Jansen, Kirstin; van de Veen, Willem; Akdis, Mübeccel

    2018-02-16

    During the past few decades, modified allergens have been developed for use in allergen-specific immunotherapy (AIT) with the aim to improve efficacy and reduce adverse effects. This review aims to provide an overview of the different types of modified allergens, their mechanism of action and their potential for improving AIT. In-depth research in the field of allergen modifications as well as the advance of recombinant DNA technology have paved the way for improved diagnosis and research on human allergic diseases. A wide range of structurally modified allergens has been generated including allergen peptides, chemically altered allergoids, adjuvant-coupled allergens, and nanoparticle-based allergy vaccines. These modified allergens show promise for the development of AIT regimens with improved safety and long-term efficacy. Certain modifications ensure reduced IgE reactivity and retained T cell reactivity, which facilities induction of immune tolerance to the allergen. To date, multiple clinical trials have been performed using modified allergens. Promising results were obtained for the modified cat, grass and birch pollen, and house dust mite allergens. The use of modified allergens holds promise for improving AIT efficacy and safety. There is however a need for larger clinical studies to reliably assess the added benefit for the patient of using modified allergens for AIT.

  19. Nonderivative Modified Gravity: a Classification

    CERN Document Server

    Comelli, Denis; Pilo, Luigi

    2014-01-01

    We analyze the theories of gravity modified by a generic nonderivative potential built from the metric, under the minimal requirement of unbroken spatial rotations. Using the canonical analysis, we classify the potentials $V$ according to the number of degrees of freedom (DoF) that propagate at the nonperturbative level. We then compare the nonperturbative results with the perturbative DoF propagating around Minkowski and FRW backgrounds. A generic $V$ implies 6 propagating DoF at the non-perturbative level, with a ghost on Minkowski background. There exist potentials which propagate 5 DoF, as already studied in previous works. Here, no $V$ with unbroken rotational invariance admitting 4 DoF is found. Theories with 3 DoF turn out to be strongly coupled on Minkowski background. Finally, potentials with only the 2 DoF of a massive graviton exist. Their effect on cosmology is simply equivalent to a cosmological constant. Potentials with 2 or 5 DoF and explicit time dependence appear to be a further viable possib...

  20. Refined Phenotyping of Modic Changes

    Science.gov (United States)

    Määttä, Juhani H.; Karppinen, Jaro; Paananen, Markus; Bow, Cora; Luk, Keith D.K.; Cheung, Kenneth M.C.; Samartzis, Dino

    2016-01-01

    Abstract Low back pain (LBP) is the world's most disabling condition. Modic changes (MC) are vertebral bone marrow changes adjacent to the endplates as noted on magnetic resonance imaging. The associations of specific MC types and patterns with prolonged, severe LBP and disability remain speculative. This study assessed the relationship of prolonged, severe LBP and back-related disability, with the presence and morphology of lumbar MC in a large cross-sectional population-based study of Southern Chinese. We addressed the topographical and morphological dimensions of MC along with other magnetic resonance imaging phenotypes (eg, disc degeneration and displacement) on the basis of axial T1 and sagittal T2-weighted imaging of L1-S1. Prolonged severe LBP was defined as LBP lasting ≥30 days during the past year, and a visual analog scale severest pain intensity of at least 6/10. An Oswestry Disability Index score of 15% was regarded as significant disability. We also assessed subject demographics, occupation, and lifestyle factors. In total, 1142 subjects (63% females, mean age 53 years) were assessed. Of these, 282 (24.7%) had MC (7.1% type I, 17.6% type II). MC subjects were older (P = 0.003), had more frequent disc displacements (P disability. The strength of the associations increased with the number of MC. This large-scale study is the first to definitively note MC types and specific morphologies to be independently associated with prolonged severe LBP and back-related disability. This proposed refined MC phenotype may have direct implications in clinical decision-making as to the development and management of LBP. Understanding of these imaging biomarkers can lead to new preventative and personalized therapeutics related to LBP. PMID:27258491

  1. Scientific background of the project

    International Nuclear Information System (INIS)

    Christofidis, I.

    1997-01-01

    The main objective of the proposed project is the development of radioimmunometric assay(s) for the determination of free and total PSA in serum samples from normal and pathological individuals (BPH, PCa). This will be achieved by: A. Selection of appropriate antibody pairs (capture and labelled antibody) for determination of total PSA (free and complex) and for determination of free PSA. From bibliography we have already spotted some antibody pairs. B. Radiolabelling of antibodies. Several labelling and purification procedures will be followed in order to obtain the required analytical sensitivity and dynamic range of the assays. Special attention will be given to the affinity constant as well as to the stability of the radiolabelled molecules. C. Development of protocols for immobilisation of capture antibodies. We will use several solid support formats (plastic tubes, beads and magnetizable particles). Direct adsorption or covalent binding will be used. Immunoadsorption through immobilised second antibody will be also tested in order to decrease the preparation cost of the solid phase reagents. D. Preparation of standards of suitable purity levels. We will test different PSA-free matrices (Bovine serum, buffer solutions etc.) in order to select the most appropriate among them in terms of low background determination and low reagents cost. E. Optimisation of the immunoassays conditions for the free PSA and total PSA (e.g. assay buffers, incubation time, temperature, one or two step procedure, washings). F. Optimisation and standardisation of assay protocols for kit production. G. Production of kits for distribution in clinical laboratories in Greece for comparison with commercial kits. H. Evaluation of the developed assays in real clinical conditions using well characterised human serum samples. This will be performed in co-operation with the Hellenic Society for Tumor Markers, and other anticancer institutions and hospital clinicians of long standing relation

  2. The phenotypic variance gradient - a novel concept.

    Science.gov (United States)

    Pertoldi, Cino; Bundgaard, Jørgen; Loeschcke, Volker; Barker, James Stuart Flinton

    2014-11-01

    Evolutionary ecologists commonly use reaction norms, which show the range of phenotypes produced by a set of genotypes exposed to different environments, to quantify the degree of phenotypic variance and the magnitude of plasticity of morphometric and life-history traits. Significant differences among the values of the slopes of the reaction norms are interpreted as significant differences in phenotypic plasticity, whereas significant differences among phenotypic variances (variance or coefficient of variation) are interpreted as differences in the degree of developmental instability or canalization. We highlight some potential problems with this approach to quantifying phenotypic variance and suggest a novel and more informative way to plot reaction norms: namely "a plot of log (variance) on the y-axis versus log (mean) on the x-axis, with a reference line added". This approach gives an immediate impression of how the degree of phenotypic variance varies across an environmental gradient, taking into account the consequences of the scaling effect of the variance with the mean. The evolutionary implications of the variation in the degree of phenotypic variance, which we call a "phenotypic variance gradient", are discussed together with its potential interactions with variation in the degree of phenotypic plasticity and canalization.

  3. Sex-specific phenotypes of hyperthyroidism and hypothyroidism in mice

    OpenAIRE

    Rakov, Helena; Engels, Kathrin; H?nes, Georg Sebastian; Strucksberg, Karl-Heinz; Moeller, Lars Christian; K?hrle, Josef; Zwanziger, Denise; F?hrer, Dagmar

    2016-01-01

    Background Thyroid dysfunction is more common in the female population, however, the impact of sex on disease characteristics has rarely been addressed. Using a murine model, we asked whether sex has an influence on phenotypes, thyroid hormone status, and thyroid hormone tissue response in hyper- and hypothyroidism. Methods Hypo- and hyperthyroidism were induced in 5-month-old female and male wildtype C57BL/6N mice, by LoI/MMI/ClO4 ? or T4 i.p. treatment over 7?weeks, and control animals unde...

  4. Phenotype of normal spirometry in an aging population.

    Science.gov (United States)

    Vaz Fragoso, Carlos A; McAvay, Gail; Van Ness, Peter H; Casaburi, Richard; Jensen, Robert L; MacIntyre, Neil; Gill, Thomas M; Yaggi, H Klar; Concato, John

    2015-10-01

    In aging populations, the commonly used Global Initiative for Chronic Obstructive Lung Disease (GOLD) may misclassify normal spirometry as respiratory impairment (airflow obstruction and restrictive pattern), including the presumption of respiratory disease (chronic obstructive pulmonary disease [COPD]). To evaluate the phenotype of normal spirometry as defined by a new approach from the Global Lung Initiative (GLI), overall and across GOLD spirometric categories. Using data from COPDGene (n = 10,131; ages 45-81; smoking history, ≥10 pack-years), we evaluated spirometry and multiple phenotypes, including dyspnea severity (Modified Medical Research Council grade 0-4), health-related quality of life (St. George's Respiratory Questionnaire total score), 6-minute-walk distance, bronchodilator reversibility (FEV1 % change), computed tomography-measured percentage of lung with emphysema (% emphysema) and gas trapping (% gas trapping), and small airway dimensions (square root of the wall area for a standardized airway with an internal perimeter of 10 mm). Among 5,100 participants with GLI-defined normal spirometry, GOLD identified respiratory impairment in 1,146 (22.5%), including a restrictive pattern in 464 (9.1%), mild COPD in 380 (7.5%), moderate COPD in 302 (5.9%), and severe COPD in none. Overall, the phenotype of GLI-defined normal spirometry included normal adjusted mean values for dyspnea grade (0.8), St. George's Respiratory Questionnaire (15.9), 6-minute-walk distance (1,424 ft [434 m]), bronchodilator reversibility (2.7%), % emphysema (0.9%), % gas trapping (10.7%), and square root of the wall area for a standardized airway with an internal perimeter of 10 mm (3.65 mm); corresponding 95% confidence intervals were similarly normal. These phenotypes remained normal for GLI-defined normal spirometry across GOLD spirometric categories. GLI-defined normal spirometry, even when classified as respiratory impairment by GOLD, included adjusted mean values in the

  5. Societal aspects of genetically modified foods

    DEFF Research Database (Denmark)

    Frewer, L.J.; Lassen, J.; Kettlitz, B.

    2004-01-01

    This paper aims to examine some of the reasons behind public controversy associated with the introduction of genetically modified foods in Europe the 1990s. The historical background to the controversy is provided to give context. The issue of public acceptance of genetically modified foods......, and indeed the emerging biosciences more generally, is considered in the context of risk perceptions and attitudes, public trust in regulatory institutions, scientists and industry, and the need to develop communication strategies that explicitly include public concerns rather than exclude them. Increased...

  6. Cattle phenotypes can disguise their maternal ancestry.

    Science.gov (United States)

    Srirattana, Kanokwan; McCosker, Kieren; Schatz, Tim; St John, Justin C

    2017-06-26

    Cattle are bred for, amongst other factors, specific traits, including parasite resistance and adaptation to climate. However, the influence and inheritance of mitochondrial DNA (mtDNA) are not usually considered in breeding programmes. In this study, we analysed the mtDNA profiles of cattle from Victoria (VIC), southern Australia, which is a temperate climate, and the Northern Territory (NT), the northern part of Australia, which has a tropical climate, to determine if the mtDNA profiles of these cattle are indicative of breed and phenotype, and whether these profiles are appropriate for their environments. A phylogenetic tree of the full mtDNA sequences of different breeds of cattle, which were obtained from the NCBI database, showed that the mtDNA profiles of cattle do not always reflect their phenotype as some cattle with Bos taurus phenotypes had Bos indicus mtDNA, whilst some cattle with Bos indicus phenotypes had Bos taurus mtDNA. Using D-loop sequencing, we were able to contrast the phenotypes and mtDNA profiles from different species of cattle from the 2 distinct cattle breeding regions of Australia. We found that 67 of the 121 cattle with Bos indicus phenotypes from NT (55.4%) had Bos taurus mtDNA. In VIC, 92 of the 225 cattle with Bos taurus phenotypes (40.9%) possessed Bos indicus mtDNA. When focusing on oocytes from cattle with the Bos taurus phenotype in VIC, their respective oocytes with Bos indicus mtDNA had significantly lower levels of mtDNA copy number compared with oocytes possessing Bos taurus mtDNA (P cattle with a Bos taurus phenotype. The phenotype of cattle is not always related to their mtDNA profiles. MtDNA profiles should be considered for breeding programmes as they also influence phenotypic traits and reproductive capacity in terms of oocyte quality.

  7. Broad phenotypic spectrum in familial adenomatous polyposis; from early onset and severe phenotypes to late onset of attenuated polyposis with the first manifestation at age 72

    DEFF Research Database (Denmark)

    Nilbert, Mef; Kristoffersson, Ulf; Ericsson, Mats

    2008-01-01

    ABSTRACT: Background Familial adenomatous polyposis (FAP) is typically characterized by multiple colonic polyps and frequent extracolonic features. Whereas the number of colonic polyps has been linked to the APC gene mutation, possible genotype-phenotype correlations largely remain to be defined...... of extracolonic manifestations was identified in most of these individuals. Two sisters with an insertion in codon 528 (c.1582_1583insGC) both showed severe phenotypes with classical polyposis, upper gastrointestinal polyps and thyroid cancer. A woman with a 3'APC mutation (c.5030_5031insAA) developed colon...

  8. Lactase persistence versus lactose intolerance: Is there an intermediate phenotype?

    Science.gov (United States)

    Dzialanski, Zbigniew; Barany, Michael; Engfeldt, Peter; Magnuson, Anders; Olsson, Lovisa A; Nilsson, Torbjörn K

    2016-02-01

    According to the prevailing theory about the genetic background to lactose intolerance, there are three genotypes but only two adult physiological phenotypes: lactase persistence in individuals with the CT and TT genotypes and lactase non-persistence in individuals with the CC genotype. However, analysis of lactase activity from intestinal biopsies has revealed three distinct levels of activity, suggesting that an intermediate physiological phenotype may exist. To assess possible disparities between different genotypes with regard to biomarkers of lactase activity and physical symptoms during an oral lactose load test. A retrospective study using an oral lactose load test (n=487). Concentrations of hydrogen in exhaled air and blood glucose were measured. Afterwards, subjects were asked to provide oral mucosa samples for genotyping and answer a questionnaire (participation rate 56%, n=274). Mean hydrogen levels in exhaled air at 120min were significantly higher in the CT genotype than in the TT genotype. There was no significant difference in blood glucose levels between the two groups. Reported symptoms, with the possible exception of abdominal pain, were equally prevalent in both groups. Subjects with the CT and TT genotypes, hitherto classified as lactase-persistent, differ in their physiological response to lactose intake, indicating differences in phenotype which could have clinical significance. Copyright © 2015 The Canadian Society of Clinical Chemists. Published by Elsevier Inc. All rights reserved.

  9. The Human Phenotype Ontology project: linking molecular biology and disease through phenotype data

    NARCIS (Netherlands)

    Kohler, S.; Doelken, S.C.; Mungall, C.J.; Bauer, S.; Firth, H.V.; Bailleul-Forestier, I.; Black, G.C.M.; Brown, D.L.; Brudno, M.; Campbell, J.; FitzPatrick, D.R.; Eppig, J.T.; Jackson, A.P.; Freson, K.; Girdea, M.; Helbig, I.; Hurst, J.A.; Jahn, J.; Jackson, L.G.; Kelly, A.M.; Ledbetter, D.H.; Mansour, S.; Martin, C.L.; Moss, C.; Mumford, A.; Ouwehand, W.H.; Park, S.M.; Riggs, E.R.; Scott, R.H.; Sisodiya, S.; Vooren, S. van der; Wapner, R.J.; Wilkie, A.O.; Wright, C.F.; Silfhout, A.T. van; Leeuw, N. de; Vries, B. de; Washingthon, N.L.; Smith, C.L.; Westerfield, M.; Schofield, P.; Ruef, B.J.; Gkoutos, G.V.; Haendel, M.; Smedley, D.; Lewis, S.E.; Robinson, P.N.

    2014-01-01

    The Human Phenotype Ontology (HPO) project, available at http://www.human-phenotype-ontology.org, provides a structured, comprehensive and well-defined set of 10,088 classes (terms) describing human phenotypic abnormalities and 13,326 subclass relations between the HPO classes. In addition we have

  10. Locating a modifier gene of Ovum mutant through crosses between ...

    Indian Academy of Sciences (India)

    modifier gene of Om in the B6 background. [Tan J., Song ... should be half the rate of those from the normal crosses,. B6 (+/+) ... the genetic background of the B6 strain. The purpose of .... Smirnov test (P > 0.05) and the reproductive rate of N2.

  11. Background Noise Reduction Using Adaptive Noise Cancellation Determined by the Cross-Correlation

    Science.gov (United States)

    Spalt, Taylor B.; Brooks, Thomas F.; Fuller, Christopher R.

    2012-01-01

    Background noise due to flow in wind tunnels contaminates desired data by decreasing the Signal-to-Noise Ratio. The use of Adaptive Noise Cancellation to remove background noise at measurement microphones is compromised when the reference sensor measures both background and desired noise. The technique proposed modifies the classical processing configuration based on the cross-correlation between the reference and primary microphone. Background noise attenuation is achieved using a cross-correlation sample width that encompasses only the background noise and a matched delay for the adaptive processing. A present limitation of the method is that a minimum time delay between the background noise and desired signal must exist in order for the correlated parts of the desired signal to be separated from the background noise in the crosscorrelation. A simulation yields primary signal recovery which can be predicted from the coherence of the background noise between the channels. Results are compared with two existing methods.

  12. Daddy issues: paternal effects on phenotype.

    Science.gov (United States)

    Rando, Oliver J

    2012-11-09

    The once popular and then heretical idea that ancestral environment can affect the phenotype of future generations is coming back into vogue due to advances in the field of epigenetic inheritance. How paternal environmental conditions influence the phenotype of progeny is now a tractable question, and researchers are exploring potential mechanisms underlying such effects. Copyright © 2012 Elsevier Inc. All rights reserved.

  13. Phenotypes of organ involvement in sarcoidosis

    NARCIS (Netherlands)

    Schupp, Jonas Christian; Freitag-Wolf, Sandra; Bargagli, Elena; Mihailović-Vučinić, Violeta; Rottoli, Paola; Grubanovic, Aleksandar; Müller, Annegret; Jochens, Arne; Tittmann, Lukas; Schnerch, Jasmin; Olivieri, Carmela; Fischer, Annegret; Jovanovic, Dragana; Filipovic, Snežana; Videnovic-Ivanovic, Jelica; Bresser, Paul; Jonkers, René; O'Reilly, Kate; Ho, Ling-Pei; Gaede, Karoline I.; Zabel, Peter; Dubaniewicz, Anna; Marshall, Ben; Kieszko, Robert; Milanowski, Janusz; Günther, Andreas; Weihrich, Anette; Petrek, Martin; Kolek, Vitezslav; Keane, Michael P.; O'Beirne, Sarah; Donnelly, Seamas; Haraldsdottir, Sigridur Olina; Jorundsdottir, Kristin B.; Costabel, Ulrich; Bonella, Francesco; Wallaert, Benoît; Grah, Christian; Peroš-Golubičić, Tatjana; Luisetti, Mauritio; Kadija, Zamir; Pabst, Stefan; Grohé, Christian; Strausz, János; Vašáková, Martina; Sterclova, Martina; Millar, Ann; Homolka, Jiří; Slováková, Alena; Kendrick, Yvonne; Crawshaw, Anjali; Wuyts, Wim; Spencer, Lisa; Pfeifer, Michael; Valeyre, Dominique; Poletti, Venerino; Wirtz, Hubertus; Prasse, Antje; Schreiber, Stefan; Krawczak, Michael; Müller-Quernheim, Joachim

    2018-01-01

    Sarcoidosis is a highly variable, systemic granulomatous disease of hitherto unknown aetiology. The GenPhenReSa (Genotype-Phenotype Relationship in Sarcoidosis) project represents a European multicentre study to investigate the influence of genotype on disease phenotypes in sarcoidosis. The baseline

  14. Emerging semantics to link phenotype and environment

    Directory of Open Access Journals (Sweden)

    Anne E. Thessen

    2015-12-01

    Full Text Available Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1 use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2 two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3 two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE and the Biological Collections Ontology (BCO; these provide a starting point for the development of a data model linking phenotypes and environments.

  15. Haptoglobin Phenotypes and Hypertension in Indigenous Zambians ...

    African Journals Online (AJOL)

    Haptoglobin Phenotypes and Hypertension in Indigenous Zambians at the University Teaching Hospital, Lusaka, Zambia. MM Phiri, T Kaile, FM Goma. Abstract. Objectives: The aim of the study was to investigate the association between presence of haptoglobin phenotypes and hypertension in indigenous Zambian patients ...

  16. Knowledge-based analysis of phenotypes

    KAUST Repository

    Hoendorf, Robert

    2016-01-01

    a formal framework to describe phenotypes. A formalized theory of phenotypes is not only useful for domain analysis, but can also be applied to assist in the diagnosis of rare genetic diseases, and I will show how our results on the ontology

  17. The Neuroanatomy of the Autistic Phenotype

    Science.gov (United States)

    Fahim, Cherine; Meguid, Nagwa A.; Nashaat, Neveen H.; Yoon, Uicheul; Mancini-Marie, Adham; Evans, Alan C.

    2012-01-01

    The autism phenotype is associated with an excess of brain volume due in part to decreased pruning during development. Here we aimed at assessing brain volume early in development to further elucidate previous findings in autism and determine whether this pattern is restricted to idiopathic autism or shared within the autistic phenotype (fragile X…

  18. Modified Nance palatal button

    Directory of Open Access Journals (Sweden)

    Nitin Arora

    2015-01-01

    Full Text Available This paper describes modified Nance palatal button by which problems encountered in the palatal region around the acrylic button during space closure and molar distalization can be minimized.

  19. Modified microdissection electrocautery needle

    OpenAIRE

    Singh, Virendra; Kumar, Pramod

    2014-01-01

    Electrocautery is routinely used in surgical procedures. The commercially available microdissection electrocautery needles are costly. To overcome this disadvantage, we have modified monopolar electrocautery tip to function as well as commercially available systems.

  20. Evolving phenotypic networks in silico.

    Science.gov (United States)

    François, Paul

    2014-11-01

    Evolved gene networks are constrained by natural selection. Their structures and functions are consequently far from being random, as exemplified by the multiple instances of parallel/convergent evolution. One can thus ask if features of actual gene networks can be recovered from evolutionary first principles. I review a method for in silico evolution of small models of gene networks aiming at performing predefined biological functions. I summarize the current implementation of the algorithm, insisting on the construction of a proper "fitness" function. I illustrate the approach on three examples: biochemical adaptation, ligand discrimination and vertebrate segmentation (somitogenesis). While the structure of the evolved networks is variable, dynamics of our evolved networks are usually constrained and present many similar features to actual gene networks, including properties that were not explicitly selected for. In silico evolution can thus be used to predict biological behaviours without a detailed knowledge of the mapping between genotype and phenotype. Copyright © 2014 The Author. Published by Elsevier Ltd.. All rights reserved.

  1. Adjusting phenotypes by noise control.

    Directory of Open Access Journals (Sweden)

    Kyung H Kim

    2012-01-01

    Full Text Available Genetically identical cells can show phenotypic variability. This is often caused by stochastic events that originate from randomness in biochemical processes involving in gene expression and other extrinsic cellular processes. From an engineering perspective, there have been efforts focused on theory and experiments to control noise levels by perturbing and replacing gene network components. However, systematic methods for noise control are lacking mainly due to the intractable mathematical structure of noise propagation through reaction networks. Here, we provide a numerical analysis method by quantifying the parametric sensitivity of noise characteristics at the level of the linear noise approximation. Our analysis is readily applicable to various types of noise control and to different types of system; for example, we can orthogonally control the mean and noise levels and can control system dynamics such as noisy oscillations. As an illustration we applied our method to HIV and yeast gene expression systems and metabolic networks. The oscillatory signal control was applied to p53 oscillations from DNA damage. Furthermore, we showed that the efficiency of orthogonal control can be enhanced by applying extrinsic noise and feedback. Our noise control analysis can be applied to any stochastic model belonging to continuous time Markovian systems such as biological and chemical reaction systems, and even computer and social networks. We anticipate the proposed analysis to be a useful tool for designing and controlling synthetic gene networks.

  2. Federated Tensor Factorization for Computational Phenotyping

    Science.gov (United States)

    Kim, Yejin; Sun, Jimeng; Yu, Hwanjo; Jiang, Xiaoqian

    2017-01-01

    Tensor factorization models offer an effective approach to convert massive electronic health records into meaningful clinical concepts (phenotypes) for data analysis. These models need a large amount of diverse samples to avoid population bias. An open challenge is how to derive phenotypes jointly across multiple hospitals, in which direct patient-level data sharing is not possible (e.g., due to institutional policies). In this paper, we developed a novel solution to enable federated tensor factorization for computational phenotyping without sharing patient-level data. We developed secure data harmonization and federated computation procedures based on alternating direction method of multipliers (ADMM). Using this method, the multiple hospitals iteratively update tensors and transfer secure summarized information to a central server, and the server aggregates the information to generate phenotypes. We demonstrated with real medical datasets that our method resembles the centralized training model (based on combined datasets) in terms of accuracy and phenotypes discovery while respecting privacy. PMID:29071165

  3. Nordic research infrastructures for plant phenotyping

    Directory of Open Access Journals (Sweden)

    Kristiina Himanen

    2018-03-01

    Full Text Available Plant phenomics refers to the systematic study of plant phenotypes. Together with closely monitored, controlled climates, it provides an essential component for the integrated analysis of genotype-phenotype-environment interactions. Currently, several plant growth and phenotyping facilities are under establishment globally, and numerous facilities are already in use. Alongside the development of the research infrastructures, several national and international networks have been established to support shared use of the new methodology. In this review, an overview is given of the Nordic plant phenotyping and climate control facilities. Since many areas of phenomics such as sensor-based phenotyping, image analysis and data standards are still developing, promotion of educational and networking activities is especially important. These facilities and networks will be instrumental in tackling plant breeding and plant protection challenges. They will also provide possibilities to study wild species and their ecological interactions under changing Nordic climate conditions.

  4. ABO blood group phenotypes influence parity specific immunity to Plasmodium falciparum malaria in Malawian women

    NARCIS (Netherlands)

    Senga, Edward; Loscertales, Maria-Paz; Makwakwa, K. E. B.; Liomba, George N.; Dzamalala, Charles; Kazembe, Peter N.; Brabin, Bernard J.

    2007-01-01

    BACKGROUND: Blood group O has been significantly associated with increased placental malaria infection in primiparae and reduced risk of infection in multiparae in the Gambia, an area with markedly seasonal malaria transmission. This study analyses the association between ABO blood group phenotypes

  5. Prevalence of weak RhD phenotype in the blood donor population ...

    African Journals Online (AJOL)

    Background: The weak RhD phenotype is a form of RhD antigen that, in routine RhD typing, does not react by agglutination with potent monoclonal anti-D serum, but requires addition of antiglobulin serum to demonstrate the presence of the antigen. However, the weak D antigen can cause immunization or sensitization ...

  6. GRIN2B encephalopathy : Novel findings on phenotype, variant clustering, functional consequences and treatment aspects

    NARCIS (Netherlands)

    Platzer, Konrad; Yuan, Hongjie; Schütz, Hannah; Winschel, Alexander; Chen, Wenjuan; Hu, Chun; Kusumoto, Hirofumi; Heyne, Henrike O; Helbig, Katherine L; Tang, Sha; Willing, Marcia C; Tinkle, Brad T; Adams, Darius J; Depienne, Christel; Keren, Boris; Mignot, Cyril; Frengen, Eirik; Strømme, Petter; Biskup, Saskia; Döcker, Dennis; Strom, Tim M.; Mefford, Heather C.; Myers, Candace T.; Muir, Alison M; LaCroix, Amy; Sadleir, Lynette G.; Scheffer, Ingrid E.; Brilstra, Eva; van Haelst, Mieke M.; van der Smagt, Jasper J.; Bok, Levinus A; Møller, Rikke S.; Jensen, Uffe Birk; Millichap, John J; Berg, Anne T; Goldberg, Ethan M; De Bie, Isabelle; Fox, Stephanie; Major, Philippe; Jones, Julie R; Zackai, Elaine H.; Abou Jamra, Rami; Rolfs, Arndt; Leventer, Richard J; Lawson, John A; Roscioli, Tony; Jansen, Floor E.; Ranza, Emmanuelle; Korff, Christian M; Lehesjoki, Anna-Elina; Courage, Carolina; Linnankivi, Tarja; Smith, Douglas R; Stanley, Christine; Mintz, Mark; McKnight, Dianalee; Decker, Amy; Tan, Wen-Hann; Tarnopolsky, Mark A; Brady, Lauren I; Wolff, Markus; Dondit, Lutz; Pedro, Helio F; Parisotto, Sarah E; Jones, Kelly L; Patel, Anup D; Franz, David N; Vanzo, Rena; Marco, Elysa; Ranells, Judith D; Di Donato, Nataliya; Dobyns, William B.; Laube, Bodo; Traynelis, Stephen F; Lemke, Johannes R.

    2017-01-01

    Background: We aimed for a comprehensive delineation of genetic, functional and phenotypic aspects of GRIN2B encephalopathy and explored potential prospects of personalised medicine. Methods: Data of 48 individuals with de novo GRIN2B variants were collected from several diagnostic and research

  7. Measurement Equivalence of the Autism Symptom Phenotype in Children and Youth

    Science.gov (United States)

    Duku, Eric; Szatmari, Peter; Vaillancourt, Tracy; Georgiades, Stelios; Thompson, Ann; Liu, Xiao-Qing; Paterson, Andrew D.; Bennett, Terry

    2013-01-01

    Background: The Autism Diagnostic Interview-Revised (ADI-R) is a gold standard assessment of Autism Spectrum Disorder (ASD) symptoms and behaviours. A key underlying assumption of studies using the ADI-R is that it measures the same phenotypic constructs across different populations (i.e. males/females, younger/older, verbal/nonverbal). The…

  8. Dietary patterns and the insulin resistance phenotype among non-diabetic adults

    Science.gov (United States)

    Background: Information on the relation between dietary patterns derived by cluster analysis and insulin resistance is scarce. Objective: To compare insulin resistance phenotypes, including waist circumference, body mass index, fasting and 2-hour post-challenge insulin, insulin sensitivity index (I...

  9. Adaptive developmental plasticity: Compartmentalized responses to environmental cues and corresponding internal signals provide phenotypic flexibility

    NARCIS (Netherlands)

    Mateus, A.R.A.; Marques-Pita, M.; Oostra, V.; Lafuente, E.; Brakefield, P.M.; Zwaan, B.J.; Beldade, P.

    2014-01-01

    Background The environmental regulation of development can result in the production of distinct phenotypes from the same genotype and provide the means for organisms to cope with environmental heterogeneity. The effect of the environment on developmental outcomes is typically mediated by hormonal

  10. Genotype-phenotype correlation in patients suspected of having Sotos syndrome

    NARCIS (Netherlands)

    de Boer, Lonneke; Kant, Sarina G.; Karperien, Marcel; van Beers, Lotte; Tjon, Jennifer; Vink, Geraldine R.; van Tol, Dewy; Dauwerse, Hans; le Cessie, Saskia; Beemer, Frits A.; van der Burgt, Ineke; Hamel, Ben C. J.; Hennekam, Raoul C.; Kuhnle, Ursula; Mathijssen, Inge B.; Veenstra-Knol, Hermine E.; Stumpel, Connie T. Schrander; Breuning, Martijn H.; Wit, Jan M.

    2004-01-01

    Background: Deletions and mutations in the NSD1 gene are the major cause of Sotos syndrome. We wanted to evaluate the genotype-phenotype correlation in patients suspected of having Sotos syndrome and determine the best discriminating parameters for the presence of a NSD1 gene alteration. Methods:

  11. Genotype-phenotype correlation in patients suspected of having sotos syndrome.

    NARCIS (Netherlands)

    Boer, L. de; Kant, S.; Karperien, M.; Beers, L. van; Tjon, J.; Vink, G.R.; Tol, D. van; Dauwerse, H.G.; Cessie, S. le; Beemer, F.A.; Burgt, C.J.A.M. van der; Hamel, B.C.J.; Hennekam, R.C.M.; Kuhnle, U.; Mathijssen, I.B.; Veenstra-Knol, H.E.; Stumpel, C.T.; Breuning, M.H.; Wit, J.M.

    2004-01-01

    BACKGROUND: Deletions and mutations in the NSD1 gene are the major cause of Sotos syndrome. We wanted to evaluate the genotype-phenotype correlation in patients suspected of having Sotos syndrome and determine the best discriminating parameters for the presence of a NSD1 gene alteration. METHODS:

  12. The Behavioural Phenotype of Smith-Magenis Syndrome: Evidence for a Gene-Environment Interaction

    Science.gov (United States)

    Taylor, L.; Oliver, C.

    2008-01-01

    Background: Behaviour problems and a preference for adult contact are reported to be prominent in the phenotype of Smith-Magenis syndrome. In this study we examined the relationship between social interactions and self-injurious and aggressive/disruptive behaviour in Smith-Magenis syndrome to explore potential operant reinforcement of problem…

  13. CARD15 in inflammatory bowel disease and Crohn's disease phenotypes : An association study and pooled analysis

    NARCIS (Netherlands)

    Oostenbrug, L. E.; Nolte, I. M.; Oosterom, E.; van der Steege, G.; Meerman, G. J. te; van Dullemen, H. M.; Drenth, J. P. H.; de Jong, D. J.; van der Linde, K.; Jansen, P. L. M.; Kleibeuker, J. H.

    2006-01-01

    Background. Three major polymorphisms of the Caspase-Activation Recruitment Domain containing protein 15 gene have been described to be associated with Crohn's disease. Genotype-phenotype studies reported in literature provide conflicting data on disease localisation and behaviour. We investigated

  14. High-throughput phenotyping of plant resistance to aphids by automated video tracking

    NARCIS (Netherlands)

    Kloth, K.J.; Broeke, ten C.J.M.; Thoen, H.P.M.; Hanhart-van den Brink, M.; Wiegers, G.L.; Krips, O.E.; Noldus, L.P.J.J.; Dicke, M.; Jongsma, M.A.

    2015-01-01

    Background: Piercing-sucking insects are major vectors of plant viruses causing significant yield losses in crops.Functional genomics of plant resistance to these insects would greatly benefit from the availability of highthroughput, quantitative phenotyping methods. Results: We have developed an

  15. The clinical phenotype of hereditary versus sporadic prostate cancer: HPC definition revisited

    NARCIS (Netherlands)

    Cremers, R.G.H.M.; Aben, K.K.H.; Oort, I.M. van; Sedelaar, J.P.M.; Vasen, H.F.A.; Vermeulen, S.H.; Kiemeney, L.A.L.M.

    2016-01-01

    BACKGROUND: The definition of hereditary prostate cancer (HPC) is based on family history and age at onset. Intuitively, HPC is a serious subtype of prostate cancer but there are only limited data on the clinical phenotype of HPC. Here, we aimed to compare the prognosis of HPC to the sporadic form

  16. Patient Age, Sex, and Inflammatory Bowel Disease Phenotype Associate With Course of Primary Sclerosing Cholangitis

    NARCIS (Netherlands)

    Weismueller, Tobias J.; Trivedi, Palak J; Bergquist, Annika; Imam, Mohamad; Lenzen, Henrike; Ponsioen, Cyriel Y.; Holm, Kristian; Gotthardt, Daniel; Faerkkilae, Martti A.; Marschall, Hanns-Ulrich; Thorburn, Douglas; Weersma, Rinse K.; Fevery, Johan; Mueller, Tobias; Chazouilleres, Olivier; Schulze, Kornelius; Lazaridis, Konstantinos N.; Almer, Sven; Pereira, Stephen P.; Levy, Cynthia; Mason, Andrew L.; Naess, Sigrid; Bowlus, Christopher L.; Floreani, Annarosa; Halilbasic, Emina; Yimam, Kidist K.; Milkiewicz, Piotr; Beuers, Ulrich; Huynh, Dep K.; Pares, Albert; Manser, Christine N.; Dalekos, George N.; Eksteen, Bertus; Invernizzi, Pietro; Berg, Christoph P.; Kirchner, Gabi I.; Sarrazin, Christoph; Zimmer, Vincent; Fabris, Luca; Braun, Felix; Marzioni, Marco; Juran, Brian D.; Said, Karouk; Rupp, Christian; Jokelainen, Kalle; de Valle, Maria Benito; Saffioti, Francesca; Cheung, Angela; Trauner, Michael; Schramm, Christoph; Chapman, Roger W.; Karlsen, Tom H.; Schrumpf, Erik; Strassburg, Christian P.; Manns, Michael P.; Lindor, Keith D; Hirschfield, Gideon M.; Hansen, Bettina E.; Boberg, Kirsten M.

    BACKGROUND & AIMS: Primary sclerosing cholangitis (PSC) is an orphan hepatobiliary disorder associated with inflammatory bowel disease (IBD). We aimed to estimate the risk of disease progression based on distinct clinical phenotypes in a large international cohort of patients with PSC. METHODS: We

  17. Weak lensing probes of modified gravity

    International Nuclear Information System (INIS)

    Schmidt, Fabian

    2008-01-01

    We study the effect of modifications to general relativity on large-scale weak lensing observables. In particular, we consider three modified gravity scenarios: f(R) gravity, the Dvali-Gabadadze-Porrati model, and tensor-vector-scalar theory. Weak lensing is sensitive to the growth of structure and the relation between matter and gravitational potentials, both of which will in general be affected by modified gravity. Restricting ourselves to linear scales, we compare the predictions for galaxy-shear and shear-shear correlations of each modified gravity cosmology to those of an effective dark energy cosmology with the same expansion history. In this way, the effects of modified gravity on the growth of perturbations are separated from the expansion history. We also propose a test which isolates the matter-potential relation from the growth factor and matter power spectrum. For all three modified gravity models, the predictions for galaxy and shear correlations will be discernible from those of dark energy with very high significance in future weak lensing surveys. Furthermore, each model predicts a measurably distinct scale dependence and redshift evolution of galaxy and shear correlations, which can be traced back to the physical foundations of each model. We show that the signal-to-noise for detecting signatures of modified gravity is much higher for weak lensing observables as compared to the integrated Sachs-Wolfe effect, measured via the galaxy-cosmic microwave background cross-correlation.

  18. Biological response modifiers

    Energy Technology Data Exchange (ETDEWEB)

    Weller, R.E.

    1991-10-01

    Much of what used to be called immunotherapy is now included in the term biological response modifiers. Biological response modifiers (BRMs) are defined as those agents or approaches that modify the relationship between the tumor and host by modifying the host's biological response to tumor cells with resultant therapeutic effects.'' Most of the early work with BRMs centered around observations of spontaneous tumor regression and the association of tumor regression with concurrent bacterial infections. The BRM can modify the host response in the following ways: Increase the host's antitumor responses through augmentation and/or restoration of effector mechanisms or mediators of the host's defense or decrease the deleterious component by the host's reaction; Increase the host's defenses by the administration of natural biologics (or the synthetic derivatives thereof) as effectors or mediators of an antitumor response; Augment the host's response to modified tumor cells or vaccines, which might stimulate a greater response by the host or increase tumor-cell sensitivity to an existing response; Decrease the transformation and/or increase differentiation (maturation) of tumor cells; or Increase the ability of the host to tolerate damage by cytotoxic modalities of cancer treatment.

  19. Fried frailty phenotype assessment components as applied to geriatric inpatients

    Directory of Open Access Journals (Sweden)

    Bieniek J

    2016-04-01

    Full Text Available Joanna Bieniek, Krzysztof Wilczynski, Jan Szewieczek Department of Geriatrics, School of Health Sciences in Katowice, Medical University of Silesia, Katowice, Poland Background: Management of geriatric patients would be simplified if a universally accepted definition of frailty for clinical use was defined. Among definitions of frailty, Fried frailty phenotype criteria constitute a common reference frame for many geriatric studies. However, this reference frame has been tested primarily in elderly patients presenting with relatively good health status. Objective: The aim of this article was to assess the usefulness and limitations of Fried frailty phenotype criteria in geriatric inpatients, characterized by comorbidity and functional impairments, and to estimate the frailty phenotype prevalence in this group. Patients and methods: Five hundred consecutive patients of the university hospital subacute geriatric ward, aged 79.0±8.4 years (67% women and 33% men, participated in this cross-sectional study. Comprehensive geriatric assessment and Fried frailty phenotype component evaluation were performed in all patients. Results: Multimorbidity (6.0±2.8 diseases characterized our study group, with a wide range of clinical conditions and functional states (Barthel Index of Activities of Daily Living 72.2±28.2 and Mini-Mental State Examination 23.6±7.1 scores. All five Fried frailty components were assessed in 65% of patients (95% confidence interval [CI] =60.8–69.2 (diagnostic group. One or more components were not feasible to be assessed in 35% of the remaining patients (nondiagnostic group because of lack of past patient’s body mass control and/or cognitive or physical impairment. Patients from the nondiagnostic group, as compared to patients from the diagnostic group, presented with more advanced age, higher prevalence of dementia, lower prevalence of hypertension, lower systolic and diastolic blood pressure, body mass index, Mini

  20. The Nature of Stable Insomnia Phenotypes

    Science.gov (United States)

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L.

    2015-01-01

    Study Objectives: We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Design: Longitudinal. Setting: Urban, community-based. Participants: Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). Interventions: None. Measurements and results: At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the “neither criterion” phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. Conclusions: By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With

  1. A study comparing chemical peeling using modified jessner′s solution and 15% trichloroacetic acid versus 15% trichloroacetic acid in the treatment of melasma

    Directory of Open Access Journals (Sweden)

    Safoury Omar

    2009-01-01

    Full Text Available Background: Melasma is a symmetric progressive hyperpigmentation of the facial skin that occurs in all races but has a predilection for darker skin phenotypes. Depigmenting agents, laser and chemical peeling as classic Jessner′s solution, modified Jessner′s solution and trichloroacetic acid have been used alone and in combination in the treatment of melasma. Objectives: The aim of the study was to compare the therapeutic effect of combined 15% Trichloroacetic acid (TCA and modified Jessner′s solution with 15% TCA on melasma. Materials and Methods: Twenty married females with melasma (epidermal type, with a mean age of 38.25 years, were included in this study. All were of skin type III or IV. Fifteen percent TCA was applied to the whole face, with the exception of the left malar area to which combined TCA 15% and modified Jessner′s solution was applied. Results: Our results revealed statistically highly significant difference between MASI Score (Melasma Area and Severity Index between the right malar area and the left malar area. Conclusion: Modified Jessner′s solution proved to be useful as an adjuvant treatment with TCA in the treatment of melasma, improving the results and minimizing postinflammatory hyperpigmentation.

  2. Invasive ecosystem engineer selects for different phenotypes of an associated native species.

    Science.gov (United States)

    Wright, Jeffrey T; Gribben, Paul E; Byers, James E; Monro, Keyne

    2012-06-01

    Invasive habitat-forming ecosystem engineers modify the abiotic environment and thus represent a major perturbation to many ecosystems. Because native species often persist in these invaded habitats but have no shared history with the ecosystem engineer, the engineer may impose novel selective pressure on native species. In this study, we used a phenotypic selection framework to determine whether an invasive habitat-forming ecosystem engineer (the seaweed Caulerpa taxifolia) selects for different phenotypes of a common co-occurring native species (the bivalve Anadara trapezia). Compared to unvegetated habitat, Caulerpa habitat has lower water flow, lower dissolved oxygen, and sediments are more silty and anoxic. We determined the performance consequences of variation in key functional traits that may be affected by these abiotic changes (shell morphology, gill mass, and palp mass) for Anadara transplanted into Caulerpa and unvegetated habitat. Both linear and nonlinear performance gradients in Anadara differed between habitats, and these gradients were stronger in Caulerpa compared to unvegetated sediment. Moreover, in Caulerpa alternate phenotypes performed well, and these phenotypes were different from the dominant phenotype in unvegetated sediment. By demonstrating that phenotype-performance gradients differ between habitats, we have highlighted a role for Caulerpa as an agent of selection on native species.

  3. Multi-dimensional discovery of biomarker and phenotype complexes

    Directory of Open Access Journals (Sweden)

    Huang Kun

    2010-10-01

    Full Text Available Abstract Background Given the rapid growth of translational research and personalized healthcare paradigms, the ability to relate and reason upon networks of bio-molecular and phenotypic variables at various levels of granularity in order to diagnose, stage and plan treatments for disease states is highly desirable. Numerous techniques exist that can be used to develop networks of co-expressed or otherwise related genes and clinical features. Such techniques can also be used to create formalized knowledge collections based upon the information incumbent to ontologies and domain literature. However, reports of integrative approaches that bridge such networks to create systems-level models of disease or wellness are notably lacking in the contemporary literature. Results In response to the preceding gap in knowledge and practice, we report upon a prototypical series of experiments that utilize multi-modal approaches to network induction. These experiments are intended to elicit meaningful and significant biomarker-phenotype complexes spanning multiple levels of granularity. This work has been performed in the experimental context of a large-scale clinical and basic science data repository maintained by the National Cancer Institute (NCI funded Chronic Lymphocytic Leukemia Research Consortium. Conclusions Our results indicate that it is computationally tractable to link orthogonal networks of genes, clinical features, and conceptual knowledge to create multi-dimensional models of interrelated biomarkers and phenotypes. Further, our results indicate that such systems-level models contain interrelated bio-molecular and clinical markers capable of supporting hypothesis discovery and testing. Based on such findings, we propose a conceptual model intended to inform the cross-linkage of the results of such methods. This model has as its aim the identification of novel and knowledge-anchored biomarker-phenotype complexes.

  4. Modified dispersion relations, inflation, and scale invariance

    Science.gov (United States)

    Bianco, Stefano; Friedhoff, Victor Nicolai; Wilson-Ewing, Edward

    2018-02-01

    For a certain type of modified dispersion relations, the vacuum quantum state for very short wavelength cosmological perturbations is scale-invariant and it has been suggested that this may be the source of the scale-invariance observed in the temperature anisotropies in the cosmic microwave background. We point out that for this scenario to be possible, it is necessary to redshift these short wavelength modes to cosmological scales in such a way that the scale-invariance is not lost. This requires nontrivial background dynamics before the onset of standard radiation-dominated cosmology; we demonstrate that one possible solution is inflation with a sufficiently large Hubble rate, for this slow roll is not necessary. In addition, we also show that if the slow-roll condition is added to inflation with a large Hubble rate, then for any power law modified dispersion relation quantum vacuum fluctuations become nearly scale-invariant when they exit the Hubble radius.

  5. How well do you know your mutation? Complex effects of genetic background on expressivity, complementation, and ordering of allelic effects.

    Directory of Open Access Journals (Sweden)

    Christopher H Chandler

    2017-11-01

    Full Text Available For a given gene, different mutations influence organismal phenotypes to varying degrees. However, the expressivity of these variants not only depends on the DNA lesion associated with the mutation, but also on factors including the genetic background and rearing environment. The degree to which these factors influence related alleles, genes, or pathways similarly, and whether similar developmental mechanisms underlie variation in the expressivity of a single allele across conditions and among alleles is poorly understood. Besides their fundamental biological significance, these questions have important implications for the interpretation of functional genetic analyses, for example, if these factors alter the ordering of allelic series or patterns of complementation. We examined the impact of genetic background and rearing environment for a series of mutations spanning the range of phenotypic effects for both the scalloped and vestigial genes, which influence wing development in Drosophila melanogaster. Genetic background and rearing environment influenced the phenotypic outcome of mutations, including intra-genic interactions, particularly for mutations of moderate expressivity. We examined whether cellular correlates (such as cell proliferation during development of these phenotypic effects matched the observed phenotypic outcome. While cell proliferation decreased with mutations of increasingly severe effects, surprisingly it did not co-vary strongly with the degree of background dependence. We discuss these findings and propose a phenomenological model to aid in understanding the biology of genes, and how this influences our interpretation of allelic effects in genetic analysis.

  6. Targeting phenotypically tolerant Mycobacterium tuberculosis

    Science.gov (United States)

    Gold, Ben; Nathan, Carl

    2016-01-01

    While the immune system is credited with averting tuberculosis in billions of individuals exposed to Mycobacterium tuberculosis, the immune system is also culpable for tempering the ability of antibiotics to deliver swift and durable cure of disease. In individuals afflicted with tuberculosis, host immunity produces diverse microenvironmental niches that support suboptimal growth, or complete growth arrest, of M. tuberculosis. The physiological state of nonreplication in bacteria is associated with phenotypic drug tolerance. Many of these host microenvironments, when modeled in vitro by carbon starvation, complete nutrient starvation, stationary phase, acidic pH, reactive nitrogen intermediates, hypoxia, biofilms, and withholding streptomycin from the streptomycin-addicted strain SS18b, render M. tuberculosis profoundly tolerant to many of the antibiotics that are given to tuberculosis patients in a clinical setting. Targeting nonreplicating persisters is anticipated to reduce the duration of antibiotic treatment and rate of post-treatment relapse. Some promising drugs to treat tuberculosis, such as rifampicin and bedaquiline, only kill nonreplicating M. tuberculosis in vitro at concentrations far greater than their minimal inhibitory concentrations against replicating bacilli. There is an urgent demand to identify which of the currently used antibiotics, and which of the molecules in academic and corporate screening collections, have potent bactericidal action on nonreplicating M. tuberculosis. With this goal, we review methods of high throughput screening to target nonreplicating M. tuberculosis and methods to progress candidate molecules. A classification based on structures and putative targets of molecules that have been reported to kill nonreplicating M. tuberculosis revealed a rich diversity in pharmacophores. However, few of these compounds were tested under conditions that would exclude the impact of adsorbed compound acting during the recovery phase of

  7. Genome-wide association study to identify potential genetic modifiers in a canine model for Duchenne muscular dystrophy.

    Science.gov (United States)

    Brinkmeyer-Langford, Candice; Balog-Alvarez, Cynthia; Cai, James J; Davis, Brian W; Kornegay, Joe N

    2016-08-22

    Duchenne muscular dystrophy (DMD) causes progressive muscle degeneration, cardiomyopathy and respiratory failure in approximately 1/5,000 boys. Golden Retriever muscular dystrophy (GRMD) resembles DMD both clinically and pathologically. Like DMD, GRMD exhibits remarkable phenotypic variation among affected dogs, suggesting the influence of modifiers. Understanding the role(s) of genetic modifiers of GRMD may identify genes and pathways that also modify phenotypes in DMD and reveal novel therapies. Therefore, our objective in this study was to identify genetic modifiers that affect discrete GRMD phenotypes. We performed a linear mixed-model (LMM) analysis using 16 variably-affected dogs from our GRMD colony (8 dystrophic, 8 non-dystrophic). All of these dogs were either full or half-siblings, and phenotyped for 19 objective, quantitative biomarkers at ages 6 and 12 months. Each biomarker was individually assessed. Gene expression profiles of 59 possible candidate genes were generated for two muscle types: the cranial tibialis and medial head of the gastrocnemius. SNPs significantly associated with GRMD biomarkers were identified on multiple chromosomes (including the X chromosome). Gene expression levels for candidate genes located near these SNPs correlated with biomarker values, suggesting possible roles as GRMD modifiers. The results of this study enhance our understanding of GRMD pathology and represent a first step toward the characterization of GRMD modifiers that may be relevant to DMD pathology. Such modifiers are likely to be useful for DMD treatment development based on their relationships to GRMD phenotypes.

  8. Canonical quantization of spinning relativistic particle in external backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Gavrilov, S.P. [Universidade Federal de Sergipe (UFS), Aracaju, SE (Brazil); Gitman, D.M. [Sao Paulo Univ. (USP), SP (Brazil). Inst. de Fisica

    2000-07-01

    Full text follows: We revise the problem of the quantization of spinning relativistic particle pseudoclassical model, using a modified consistent canonical scheme. It allows one not only to include arbitrary electromagnetic and gravitational backgrounds in the consideration but to get in course of the quantization a consistent relativistic quantum mechanics, which reproduces literally the behavior of the one-particle sector of quantized spinor field. In particular, in a physical sector of the Hilbert space a complete positive spectrum of energies of relativistic particles and antiparticles is reproduced. Requirement to maintain all classical symmetries under the coordinate transformations and under U(1) transformations allows one to realize operator algebra without any ambiguities. (author)

  9. Kinetics of spontaneous baryogenesis in non-stationary background

    Directory of Open Access Journals (Sweden)

    Arbuzova Elena

    2016-01-01

    Full Text Available Generation of the cosmological baryon asymmetry in frameworks of spontaneous baryogenesis is studied in detail. It is shown that the relation between baryonic chemical potential and the time derivative of the (pseudoGoldstone field essentially depends upon the representation chosen for the fermionic fields with non-zero baryonic number (quarks. Kinetic equation is modified and numerically solved in equilibrium for the case of time dependent external background or finite integration time to be applicable to the case when energy conservation law is formally violated.

  10. Phenotype comparison of MLH1 and MSH2 mutation carriers in a cohort of 1,914 individuals undergoing clinical genetic testing in the United States

    NARCIS (Netherlands)

    F. Kastrinos (Fay); E.M. Stoffel (Elena); J. Balmana (Judith); E.W. Steyerberg (Ewout); R. Mercado (Rowena); S. Syngal (Sapna)

    2008-01-01

    textabstractBackground and Aims: Lynch syndrome is caused by germ-line mismatch repair gene mutations. We examined the phenotypic differences between MLH1 and MSH2 gene mutation carriers and whether mutation type (point versus large rearrangement) affected phenotypic expression. Methods: This is a

  11. Redefining Aging in HIV Infection Using Phenotypes.

    Science.gov (United States)

    Stoff, David M; Goodkin, Karl; Jeste, Dilip; Marquine, Maria

    2017-10-01

    This article critically reviews the utility of "phenotypes" as behavioral descriptors in aging/HIV research that inform biological underpinnings and treatment development. We adopt a phenotypic redefinition of aging conceptualized within a broader context of HIV infection and of aging. Phenotypes are defined as dimensions of behavior, closely related to fundamental mechanisms, and, thus, may be more informative than chronological age. Primary emphasis in this review is given to comorbid aging and cognitive aging, though other phenotypes (i.e., disability, frailty, accelerated aging, successful aging) are also discussed in relation to comorbid aging and cognitive aging. The main findings that emerged from this review are as follows: (1) the phenotypes, comorbid aging and cognitive aging, are distinct from each other, yet overlapping; (2) associative relationships are the rule in HIV for comorbid and cognitive aging phenotypes; and (3) HIV behavioral interventions for both comorbid aging and cognitive aging have been limited. Three paths for research progress are identified for phenotype-defined aging/HIV research (i.e., clinical and behavioral specification, biological mechanisms, intervention targets), and some important research questions are suggested within each of these research paths.

  12. Evolution of molecular phenotypes under stabilizing selection

    International Nuclear Information System (INIS)

    Nourmohammad, Armita; Schiffels, Stephan; Lässig, Michael

    2013-01-01

    Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution builds on genome evolution in a complicated way, which involves selection, genetic drift, mutations and recombination. Here we develop a coarse-grained evolutionary statistics for phenotypes, which decouples from details of the underlying genotypes. We derive approximate evolution equations for the distribution of phenotype values within and across populations. This dynamics covers evolutionary processes at high and low recombination rates, that is, it applies to sexual and asexual populations. In a fitness landscape with a single optimal phenotype value, the phenotypic diversity within populations and the divergence between populations reach evolutionary equilibria, which describe stabilizing selection. We compute the equilibrium distributions of both quantities analytically and we show that the ratio of mean divergence and diversity depends on the strength of selection in a universal way: it is largely independent of the phenotype’s genomic encoding and of the recombination rate. This establishes a new method for the inference of selection on molecular phenotypes beyond the genome level. We discuss the implications of our findings for the predictability of evolutionary processes. (paper)

  13. Modified blank ammunition injuries.

    Science.gov (United States)

    Ogunc, Gokhan I; Ozer, M Tahir; Coskun, Kagan; Uzar, Ali Ihsan

    2009-12-15

    Blank firing weapons are designed only for discharging blank ammunition cartridges. Because they are cost-effective, are easily accessible and can be modified to live firearms plus their unclear legal situation in Turkish Law makes them very popular in Turkey. 2004 through 2008, a total of 1115 modified blank weapons were seized in Turkey. Blank firing weapons are easily modified by owners, making them suitable for discharging live firearm ammunition or modified blank ammunitions. Two common methods are used for modification of blank weapons. After the modification, these weapons can discharge the live ammunition. However, due to compositional durability problems with these types of weapons; the main trend is to use the modified blank ammunitions rather than live firearm ammunition fired from modified blank firing weapons. In this study, two types of modified blank weapons and two types of modified blank cartridges were tested on three different target models. Each of the models' shooting side was coated with 1.3+/-2 mm thickness chrome tanned cowhide as a skin simulant. The first model was only coated with skin simulant. The second model was coated with skin simulant and 100% cotton police shirt. The third model was coated with skin simulant and jean denim. After the literature evaluation four high risky anatomic locations (the neck area; the eyes; the thorax area and inguinal area) were pointed out for the steel and lead projectiles are discharged from the modified blank weapons especially in close range (0-50 cm). The target models were designed for these anatomic locations. For the target models six Transparent Ballistic Candle blocks (TCB) were prepared and divided into two test groups. The first group tests were performed with lead projectiles and second group with steel projectile. The shortest penetration depth (lead projectile: 4.358 cm; steel projectile 8.032 cm) was recorded in the skin simulant and jean denim coated block for both groups. In both groups

  14. The nature of stable insomnia phenotypes.

    Science.gov (United States)

    Pillai, Vivek; Roth, Thomas; Drake, Christopher L

    2015-01-01

    We examined the 1-y stability of four insomnia symptom profiles: sleep onset insomnia; sleep maintenance insomnia; combined onset and maintenance insomnia; and neither criterion (i.e., insomnia cases that do not meet quantitative thresholds for onset or maintenance problems). Insomnia cases that exhibited the same symptom profile over a 1-y period were considered to be phenotypes, and were compared in terms of clinical and demographic characteristics. Longitudinal. Urban, community-based. Nine hundred fifty-four adults with Diagnostic and Statistical Manual of Mental Disorders, Fifth Edition based current insomnia (46.6 ± 12.6 y; 69.4% female). None. At baseline, participants were divided into four symptom profile groups based on quantitative criteria. Follow-up assessment 1 y later revealed that approximately 60% of participants retained the same symptom profile, and were hence judged to be phenotypes. Stability varied significantly by phenotype, such that sleep onset insomnia (SOI) was the least stable (42%), whereas combined insomnia (CI) was the most stable (69%). Baseline symptom groups (cross-sectionally defined) differed significantly across various clinical indices, including daytime impairment, depression, and anxiety. Importantly, however, a comparison of stable phenotypes (longitudinally defined) did not reveal any differences in impairment or comorbid psychopathology. Another interesting finding was that whereas all other insomnia phenotypes showed evidence of an elevated wake drive both at night and during the day, the 'neither criterion' phenotype did not; this latter phenotype exhibited significantly higher daytime sleepiness despite subthreshold onset and maintenance difficulties. By adopting a stringent, stability-based definition, this study offers timely and important data on the longitudinal trajectory of specific insomnia phenotypes. With the exception of daytime sleepiness, few clinical differences are apparent across stable phenotypes.

  15. Asymmetry in dentition and shape of pharyngeal arches in the clonal fish Chrosomus eos-neogaeus: Phenotypic plasticity and developmental instability.

    Directory of Open Access Journals (Sweden)

    Christelle Leung

    Full Text Available The effect of the environment may result in different developmental outcomes. Extrinsic signals can modify developmental pathways and result in alternative phenotypes (phenotypic plasticity. The environment can also be interpreted as a stressor and increase developmental instability (developmental noise. Directional and fluctuating asymmetry provide a conceptual background to discriminate between these results. This study aims at assessing whether variation in dentition and shape of pharyngeal arches of the clonal fish Chrosomus eos-neogaeus results from developmental instability or environmentally induced changes. A total of 262 specimens of the Chrosomus eos-neogaeus complex from 12 natural sites were analysed. X-ray microcomputed tomography (X-ray micro-CT was used to visualize the pharyngeal arches in situ with high resolution. Variation in the number of pharyngeal teeth is high in hybrids in contrast to the relative stability observed in both parental species. The basal dental formula is symmetric while the most frequent alternative dental formula is asymmetric. Within one lineage, large variation in the proportion of individuals bearing basal or alternative dental formulae was observed among sites in the absence of genetic difference. Both dentition and arch shape of this hybrid lineage were explained significantly by environmental differences. Only individuals bearing asymmetric dental formula displayed fluctuating asymmetry as well as directional left-right asymmetry for the arches. The hybrids appeared sensitive to environmental signals and intraspecific variation on pharyngeal teeth was not random but reflects phenotypic plasticity. Altogether, these results support the influence of the environment as a trigger for an alternative developmental pathway resulting in left-right asymmetry in dentition and shape of pharyngeal arches.

  16. Phenotyping animal models of diabetic neuropathy

    DEFF Research Database (Denmark)

    Biessels, G J; Bril, V; Calcutt, N A

    2014-01-01

    NIDDK, JDRF, and the Diabetic Neuropathy Study Group of EASD sponsored a meeting to explore the current status of animal models of diabetic peripheral neuropathy. The goal of the workshop was to develop a set of consensus criteria for the phenotyping of rodent models of diabetic neuropathy...... with a discussion on the merits and limitations of a unified approach to phenotyping rodent models of diabetic neuropathy and a consensus formed on the definition of the minimum criteria required for establishing the presence of the disease. A neuropathy phenotype in rodents was defined as the presence...

  17. Managing major data of genetically modified mice: from scientific demands to legal obligations.

    Science.gov (United States)

    Staudt, Michael; Trauth, Jürgen; Hindi, Iris El; Galuschka, Claudia; Sitek, Dagmar; Schenkel, Johannes

    2012-10-01

    The number of genetically modified mice is increasing rapidly. Several limitations when working with these animals are to be considered: small colonies, the continued danger of loss, often a limited breeding-success, the need to keep those mutants in stock, difficult and costly import-procedures, and also a major (scientific) value of those mutants often available only with major restrictions. To gather relevant information about all active and archived genetically modified mouse lines available in-house (>1.500) and to deal with a unique resource for several, quite different purposes, a data base was developed enabling optimum knowledge management and easy access. The data base covers also legal restraints and is being linked with the institutional publication repository. To identify the lines available detailed information is provided for each line, as the international designation, a short name, the characterization/description, and the genetic modification including the technique used therefore. The origin of the mutation (gene-ID# and donor organism), the origin of regulatory elements and their donors are listed as well as the genetic background, back-cross generation, phenotype, possible publications, keywords, and some in-house information. Also aspects of animal welfare, obligations to record genetically modified organisms, and technology transfer are displayed; the latter to make licenses possible (if legally permitted). Material transfer agreements, patents, or legal restrictions are listed. This data base helps to avoid double-imports, saves animals and costs since a redundant generation or import can be omitted. However, this is a contribution to the 3R principles developed by Russell and Burch.

  18. Modified nasolacrimal duct stenting

    International Nuclear Information System (INIS)

    Tian Min; Jin Mei; Chen Huanjun; Li Yi

    2008-01-01

    Objective: Traditional nasolacrimal duct stenting possesses some shortcoming including difficulty of pulling ball head guide wire from the nasal cavity with turbinate hypertrophy and nasal septal deviation. The new method of nose-oral tube track establishment can overcome the forementioned and increase the successful rate. Methods: 5 F catheter and arterial sheath were modified to be nasolacrimal duct stent delivery device respectively. Antegrade dacryocystography was taken firstly to display the obstructed site and followed by the modified protocol of inserting the guide wire through nasolacrimal duct and nasal cavity, and establishing the stent delivery track for retrograde stent placement. Results: 5 epiphora patients with failure implantation by traditional method were all succeeded through the modified stenting (100%). During 6-mouth follow-up, no serious complications and reocclusion occurred. Conclusion: The establishment of eye-nose-mouth-nose of external nasal guide wire track can improve the successful rate of nasolacrimal duct stenting. (authors)

  19. Absorbing systematic effects to obtain a better background model in a search for new physics

    International Nuclear Information System (INIS)

    Caron, S; Horner, S; Sundermann, J E; Cowan, G; Gross, E

    2009-01-01

    This paper presents a novel approach to estimate the Standard Model backgrounds based on modifying Monte Carlo predictions within their systematic uncertainties. The improved background model is obtained by altering the original predictions with successively more complex correction functions in signal-free control selections. Statistical tests indicate when sufficient compatibility with data is reached. In this way, systematic effects are absorbed into the new background model. The same correction is then applied on the Monte Carlo prediction in the signal region. Comparing this method to other background estimation techniques shows improvements with respect to statistical and systematic uncertainties. The proposed method can also be applied in other fields beyond high energy physics.

  20. Exome sequencing identifies mutations in ABCD1 and DACH2 in two brothers with a distinct phenotype

    OpenAIRE

    Zhang, Yanliang; Liu, Yanhui; Li, Ya; Duan, Yong; Zhang, Keyun; Wang, Junwang; Dai, Yong

    2014-01-01

    Background We report on two brothers with a distinct syndromic phenotype and explore the potential pathogenic cause. Methods Cytogenetic tests and exome sequencing were performed on the two brothers and their parents. Variants detected by exome sequencing were validated by Sanger sequencing. Results The main phenotype of the two brothers included congenital language disorder, growth retardation, intellectual disability, difficulty in standing and walking, and urinary and fecal incontinence. T...

  1. Leaf-GP: an open and automated software application for measuring growth phenotypes for arabidopsis and wheat

    OpenAIRE

    Zhou, Ji; Applegate, Christopher; Alonso, Albor Dobon; Reynolds, Daniel; Orford, Simon; Mackiewicz, Michal; Griffiths, Simon; Penfield, Steven; Pullen, Nick

    2017-01-01

    Background Plants demonstrate dynamic growth phenotypes that are determined by genetic and environmental factors. Phenotypic analysis of growth features over time is a key approach to understand how plants interact with environmental change as well as respond to different treatments. Although the importance of measuring dynamic growth traits is widely recognised, available open software tools are limited in terms of batch image processing, multiple traits analyses, software usability and cros...

  2. Phenotypic plasticity as an adaptive response to predictable and unpredictable environmental changes

    DEFF Research Database (Denmark)

    Manenti, Tommaso

    Phenotypic plasticity is the ability of a genotype to modify its phenotype in response to environmental changes as a consequence of an interaction between genes and environment (Bradshaw, 1965). Plasticity contributes to the vast phenotypic variation observed in natural populations. Many examples...... of a plastic response are expected to depend on the environmental conditions experienced by organisms. Thus, in populations exposed to a non-changing environment, the plastic machinery might be a waste of resources. Contrary, in populations experiencing varying environmental conditions, plasticity is expected...... such as anti-predator behaviours or the activation of mechanisms to prevent thermal stress injuries suggest that plasticity is an adaptive response, favoured by natural selection. At the same time, organisms do show limited plastic responses, indicating that this ability is not for free. Costs and benefits...

  3. a Systematic Review of Phenotypes

    Directory of Open Access Journals (Sweden)

    Yoonju Lee

    2017-01-01

    Full Text Available Familial hyperekplexia, also called startle disease, is a rare neurological disorder characterized by excessive startle responses to noise or touch. It can be associated with serious injury from frequent falls, apnea spells, and aspiration pneumonia. Familial hyperekplexia has a heterogeneous genetic background with several identified causative genes; it demonstrates both dominant and recessive inheritance in the α1 subunit of the glycine receptor (GLRA1, the β subunit of the glycine receptor and the presynaptic sodium and chloride-dependent glycine transporter 2 genes. Clonazepam is an effective medical treatment for hyperekplexia. Here, we report genetically confirmed familial hyperekplexia patients presenting early adult cautious gait. Additionally, we review clinical features, mode of inheritance, ethnicity and the types and locations of mutations of previously reported hyperekplexia cases with a GLRA1 gene mutation.

  4. Normal modified stable processes

    DEFF Research Database (Denmark)

    Barndorff-Nielsen, Ole Eiler; Shephard, N.

    2002-01-01

    Gaussian (NGIG) laws. The wider framework thus established provides, in particular, for added flexibility in the modelling of the dynamics of financial time series, of importance especially as regards OU based stochastic volatility models for equities. In the special case of the tempered stable OU process......This paper discusses two classes of distributions, and stochastic processes derived from them: modified stable (MS) laws and normal modified stable (NMS) laws. This extends corresponding results for the generalised inverse Gaussian (GIG) and generalised hyperbolic (GH) or normal generalised inverse...

  5. Phenotypic profiles of Armenian grape cultivars

    Directory of Open Access Journals (Sweden)

    Aroutiounian Rouben

    2015-01-01

    Full Text Available The conservation and sustainable use of grapevine biodiversity in Armenia is particularly important due to the large number of traditional local varieties. Being partially different from European grapevine gene pool, the material of Armenian local cultivars significantly contributes to the understanding of the genetic variation and is valuable source for target selection. During last years many Armenian grapevine cultivars have been already described and their genotypes determined, but some local varieties and wild accessions remain unidentified and their phenotypic characteristics overlooked. The comprehensive analysis of phenotypes is essential for research, including genetic association studies, cultivar evaluation and selection. The goal of our research was the phenotyping on the base of reproductive, carpological and analytical characteristics of 80 Armenian aboriginal and new grape cultivars. Description of phenotypic profiles is important step towards identification and conservation of genetic resources of Armenian grapes. In future, these data can be applied for breeding of improved grape varieties targeted to fresh consumption and wine production.

  6. Phenotypic diversity and phylogenetic relationship between the ...

    African Journals Online (AJOL)

    Phenotypic diversity and phylogenetic relationship between the Bakosi/Baweri and other pig breeds ( Sus scrofa Domesticus ) in the humid forest with monomodal rainfall agro-ecological zone of Cameroon.

  7. Mining skeletal phenotype descriptions from scientific literature.

    Directory of Open Access Journals (Sweden)

    Tudor Groza

    Full Text Available Phenotype descriptions are important for our understanding of genetics, as they enable the computation and analysis of a varied range of issues related to the genetic and developmental bases of correlated characters. The literature contains a wealth of such phenotype descriptions, usually reported as free-text entries, similar to typical clinical summaries. In this paper, we focus on creating and making available an annotated corpus of skeletal phenotype descriptions. In addition, we present and evaluate a hybrid Machine Learning approach for mining phenotype descriptions from free text. Our hybrid approach uses an ensemble of four classifiers and experiments with several aggregation techniques. The best scoring technique achieves an F-1 score of 71.52%, which is close to the state-of-the-art in other domains, where training data exists in abundance. Finally, we discuss the influence of the features chosen for the model on the overall performance of the method.

  8. Integrating phenotype ontologies with PhenomeNET

    KAUST Repository

    Rodriguez-Garcia, Miguel Angel; Gkoutos, Georgios V.; Schofield, Paul N.; Hoehndorf, Robert

    2017-01-01

    in clinical and model organism databases presents complex problems when attempting to match classes across species and across phenotypes as diverse as behaviour and neoplasia. We have previously developed PhenomeNET, a system for disease gene prioritization

  9. Wiedemann-Rautenstrauch syndrome: A phenotype analysis

    NARCIS (Netherlands)

    Paolacci, Stefano; Bertola, Debora; Franco, José; Mohammed, Shehla; Tartaglia, Marco; Wollnik, Bernd; Hennekam, Raoul C.

    2017-01-01

    Wiedemann-Rautenstrauch syndrome (WRS) is a neonatal progeroid disorder characterized by growth retardation, lipodystrophy, a distinctive face, and dental anomalies. Patients reported to date demonstrate a remarkable variability in phenotype, which hampers diagnostics. We performed a literature

  10. The spatial patterns of directional phenotypic selection

    KAUST Repository

    Siepielski, Adam M.; Gotanda, Kiyoko M.; Morrissey, Michael B.; Diamond, Sarah E.; DiBattista, Joseph; Carlson, Stephanie Marie

    2013-01-01

    the spatial patterns of selection, namely the extent of variation among populations in the strength and direction of selection. Here, we analyse a data set of spatially replicated studies of directional phenotypic selection from natural populations. The data

  11. Phenotypic variability among strains of Pasteurella multocida ...

    African Journals Online (AJOL)

    STORAGESEVER

    2008-05-02

    May 2, 2008 ... Available online at http://www.academicjournals.org/AJB. ISSN 1684–5315 ... extended phenotypic characterization methods supported by DNA ... septicaemia African (Obudu) strain (E:2) which are currently employed as ...

  12. Computer vision and machine learning for robust phenotyping in genome-wide studies.

    Science.gov (United States)

    Zhang, Jiaoping; Naik, Hsiang Sing; Assefa, Teshale; Sarkar, Soumik; Reddy, R V Chowda; Singh, Arti; Ganapathysubramanian, Baskar; Singh, Asheesh K

    2017-03-08

    Traditional evaluation of crop biotic and abiotic stresses are time-consuming and labor-intensive limiting the ability to dissect the genetic basis of quantitative traits. A machine learning (ML)-enabled image-phenotyping pipeline for the genetic studies of abiotic stress iron deficiency chlorosis (IDC) of soybean is reported. IDC classification and severity for an association panel of 461 diverse plant-introduction accessions was evaluated using an end-to-end phenotyping workflow. The workflow consisted of a multi-stage procedure including: (1) optimized protocols for consistent image capture across plant canopies, (2) canopy identification and registration from cluttered backgrounds, (3) extraction of domain expert informed features from the processed images to accurately represent IDC expression, and (4) supervised ML-based classifiers that linked the automatically extracted features with expert-rating equivalent IDC scores. ML-generated phenotypic data were subsequently utilized for the genome-wide association study and genomic prediction. The results illustrate the reliability and advantage of ML-enabled image-phenotyping pipeline by identifying previously reported locus and a novel locus harboring a gene homolog involved in iron acquisition. This study demonstrates a promising path for integrating the phenotyping pipeline into genomic prediction, and provides a systematic framework enabling robust and quicker phenotyping through ground-based systems.

  13. Cluster analysis in severe emphysema subjects using phenotype and genotype data: an exploratory investigation

    Directory of Open Access Journals (Sweden)

    Martinez Fernando J

    2010-03-01

    Full Text Available Abstract Background Numerous studies have demonstrated associations between genetic markers and COPD, but results have been inconsistent. One reason may be heterogeneity in disease definition. Unsupervised learning approaches may assist in understanding disease heterogeneity. Methods We selected 31 phenotypic variables and 12 SNPs from five candidate genes in 308 subjects in the National Emphysema Treatment Trial (NETT Genetics Ancillary Study cohort. We used factor analysis to select a subset of phenotypic variables, and then used cluster analysis to identify subtypes of severe emphysema. We examined the phenotypic and genotypic characteristics of each cluster. Results We identified six factors accounting for 75% of the shared variability among our initial phenotypic variables. We selected four phenotypic variables from these factors for cluster analysis: 1 post-bronchodilator FEV1 percent predicted, 2 percent bronchodilator responsiveness, and quantitative CT measurements of 3 apical emphysema and 4 airway wall thickness. K-means cluster analysis revealed four clusters, though separation between clusters was modest: 1 emphysema predominant, 2 bronchodilator responsive, with higher FEV1; 3 discordant, with a lower FEV1 despite less severe emphysema and lower airway wall thickness, and 4 airway predominant. Of the genotypes examined, membership in cluster 1 (emphysema-predominant was associated with TGFB1 SNP rs1800470. Conclusions Cluster analysis may identify meaningful disease subtypes and/or groups of related phenotypic variables even in a highly selected group of severe emphysema subjects, and may be useful for genetic association studies.

  14. Highly efficient transduction of human plasmacytoid dendritic cells without phenotypic and functional maturation

    Directory of Open Access Journals (Sweden)

    Plumas Joel

    2009-01-01

    Full Text Available Abstract Background Gene modified dendritic cells (DC are able to modulate DC functions and induce therapeutic immunity or tolerance in an antigen-specific manner. Among the different DC subsets, plasmacytoid DC (pDC are well known for their ability to recognize and respond to a variety of viruses by secreting high levels of type I interferon. Methods We analyzed here, the transduction efficiency of a pDC cell line, GEN2.2, and of pDC derived from CD34+ progenitors, using lentiviral vectors (LV pseudotyped with different envelope glycoproteins such as the vesicular stomatitis virus envelope (VSVG, the gibbon ape leukaemia virus envelope (GaLV or the feline endogenous virus envelope (RD114. At the same time, we evaluated transgene expression (E-GFP reporter gene under the control of different promoters. Results We found that efficient gene transfer into pDC can be achieved with VSVG-pseudotyped lentiviral vectors (LV under the control of phoshoglycerate kinase (PGK and elongation factor-1 (EF1α promoters (28% to 90% of E-GFP+ cells, respectively in the absence of phenotypic and functional maturation. Surprisingly, promoters (desmin or synthetic C5–12 described as muscle-specific and which drive gene expression in single strand AAV vectors in gene therapy protocols were very highly active in pDC using VSVG-LV. Conclusion Taken together, our results indicate that LV vectors can serve to design pDC-based vaccines in humans, and they are also useful in vitro to evaluate the immunogenicity of the vector preparations, and the specificity and safety of given promoters used in gene therapy protocols.

  15. Atypical disease phenotypes in pediatric ulcerative colitis

    DEFF Research Database (Denmark)

    Levine, Arie; de Bie, Charlotte I; Turner, Dan

    2013-01-01

    Definitive diagnosis of pediatric ulcerative colitis (UC) may be particularly challenging since isolated colitis with overlapping features is common in pediatric Crohn's disease (CD), while atypical phenotypes of UC are not uncommon. The Paris classification allows more accurate phenotyping...... of atypical inflammatory bowel disease (IBD) patients. Our aim was to identify the prevalence of atypical disease patterns in new-onset pediatric UC using the Paris classification....

  16. Increased entropy of signal transduction in the cancer metastasis phenotype

    Directory of Open Access Journals (Sweden)

    Teschendorff Andrew E

    2010-07-01

    Full Text Available Abstract Background The statistical study of biological networks has led to important novel biological insights, such as the presence of hubs and hierarchical modularity. There is also a growing interest in studying the statistical properties of networks in the context of cancer genomics. However, relatively little is known as to what network features differ between the cancer and normal cell physiologies, or between different cancer cell phenotypes. Results Based on the observation that frequent genomic alterations underlie a more aggressive cancer phenotype, we asked if such an effect could be detectable as an increase in the randomness of local gene expression patterns. Using a breast cancer gene expression data set and a model network of protein interactions we derive constrained weighted networks defined by a stochastic information flux matrix reflecting expression correlations between interacting proteins. Based on this stochastic matrix we propose and compute an entropy measure that quantifies the degree of randomness in the local pattern of information flux around single genes. By comparing the local entropies in the non-metastatic versus metastatic breast cancer networks, we here show that breast cancers that metastasize are characterised by a small yet significant increase in the degree of randomness of local expression patterns. We validate this result in three additional breast cancer expression data sets and demonstrate that local entropy better characterises the metastatic phenotype than other non-entropy based measures. We show that increases in entropy can be used to identify genes and signalling pathways implicated in breast cancer metastasis and provide examples of de-novo discoveries of gene modules with known roles in apoptosis, immune-mediated tumour suppression, cell-cycle and tumour invasion. Importantly, we also identify a novel gene module within the insulin growth factor signalling pathway, alteration of which may

  17. Phenex: ontological annotation of phenotypic diversity.

    Directory of Open Access Journals (Sweden)

    James P Balhoff

    2010-05-01

    Full Text Available Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices.Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  18. Phenex: ontological annotation of phenotypic diversity.

    Science.gov (United States)

    Balhoff, James P; Dahdul, Wasila M; Kothari, Cartik R; Lapp, Hilmar; Lundberg, John G; Mabee, Paula; Midford, Peter E; Westerfield, Monte; Vision, Todd J

    2010-05-05

    Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution. Traditionally, these descriptions have been expressed in natural language within the context of individual journal publications or monographs. As such, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge. Here we describe Phenex, a platform-independent desktop application designed to facilitate efficient and consistent annotation of phenotypic similarities and differences using Entity-Quality syntax, drawing on terms from community ontologies for anatomical entities, phenotypic qualities, and taxonomic names. Phenex can be configured to load only those ontologies pertinent to a taxonomic group of interest. The graphical user interface was optimized for evolutionary biologists accustomed to working with lists of taxa, characters, character states, and character-by-taxon matrices. Annotation of phenotypic data using ontologies and globally unique taxonomic identifiers will allow biologists to integrate phenotypic data from different organisms and studies, leveraging decades of work in systematics and comparative morphology.

  19. EAMJ Modifiable 10.indd

    African Journals Online (AJOL)

    2010-02-02

    Feb 2, 2010 ... MODIFIABLE FACTORS ASSOCIATED WITH ACTIVE PULMONARY TUBERCULOSIS IN A KENYAN PRISON. A. S. Amwayi, MBChB, MSc., ... University of Agriculture and Technology, P.O. Box 62000- 0200, Nairobi, Kenya and E. M. Muchiri, MSc, PhD., Division ..... Diabetes and low BMI. 223452.81.

  20. Isotopically modified compounds

    International Nuclear Information System (INIS)

    Kuruc, J.

    2009-01-01

    In this chapter the nomenclature of isotopically modified compounds in Slovak language is described. This chapter consists of following parts: (1) Isotopically substituted compounds; (2) Specifically isotopically labelled compounds; (3) Selectively isotopically labelled compounds; (4) Non-selectively isotopically labelled compounds; (5) Isotopically deficient compounds.

  1. Modifiable Combining Functions

    OpenAIRE

    Cohen, Paul; Shafer, Glenn; Shenoy, Prakash P.

    2013-01-01

    Modifiable combining functions are a synthesis of two common approaches to combining evidence. They offer many of the advantages of these approaches and avoid some disadvantages. Because they facilitate the acquisition, representation, explanation, and modification of knowledge about combinations of evidence, they are proposed as a tool for knowledge engineers who build systems that reason under uncertainty, not as a normative theory of evidence.

  2. Modifying Cookbook Labs.

    Science.gov (United States)

    Clark, Robert, L.; Clough, Michael P.; Berg, Craig A.

    2000-01-01

    Modifies an extended lab activity from a cookbook approach for determining the percent mass of water in copper sulfate pentahydrate crystals to one which incorporates students' prior knowledge, engenders active mental struggling with prior knowledge and new experiences, and encourages metacognition. (Contains 12 references.) (ASK)

  3. Phenotypic heterogeneity in a bacteriophage population only appears as stress-induced mutagenesis.

    Science.gov (United States)

    Yosef, Ido; Edgar, Rotem; Qimron, Udi

    2016-11-01

    Stress-induced mutagenesis has been studied in cancer cells, yeast, bacteria, and archaea, but not in viruses. In a recent publication, we present a bacteriophage model showing an apparent stress-induced mutagenesis. We show that the stress does not drive the mutagenesis, but only selects the fittest mutants. The mechanism underlying the observed phenomenon is a phenotypic heterogeneity that resembles persistence of the viral population. The new findings, the background for the ongoing debate on stress-induced mutagenesis, and the phenotypic heterogeneity underlying a novel phage infection strategy are discussed in this short manuscript.

  4. Mesenchymal Stromal Cell Phenotype is not Influenced by Confluence during Culture Expansion

    DEFF Research Database (Denmark)

    Haack-Sørensen, Mandana; Hansen, Susanne Kofoed; Hansen, Louise

    2013-01-01

    BACKGROUND: Accumulating preclinical and clinical evidence indicates that human mesenchymal stromal cells (MSCs) are good candidates for cell therapy. For clinical applications of MSCs extensive in vitro expansion is required to obtain an adequate number of cells. It is evident that the pursuit...... differentiation. This phenotype persisted independent of increasing cell densities. DISCUSSION: These data demonstrate that MSC characteristics and plasticity can be maintained during culture expansion from bone marrow mononuclear cells to MSCs and that a homogeneous phenotype of undifferentiated MSCs which...... persists independent of cell density can be used for clinical therapies....

  5. Hemizygous Le-Cre Transgenic Mice Have Severe Eye Abnormalities on Some Genetic Backgrounds in the Absence of LoxP Sites

    Science.gov (United States)

    Dorà, Natalie J.; Collinson, J. Martin; Hill, Robert E.; West, John D.

    2014-01-01

    Eye phenotypes were investigated in Le-CreTg/−; Pax6fl/+ mice, which were expected to show tissue-specific reduction of Pax6 in surface ectoderm derivatives. To provide a better comparison with our previous studies of Pax6+/− eye phenotypes, hemizygous Le-CreTg/− and heterozygous Pax6fl/+mice were crossed onto the CBA/Ca genetic background. After the Le-Cre transgene had been backcrossed to CBA/Ca for seven generations, significant eye abnormalities occurred in some hemizygous Le-CreTg/−; Pax6+/+ controls (without a floxed Pax6fl allele) as well as experimental Le-CreTg/−; Pax6fl/+ mice. However, no abnormalities were seen in Le-Cre−/−; Pax6fl/+ or Le-Cre−/−; Pax6+/+ controls (without the Le-Cre transgene). The severity and frequency of the eye abnormalities in Le-CreTg/−; Pax6+/+ control mice diminished after backcrossing Le-CreTg/− mice to the original FVB/N strain for two generations, showing that the effect was reversible. This genetic background effect suggests that the eye abnormalities are a consequence of an interaction between the Le-Cre transgene and alleles of unknown modifier genes present in certain genetic backgrounds. The abnormalities were also ameliorated by introducing additional Pax6 gene copies on a CBA/Ca background, suggesting involvement of Pax6 depletion in Le-CreTg/−; Pax6+/+ mice rather than direct action of Cre recombinase on cryptic pseudo-loxP sites. One possibility is that expression of Cre recombinase from the Pax6-Le regulatory sequences in the Le-Cre transgene depletes cofactors required for endogenous Pax6 gene expression. Our observation that eye abnormalities can occur in hemizygous Le-CreTg/−; Pax6+/+ mice, in the absence of a floxed allele, demonstrates the importance of including all the relevant genetic controls in Cre-loxP experiments. PMID:25272013

  6. Simulation of Experimental Background using FLUKA

    Energy Technology Data Exchange (ETDEWEB)

    Rokni, Sayed

    1999-05-11

    In November 1997, Experiment T423 began acquiring data with the intentions of understanding the energy spectra of high-energy neutrons generated in the interaction of electrons with lead. The following describes a series of FLUKA simulations studying (1) particle yields in the absence of all background; (2) the background caused from scattering in the room; (3) the effects of the thick lead shielding which surrounded the detector; (4) the sources of neutron background created in this lead shielding; and (5) the ratio of the total background to the ideal yield. In each case, particular attention is paid to the neutron yield.

  7. Modeling the Thermal Signature of Natural Backgrounds

    National Research Council Canada - National Science Library

    Gamborg, Marius

    2002-01-01

    Two measuring stations have been established the purpose being to collect comprehensive databases of thermal signatures of background elements in addition to the prevailing meteorological conditions...

  8. Meta-analysis of melanin-concentrating hormone signaling-deficient mice on behavioral and metabolic phenotypes.

    Directory of Open Access Journals (Sweden)

    Kenkichi Takase

    Full Text Available The demand for meta-analyses in basic biomedical research has been increasing because the phenotyping of genetically modified mice does not always produce consistent results. Melanin-concentrating hormone (MCH has been reported to be involved in a variety of behaviors that include feeding, body-weight regulation, anxiety, sleep, and reward behavior. However, the reported behavioral and metabolic characteristics of MCH signaling-deficient mice, such as MCH-deficient mice and MCH receptor 1 (MCHR1-deficient mice, are not consistent with each other. In the present study, we performed a meta-analysis of the published data related to MCH-deficient and MCHR1-deficient mice to obtain robust conclusions about the role of MCH signaling. Overall, the meta-analysis revealed that the deletion of MCH signaling enhanced wakefulness, locomotor activity, aggression, and male sexual behavior and that MCH signaling deficiency suppressed non-REM sleep, anxiety, responses to novelty, startle responses, and conditioned place preferences. In contrast to the acute orexigenic effect of MCH, MCH signaling deficiency significantly increased food intake. Overall, the meta-analysis also revealed that the deletion of MCH signaling suppressed the body weight, fat mass, and plasma leptin, while MCH signaling deficiency increased the body temperature, oxygen consumption, heart rate, and mean arterial pressure. The lean phenotype of the MCH signaling-deficient mice was also confirmed in separate meta-analyses that were specific to sex and background strain (i.e., C57BL/6 and 129Sv. MCH signaling deficiency caused a weak anxiolytic effect as assessed with the elevated plus maze and the open field test but also caused a weak anxiogenic effect as assessed with the emergence test. MCH signaling-deficient mice also exhibited increased plasma corticosterone under non-stressed conditions, which suggests enhanced activity of the hypothalamic-pituitary-adrenal axis. To the best of our

  9. Biotechnology: Two Decades of Experimentation with Genetically Modified Foods

    Directory of Open Access Journals (Sweden)

    Marjan Ajami

    2016-10-01

    Full Text Available Background and Objective: Over the recent years, genetically modified food in varieties of corn, soybeans, canola and cotton have been introduced to the global market. This study reviews the health and nutritional value of genetically modified foods in the past two decades.Results and Conclusions: Contrary to the present biotechnological claims, transgenic products did not prove to be so flawless, and actually failed to maintain social satisfaction. Genetically modified foods could not gain an increase in the yield potential. Planting natural products and genetically modified products in parallel lines will absolutely result in genetic infection from the side of genetically modified foods. One of the major anxieties of the anti- genetically modified foods activism is the claim that genetically modified crops would alter the consumable parts of the plant quality and safety. Genetically modified foods have shown to have inadequate efficiency and potential adverse effects in both fields of health and biodiversity. This review has presented studies of genetically modified foods performances in the past two decades, and concludes that the wide application and the over generalization of genetically modified foods are not fundamentally recommended.Conflict of interest: Authors declare that there is no conflict of interest.

  10. A statistical background noise correction sensitive to the steadiness of background noise.

    Science.gov (United States)

    Oppenheimer, Charles H

    2016-10-01

    A statistical background noise correction is developed for removing background noise contributions from measured source levels, producing a background noise-corrected source level. Like the standard background noise corrections of ISO 3741, ISO 3744, ISO 3745, and ISO 11201, the statistical background correction increases as the background level approaches the measured source level, decreasing the background noise-corrected source level. Unlike the standard corrections, the statistical background correction increases with steadiness of the background and is excluded from use when background fluctuation could be responsible for measured differences between the source and background noise levels. The statistical background noise correction has several advantages over the standard correction: (1) enveloping the true source with known confidence, (2) assuring physical source descriptions when measuring sources in fluctuating backgrounds, (3) reducing background corrected source descriptions by 1 to 8 dB for sources in steady backgrounds, and (4) providing a means to replace standardized background correction caps that incentivize against high precision grade methods.

  11. Hanford Site background: Part 1, Soil background for nonradioactive analytes. Revision 1, Volume 2

    Energy Technology Data Exchange (ETDEWEB)

    1993-04-01

    Volume two contains the following appendices: Description of soil sampling sites; sampling narrative; raw data soil background; background data analysis; sitewide background soil sampling plan; and use of soil background data for the detection of contamination at waste management unit on the Hanford Site.

  12. iBeetle-Base: a database for RNAi phenotypes in the red flour beetle Tribolium castaneum.

    Science.gov (United States)

    Dönitz, Jürgen; Schmitt-Engel, Christian; Grossmann, Daniela; Gerischer, Lizzy; Tech, Maike; Schoppmeier, Michael; Klingler, Martin; Bucher, Gregor

    2015-01-01

    The iBeetle-Base (http://ibeetle-base.uni-goettingen.de) makes available annotations of RNAi phenotypes, which were gathered in a large scale RNAi screen in the red flour beetle Tribolium castaneum (iBeetle screen). In addition, it provides access to sequence information and links for all Tribolium castaneum genes. The iBeetle-Base contains the annotations of phenotypes of several thousands of genes knocked down during embryonic and metamorphic epidermis and muscle development in addition to phenotypes linked to oogenesis and stink gland biology. The phenotypes are described according to the EQM (entity, quality, modifier) system using controlled vocabularies and the Tribolium morphological ontology (TrOn). Furthermore, images linked to the respective annotations are provided. The data are searchable either for specific phenotypes using a complex 'search for morphological defects' or a 'quick search' for gene names and IDs. The red flour beetle Tribolium castaneum has become an important model system for insect functional genetics and is a representative of the most species rich taxon, the Coleoptera, which comprise several devastating pests. It is used for studying insect typical development, the evolution of development and for research on metabolism and pest control. Besides Drosophila, Tribolium is the first insect model organism where large scale unbiased screens have been performed. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  13. Background based Gaussian mixture model lesion segmentation in PET

    Energy Technology Data Exchange (ETDEWEB)

    Soffientini, Chiara Dolores, E-mail: chiaradolores.soffientini@polimi.it; Baselli, Giuseppe [DEIB, Department of Electronics, Information, and Bioengineering, Politecnico di Milano, Piazza Leonardo da Vinci 32, Milan 20133 (Italy); De Bernardi, Elisabetta [Department of Medicine and Surgery, Tecnomed Foundation, University of Milano—Bicocca, Monza 20900 (Italy); Zito, Felicia; Castellani, Massimo [Nuclear Medicine Department, Fondazione IRCCS Ca’ Granda Ospedale Maggiore Policlinico, via Francesco Sforza 35, Milan 20122 (Italy)

    2016-05-15

    Purpose: Quantitative {sup 18}F-fluorodeoxyglucose positron emission tomography is limited by the uncertainty in lesion delineation due to poor SNR, low resolution, and partial volume effects, subsequently impacting oncological assessment, treatment planning, and follow-up. The present work develops and validates a segmentation algorithm based on statistical clustering. The introduction of constraints based on background features and contiguity priors is expected to improve robustness vs clinical image characteristics such as lesion dimension, noise, and contrast level. Methods: An eight-class Gaussian mixture model (GMM) clustering algorithm was modified by constraining the mean and variance parameters of four background classes according to the previous analysis of a lesion-free background volume of interest (background modeling). Hence, expectation maximization operated only on the four classes dedicated to lesion detection. To favor the segmentation of connected objects, a further variant was introduced by inserting priors relevant to the classification of neighbors. The algorithm was applied to simulated datasets and acquired phantom data. Feasibility and robustness toward initialization were assessed on a clinical dataset manually contoured by two expert clinicians. Comparisons were performed with respect to a standard eight-class GMM algorithm and to four different state-of-the-art methods in terms of volume error (VE), Dice index, classification error (CE), and Hausdorff distance (HD). Results: The proposed GMM segmentation with background modeling outperformed standard GMM and all the other tested methods. Medians of accuracy indexes were VE <3%, Dice >0.88, CE <0.25, and HD <1.2 in simulations; VE <23%, Dice >0.74, CE <0.43, and HD <1.77 in phantom data. Robustness toward image statistic changes (±15%) was shown by the low index changes: <26% for VE, <17% for Dice, and <15% for CE. Finally, robustness toward the user-dependent volume initialization was

  14. Age is associated with asthma phenotypes.

    Science.gov (United States)

    Ponte, Eduardo V; Lima, Aline; Almeida, Paula C A; de Jesus, Juliana P V; Lima, Valmar B; Scichilone, Nicola; Souza-Machado, Adelmir; Cruz, Álvaro A

    2017-11-01

    The relationship between age and asthma phenotypes is important as population is ageing, asthma is becoming common in older ages and recently developed treatments for asthma are guided by phenotypes. The aim of this study is to evaluate whether age is associated with specific asthma phenotypes. This is a cross-sectional study. We included subjects with asthma of varied degrees of severity. Subjects underwent spirometry, skin prick test to aeroallergens, answered the Asthma Control Questionnaire and had blood samples collected. We performed binary logistic regression analysis to evaluate whether age is associated with asthma phenotypes. We enrolled 868 subjects. In comparison with subjects ≤ 40 years, older subjects had high odds of irreversible airway obstruction (from 41 to 64 years, OR: 1.83 (95% CI: 1.32-2.54); ≥65 years, OR: 3.45 (2.12-5.60)) and severe asthma phenotypes (from 41 to 64 years, OR: 3.23 (2.26-4.62); ≥65 years, OR: 4.55 (2.39-8.67)). Older subjects had low odds of atopic (from 41 to 64 years, OR: 0.56 (0.39-0.79); ≥65 years, OR: 0.47 (0.27-0.84)) and eosinophilic phenotypes (from 41 to 64 years, OR: 0.63 (0.46-0.84); ≥65 years, OR: 0.39 (0.24-0.64)). Older subjects with asthma have low odds of atopic and eosinophilic phenotypes, whereas they present high odds of irreversible airway obstruction and severe asthma. © 2017 Asian Pacific Society of Respirology.

  15. Genotypic and Phenotypic Analysis of Fasciola Isolates

    Directory of Open Access Journals (Sweden)

    SN Mosavinasab

    2009-07-01

    Full Text Available "nBackground: To identify the fasciolid species by morphometric and molecular methods in Zanjan, north­west of Iran. "nMethods: Adult Fasciola worms (n=584 were obtained from cattle and sheep in Zanjan slaughterhouse in 2007. Living flukes were washed, then worms' images were taken by 3CCD camera and finally apical zone of each worm was obtained. Morphometric values such as body length, body width, body area, body pe­rimeter and the distance between ventral sucker and posterior end of body were obtained using Auto­CAD image analysis software. Total gDNA was extracted from individual flukes by modified phenol-chloroform method. PCR amplification of ITS2 fragment was performed the isolated DNA samples and the amplicons were consequently subjected to RFLP assay and nucleotide sequencing to distinguish be­tween fasciolid species. "nResults: Mean of morphometric values in flukes from sheep was greater than those of cattle. Accordingly, the identified species included 31% F. hepatica-like, 7% F. gigantica-like and 62% intermediate forms. How­ever, ITS2 fragment of 535 amplified specimens, showed no variation at the species-specific nucleo­tide sites 230, 340 and 341. The amplified fragment composed of partial 5.8S sequence (62bp, the com­plete ITS2 sequence (361bp and partial 28S sequence (34bp. The nucleotide contents of ITS2 region were 69 A, 116 T, 81 C and 95 G and the average G+C content was approximately 49%. Comparing of ITS2 sequences with the BLAST GenBank database, also confirmed that all specimens were F. hepatica. "nConclusion: A simple and rapid PCR-RFLP assay can be used for distinguishing between these species.

  16. Phenotypic and functional markers for 1alpha,25-dihydroxyvitamin D(3)-modified regulatory dendritic cells

    DEFF Research Database (Denmark)

    Pedersen, A W; Holmstrøm, K; Jensen, S S

    2009-01-01

    The clinical use of dendritic cells (DCs) to induce antigen-specific immune tolerance has been hampered by the lack of a widely acknowledged method for generating human regulatory DCs but even more so by the non-existence of reliable markers. Thus, we set out to find reliable markers that can...... CD14 and reduced CD1a on the cell surface. These VD3-treated DCs exert a long-lasting inefficient T cell stimulation and induce T cell hyporesponsiveness with regulatory potential. Importantly, such VD3-treated DCs were readily distinguishable from untreated DCs by low levels of interleukin-23...

  17. 41 CFR 128-1.8001 - Background.

    Science.gov (United States)

    2010-07-01

    ... 41 Public Contracts and Property Management 3 2010-07-01 2010-07-01 false Background. 128-1.8001 Section 128-1.8001 Public Contracts and Property Management Federal Property Management Regulations System (Continued) DEPARTMENT OF JUSTICE 1-INTRODUCTION 1.80-Seismic Safety Program § 128-1.8001 Background. The...

  18. Introduction to the background field method

    International Nuclear Information System (INIS)

    Abbott, L.F.; Brandeis Univ., Waltham, MA

    1982-01-01

    The background field approach to calculations in gauge field theories is presented. Conventional functional techniques are reviewed and the background field method is introduced. Feynman rules and renormalization are discussed and, as an example, the Yang-Mills β function is computed. (author)

  19. 12 CFR 408.1 - Background.

    Science.gov (United States)

    2010-01-01

    ... 12 Banks and Banking 4 2010-01-01 2010-01-01 false Background. 408.1 Section 408.1 Banks and Banking EXPORT-IMPORT BANK OF THE UNITED STATES PROCEDURES FOR COMPLIANCE WITH THE NATIONAL ENVIRONMENTAL POLICY ACT General § 408.1 Background. (a) The National Environmental Policy Act (NEPA) of 1969 (42 U.S.C...

  20. Observing a Gravitational Wave Background With Lisa

    National Research Council Canada - National Science Library

    Tinto, M; Armstrong, J; Estabrook, F

    2000-01-01

    .... Comparison of the conventional Michelson interferometer observable with the fully-symmetric Sagnac data-type allows unambiguous discrimination between a gravitational wave background and instrumental noise. The method presented here can be used to detect a confusion-limited gravitational wave background.

  1. 28 CFR 23.2 - Background.

    Science.gov (United States)

    2010-07-01

    ... 28 Judicial Administration 1 2010-07-01 2010-07-01 false Background. 23.2 Section 23.2 Judicial Administration DEPARTMENT OF JUSTICE CRIMINAL INTELLIGENCE SYSTEMS OPERATING POLICIES § 23.2 Background. It is... potential threats to the privacy of individuals to whom such data relates, policy guidelines for Federally...

  2. 16 CFR 1404.2 - Background.

    Science.gov (United States)

    2010-01-01

    ... 16 Commercial Practices 2 2010-01-01 2010-01-01 false Background. 1404.2 Section 1404.2 Commercial Practices CONSUMER PRODUCT SAFETY COMMISSION CONSUMER PRODUCT SAFETY ACT REGULATIONS CELLULOSE INSULATION § 1404.2 Background. Based on available fire incident information, engineering analysis of the probable...

  3. Modeling Lost-Particle Accelerator Backgrounds in PEP-II Using LPTURTLE

    CERN Document Server

    Fieguth, Theodore; Kozanecki, Witold

    2005-01-01

    Background studies during the design, construction, commissioning, operation and improvement of BaBar and PEP-II have been greatly influenced by results from a program referred to as LPTURTLE (Lost Particle TURTLE a modified version of Decay TURTLE) which was originally conceived for the purpose of studying gas background for SLC. This venerable program is still in use today. We describe its use, capabilities and improvements and refer to current results now being applied to BaBar.

  4. Luminosity distance for Born-Infeld electromagnetic waves propagating in a cosmological magnetic background

    Energy Technology Data Exchange (ETDEWEB)

    Aiello, Matias; Bengochea, Gabriel R; Ferraro, Rafael, E-mail: aiello@iafe.uba.ar, E-mail: gabriel@iafe.uba.ar, E-mail: ferraro@iafe.uba.ar [Instituto de Astronomia y Fisica del Espacio, Casilla de Correo 67, Sucursal 28, 1428 Buenos Aires (Argentina); Departamento de Fisica, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pabellon I, 1428 Buenos Aires (Argentina)

    2008-06-15

    Born-Infeld electromagnetic waves interacting with a static magnetic background in an expanding universe are studied. The non-linear character of Born-Infeld electrodynamics modifies the relation between the energy flux and the distance to the source, which gains a new dependence on the redshift that is governed by the background field. We compute the luminosity distance as a function of the redshift and compare with Maxwellian curves for supernovae type Ia.

  5. IL6R Variation Asp358Ala Is a Potential Modifier of Lung Function in Asthma

    Science.gov (United States)

    Hawkins, Gregory A; Robinson, Mac B; Hastie, Annette T; Li, Xingnan; Li, Huashi; Moore, Wendy C; Howard, Timothy D; Busse, William W.; Erzurum, Serpil C.; Wenzel, Sally E.; Peters, Stephen P; Meyers, Deborah A; Bleecker, Eugene R

    2012-01-01

    Background The IL6R SNP rs4129267 has recently been identified as an asthma susceptibility locus in subjects of European ancestry but has not been characterized with respect to asthma severity. The SNP rs4129267 is in linkage disequilibrium (r2=1) with the IL6R coding SNP rs2228145 (Asp358Ala). This IL6R coding change increases IL6 receptor shedding and promotes IL6 transsignaling. Objectives To evaluate the IL6R SNP rs2228145 with respect to asthma severity phenotypes. Methods The IL6R SNP rs2228145 was evaluated in subjects of European ancestry with asthma from the Severe Asthma Research Program (SARP). Lung function associations were replicated in the Collaborative Study on the Genetics of Asthma (CSGA) cohort. Serum soluble IL6 receptor (sIL6R) levels were measured in subjects from SARP. Immunohistochemistry was used to qualitatively evaluate IL6R protein expression in BAL cells and endobronchial biopsies. Results The minor C allele of IL6R SNP rs2228145 was associated with lower ppFEV1 in the SARP cohort (p=0.005), the CSGA cohort (0.008), and in combined cohort analysis (p=0.003). Additional associations with ppFVC, FEV1/FVC, and PC20 were observed. The rs2228145 C allele (Ala358) was more frequent in severe asthma phenotypic clusters. Elevated serum sIL6R was associated with lower ppFEV1 (p=0.02) and lower ppFVC (p=0.008) (N=146). IL6R protein expression was observed in BAL macrophages, airway epithelium, vascular endothelium, and airway smooth muscle. Conclusions The IL6R coding SNP rs2228145 (Asp358Ala) is a potential modifier of lung function in asthma and may identify subjects at risk for more severe asthma. IL6 transsignaling may have a pathogenic role in the lung. PMID:22554704

  6. Modified Faraday cup

    Science.gov (United States)

    Elmer, John W.; Teruya, Alan T.; O'Brien, Dennis W.

    1996-01-01

    A tomographic technique for measuring the current density distribution in electron beams using electron beam profile data acquired from a modified Faraday cup to create an image of the current density in high and low power beams. The modified Faraday cup includes a narrow slit and is rotated by a stepper motor and can be moved in the x, y and z directions. The beam is swept across the slit perpendicular thereto and controlled by deflection coils, and the slit rotated such that waveforms are taken every few degrees form 0.degree. to 360.degree. and the waveforms are recorded by a digitizing storage oscilloscope. Two-din-tensional and three-dimensional images of the current density distribution in the beam can be reconstructed by computer tomography from this information, providing quantitative information about the beam focus and alignment.

  7. Beam-gas Background Observations at LHC

    CERN Document Server

    AUTHOR|(INSPIRE)INSPIRE-00214737; The ATLAS collaboration; Alici, Andrea; Lazic, Dragoslav-Laza; Alemany Fernandez, Reyes; Alessio, Federico; Bregliozzi, Giuseppe; Burkhardt, Helmut; Corti, Gloria; Guthoff, Moritz; Manousos, Athanasios; Sjoebaek, Kyrre; D'Auria, Saverio

    2017-01-01

    Observations of beam-induced background at LHC during 2015 and 2016 are presented in this paper. The four LHC experiments use the non-colliding bunches present in the physics-filling pattern of the accelerator to trigger on beam-gas interactions. During luminosity production the LHC experiments record the beam-gas interactions using dedicated background monitors. These data are sent to the LHC control system and are used to monitor the background levels at the experiments during accelerator operation. This is a very important measurement, since poor beam-induced background conditions can seriously affect the performance of the detectors. A summary of the evolution of the background levels during 2015 and 2016 is given in these proceedings.

  8. Tip-modified Propellers

    DEFF Research Database (Denmark)

    Andersen, Poul

    1999-01-01

    The paper deals with tip-modified propellers and the methods which, over a period of two decades, have been applied to develop such propellers. The development is driven by the urge to increase the efficiency of propellers and can be seen as analogous to fitting end plates and winglets to aircraft...... propeller, have efficiency increases of a reasonable magnitude in both open-water and behind-ship conditions....

  9. PENGARUH BACKGROUND MAHASISWA TERHADAP KINERJA AKADEMIK

    Directory of Open Access Journals (Sweden)

    Trianasari Angkawijaya

    2014-09-01

    Full Text Available Abstract: The Effect of Students’ Background on Academic Performance. This study examines the effect of background variables on the academic performance of accounting students in a private university in Surabaya. The background variables under study included previous academic performance, prior knowledge on accounting, sex, motivation, preparedness, and expectations. The results show that previous academic performance, motivation, and expectations have positive and significant effects on the students’ overall academic performance in accounting, while preparedness affects only the students’ performance in management accounting. In contrast, prior knowledge on accounting and sex do not give significant impacts to the students’ overall academic performance.These findings indicate the importance of previous aca­demic performance as well as motivation and expectations as background variables in current academic performance. Keywords: students’ background, academic performance, accounting Abstrak: Pengaruh Background Mahasiswa terhadap Kinerja Akademik. Penelitian ini mengkaji pengaruh variabel background terhadap kinerja akademik mahasiswa akuntansi di Universitas Surabaya. Lima variabel background utama dipergunakan, yaitu kinerja akademik sebelumnya, pengetahuan akun­tansi sebelumnya, jenis kelamin, motivasi, kesiapan, dan ekspektasi. Hipotesis diuji menggunakan model regresi linier berganda OLS dan Robust Standar Error. Hasil penelitian memerlihatkan bahwa kinerja akademik sebelumnya, motivasi, dan ekspektasi memiliki pengaruh positif signifikan terhadap kinerja akademik keseluruhan, sementara kesiapan memberikan pengaruh positif hanya pada kinerja akademik akuntansi manajemen. Sebaliknya, pengetahuan akuntansi sebelumnya dan jenis kelamin tidak memberi­kan pengaruh signifikan terhadap kinerja akademik keseluruhan. Temuan ini mengindikasikan bahwa kinerja akademik sebelumnya beserta motivasi dan ekspektasi adalah variabel background

  10. Modified Firefly Algorithm

    Directory of Open Access Journals (Sweden)

    Surafel Luleseged Tilahun

    2012-01-01

    Full Text Available Firefly algorithm is one of the new metaheuristic algorithms for optimization problems. The algorithm is inspired by the flashing behavior of fireflies. In the algorithm, randomly generated solutions will be considered as fireflies, and brightness is assigned depending on their performance on the objective function. One of the rules used to construct the algorithm is, a firefly will be attracted to a brighter firefly, and if there is no brighter firefly, it will move randomly. In this paper we modify this random movement of the brighter firefly by generating random directions in order to determine the best direction in which the brightness increases. If such a direction is not generated, it will remain in its current position. Furthermore the assignment of attractiveness is modified in such a way that the effect of the objective function is magnified. From the simulation result it is shown that the modified firefly algorithm performs better than the standard one in finding the best solution with smaller CPU time.

  11. Genetically Modified Organisms

    Directory of Open Access Journals (Sweden)

    Claro Llaguno

    2001-06-01

    Full Text Available Recent reports have brought to public attention concerns about Bt corn and genetically modified organisms (GMO in general. The timing, it seems, is most appropriate considering two related developments early this year: the final approval of the Cartagena Protocol on Biosafety in Montreal on January 29, 2001, and the OECD Edinburgh Conference on GM food safety last February 28- March 1, 2001. The protocol makes clear that GMOs include all living modified organisms (LMO defined as "any living organism that possesses a novel combination of genetic material obtained through the use of modern biotechnology". This includes seeds, live fish, and other organisms intentionally obtained for release to the environment. It would seem that the common understanding about GMOs as referring to farm-to-table products is perforce expanded to embrace genetically modified farm animals and aquatic resources. Being a trade agreement, the Montreal accord primarily deals with the safety issues related to the transboundary movement of LMOs around the globe. The OECD conference on the other hand, called for an international body "to address all sides of the GM debate" in response to the public outcry, particularly in Western Europe, regarding the risks the new products pose to human health and the environment. Some points of contention, which remain unresolved, include issues such as whether countries should be allowed to develop their own GM food based on their needs, and whether a global moratorium on GMOs and mandatory labeling should be enforced worldwide.

  12. GABA(A)-benzodiazepine receptor complex sensitivity in 5-HT(1A) receptor knockout mice on a 129/Sv background.

    NARCIS (Netherlands)

    Pattij, T.; Groenink, L.; Oosting, R.S.; Gugten, J. van der; Maes, R.A.A.; Olivier, B.

    2002-01-01

    Previous studies in 5-HT(1A) receptor knockout (1AKO) mice on a mixed Swiss Websterx129/Sv (SWx129/Sv) and a pure 129/Sv genetic background suggest a differential gamma-aminobutyric acid (GABA(A))-benzodiazepine receptor complex sensitivity in both strains, independent from the anxious phenotype. To

  13. Overeating phenotypes in overweight and obese children.

    Science.gov (United States)

    Boutelle, Kerri N; Peterson, Carol B; Crosby, Ross D; Rydell, Sarah A; Zucker, Nancy; Harnack, Lisa

    2014-05-01

    The purpose of this study was to identify overeating phenotypes and their correlates in overweight and obese children. One hundred and seventeen treatment-seeking overweight and obese 8-12year-old children and their parents completed the study. Children completed an eating in the absence of hunger (EAH) paradigm, the Eating Disorder Examination interview, and measurements of height and weight. Parents and children completed questionnaires that evaluated satiety responsiveness, food responsiveness, negative affect eating, external eating and eating in the absence of hunger. Latent profile analysis was used to identify heterogeneity in overeating phenotypes in the child participants. Latent classes were then compared on measures of demographics, obesity status and nutritional intake. Three latent classes of overweight and obese children were identified: High Satiety Responsive, High Food Responsive, and Moderate Satiety and Food Responsive. Results indicated that the High Food Responsive group had higher BMI and BMI-Z scores compared to the High Satiety Responsive group. No differences were found among classes in demographics or nutritional intake. This study identified three overeating phenotypes, supporting the heterogeneity of eating patterns associated with overweight and obesity in treatment-seeking children. These finding suggest that these phenotypes can potentially be used to identify high risk groups, inform prevention and intervention targets, and develop specific treatments for these behavioral phenotypes. Copyright © 2014. Published by Elsevier Ltd.

  14. Advanced phenotyping offers opportunities for improved breeding of forage and turf species

    DEFF Research Database (Denmark)

    Walter, Achim; Studer, Bruno; Kölliker, Roland

    2012-01-01

    Background and Aims Advanced phenotyping, i.e. the application of automated, high-throughput methods to characterize plant architecture and performance, has the potential to accelerate breeding progress but is far from being routinely used in current breeding approaches. In forage and turf...... improvement programmes, in particular, where breeding populations and cultivars are characterized by high genetic diversity and substantial genotype × environment interactions, precise and efficient phenotyping is essential to meet future challenges imposed by climate change, growing demand and declining...... resources. Scope This review highlights recent achievements in the establishment of phenotyping tools and platforms. Some of these tools have originally been established in remote sensing, some in precision agriculture, while others are laboratory-based imaging procedures. They quantify plant colour...

  15. DeepPVP: phenotype-based prioritization of causative variants using deep learning

    KAUST Repository

    Boudellioua, Imene

    2018-05-02

    Background: Prioritization of variants in personal genomic data is a major challenge. Recently, computational methods that rely on comparing phenotype similarity have shown to be useful to identify causative variants. In these methods, pathogenicity prediction is combined with a semantic similarity measure to prioritize not only variants that are likely to be dysfunctional but those that are likely involved in the pathogenesis of a patient\\'s phenotype. Results: We have developed DeepPVP, a variant prioritization method that combined automated inference with deep neural networks to identify the likely causative variants in whole exome or whole genome sequence data. We demonstrate that DeepPVP performs significantly better than existing methods, including phenotype-based methods that use similar features. DeepPVP is freely available at https://github.com/bio-ontology-research-group/phenomenet-vp Conclusions: DeepPVP further improves on existing variant prioritization methods both in terms of speed as well as accuracy.

  16. Familial adenomatous polyposis patients without an identified APC germline mutation have a severe phenotype

    DEFF Research Database (Denmark)

    Bisgaard, M L; Ripa, R; Knudsen, Anne Louise

    2004-01-01

    BACKGROUND: Development of more than 100 colorectal adenomas is diagnostic of the dominantly inherited autosomal disease familial adenomatous polyposis (FAP). Germline mutations can be identified in the adenomatous polyposis coli (APC) gene in approximately 80% of patients. The APC protein...... comprises several regions and domains for interaction with other proteins, and specific clinical manifestations are associated with the mutation assignment to one of these regions or domains. AIMS: The phenotype in patients without an identified causative APC mutation was compared with the phenotype...... in patients with a known APC mutation and with the phenotypes characteristic of patients with mutations in specific APC regions and domains. PATIENTS: Data on 121 FAP probands and 149 call up patients from 70 different families were extracted from the Danish Polyposis register. METHODS: Differences in 16...

  17. Experimental evolution and the dynamics of genomic mutation rate modifiers.

    Science.gov (United States)

    Raynes, Y; Sniegowski, P D

    2014-11-01

    Because genes that affect mutation rates are themselves subject to mutation, mutation rates can be influenced by natural selection and other evolutionary forces. The population genetics of mutation rate modifier alleles has been a subject of theoretical interest for many decades. Here, we review experimental contributions to our understanding of mutation rate modifier dynamics. Numerous evolution experiments have shown that mutator alleles (modifiers that elevate the genomic mutation rate) can readily rise to high frequencies via genetic hitchhiking in non-recombining microbial populations. Whereas these results certainly provide an explanatory framework for observations of sporadically high mutation rates in pathogenic microbes and in cancer lineages, it is nonetheless true that most natural populations have very low mutation rates. This raises the interesting question of how mutator hitchhiking is suppressed or its phenotypic effect reversed in natural populations. Very little experimental work has addressed this question; with this in mind, we identify some promising areas for future experimental investigation.

  18. Pathophysiology-based phenotyping in type 2 diabetes

    DEFF Research Database (Denmark)

    Stidsen, Jacob V; Henriksen, Jan E; Olsen, Michael H

    2018-01-01

    clinically diagnosed type 2 diabetes. METHODS: We first identified all patients with rare subtypes of diabetes, latent autoimmune diabetes of adults (LADA), secondary diabetes, or glucocorticoid-associated diabetes. We then used the homeostatic assessment model to subphenotype all remaining patients......BACKGROUND: Type 2 diabetes may be a more heterogeneous disease than previously thought. Better understanding of pathophysiological subphenotypes could lead to more individualized diabetes treatment. We examined the characteristics of different phenotypes among 5813 Danish patients with new...... into insulinopenic (high insulin sensitivity and low beta cell function), classical (low insulin sensitivity and low beta cell function), or hyperinsulinemic (low insulin sensitivity and high beta cell function) type 2 diabetes. RESULTS: Among 5813 patients diagnosed with incident type 2 diabetes in the community...

  19. Bone phenotypes of P2 receptor knockout mice

    DEFF Research Database (Denmark)

    Orriss, Isabel; Syberg, Susanne; Wang, Ning

    2011-01-01

    The action of extracellular nucleotides is mediated by ionotropic P2X receptors and G-protein coupled P2Y receptors. The human genome contains 7 P2X and 8 P2Y receptor genes. Knockout mice strains are available for most of them. As their phenotypic analysis is progressing, bone abnormalities have...... been observed in an impressive number of these mice: distinct abnormalities in P2X7-/- mice, depending on the gene targeting construct and the genetic background, decreased bone mass in P2Y1-/- mice, increased bone mass in P2Y2-/- mice, decreased bone resorption in P2Y6-/- mice, decreased bone...... formation and bone resorption in P2Y13-/- mice. These findings demonstrate the unexpected importance of extracellular nucleotide signalling in the regulation of bone metabolism via multiple P2 receptors and distinct mechanisms involving both osteoblasts and osteoclasts....

  20. Dyslipidemias and Cardiovascular Prevention: Tailoring Treatment According to Lipid Phenotype.

    Science.gov (United States)

    Sanin, Veronika; Pfetsch, Vanessa; Koenig, Wolfgang

    2017-07-01

    This study aimed to present the current information on the genetic background of dyslipidemias and provide insights into the complex pathophysiological role of several plasma lipids/lipoproteins in the pathogenesis of atherosclerotic cardiovascular disease. Furthermore, we aim to summarize established therapies and describe the scientific rationale for the development of novel therapeutic strategies. Evidence from genetic studies suggests that besides lowering low-density lipoprotein cholesterol, pharmacological reduction of triglyceride-rich lipoproteins, or lipoprotein(a) will reduce risk for coronary heart disease. Dyslipidemia, in particular hypercholesterolemia, is a common clinical condition and represents an important determinant of atherosclerotic vascular disease. Treatment decisions are currently guided by the causative lipid phenotype and the presence of other risk factors suggesting a very high cardiovascular risk. Therefore, the identification of lipid disorders and the optimal combination of therapeutic strategies provide an outstanding opportunity for reducing the onset and burden of cardiovascular disease.

  1. String pair production in non homogeneous backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Bolognesi, S. [Department of Physics “E. Fermi” University of Pisa, and INFN - Sezione di Pisa,Largo Pontecorvo, 3, Ed. C, 56127 Pisa (Italy); Rabinovici, E. [Racah Institute of Physics, The Hebrew University of Jerusalem,91904 Jerusalem (Israel); Tallarita, G. [Departamento de Ciencias, Facultad de Artes Liberales,Universidad Adolfo Ibáñez, Santiago 7941169 (Chile)

    2016-04-28

    We consider string pair production in non homogeneous electric backgrounds. We study several particular configurations which can be addressed with the Euclidean world-sheet instanton technique, the analogue of the world-line instanton for particles. In the first case the string is suspended between two D-branes in flat space-time, in the second case the string lives in AdS and terminates on one D-brane (this realizes the holographic Schwinger effect). In some regions of parameter space the result is well approximated by the known analytical formulas, either the particle pair production in non-homogeneous background or the string pair production in homogeneous background. In other cases we see effects which are intrinsically stringy and related to the non-homogeneity of the background. The pair production is enhanced already for particles in time dependent electric field backgrounds. The string nature enhances this even further. For spacial varying electrical background fields the string pair production is less suppressed than the rate of particle pair production. We discuss in some detail how the critical field is affected by the non-homogeneity, for both time and space dependent electric field backgrouds. We also comment on what could be an interesting new prediction for the small field limit. The third case we consider is pair production in holographic confining backgrounds with homogeneous and non-homogeneous fields.

  2. String pair production in non homogeneous backgrounds

    International Nuclear Information System (INIS)

    Bolognesi, S.; Rabinovici, E.; Tallarita, G.

    2016-01-01

    We consider string pair production in non homogeneous electric backgrounds. We study several particular configurations which can be addressed with the Euclidean world-sheet instanton technique, the analogue of the world-line instanton for particles. In the first case the string is suspended between two D-branes in flat space-time, in the second case the string lives in AdS and terminates on one D-brane (this realizes the holographic Schwinger effect). In some regions of parameter space the result is well approximated by the known analytical formulas, either the particle pair production in non-homogeneous background or the string pair production in homogeneous background. In other cases we see effects which are intrinsically stringy and related to the non-homogeneity of the background. The pair production is enhanced already for particles in time dependent electric field backgrounds. The string nature enhances this even further. For spacial varying electrical background fields the string pair production is less suppressed than the rate of particle pair production. We discuss in some detail how the critical field is affected by the non-homogeneity, for both time and space dependent electric field backgrouds. We also comment on what could be an interesting new prediction for the small field limit. The third case we consider is pair production in holographic confining backgrounds with homogeneous and non-homogeneous fields.

  3. Slavnov-Taylor constraints for nontrivial backgrounds

    International Nuclear Information System (INIS)

    Binosi, D.; Quadri, A.

    2011-01-01

    We devise an algebraic procedure for the evaluation of Green's functions in SU(N) Yang-Mills theory in the presence of a nontrivial background field. In the ghost-free sector the dependence of the vertex functional on the background is shown to be uniquely determined by the Slavnov-Taylor identities in terms of a certain 1-PI correlator of the covariant derivatives of the ghost and the antighost fields. At nonvanishing background this amplitude is shown to encode the quantum deformations to the tree-level background-quantum splitting. The approach only relies on the functional identities of the model (Slavnov-Taylor identities, b-equation, antighost equation) and thus it is valid beyond perturbation theory, and, in particular, in a lattice implementation of the background field method. As an example of the formalism we analyze the ghost two-point function and the Kugo-Ojima function in an instanton background in SU(2) Yang-Mills theory, quantized in the background Landau gauge.

  4. Sources of the Radio Background Considered

    Energy Technology Data Exchange (ETDEWEB)

    Singal, J.; /KIPAC, Menlo Park /Stanford U.; Stawarz, L.; /KIPAC, Menlo Park /Stanford U. /Jagiellonian U., Astron. Observ.; Lawrence, A.; /Edinburgh U., Inst. Astron. /KIPAC, Menlo Park /Stanford U.; Petrosian, V.; /KIPAC, Menlo Park /Stanford U., Phys. Dept. /Stanford U., Appl. Phys. Dept.

    2011-08-22

    We investigate possible origins of the extragalactic radio background reported by the ARCADE 2 collaboration. The surface brightness of the background is several times higher than that which would result from currently observed radio sources. We consider contributions to the background from diffuse synchrotron emission from clusters and the intergalactic medium, previously unrecognized flux from low surface brightness regions of radio sources, and faint point sources below the flux limit of existing surveys. By examining radio source counts available in the literature, we conclude that most of the radio background is produced by radio point sources that dominate at sub {mu}Jy fluxes. We show that a truly diffuse background produced by elections far from galaxies is ruled out because such energetic electrons would overproduce the observed X-ray/{gamma}-ray background through inverse Compton scattering of the other photon fields. Unrecognized flux from low surface brightness regions of extended radio sources, or moderate flux sources missed entirely by radio source count surveys, cannot explain the bulk of the observed background, but may contribute as much as 10%. We consider both radio supernovae and radio quiet quasars as candidate sources for the background, and show that both fail to produce it at the observed level because of insufficient number of objects and total flux, although radio quiet quasars contribute at the level of at least a few percent. We conclude that the most important population for production of the background is likely ordinary starforming galaxies above redshift 1 characterized by an evolving radio far-infrared correlation, which increases toward the radio loud with redshift.

  5. Extragalactic background light measurements and applications.

    Science.gov (United States)

    Cooray, Asantha

    2016-03-01

    This review covers the measurements related to the extragalactic background light intensity from γ-rays to radio in the electromagnetic spectrum over 20 decades in wavelength. The cosmic microwave background (CMB) remains the best measured spectrum with an accuracy better than 1%. The measurements related to the cosmic optical background (COB), centred at 1 μm, are impacted by the large zodiacal light associated with interplanetary dust in the inner Solar System. The best measurements of COB come from an indirect technique involving γ-ray spectra of bright blazars with an absorption feature resulting from pair-production off of COB photons. The cosmic infrared background (CIB) peaking at around 100 μm established an energetically important background with an intensity comparable to the optical background. This discovery paved the way for large aperture far-infrared and sub-millimetre observations resulting in the discovery of dusty, starbursting galaxies. Their role in galaxy formation and evolution remains an active area of research in modern-day astrophysics. The extreme UV (EUV) background remains mostly unexplored and will be a challenge to measure due to the high Galactic background and absorption of extragalactic photons by the intergalactic medium at these EUV/soft X-ray energies. We also summarize our understanding of the spatial anisotropies and angular power spectra of intensity fluctuations. We motivate a precise direct measurement of the COB between 0.1 and 5 μm using a small aperture telescope observing either from the outer Solar System, at distances of 5 AU or more, or out of the ecliptic plane. Other future applications include improving our understanding of the background at TeV energies and spectral distortions of CMB and CIB.

  6. Constraints on the evolution of phenotypic plasticity

    DEFF Research Database (Denmark)

    Murren, Courtney J; Auld, Josh R.; Callahan, Hilary S

    2015-01-01

    Phenotypic plasticity is ubiquitous and generally regarded as a key mechanism for enabling organisms to survive in the face of environmental change. Because no organism is infinitely or ideally plastic, theory suggests that there must be limits (for example, the lack of ability to produce...... an optimal trait) to the evolution of phenotypic plasticity, or that plasticity may have inherent significant costs. Yet numerous experimental studies have not detected widespread costs. Explicitly differentiating plasticity costs from phenotype costs, we re-evaluate fundamental questions of the limits...... to the evolution of plasticity and of generalists vs specialists. We advocate for the view that relaxed selection and variable selection intensities are likely more important constraints to the evolution of plasticity than the costs of plasticity. Some forms of plasticity, such as learning, may be inherently...

  7. Phenotype Development in Adolescents With Tourette Syndrome

    DEFF Research Database (Denmark)

    Groth, Camilla; Debes, Nanette Mol; Skov, Liselotte

    2017-01-01

    Tourette syndrome (TS) is a neurodevelopmental disorder characterized by frequent comorbidities and a wide spectrum of phenotype presentations. This study aimed to describe the development of phenotypes in TS and tic-related impairment in a large longitudinal study of 226 children and adolescents...... followed up after 6 years. The participants were clinically examined to assess tic severity and impairment, obsessive compulsive disorder (OCD), and attention-deficit/hyperactivity disorder (ADHD). The development in phenotypes changed toward less comorbidity with 40% TS-only (no OCD or ADHD) (TS without...... OCD or ADHD) at baseline and 55% at follow-up.Tic-related impairment was expected to improve with an age-related tic decline, but surprisingly the impairment score did not reflect the tic decline. Sex, vocal and motor tics, and OCD and ADHD severity were highly significantly correlated...

  8. Delineating the GRIN1 phenotypic spectrum

    DEFF Research Database (Denmark)

    Lemke, Johannes R; Geider, Kirsten; Helbig, Katherine L

    2016-01-01

    consequences of GRIN1 mutations were investigated in Xenopus laevis oocytes. RESULTS: We identified heterozygous de novo GRIN1 mutations in 14 individuals and reviewed the phenotypes of all 9 previously reported patients. These 23 individuals presented with a distinct phenotype of profound developmental delay......, severe intellectual disability with absent speech, muscular hypotonia, hyperkinetic movement disorder, oculogyric crises, cortical blindness, generalized cerebral atrophy, and epilepsy. Mutations cluster within transmembrane segments and result in loss of channel function of varying severity...... impairment as well as oculomotor and movement disorders being discriminating phenotypic features. Loss of NMDA receptor function appears to be the underlying disease mechanism. The identification of both heterozygous and homozygous mutations blurs the borders of dominant and recessive inheritance of GRIN1...

  9. Semi-supervised Learning for Phenotyping Tasks.

    Science.gov (United States)

    Dligach, Dmitriy; Miller, Timothy; Savova, Guergana K

    2015-01-01

    Supervised learning is the dominant approach to automatic electronic health records-based phenotyping, but it is expensive due to the cost of manual chart review. Semi-supervised learning takes advantage of both scarce labeled and plentiful unlabeled data. In this work, we study a family of semi-supervised learning algorithms based on Expectation Maximization (EM) in the context of several phenotyping tasks. We first experiment with the basic EM algorithm. When the modeling assumptions are violated, basic EM leads to inaccurate parameter estimation. Augmented EM attenuates this shortcoming by introducing a weighting factor that downweights the unlabeled data. Cross-validation does not always lead to the best setting of the weighting factor and other heuristic methods may be preferred. We show that accurate phenotyping models can be trained with only a few hundred labeled (and a large number of unlabeled) examples, potentially providing substantial savings in the amount of the required manual chart review.

  10. Do instantons like a colorful background?

    Energy Technology Data Exchange (ETDEWEB)

    Gies, H.; Pawlowski, J.M.; Wetterich, C. [Heidelberg Univ. (Germany). Inst. fuer Theoretische Physik; Jaeckel, J. [Deutsches Elektronen-Synchrotron (DESY), Hamburg (Germany)

    2006-08-15

    We investigate chiral symmetry breaking and color symmetry breaking in QCD. The effective potential of the corresponding scalar condensates is discussed in the presence of non-perturbative contributions from the semiclassical one-instanton sector. We concentrate on a color singlet scalar background which can describe chiral condensation, as well as a color cotet scalar background which can generate mass for the gluons. Whereas a non-vanishing singlet chiral field is favored by the instantons, we have found no indication for a preference of color octet backgrounds. (orig.)

  11. The investigation for potential modifier genes in patients with neurofibromatosis type 1 based on next-generation sequencing

    Directory of Open Access Journals (Sweden)

    Yang F

    2018-02-01

    , phosphoinositide-3-kinase-Akt pathway was altered in both the public plexiform neurofibroma sample and in our proband patient. Conclusion: This study reexamined the background germline mutations and suggested their potential value as modifier genes that may influence the phenotype heterogenity. Keywords: plexiform, neurofibroma type 1, mutation, modifier gene, next-generation sequencing

  12. Genotypic and phenotypic characterization of the Sdccag8Tn(sb-Tyr2161B.CA1C2Ove mouse model.

    Directory of Open Access Journals (Sweden)

    Katie Weihbrecht

    Full Text Available Nephronophthisis-related ciliopathies (NPHP-RC are a group of disorders that present with end-stage renal failure in childhood/adolescence, kidney cysts, retinal degeneration, and cerebellar hypoplasia. One disorder that shares clinical features with NPHP-RC is Bardet-Biedl Syndrome (BBS. Serologically defined colon cancer antigen 8 (SDCCAG8; also known as NPHP10 and BBS16 is an NPHP gene that is also associated with BBS. To better understand the patho-mechanisms of NPHP and BBS caused by loss of SDCCAG8 function, we characterized an SDCCAG8 mouse model (Sdccag8Tn(sb-Tyr2161B.CA1C2Ove generated by Sleeping Beauty Transposon (SBT-mediated insertion mutagenesis. Consistent with the previously reported, independent SDCCAG8 mouse models, our mutant mice display pre-axial polydactyly in their hind limbs. In addition, we report patterning defects in the secondary palate, brain abnormalities, as well as neonatal lethality associated with developmental defects in the lung in our mouse model. The neonatal lethality phenotype is genetic background dependent and rescued by introducing 129S6/SvEvTac background. Genetic modifier(s responsible for this effect were mapped to a region between SNPs rs3714172 and rs3141832 on chromosome 11. While determining the precise genetic lesion in our mouse model, we found that SBT insertion resulted in a deletion of multiple exons from both Sdccag8 and its neighboring gene Akt3. We ascribe the patterning defects in the limb and the secondary palate as well as lung abnormalities to loss of SDCCAG8, while the developmental defects in the brain are likely due to the loss of AKT3. This mouse model may be useful to study features not observed in other SDCCAG8 models but cautions are needed in interpreting data.

  13. On the microwave background spectrum and noise

    International Nuclear Information System (INIS)

    De Bernardis, P.; Masi, S.

    1982-01-01

    We show that the combined measurement of the cosmic background radiation (CBR) intensity and noise can provide direct information on the temperature and the emissivity of the source responsible for the CBR. (orig.)

  14. Quantum background independence in string theory

    International Nuclear Information System (INIS)

    Witten, E.

    1994-01-01

    Not only in physical string theories, but also in some highly simplified situations, background independence has been difficult to understand. It is argued that the ''holomorphic anomaly'' of Bershadsky, Cecotti, Ooguri and Vafa gives a fundamental explanation of some of the problems. Moreover, their anomaly equation can be interpreted in terms of a rather peculiar quantum version of background independence: in systems afflicted by the anomaly, background independence does not hold order by order in perturbation theory, but the exact partition function as a function of the coupling constants has a background independent interpretation as a state in an auxiliary quantum Hilbert space. The significance of this auxiliary space is otherwise unknown. (author). 23 refs

  15. Background-cross-section-dependent subgroup parameters

    International Nuclear Information System (INIS)

    Yamamoto, Toshihisa

    2003-01-01

    A new set of subgroup parameters was derived that can reproduce the self-shielded cross section against a wide range of background cross sections. The subgroup parameters are expressed with a rational equation which numerator and denominator are expressed as the expansion series of background cross section, so that the background cross section dependence is exactly taken into account in the parameters. The advantage of the new subgroup parameters is that they can reproduce the self-shielded effect not only by group basis but also by subgroup basis. Then an adaptive method is also proposed which uses fitting procedure to evaluate the background-cross-section-dependence of the parameters. One of the simple fitting formula was able to reproduce the self-shielded subgroup cross section by less than 1% error from the precise evaluation. (author)

  16. REQUEST FOR EXPRESSIONS OF INTEREST For Background ...

    International Development Research Centre (IDRC) Digital Library (Canada)

    sbickram

    2012-07-10

    Jul 10, 2012 ... the applicant's qualifications and ability to undertake the hot spot background study. ... any interviews, presentations and subsequent proposals, are the sole ... The program will focus on increasing the resilience of the most ...

  17. Background music: effects on attention performance.

    Science.gov (United States)

    Shih, Yi-Nuo; Huang, Rong-Hwa; Chiang, Hsin-Yu

    2012-01-01

    Previous studies indicate that noise may affect worker attention. However, some background music in the work environment can increase worker satisfaction and productivity. This study compared how music with, and without, lyrics affects human attention. One hundred and two participants, aged 20-24 years, were recruited into this study. Fifty-six males and 46 females participated in this study. Background music with, and without lyrics, was tested for effects on listener concentration in attention testing using a randomized controlled trial (RCT) study. The comparison results revealed that background music with lyrics had significant negative effects on concentration and attention. The findings suggest that, if background music is played in the work environment, music without lyrics is preferable because songs with lyrics are likely to reduce worker attention and performance.

  18. History and background of the project

    Digital Repository Service at National Institute of Oceanography (India)

    Jauhari, P.; Nair, R.R.

    The history of oceanography, the discovery of manganese nodules and the background of the developments in nodule research and mining is given The first nodules were collected in 1981 on board the research vessel R V Gaveshani Following the success...

  19. 47 CFR 215.1 - Background.

    Science.gov (United States)

    2010-10-01

    ... POINT FOR ELECTROMAGNETIC PULSE (EMP) INFORMATION § 215.1 Background. (a) The nuclear electromagnetic pulse (EMP) is part of the complex environment produced by nuclear explosions. It consists of transient...

  20. 32 CFR 770.49 - Background.

    Science.gov (United States)

    2010-07-01

    ..., Washington § 770.49 Background. (a) Puget Sound Naval Shipyard is a major naval ship repair facility, with... interruption. Additionally, most of Puget Sound Naval Shipyard is dedicated to heavy industrial activity where...

  1. Modified harmony search

    Science.gov (United States)

    Mohamed, Najihah; Lutfi Amri Ramli, Ahmad; Majid, Ahmad Abd; Piah, Abd Rahni Mt

    2017-09-01

    A metaheuristic algorithm, called Harmony Search is quite highly applied in optimizing parameters in many areas. HS is a derivative-free real parameter optimization algorithm, and draws an inspiration from the musical improvisation process of searching for a perfect state of harmony. Propose in this paper Modified Harmony Search for solving optimization problems, which employs a concept from genetic algorithm method and particle swarm optimization for generating new solution vectors that enhances the performance of HS algorithm. The performances of MHS and HS are investigated on ten benchmark optimization problems in order to make a comparison to reflect the efficiency of the MHS in terms of final accuracy, convergence speed and robustness.

  2. Modified puestow lateral pancreaticojejunostomy.

    Science.gov (United States)

    Ceppa, Eugene P; Pappas, Theodore N

    2009-05-01

    There are various surgical options for the treatment of pain associated with chronic pancreatitis. The modified Puestow lateral pancreaticojejunostomy has been proven to be effective in ameliorating symptoms and expediting return to normal lifestyle while maintaining a low rate of morbidity and mortality. However, the debate regarding which surgical treatment provides the best outcomes is controversial. The aims of this manuscript are to identify the patient population for which the Puestow benefits the most and discuss the pertinent technical aspects of the surgical procedure.

  3. Mathematical Background of Public Key Cryptography

    DEFF Research Database (Denmark)

    Frey, Gerhard; Lange, Tanja

    2005-01-01

    The two main systems used for public key cryptography are RSA and protocols based on the discrete logarithm problem in some cyclic group. We focus on the latter problem and state cryptographic protocols and mathematical background material.......The two main systems used for public key cryptography are RSA and protocols based on the discrete logarithm problem in some cyclic group. We focus on the latter problem and state cryptographic protocols and mathematical background material....

  4. A Practical Theorem on Gravitational Wave Backgrounds

    OpenAIRE

    Phinney, E. S.

    2001-01-01

    There is an extremely simple relationship between the spectrum of the gravitational wave background produced by a cosmological distribution of discrete gravitational wave sources, the total time-integrated energy spectrum of an individual source, and the present-day comoving number density of remnants. Stated in this way, the background is entirely independent of the cosmology, and only weakly dependent on the evolutionary history of the sources. This relationship allows one easily to compute...

  5. Isotherms clustering in cosmic microwave background

    International Nuclear Information System (INIS)

    Bershadskii, A.

    2006-01-01

    Isotherms clustering in cosmic microwave background (CMB) has been studied using the 3-year WMAP data on cosmic microwave background radiation. It is shown that the isotherms clustering could be produced by the baryon-photon fluid turbulence in the last scattering surface. The Taylor-microscale Reynolds number of the turbulence is estimated directly from the CMB data as Re λ ∼10 2

  6. Classification of supersymmetric backgrounds of string theory

    International Nuclear Information System (INIS)

    Gran, U.; Gutowski, J.; Papadopoulos, G.; Roest, D.

    2007-01-01

    We review the recent progress made towards the classification of supersymmetric solutions in ten and eleven dimensions with emphasis on those of IIB supergravity. In particular, the spinorial geometry method is outlined and adapted to nearly maximally supersymmetric backgrounds. We then demonstrate its effectiveness by classifying the maximally supersymmetric IIB G-backgrounds and by showing that N=31 IIB solutions do not exist. (Abstract Copyright [2007], Wiley Periodicals, Inc.)

  7. Superstring gravitational wave backgrounds with spacetime supersymmetry

    CERN Document Server

    Kiritsis, Elias B; Lüst, Dieter; Kiritsis, E; Kounnas, C; Lüst, D

    1994-01-01

    We analyse the stringy gravitational wave background based on the current algebra E.sup(c).sub(2). We determine its exact spectrum and construct the modular invariant vacuum energy. The corresponding N=1 extension is also constructed. The algebra is again mapped to free bosons and fermions and we show that this background has N=4 (N=2) unbroken spacetime supersymmetry in the type II (heterotic case).

  8. Background dose subtraction in personnel dosimetry

    International Nuclear Information System (INIS)

    Picazo, T.; Llorca, N.; Alabau, J.

    1997-01-01

    In this paper it is proposed to consider the mode of the frequency distribution of the low dose dosemeters from each clinic that uses X rays as the background environmental dose that should be subtracted from the personnel dosimetry to evaluate the doses due to practice. The problems and advantages of this indirect method to estimate the environmental background dose are discussed. The results for 60 towns are presented. (author)

  9. Moving object detection using background subtraction

    CERN Document Server

    Shaikh, Soharab Hossain; Chaki, Nabendu

    2014-01-01

    This Springer Brief presents a comprehensive survey of the existing methodologies of background subtraction methods. It presents a framework for quantitative performance evaluation of different approaches and summarizes the public databases available for research purposes. This well-known methodology has applications in moving object detection from video captured with a stationery camera, separating foreground and background objects and object classification and recognition. The authors identify common challenges faced by researchers including gradual or sudden illumination change, dynamic bac

  10. Phenotype Clustering of Breast Epithelial Cells in Confocal Imagesbased on Nuclear Protein Distribution Analysis

    Energy Technology Data Exchange (ETDEWEB)

    Long, Fuhui; Peng, Hanchuan; Sudar, Damir; Levievre, Sophie A.; Knowles, David W.

    2006-09-05

    Background: The distribution of the chromatin-associatedproteins plays a key role in directing nuclear function. Previously, wedeveloped an image-based method to quantify the nuclear distributions ofproteins and showed that these distributions depended on the phenotype ofhuman mammary epithelial cells. Here we describe a method that creates ahierarchical tree of the given cell phenotypes and calculates thestatistical significance between them, based on the clustering analysisof nuclear protein distributions. Results: Nuclear distributions ofnuclear mitotic apparatus protein were previously obtained fornon-neoplastic S1 and malignant T4-2 human mammary epithelial cellscultured for up to 12 days. Cell phenotype was defined as S1 or T4-2 andthe number of days in cultured. A probabilistic ensemble approach wasused to define a set of consensus clusters from the results of multipletraditional cluster analysis techniques applied to the nucleardistribution data. Cluster histograms were constructed to show how cellsin any one phenotype were distributed across the consensus clusters.Grouping various phenotypes allowed us to build phenotype trees andcalculate the statistical difference between each group. The resultsshowed that non-neoplastic S1 cells could be distinguished from malignantT4-2 cells with 94.19 percent accuracy; that proliferating S1 cells couldbe distinguished from differentiated S1 cells with 92.86 percentaccuracy; and showed no significant difference between the variousphenotypes of T4-2 cells corresponding to increasing tumor sizes.Conclusion: This work presents a cluster analysis method that canidentify significant cell phenotypes, based on the nuclear distributionof specific proteins, with high accuracy.

  11. Aircraft and background noise annoyance effects

    Science.gov (United States)

    Willshire, K. F.

    1984-01-01

    To investigate annoyance of multiple noise sources, two experiments were conducted. The first experiment, which used 48 subjects, was designed to establish annoyance-noise level functions for three community noise sources presented individually: jet aircraft flyovers, air conditioner, and traffic. The second experiment, which used 216 subjects, investigated the effects of background noise on aircraft annoyance as a function of noise level and spectrum shape; and the differences between overall, aircraft, and background noise annoyance. In both experiments, rated annoyance was the dependent measure. Results indicate that the slope of the linear relationship between annoyance and noise level for traffic is significantly different from that of flyover and air conditioner noise and that further research was justified to determine the influence of the two background noises on overall, aircraft, and background noise annoyance (e.g., experiment two). In experiment two, total noise exposure, signal-to-noise ratio, and background source type were found to have effects on all three types of annoyance. Thus, both signal-to-noise ratio, and the background source must be considered when trying to determine community response to combined noise sources.

  12. Low energy background radiation in India

    International Nuclear Information System (INIS)

    Gopinath, D.V.

    1980-01-01

    Spectral distribution of background radiation at 9 locations spread all over India has been measured. Specifications of the counting set-up standardised for measurement are given. At one of the places, the background spectrum was measured with four different types of detectors. A broad peak in 60-100 keV with differing intensity and standard deviation is observed in all the spectra. In the Kalpakkam area, the peak near the seashore is observed to be more intense than away from the shore. This could be due to the presence of monazite sands on the seashore. The natural background radiation is observed to have a steep rise below 20 keV. Peak intensity is found to be independent of both the location (i.e. the source of energy) and the type of detector used for measurement. The calculated spectra due to multiple scattered radiation (with a nominal source energy of 1 MeV) through paraffin wax and the measured background spectrum with the detector shielded with 20 cm wax show good agreement above 40 keV. This shows that 80 keV hump in the natural background radiation is a property of air. The peak, therefore, in the spectra of natural background radiation is essentially a property of medium and it is independent of location or detector. (M.G.B.)

  13. Background of SAM atom-fraction profiles

    International Nuclear Information System (INIS)

    Ernst, Frank

    2017-01-01

    Atom-fraction profiles acquired by SAM (scanning Auger microprobe) have important applications, e.g. in the context of alloy surface engineering by infusion of carbon or nitrogen through the alloy surface. However, such profiles often exhibit an artifact in form of a background with a level that anti-correlates with the local atom fraction. This article presents a theory explaining this phenomenon as a consequence of the way in which random noise in the spectrum propagates into the discretized differentiated spectrum that is used for quantification. The resulting model of “energy channel statistics” leads to a useful semi-quantitative background reduction procedure, which is validated by applying it to simulated data. Subsequently, the procedure is applied to an example of experimental SAM data. The analysis leads to conclusions regarding optimum experimental acquisition conditions. The proposed method of background reduction is based on general principles and should be useful for a broad variety of applications. - Highlights: • Atom-fraction–depth profiles of carbon measured by scanning Auger microprobe • Strong background, varies with local carbon concentration. • Needs correction e.g. for quantitative comparison with simulations • Quantitative theory explains background. • Provides background removal strategy and practical advice for acquisition

  14. Background of SAM atom-fraction profiles

    Energy Technology Data Exchange (ETDEWEB)

    Ernst, Frank

    2017-03-15

    Atom-fraction profiles acquired by SAM (scanning Auger microprobe) have important applications, e.g. in the context of alloy surface engineering by infusion of carbon or nitrogen through the alloy surface. However, such profiles often exhibit an artifact in form of a background with a level that anti-correlates with the local atom fraction. This article presents a theory explaining this phenomenon as a consequence of the way in which random noise in the spectrum propagates into the discretized differentiated spectrum that is used for quantification. The resulting model of “energy channel statistics” leads to a useful semi-quantitative background reduction procedure, which is validated by applying it to simulated data. Subsequently, the procedure is applied to an example of experimental SAM data. The analysis leads to conclusions regarding optimum experimental acquisition conditions. The proposed method of background reduction is based on general principles and should be useful for a broad variety of applications. - Highlights: • Atom-fraction–depth profiles of carbon measured by scanning Auger microprobe • Strong background, varies with local carbon concentration. • Needs correction e.g. for quantitative comparison with simulations • Quantitative theory explains background. • Provides background removal strategy and practical advice for acquisition.

  15. Non-collision backgrounds in ATLAS

    CERN Document Server

    Gibson, S M; The ATLAS collaboration

    2012-01-01

    The proton-proton collision events recorded by the ATLAS experiment are on top of a background that is due to both collision debris and non-collision components. The latter comprises of three types: beam-induced backgrounds, cosmic particles and detector noise. We present studies that focus on the first two of these. We give a detailed description of beam-related and cosmic backgrounds based on the full 2011 ATLAS data set, and present their rates throughout the whole data-taking period. Studies of correlations between tertiary proton halo and muon backgrounds, as well as, residual pressure and resulting beam-gas events seen in beam-condition monitors will be presented. Results of simulations based on the LHC geometry and its parameters will be presented. They help to better understand the features of beam-induced backgrounds in each ATLAS sub-detector. The studies of beam-induced backgrounds in ATLAS reveal their characteristics and serve as a basis for designing rejection tools that can be applied in physic...

  16. Moral Education USA: Background and Trends.

    Science.gov (United States)

    Parker, Franklin

    Current trends in ethical/moral instruction are placed in context by tracing educational and social change from the 19th century to the present. The focus on religion for salvation and on good behavior lasted in modified form well into the 19th century. In the late 19th century curriculum in the schools changed due to immigration, industrialism,…

  17. Stochastic background of negative binomial distribution

    International Nuclear Information System (INIS)

    Suzuki, N.; Biyajima, M.; Wilk, G.

    1991-01-01

    A branching equations of the birth process with immigration is taken as a model for the particle production process. Using it we investigate cases in which its solution becomes the negative binomial distribution. Furthermore, we compare our approach with the modified negative binomial distribution proposed recently by Chliapnikov and Tchikilev and use it to analyse the observed multiplicity distributions. (orig.)

  18. Background enhancement in breast MR: Correlation with breast density in mammography and background echotexture in ultrasound

    International Nuclear Information System (INIS)

    Ko, Eun Sook; Lee, Byung Hee; Choi, Hye Young; Kim, Rock Bum; Noh, Woo-Chul

    2011-01-01

    Objective: This study aimed to determine whether background enhancement on MR was related to mammographic breast density or ultrasonographic background echotexture in premenopausal and postmenopausal women. Materials and methods: We studied 142 patients (79 premenopausal, 63 postmenopausal) who underwent mammography, ultrasonography, and breast MR. We reviewed the mammography for overall breast density of the contralateral normal breast according to the four-point scale of the BI-RADS classification. Ultrasound findings were classified as homogeneous or heterogeneous background echotexture according to the BI-RADS lexicon. We rated background enhancement on a contralateral breast MR into four categories based on subtraction images: absent, mild, moderate, and marked. All imaging findings were interpreted independently by two readers without knowledge of menstrual status, imaging findings of other modalities. Results: There were significant differences between the premenopausal and postmenopausal group in distribution of mammographic breast density, ultrasonographic background echotexture, and degree of background enhancement. Regarding the relationship between mammographic density and background enhancement, there was no significant correlation. There was significant relationship between ultrasonographic background echotexture and background enhancement in both premenopausal and postmenopausal groups. Conclusion: There is a significant correlation between ultrasonographic background echotexture and background enhancement in MR regardless of menopausal status. Interpreting breast MR, or scheduling for breast MR of women showing heterogeneous background echotexture needs more caution.

  19. Searching for stringy topologies in the cosmic microwave background

    International Nuclear Information System (INIS)

    Ben-David, Assaf; Rathaus, Ben; Itzhaki, Nissan

    2012-01-01

    We consider a universe with a non-classical stringy topology that has fixed points. We concentrate on the simplest example, an orbifold point, and study its observable imprints on the cosmic microwave background (CMB). We show that an orbifold preserves the Gaussian nature of the temperature fluctuations, yet modifies the angular correlation function. A direct signature of an orbifold is a single circle in the CMB that is invariant under rotation by 180°. Searching the 7-year ILC map of WMAP, we find one candidate circle with high statistical significance. However, a closer look reveals that the temperature profile does not fit an orbifold. We place a lower bound on the distance to an orbifold point at ∼ 85% of the distance to the surface of last scattering

  20. Searching for stringy topologies in the cosmic microwave background

    Energy Technology Data Exchange (ETDEWEB)

    Ben-David, Assaf; Rathaus, Ben; Itzhaki, Nissan, E-mail: bd.assaf@gmail.com, E-mail: ben.rathaus@gmail.com, E-mail: nitzhaki@post.tau.ac.il [Raymond and Beverly Sackler Faculty of Exact Sciences, School of Physics and Astronomy, Tel-Aviv University, Ramat-Aviv, 69978 (Israel)

    2012-11-01

    We consider a universe with a non-classical stringy topology that has fixed points. We concentrate on the simplest example, an orbifold point, and study its observable imprints on the cosmic microwave background (CMB). We show that an orbifold preserves the Gaussian nature of the temperature fluctuations, yet modifies the angular correlation function. A direct signature of an orbifold is a single circle in the CMB that is invariant under rotation by 180°. Searching the 7-year ILC map of WMAP, we find one candidate circle with high statistical significance. However, a closer look reveals that the temperature profile does not fit an orbifold. We place a lower bound on the distance to an orbifold point at ∼ 85% of the distance to the surface of last scattering.

  1. The coupling of Poisson sigma models to topological backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Rosa, Dario [School of Physics, Korea Institute for Advanced Study,Seoul 02455 (Korea, Republic of)

    2016-12-13

    We extend the coupling to the topological backgrounds, recently worked out for the 2-dimensional BF-model, to the most general Poisson sigma models. The coupling involves the choice of a Casimir function on the target manifold and modifies the BRST transformations. This in turn induces a change in the BRST cohomology of the resulting theory. The observables of the coupled theory are analyzed and their geometrical interpretation is given. We finally couple the theory to 2-dimensional topological gravity: this is the first step to study a topological string theory in propagation on a Poisson manifold. As an application, we show that the gauge-fixed vectorial supersymmetry of the Poisson sigma models has a natural explanation in terms of the theory coupled to topological gravity.

  2. Phenotypic characterisation and molecular polymorphism of ...

    African Journals Online (AJOL)

    The study of the phenotypic characterisation and molecular polymorphism of local chicken populations was carried out in Benin on 326 chickens of the Forest ecological area and 316 of the Savannah ecological area, all were 7 months old at least. The collection of blood for the molecular typing was achieved on 121 ...

  3. Evidence for a Broad Autism Phenotype

    NARCIS (Netherlands)

    K. de Groot (Kristel); J.W. van Strien (Jan)

    2017-01-01

    textabstractThe broad autism phenotype implies the existence of a continuum ranging from individuals displaying almost no autistic traits to severely impaired diagnosed individuals. Recent studies have linked this variation in autistic traits to several domains of functioning. However, studies

  4. phenotype correlation of methylene tetrahydrofolate reductase ...

    African Journals Online (AJOL)

    Rabah M. Shawky

    2014-06-21

    Jun 21, 2014 ... children with autism and to correlate them with different phenotypes. Subjects and ... of impairments in communication, reciprocal social interac- tions, and ... isolation was obtained from peripheral blood samples using the spin ... IQ, while ten of them (50%) had mild mental retardation and six patients (30%) ...

  5. Phenotype Presentation of Hypophosphatemic Rickets in Adults

    DEFF Research Database (Denmark)

    Beck-Nielsen, Signe S; Brusgaard, Klaus; Rasmussen, Lars M

    2010-01-01

    Hypophosphatemic rickets (HR) is a group of rare disorders caused by excessive renal phosphate wasting. The purpose of this cross-sectional study of 38 HR patients was to characterize the phenotype of adult HR patients. Moreover, skeletal and endodontic severity scores were defined to assess poss...

  6. Phenotypic and molecular characterization of Salmonella serotypes ...

    African Journals Online (AJOL)

    The presence of Salmonella and human pathogens in unpasteurized milk remains a public health hazard. The study reported the phenotypic and molecular characterization of Salmonella serotypes in cow raw milk, cheese and traditional yoghurt marketed for man's consumption in Nigeria. Isolation of Salmonella was done ...

  7. (RR) soybean cultivars estimated by phenotypic characteristics

    African Journals Online (AJOL)

    SAM

    2014-06-25

    Jun 25, 2014 ... phenotypic characteristics and microsatellite molecular markers (SSR). ... discriminatory analysis, principal components, coordinate and cluster analysis .... were employed with 10.000 simulations to attribute significance values to ...... association analysis of protein and oil content in food-grade soybeans ...

  8. Colorectal Cancer "Methylator Phenotype": Fact or Artifact?

    Directory of Open Access Journals (Sweden)

    Charles Anacleto

    2005-04-01

    Full Text Available It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI. We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.

  9. A single point-mutation within the melanophilin gene causes the lavender plumage colour dilution phenotype in the chicken

    Directory of Open Access Journals (Sweden)

    Tixier-Boichard Michèle

    2008-01-01

    Full Text Available Abstract Background The lavender phenotype in the chicken causes the dilution of both black (eumelanin and red/brown (phaeomelanin pigments. Defects in three genes involved in intracellular melanosomal transport, previously described in mammals, give rise to similar diluted pigmentation phenotypes as those seen in lavender chickens. Results We have used a candidate-gene approach based on an expectation of homology with mammals to isolate a gene involved in pigmentation in chicken. Comparative sequence analysis of candidate genes in the chicken identified a strong association between a mutation in the MLPH gene and the diluted pigmentation phenotype. This mutation results in the amino acid change R35W, at a site also associated with similar phenotypes in mice, humans and cats. Conclusion This is the first time that an avian species with a mutation in the MLPH gene has been reported.

  10. SMAD4 Loss triggers the phenotypic changes of pancreatic ductal adenocarcinoma cells

    OpenAIRE

    Chen, Yu-Wen; Hsiao, Pi-Jung; Weng, Ching-Chieh; Kuo, Kung-Kai; Kuo, Tzu-Lei; Wu, Deng-Chyang; Hung, Wen-Chun; Cheng, Kuang-Hung

    2014-01-01

    Background SMAD4 is a gastrointestinal malignancy-specific tumor suppressor gene found mutated in one third of colorectal cancer specimens and half of pancreatic tumors. SMAD4 inactivation by allelic deletion or intragenic mutation mainly occurs in the late stage of human pancreatic ductal adenocarcinoma (PDAC). Various studies have proposed potential SMAD4-mediated anti-tumor effects in human malignancy; however, the relevance of SMAD4 in the PDAC molecular phenotype has not yet been fully c...

  11. Phenotypic and Genotypic Characteristics of Listeria monocytogenes Isolated From Dairy and Meat Products

    OpenAIRE

    Bahador; Sadeghi Kalani; Valian; Irajian; Lotfollahi

    2015-01-01

    Background Listeria monocytogenes is a foodborne pathogen and a serious threat to the public health in the world. Consumption of traditional foods such as dairy and meat products can be a major reason for relative abundance and isolation of these bacteria. Objectives The purpose of this study was to determine the phenotypic and genotypic characteristics of L. monocytogenes strains isolated from dairy and meat products. ...

  12. Protein structure and phenotypic analysis of pathogenic and population missense variants in STXBP1

    OpenAIRE

    Suri, Mohnish; Evers, Jochem M. G.; Laskowski, Roman A.; O'Brien, Sinead; Baker, Kate; Clayton‐Smith, Jill; Dabir, Tabib; Josifova, Dragana; Joss, Shelagh; Kerr, Bronwyn; Kraus, Alison; McEntagart, Meriel; Morton, Jenny; Smith, Audrey; Splitt, Miranda

    2017-01-01

    Abstract Background Syntaxin‐binding protein 1, encoded by STXBP1, is highly expressed in the brain and involved in fusing synaptic vesicles with the plasma membrane. Studies have shown that pathogenic loss‐of‐function variants in this gene result in various types of epilepsies, mostly beginning early in life. We were interested to model pathogenic missense variants on the protein structure to investigate the mechanism of pathogenicity and genotype–phenotype correlations. Methods We report 11...

  13. Continuity of aggressive antisocial behavior from childhood to adulthood: The question of phenotype definition.

    OpenAIRE

    Hofvander, Björn; Ossowski, Daniel; Lundström, Sebastian; Anckarsäter, Henrik

    2009-01-01

    Aiming to clarify the adult phenotype of antisocial personality disorder (ASPD), the empirical literature on its childhood background among the disruptive behaviour disorders, such as attention deficit/hyperactivity disorder (AD/HD), oppositional defiant disorder (ODD), conduct disorder (CD), or hyperkinetic conduct disorder (HKCD), was reviewed according to the Robins and Guze criteria for nosological validity. At least half of hyperactive children develop ODD and about a third CD (i.e. AD/H...

  14. The background in the experiment Gerda

    Science.gov (United States)

    Agostini, M.; Allardt, M.; Andreotti, E.; Bakalyarov, A. M.; Balata, M.; Barabanov, I.; Barnabé Heider, M.; Barros, N.; Baudis, L.; Bauer, C.; Becerici-Schmidt, N.; Bellotti, E.; Belogurov, S.; Belyaev, S. T.; Benato, G.; Bettini, A.; Bezrukov, L.; Bode, T.; Brudanin, V.; Brugnera, R.; Budjáš, D.; Caldwell, A.; Cattadori, C.; Chernogorov, A.; Cossavella, F.; Demidova, E. V.; Domula, A.; Egorov, V.; Falkenstein, R.; Ferella, A.; Freund, K.; Frodyma, N.; Gangapshev, A.; Garfagnini, A.; Gotti, C.; Grabmayr, P.; Gurentsov, V.; Gusev, K.; Guthikonda, K. K.; Hampel, W.; Hegai, A.; Heisel, M.; Hemmer, S.; Heusser, G.; Hofmann, W.; Hult, M.; Inzhechik, L. V.; Ioannucci, L.; Csáthy, J. Janicskó; Jochum, J.; Junker, M.; Kihm, T.; Kirpichnikov, I. V.; Kirsch, A.; Klimenko, A.; Knöpfle, K. T.; Kochetov, O.; Kornoukhov, V. N.; Kuzminov, V. V.; Laubenstein, M.; Lazzaro, A.; Lebedev, V. I.; Lehnert, B.; Liao, H. Y.; Lindner, M.; Lippi, I.; Liu, X.; Lubashevskiy, A.; Lubsandorzhiev, B.; Lutter, G.; Macolino, C.; Machado, A. A.; Majorovits, B.; Maneschg, W.; Nemchenok, I.; Nisi, S.; O'Shaughnessy, C.; Palioselitis, D.; Pandola, L.; Pelczar, K.; Pessina, G.; Pullia, A.; Riboldi, S.; Sada, C.; Salathe, M.; Schmitt, C.; Schreiner, J.; Schulz, O.; Schwingenheuer, B.; Schönert, S.; Shevchik, E.; Shirchenko, M.; Simgen, H.; Smolnikov, A.; Stanco, L.; Strecker, H.; Tarka, M.; Ur, C. A.; Vasenko, A. A.; Volynets, O.; von Sturm, K.; Wagner, V.; Walter, M.; Wegmann, A.; Wester, T.; Wojcik, M.; Yanovich, E.; Zavarise, P.; Zhitnikov, I.; Zhukov, S. V.; Zinatulina, D.; Zuber, K.; Zuzel, G.

    2014-04-01

    The GERmanium Detector Array ( Gerda) experiment at the Gran Sasso underground laboratory (LNGS) of INFN is searching for neutrinoless double beta () decay of Ge. The signature of the signal is a monoenergetic peak at 2039 keV, the value of the decay. To avoid bias in the signal search, the present analysis does not consider all those events, that fall in a 40 keV wide region centered around . The main parameters needed for the analysis are described. A background model was developed to describe the observed energy spectrum. The model contains several contributions, that are expected on the basis of material screening or that are established by the observation of characteristic structures in the energy spectrum. The model predicts a flat energy spectrum for the blinding window around with a background index ranging from 17.6 to 23.8 cts/(keV kg yr). A part of the data not considered before has been used to test if the predictions of the background model are consistent. The observed number of events in this energy region is consistent with the background model. The background at is dominated by close sources, mainly due to K, Bi, Th, Co and emitting isotopes from the Ra decay chain. The individual fractions depend on the assumed locations of the contaminants. It is shown, that after removal of the known peaks, the energy spectrum can be fitted in an energy range of 200 keV around with a constant background. This gives a background index consistent with the full model and uncertainties of the same size.

  15. The spinorial geometry of supersymmetric backgrounds

    International Nuclear Information System (INIS)

    Gillard, J; Gran, U; Papadopoulos, G

    2005-01-01

    We propose a new method to solve the Killing spinor equations of 11-dimensional supergravity based on a description of spinors in terms of forms and on the Spin(1, 10) gauge symmetry of the supercovariant derivative. We give the canonical form of Killing spinors for backgrounds preserving two supersymmetries, N = 2, provided that one of the spinors represents the orbit of Spin(1, 10) with stability subgroup SU(5). We directly solve the Killing spinor equations of N = 1 and some N = 2, N = 3 and N = 4 backgrounds. In the N = 2 case, we investigate backgrounds with SU(5) and SU(4) invariant Killing spinors and compute the associated spacetime forms. We find that N = 2 backgrounds with SU(5) invariant Killing spinors admit a timelike Killing vector and that the space transverse to the orbits of this vector field is a Hermitian manifold with an SU(5)-structure. Furthermore, N = 2 backgrounds with SU(4) invariant Killing spinors admit two Killing vectors, one timelike and one spacelike. The space transverse to the orbits of the former is an almost Hermitian manifold with an SU(4)-structure. The spacelike Killing vector field leaves the almost complex structure invariant. We explore the canonical form of Killing spinors for backgrounds preserving more than two supersymmetries, N > 2. We investigate a class of N = 3 and N = 4 backgrounds with SU(4) invariant spinors. We find that in both cases the space transverse to a timelike vector field is a Hermitian manifold equipped with an SU(4)-structure and admits two holomorphic Killing vector fields. We also present an application to M-theory Calabi-Yau compactifications with fluxes to one dimension

  16. The spinorial geometry of supersymmetric backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Gillard, J; Gran, U; Papadopoulos, G [Department of Mathematics, King' s College London, Strand, London WC2R 2LS (United Kingdom)

    2005-03-21

    We propose a new method to solve the Killing spinor equations of 11-dimensional supergravity based on a description of spinors in terms of forms and on the Spin(1, 10) gauge symmetry of the supercovariant derivative. We give the canonical form of Killing spinors for backgrounds preserving two supersymmetries, N = 2, provided that one of the spinors represents the orbit of Spin(1, 10) with stability subgroup SU(5). We directly solve the Killing spinor equations of N = 1 and some N = 2, N = 3 and N = 4 backgrounds. In the N = 2 case, we investigate backgrounds with SU(5) and SU(4) invariant Killing spinors and compute the associated spacetime forms. We find that N = 2 backgrounds with SU(5) invariant Killing spinors admit a timelike Killing vector and that the space transverse to the orbits of this vector field is a Hermitian manifold with an SU(5)-structure. Furthermore, N = 2 backgrounds with SU(4) invariant Killing spinors admit two Killing vectors, one timelike and one spacelike. The space transverse to the orbits of the former is an almost Hermitian manifold with an SU(4)-structure. The spacelike Killing vector field leaves the almost complex structure invariant. We explore the canonical form of Killing spinors for backgrounds preserving more than two supersymmetries, N > 2. We investigate a class of N = 3 and N = 4 backgrounds with SU(4) invariant spinors. We find that in both cases the space transverse to a timelike vector field is a Hermitian manifold equipped with an SU(4)-structure and admits two holomorphic Killing vector fields. We also present an application to M-theory Calabi-Yau compactifications with fluxes to one dimension.

  17. Effect of culture medium on propagation and phenotype of corneal stroma-derived stem cells.

    Science.gov (United States)

    Sidney, Laura E; Branch, Matthew J; Dua, Harminder S; Hopkinson, Andrew

    2015-12-01

    The limbal area of the corneal stroma has been identified as a source of mesenchymal-like stem cells, which have potential for exploitation as a cell therapy. However, the optimal culture conditions are disputed and few direct media comparisons have been performed. In this report, we evaluated several media types to identify the optimal for inducing an in vitro stem cell phenotype. Primary human corneal stroma-derived stem cells (CSSCs) were extracted from corneoscleral rims. Culture in seven different media types was compared: Dulbecco's modified Eagle's medium (DMEM) with 10% fetal bovine serum (FBS); M199 with 20% FBS; DMEM-F12 with 20% serum replacement, basic fibroblast growth factor and leukemia inhibitory factor (SCM); endothelial growth medium (EGM); semi-solid MethoCult; serum-free keratinocyte medium (K-SFM); and StemPro-34. Effects on proliferation, morphology, protein and messenger RNA expression were evaluated. All media supported proliferation of CSSCs with the exception of K-SFM and StemPro-34. Morphology differed between media: DMEM produced large cells, whereas EGM produced very small cells. Culture in M199 produced a typical mesenchymal stromal cell phenotype with high expression of CD105, CD90 and CD73 but not CD34. Culture in SCM produced a phenotype more reminiscent of a progenitor cell type with expression of CD34, ABCG2, SSEA-4 and PAX6. Culture medium can significantly influence CSSC phenotype. SCM produced a cell phenotype closest to that of a pluripotent stem cell, and we consider it to be the most appropriate for development as a clinical-grade medium for the production of CSSC phenotypes suitable for cell therapy. Copyright © 2015 International Society for Cellular Therapy. Published by Elsevier Inc. All rights reserved.

  18. Investigating genotype-phenotype relationships in Rett syndrome using an international data set.

    Science.gov (United States)

    Bebbington, A; Anderson, A; Ravine, D; Fyfe, S; Pineda, M; de Klerk, N; Ben-Zeev, B; Yatawara, N; Percy, A; Kaufmann, W E; Leonard, H

    2008-03-11

    Rett syndrome is an uncommon neurodevelopmental disorder with an incidence of 1:9,000 live female births. The principal genetic cause was first reported in 1999 when the association with mutations in the methyl-CpG-binding protein 2 (or MECP2) gene was identified. This study uses data from a large international database, InterRett, to examine genotype-phenotype relationships and compares these with previous findings in a population-based cohort. The data set for these analyses was derived from a subset of InterRett cases with subject information collected from the family, the clinician, or both. Individual phenotypic characteristics and clinical severity using three scales were compared among those with eight known recurrent pathogenic MECP2 mutations as well as those with C-terminal deletions (n = 272). Overall, p.R270X and p.R255X were the most severe and p.R133C and p.R294X were the mildest mutations. Significant differences by mutation were seen for individual phenotypic characteristics such as hand use, ambulation, and language. This multicenter investigation into the phenotypic correlates of MECP2 mutations in Rett syndrome has provided a greater depth of understanding than hitherto available about the specific phenotypic characteristics associated with commonly occurring mutations. Although the modifying influence of X inactivation on clinical severity could not be included in the analysis, the findings confirm clear genotype-phenotype relationships in Rett syndrome and show the benefits of collaboration crucial to effective research in rare disorders.

  19. Metabolomics to unveil and understand phenotypic diversity between pathogen populations.

    Directory of Open Access Journals (Sweden)

    Ruben t'Kindt

    Full Text Available Leishmaniasis is a debilitating disease caused by the parasite Leishmania. There is extensive clinical polymorphism, including variable responsiveness to treatment. We study Leishmania donovani parasites isolated from visceral leishmaniasis patients in Nepal that responded differently to antimonial treatment due to differing intrinsic drug sensitivity of the parasites. Here, we present a proof-of-principle study in which we applied a metabolomics pipeline specifically developed for L. donovani to characterize the global metabolic differences between antimonial-sensitive and antimonial-resistant L. donovani isolates. Clones of drug-sensitive and drug-resistant parasite isolates from clinical samples were cultured in vitro and harvested for metabolomics analysis. The relative abundance of 340 metabolites was determined by ZIC-HILIC chromatography coupled to LTQ-Orbitrap mass spectrometry. Our measurements cover approximately 20% of the predicted core metabolome of Leishmania and additionally detected a large number of lipids. Drug-sensitive and drug-resistant parasites showed distinct metabolic profiles, and unsupervised clustering and principal component analysis clearly distinguished the two phenotypes. For 100 metabolites, the detected intensity differed more than three-fold between the 2 phenotypes. Many of these were in specific areas of lipid metabolism, suggesting that the membrane composition of the drug-resistant parasites is extensively modified. Untargeted metabolomics has been applied on clinical Leishmania isolates to uncover major metabolic differences between drug-sensitive and drug-resistant isolates. The identified major differences provide novel insights into the mechanisms involved in resistance to antimonial drugs, and facilitate investigations using targeted approaches to unravel the key changes mediating drug resistance.

  20. Ablation plume dynamics in a background gas

    DEFF Research Database (Denmark)

    Amoruso, Salvatore; Schou, Jørgen; Lunney, James G.

    2010-01-01

    The expansion of a plume in a background gas of pressure comparable to that used in pulsed laser deposition (PLD) has been analyzed in terms of the model of Predtechensky and Mayorov (PM). This approach gives a relatively clear and simple description of the essential hydrodynamics during the expa......The expansion of a plume in a background gas of pressure comparable to that used in pulsed laser deposition (PLD) has been analyzed in terms of the model of Predtechensky and Mayorov (PM). This approach gives a relatively clear and simple description of the essential hydrodynamics during...... the expansion. The model also leads to an insightful treatment of the stopping behavior in dimensionless units for plumes and background gases of different atomic/molecular masses. The energetics of the plume dynamics can also be treated with this model. Experimental time-of-flight data of silver ions in a neon...... background gas show a fair agreement with predictions from the PM-model. Finally we discuss the validity of the model, if the work done by the pressure of the background gas is neglected....

  1. Measurements of the cosmic background radiation

    International Nuclear Information System (INIS)

    Weiss, R.

    1980-01-01

    Measurements of the attributes of the 2.7-K microwave background radiation (CBR) are reviewed, with emphasis on the analytic phase of CBR studies. Methods for the direct measurement of the CBR spectrum are discussed. Attention is given to receivers, antennas, absolute receiver calibration, atmospheric emission and absorption, the galactic background contribution, the analysis of LF measurements, and recent HF observations of the CBR spectrum. Measurements of the large-angular-scale intensity distribution of the CBR (the most convincing evidence that the radiation is of cosmological origin) are examined, along with limits on the linear polarization of the CBR. A description is given of the NASA-sponsored Cosmic Background Explorer (COBE) satellite mission. The results of the COBE mission will be a set of sky maps showing, in the wave number range from 1 to 10,000 kaysers, the galactic background radiation due to synchrotron emission from galactic cosmic rays, to diffuse thermal emission from H II regions, and to diffuse thermal emission from interstellar and interplanetary dust, as well as a residue consisting of the CBR and whatever other cosmological background might exist

  2. General Relativity solutions in modified gravity

    Science.gov (United States)

    Motohashi, Hayato; Minamitsuji, Masato

    2018-06-01

    Recent gravitational wave observations of binary black hole mergers and a binary neutron star merger by LIGO and Virgo Collaborations associated with its optical counterpart constrain deviation from General Relativity (GR) both on strong-field regime and cosmological scales with high accuracy, and further strong constraints are expected by near-future observations. Thus, it is important to identify theories of modified gravity that intrinsically possess the same solutions as in GR among a huge number of theories. We clarify the three conditions for theories of modified gravity to allow GR solutions, i.e., solutions with the metric satisfying the Einstein equations in GR and the constant profile of the scalar fields. Our analysis is quite general, as it applies a wide class of single-/multi-field scalar-tensor theories of modified gravity in the presence of matter component, and any spacetime geometry including cosmological background as well as spacetime around black hole and neutron star, for the latter of which these conditions provide a necessary condition for no-hair theorem. The three conditions will be useful for further constraints on modified gravity theories as they classify general theories of modified gravity into three classes, each of which possesses i) unique GR solutions (i.e., no-hair cases), ii) only hairy solutions (except the cases that GR solutions are realized by cancellation between singular coupling functions in the Euler-Lagrange equations), and iii) both GR and hairy solutions, for the last of which one of the two solutions may be selected dynamically.

  3. Bitumen based modified substance

    International Nuclear Information System (INIS)

    Kostolanyi, P.

    1987-01-01

    The necessary amounts of tetrahydrosilicic acid and methyl phenyl silicon oil are added to molten bitumen heated to temperatures of 50 to 200 degC. The mixture is thoroughly mixed and let to cool. The structure of the product comes close to gel and its properties (penetration, softening point, workability time, penetration index) may be changed in dependence on the amount of additions and on the time and temperature of heating. The advantage of the thus prepared modified material is its shorter workability time, its ability to bind materials with a certain water content, and its relatively low price. It may be used for fixing and storing low-and medium-level radioactive organic and thickened waste waters. (E.S.)

  4. Biodegradable modified Phba systems

    International Nuclear Information System (INIS)

    Aniscenko, L.; Dzenis, M.; Erkske, D.; Tupureina, V.; Savenkova, L.; Muizniece - Braslava, S.

    2004-01-01

    Compositions as well as production technology of ecologically sound biodegradable multicomponent polymer systems were developed. Our objective was to design some bio plastic based composites with required mechanical properties and biodegradability intended for use as biodegradable packaging. Significant characteristics required for food packaging such as barrier properties (water and oxygen permeability) and influence of γ-radiation on the structure and changes of main characteristics of some modified PHB matrices was evaluated. It was found that barrier properties were plasticizers chemical nature and sterilization with γ-radiation dependent and were comparable with corresponding values of typical polymeric packaging films. Low γ-radiation levels (25 kGy) can be recommended as an effective sterilization method of PHB based packaging materials. Purposely designed bio plastic packaging may provide an alternative to traditional synthetic packaging materials without reducing the comfort of the end-user due to specific qualities of PHB - biodegradability, Biocompatibility and hydrophobic nature

  5. Modified Clipped LMS Algorithm

    Directory of Open Access Journals (Sweden)

    Lotfizad Mojtaba

    2005-01-01

    Full Text Available Abstract A new algorithm is proposed for updating the weights of an adaptive filter. The proposed algorithm is a modification of an existing method, namely, the clipped LMS, and uses a three-level quantization ( scheme that involves the threshold clipping of the input signals in the filter weight update formula. Mathematical analysis shows the convergence of the filter weights to the optimum Wiener filter weights. Also, it can be proved that the proposed modified clipped LMS (MCLMS algorithm has better tracking than the LMS algorithm. In addition, this algorithm has reduced computational complexity relative to the unmodified one. By using a suitable threshold, it is possible to increase the tracking capability of the MCLMS algorithm compared to the LMS algorithm, but this causes slower convergence. Computer simulations confirm the mathematical analysis presented.

  6. Modified arthroscopic Brostrom procedure.

    Science.gov (United States)

    Lui, Tun Hing

    2015-09-01

    The open modified Brostrom anatomic repair technique is widely accepted as the reference standard for lateral ankle stabilization. However, there is high incidence of intra-articular pathologies associated with chronic lateral ankle instability which may not be addressed by an isolated open Brostrom procedure. Arthroscopic Brostrom procedure with suture anchor has been described for anatomic repair of chronic lateral ankle instability and management of intra-articular lesions. However, the complication rates seemed to be higher than open Brostrom procedure. Modification of the arthroscopic Brostrom procedure with the use of bone tunnel may reduce the risk of certain complications. Copyright © 2015 European Foot and Ankle Society. Published by Elsevier Ltd. All rights reserved.

  7. Modified circular velocity law

    Science.gov (United States)

    Djeghloul, Nazim

    2018-05-01

    A modified circular velocity law is presented for a test body orbiting around a spherically symmetric mass. This law exhibits a distance scale parameter and allows to recover both usual Newtonian behaviour for lower distances and a constant velocity limit at large scale. Application to the Galaxy predicts the known behaviour and also leads to a galactic mass in accordance with the measured visible stellar mass so that additional dark matter inside the Galaxy can be avoided. It is also shown that this circular velocity law can be embedded in a geometrical description of spacetime within the standard general relativity framework upon relaxing the usual asymptotic flatness condition. This formulation allows to redefine the introduced Newtonian scale limit in term of the central mass exclusively. Moreover, a satisfactory answer to the galactic escape speed problem can be provided indicating the possibility that one can also get rid of dark matter halo outside the Galaxy.

  8. Stabilization of the wheel running phenotype in mice.

    Science.gov (United States)

    Bowen, Robert S; Cates, Brittany E; Combs, Eric B; Dillard, Bryce M; Epting, Jessica T; Foster, Brittany R; Patterson, Shawnee V; Spivey, Thomas P

    2016-03-01

    Increased physical activity is well known to improve health and wellness by modifying the risks for many chronic diseases. Rodent wheel running behavior is a beneficial surrogate model to evaluate the biology of daily physical activity in humans. Upon initial exposure to a running wheel, individual mice differentially respond to the experience, which confounds the normal activity patterns exhibited in this otherwise repeatable phenotype. To promote phenotypic stability, a minimum seven-day (or greater) acclimation period is utilized. Although phenotypic stabilization is achieved during this 7-day period, data to support acclimation periods of this length are not currently available in the literature. The purpose of this project is to evaluate the wheel running response in C57BL/6j mice immediately following exposure to a running wheel. Twenty-eight male and thirty female C57BL/6j mice (Jackson Laboratory, Bar Harbor, ME) were acquired at eight weeks of age and were housed individually with free access to running wheels. Wheel running distance (km), duration (min), and speed (m∙min(-1)) were measured daily for fourteen days following initial housing. One-way ANOVAs were used to evaluate day-to-day differences in each wheel running character. Limits of agreement and mean difference statistics were calculated between days 1-13 (acclimating) and day 14 (acclimated) to assess day-to-day agreement between each parameter. Wheel running distance (males: F=5.653, p=2.14 × 10(-9); females: F=8.217, p=1.20 × 10(-14)), duration (males: F=2.613, p=0.001; females: F=4.529, p=3.28 × 10(-7)), and speed (males: F=7.803, p=1.22 × 10(-13); females: F=13.140, p=2.00 × 10(-16)) exhibited day-to-day differences. Tukey's HSD post-hoc testing indicated differences between early (males: days 1-3; females: days 1-6) and later (males: days >3; females: days >6) wheel running periods in distance and speed. Duration only exhibited an anomalous difference between wheel running on day 13

  9. Monte Carlo simulations of low background detectors

    International Nuclear Information System (INIS)

    Miley, H.S.; Brodzinski, R.L.; Hensley, W.K.; Reeves, J.H.

    1995-01-01

    An implementation of the Electron Gamma Shower 4 code (EGS4) has been developed to allow convenient simulation of typical gamma ray measurement systems. Coincidence gamma rays, beta spectra, and angular correlations have been added to adequately simulate a complete nuclear decay and provide corrections to experimentally determined detector efficiencies. This code has been used to strip certain low-background spectra for the purpose of extremely low-level assay. Monte Carlo calculations of this sort can be extremely successful since low background detectors are usually free of significant contributions from poorly localized radiation sources, such as cosmic muons, secondary cosmic neutrons, and radioactive construction or shielding materials. Previously, validation of this code has been obtained from a series of comparisons between measurements and blind calculations. An example of the application of this code to an exceedingly low background spectrum stripping will be presented. (author) 5 refs.; 3 figs.; 1 tab

  10. Background harmonic superfields in N=2 supergravity

    International Nuclear Information System (INIS)

    Zupnik, B.M.

    1998-01-01

    A modification of the harmonic superfield formalism in D=4, N=2 supergravity using a subsidiary condition of covariance under the background supersymmetry with a central charge (B-covariance) is considered. Conservation of analyticity together with the B-covariance leads to the appearance of linear gravitational superfields. Analytic prepotentials arise in a decomposition of the background linear superfields in terms of spinor coordinates and transform in a nonstandard way under the background supersymmetry. The linear gravitational superfields can be written via spinor derivatives of nonanalytic spinor prepotentials. The perturbative expansion of supergravity action in terms of the B-covariant superfields and the corresponding version of the differential-geometric formalism are considered. We discuss the dual harmonic representation of the linearized extended supergravity, which corresponds to the dynamical condition of Grassmann analyticity

  11. Background modeling for the GERDA experiment

    Science.gov (United States)

    Becerici-Schmidt, N.; Gerda Collaboration

    2013-08-01

    The neutrinoless double beta (0νββ) decay experiment GERDA at the LNGS of INFN has started physics data taking in November 2011. This paper presents an analysis aimed at understanding and modeling the observed background energy spectrum, which plays an essential role in searches for a rare signal like 0νββ decay. A very promising preliminary model has been obtained, with the systematic uncertainties still under study. Important information can be deduced from the model such as the expected background and its decomposition in the signal region. According to the model the main background contributions around Qββ come from 214Bi, 228Th, 42K, 60Co and α emitting isotopes in the 226Ra decay chain, with a fraction depending on the assumed source positions.

  12. Background modeling for the GERDA experiment

    Energy Technology Data Exchange (ETDEWEB)

    Becerici-Schmidt, N. [Max-Planck-Institut für Physik, München (Germany); Collaboration: GERDA Collaboration

    2013-08-08

    The neutrinoless double beta (0νββ) decay experiment GERDA at the LNGS of INFN has started physics data taking in November 2011. This paper presents an analysis aimed at understanding and modeling the observed background energy spectrum, which plays an essential role in searches for a rare signal like 0νββ decay. A very promising preliminary model has been obtained, with the systematic uncertainties still under study. Important information can be deduced from the model such as the expected background and its decomposition in the signal region. According to the model the main background contributions around Q{sub ββ} come from {sup 214}Bi, {sup 228}Th, {sup 42}K, {sup 60}Co and α emitting isotopes in the {sup 226}Ra decay chain, with a fraction depending on the assumed source positions.

  13. In-beam background suppression shield

    DEFF Research Database (Denmark)

    Santoro, V.; Cai, Xiao Xiao; DiJulio, D. D.

    2015-01-01

    The long (3 ms) proton pulse of the European Spallation Source (ESS) gives rise to unique and potentially high backgrounds for the instrument suite. In such a source an instrument's capabilities will be limited by its Signal to Noise (S/N) ratio. The instruments with a direct view of the moderator......, which do not use a bender to help mitigate the fast neutron background, are the most challenging. For these beam lines we propose the innovative shielding of placing blocks of material directly into the guide system, which allow a minimum attenuation of the cold and thermal fluxes relative...... to the background suppression. This shielding configuration has been worked into a beam line model using Geant4. We study particularly the advantages of single crystal sapphire and silicon blocks....

  14. Background Model for the Majorana Demonstrator

    Science.gov (United States)

    Cuesta, C.; Abgrall, N.; Aguayo, E.; Avignone, F. T.; Barabash, A. S.; Bertrand, F. E.; Boswell, M.; Brudanin, V.; Busch, M.; Byram, D.; Caldwell, A. S.; Chan, Y.-D.; Christofferson, C. D.; Combs, D. C.; Detwiler, J. A.; Doe, P. J.; Efremenko, Yu.; Egorov, V.; Ejiri, H.; Elliott, S. R.; Fast, J. E.; Finnerty, P.; Fraenkle, F. M.; Galindo-Uribarri, A.; Giovanetti, G. K.; Goett, J.; Green, M. P.; Gruszko, J.; Guiseppe, V. E.; Gusev, K.; Hallin, A. L.; Hazama, R.; Hegai, A.; Henning, R.; Hoppe, E. W.; Howard, S.; Howe, M. A.; Keeter, K. J.; Kidd, M. F.; Kochetov, O.; Konovalov, S. I.; Kouzes, R. T.; LaFerriere, B. D.; Leon, J.; Leviner, L. E.; Loach, J. C.; MacMullin, J.; MacMullin, S.; Martin, R. D.; Meijer, S.; Mertens, S.; Nomachi, M.; Orrell, J. L.; O'Shaughnessy, C.; Overman, N. R.; Phillips, D. G.; Poon, A. W. P.; Pushkin, K.; Radford, D. C.; Rager, J.; Rielage, K.; Robertson, R. G. H.; Romero-Romero, E.; Ronquest, M. C.; Schubert, A. G.; Shanks, B.; Shima, T.; Shirchenko, M.; Snavely, K. J.; Snyder, N.; Suriano, A. M.; Thompson, J.; Timkin, V.; Tornow, W.; Trimble, J. E.; Varner, R. L.; Vasilyev, S.; Vetter, K.; Vorren, K.; White, B. R.; Wilkerson, J. F.; Wiseman, C.; Xu, W.; Yakushev, E.; Young, A. R.; Yu, C.-H.; Yumatov, V.

    The Majorana Collaboration is constructing a system containing 40 kg of HPGe detectors to demonstrate the feasibility and potential of a future tonne-scale experiment capable of probing the neutrino mass scale in the inverted-hierarchy region. To realize this, a major goal of the Majorana Demonstrator is to demonstrate a path forward to achieving a background rate at or below 1 cnt/(ROI-t-y) in the 4 keV region of interest around the Q-value at 2039 keV. This goal is pursued through a combination of a significant reduction of radioactive impurities in construction materials with analytical methods for background rejection, for example using powerful pulse shape analysis techniques profiting from the p-type point contact HPGe detectors technology. The effectiveness of these methods is assessed using simulations of the different background components whose purity levels are constrained from radioassay measurements.

  15. Background compensation for a radiation level monitor

    Science.gov (United States)

    Keefe, D.J.

    1975-12-01

    Background compensation in a device such as a hand and foot monitor is provided by digital means using a scaler. With no radiation level test initiated, a scaler is down-counted from zero according to the background measured. With a radiation level test initiated, the scaler is up-counted from the previous down-count position according to the radiation emitted from the monitored object and an alarm is generated if, with the scaler having crossed zero in the positive going direction, a particular number is exceeded in a specific time period after initiation of the test. If the test is initiated while the scale is down-counting, the background count from the previous down- count stored in a memory is used as the initial starting point for the up-count.

  16. Non-perturbative background field calculations

    International Nuclear Information System (INIS)

    Stephens, C.R.; Department of Physics, University of Utah, Salt Lake City, Utah 84112)

    1988-01-01

    New methods are developed for calculating one loop functional determinants in quantum field theory. Instead of relying on a calculation of all the eigenvalues of the small fluctuation equation, these techniques exploit the ability of the proper time formalism to reformulate an infinite dimensional field theoretic problem into a finite dimensional covariant quantum mechanical analog, thereby allowing powerful tools such as the method of Jacobi fields to be used advantageously in a field theory setting. More generally the methods developed herein should be extremely valuable when calculating quantum processes in non-constant background fields, offering a utilitarian alternative to the two standard methods of calculation: perturbation theory in the background field or taking the background field into account exactly. The formalism developed also allows for the approximate calculation of covariances of partial differential equations from a knowledge of the solutions of a homogeneous ordinary differential equation. copyright 1988 Academic Press, Inc

  17. Origin of the diffuse background gamma radiation

    International Nuclear Information System (INIS)

    Stecker, F.W.; Puget, J.L.

    1974-05-01

    Recent observations have now provided evidence for diffuse background gamma radiation extending to energies beyond 100 MeV. There is some evidence of isotropy and implied cosmological origin. Significant features in the spectrum of this background radiation were observed which provide evidence for its origin in nuclear processes in the early stages of the big-band cosmology and tie in these processes with galaxy formation theory. A crucial test of the theory may lie in future observations of the background radiation in the 100 MeV to 100 GeV energy range which may be made with large orbiting spark-chamber satellite detectors. A discussion of the theoretical interpretations of present data, their connection with baryon symmetric cosmology and galaxy formation theory, and the need for future observations are given. (U.S.)

  18. Cosmic microwave background distortions at high frequencies

    International Nuclear Information System (INIS)

    Peter, W.; Peratt, A.L.

    1988-01-01

    The authors analyze the deviation of the cosmic background radiation spectrum from the 2.76+-0.02 0 Κ blackbody curve. If the cosmic background radiation is due to absorption and re-emission of synchrotron radiation from galactic-width current filaments, higher-order synchrotron modes are less thermalized than lower-order modes, causing a distortion of the blackbody curve at higher frequencies. New observations of the microwave background spectrum at short wavelengths should provide an indication of the number of synchrotron modes thermalized in this process. The deviation of the spectrum from that of a perfect blackbody can thus be correlated with astronomical observations such as filament temperatures and electron energies. The results are discussed and compared with the theoretical predictions of other models which assume the presence of intergalactic superconducting cosmic strings

  19. Non-perturbative background field calculations

    Science.gov (United States)

    Stephens, C. R.

    1988-01-01

    New methods are developed for calculating one loop functional determinants in quantum field theory. Instead of relying on a calculation of all the eigenvalues of the small fluctuation equation, these techniques exploit the ability of the proper time formalism to reformulate an infinite dimensional field theoretic problem into a finite dimensional covariant quantum mechanical analog, thereby allowing powerful tools such as the method of Jacobi fields to be used advantageously in a field theory setting. More generally the methods developed herein should be extremely valuable when calculating quantum processes in non-constant background fields, offering a utilitarian alternative to the two standard methods of calculation—perturbation theory in the background field or taking the background field into account exactly. The formalism developed also allows for the approximate calculation of covariances of partial differential equations from a knowledge of the solutions of a homogeneous ordinary differential equation.

  20. Relation between genotype, phenotype and therapeutic drug concentrations of nortriptyline or venlafaxine users in old age psychiatry

    NARCIS (Netherlands)

    Berm, E.J.J.; Kok, R.M.; Hak, E.; Wilffert, B.

    2015-01-01

    Background The relationship between phenotype and genotype of the polymorphic cytochrome P450 2D6 enzyme (CYP2D6) has been intensively studied, however few studies are conducted among older persons. In a study among 900 relatively young venlafaxine users (mean age 45 years), 83% were genotyped as an

  1. High proportion of large genomic deletions and a genotype phenotype update in 80 unrelated families with juvenile polyposis syndrome

    DEFF Research Database (Denmark)

    Aretz, S; Stienen, D; Uhlhaas, S

    2007-01-01

    BACKGROUND: In patients with juvenile polyposis syndrome (JPS) the frequency of large genomic deletions in the SMAD4 and BMPR1A genes was unknown. METHODS: Mutation and phenotype analysis was used in 80 unrelated patients of whom 65 met the clinical criteria for JPS (typical JPS) and 15 were susp...

  2. Of monkeys and men: A metabolomic analysis of static and dynamic urinary metabolic phenotypes in two species

    NARCIS (Netherlands)

    Saccenti, E.; Tenori, L.; Verbruggen, P.; Timmerman, M.E.; Bouwman, J.; Greef, J. van der; Luchinat, C.; Smilde, A.K.

    2014-01-01

    Background: Metabolomics has attracted the interest of the medical community for its potential in predicting early derangements from a healthy to a diseased metabolic phenotype. One key issue is the diversity observed in metabolic profiles of different healthy individuals, commonly attributed to the

  3. High level of molecular and phenotypic biodiversity in Jatropha curcas from Central America compared to Africa, Asia and South America

    NARCIS (Netherlands)

    Montes Osorio, L.R.; Torres Salvador, A.F.; Jongschaap, R.E.E.; Azurdia, C.; Berduo, J.; Trindade, L.M.; Visser, R.G.F.; Loo, van E.N.

    2014-01-01

    Background The main bottleneck to elevate jatropha (Jatropha curcas L.) from a wild species to a profitable biodiesel crop is the low genetic and phenotypic variation found in different regions of the world, hampering efficient plant breeding for productivity traits. In this study, 182 accessions

  4. Genetic and phenotypic overlap of specific obsessive-compulsive and attention-deficit/hyperactive subtypes with Tourette syndrome

    NARCIS (Netherlands)

    Hirschtritt, M. E.; Darrow, S. M.; Illmann, C.; Osiecki, L.; Grados, M.; Sandor, P.; Dion, Y.; King, R. A.; Pauls, D.; Budman, C. L.; Cath, D. C.; Greenberg, E.; Lyon, G. J.; Yu, D.; McGrath, L. M.; McMahon, W. M.; Lee, P. C.; Delucchi, K. L.; Scharf, J. M.; Mathews, C. A.

    Background. The unique phenotypic and genetic aspects of obsessive-compulsive (OCD) and attention-deficit/hyperactivity disorder (ADHD) among individuals with Tourette syndrome (TS) are not well characterized. Here, we examine symptom patterns and heritability of OCD and ADHD in TS families. Method.

  5. Of Monkeys and Men: A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species

    NARCIS (Netherlands)

    Saccenti, E.; Tenori, L.; Verbruggen, P.; Timmerman, M.E.; Bouwman, J.; Greef, de J.; Luchinat, C.; Smilde, A.K.

    2014-01-01

    Background Metabolomics has attracted the interest of the medical community for its potential in predicting early derangements from a healthy to a diseased metabolic phenotype. One key issue is the diversity observed in metabolic profiles of different healthy individuals, commonly attributed to the

  6. Of Monkeys and Men : A Metabolomic Analysis of Static and Dynamic Urinary Metabolic Phenotypes in Two Species

    NARCIS (Netherlands)

    Saccenti, E.; Tenori, L.; Verbruggen, P.; Timmerman, Marieke; Bouwman, J.; van der Greef, J.; Luchinat, C.; Smilde, Age K.

    2014-01-01

    Background Metabolomics has attracted the interest of the medical community for its potential in predicting early derangements from a healthy to a diseased metabolic phenotype. One key issue is the diversity observed in metabolic profiles of different healthy individuals, commonly attributed to the

  7. Factor analysis in the Genetics of Asthma International Network family study identifies five major quantitative asthma phenotypes

    NARCIS (Netherlands)

    Pillai, S. G.; Tang, Y.; van den Oord, E.; Klotsman, M.; Barnes, K.; Carlsen, K.; Gerritsen, J.; Lenney, W.; Silverman, M.; Sly, P.; Sundy, J.; Tsanakas, J.; von Berg, A.; Whyte, M.; Ortega, H. G.; Anderson, W. H.; Helms, P. J.

    Background Asthma is a clinically heterogeneous disease caused by a complex interaction between genetic susceptibility and diverse environmental factors. In common with other complex diseases the lack of a standardized scheme to evaluate the phenotypic variability poses challenges in identifying the

  8. Body size, physical activity and risk of colorectal cancer with or without the CpG island methylator phenotype (CIMP)

    NARCIS (Netherlands)

    Hughes, L.A.E.; Simons, C.C.J.M.; Brandt, P.A. van den; Goldbohm, R.A.; Goeij, A.F. de; Bruïne, A.P. de; Engeland, M. van; Weijenberg, M.P.

    2011-01-01

    Background: We investigated how body size and physical activity influence the risk of the CpG island methylator phenotype (CIMP) in colorectal cancer (CRC). Methods: In the Netherlands Cohort Study (n = 120,852), risk factors were self-reported at baseline in 1986. After 7.3 years of follow-up, 603

  9. Sex-specific phenotypes of hyperthyroidism and hypothyroidism in mice.

    Science.gov (United States)

    Rakov, Helena; Engels, Kathrin; Hönes, Georg Sebastian; Strucksberg, Karl-Heinz; Moeller, Lars Christian; Köhrle, Josef; Zwanziger, Denise; Führer, Dagmar

    2016-01-01

    in line with altered functional and metabolic traits of hyper- and hypothyroidism. These data demonstrate that the phenotypes of hypo- and hyperthyroidism differ between male and female mice and indicate that sex is an important modifier of phenotypic manifestations.

  10. Phenotypic equilibrium as probabilistic convergence in multi-phenotype cell population dynamics.

    Directory of Open Access Journals (Sweden)

    Da-Quan Jiang

    Full Text Available We consider the cell population dynamics with n different phenotypes. Both the Markovian branching process model (stochastic model and the ordinary differential equation (ODE system model (deterministic model are presented, and exploited to investigate the dynamics of the phenotypic proportions. We will prove that in both models, these proportions will tend to constants regardless of initial population states ("phenotypic equilibrium" under weak conditions, which explains the experimental phenomenon in Gupta et al.'s paper. We also prove that Gupta et al.'s explanation is the ODE model under a special assumption. As an application, we will give sufficient and necessary conditions under which the proportion of one phenotype tends to 0 (die out or 1 (dominate. We also extend our results to non-Markovian cases.

  11. Sensorimotor adaptation is influenced by background music.

    Science.gov (United States)

    Bock, Otmar

    2010-06-01

    It is well established that listening to music can modify subjects' cognitive performance. The present study evaluates whether this so-called Mozart Effect extends beyond cognitive tasks and includes sensorimotor adaptation. Three subject groups listened to musical pieces that in the author's judgment were serene, neutral, or sad, respectively. This judgment was confirmed by the subjects' introspective reports. While listening to music, subjects engaged in a pointing task that required them to adapt to rotated visual feedback. All three groups adapted successfully, but the speed and magnitude of adaptive improvement was more pronounced with serene music than with the other two music types. In contrast, aftereffects upon restoration of normal feedback were independent of music type. These findings support the existence of a "Mozart effect" for strategic movement control, but not for adaptive recalibration. Possibly, listening to music modifies neural activity in an intertwined cognitive-emotional network.

  12. Background characterization for the GERDA experiment

    Energy Technology Data Exchange (ETDEWEB)

    Becerici-Schmidt, Neslihan [Max-Planck-Institut fuer Physik, Muenchen (Germany); Collaboration: GERDA-Collaboration

    2013-07-01

    The GERmanium Detector Array (Gerda) experiment at the LNGS laboratory of INFN searches for the neutrinoless double beta (0νββ) decay of {sup 76}Ge. A discovery of this decay can greatly advance our knowledge on the nature and properties of neutrinos. The current best limit on the half-life of {sup 76}Ge 0νββ decay is 1.9 . 10{sup 25} years (90% C.L.). In order to increase the sensitivity on the half-life with respect to past experiments, the background rate in the energy region of interest (ROI) around Q{sub ββ} = 2039 keV has been reduced by a factor 10. Gerda started data-taking with the full set of Phase I detectors in November 2011. Identification of the background in the first phase of the experiment is of major importance to further mitigate the background for Gerda Phase II. An analysis of the Phase I data resulted in a good understanding of the individual components in the Gerda background spectrum. The background components in the ROI have been identified to be mainly due to β- and γ-induced events originating from {sup 214}Bi ({sup 238}U-series), {sup 208}Tl ({sup 232}Th-series), {sup 42}K (progeny of {sup 42}Ar) and α-induced events coming from isotopes in the {sup 226}Ra decay chain. A background decomposition in the ROI will be presented, with a special emphasis on the contribution from α-induced events.

  13. Decomposing phenotype descriptions for the human skeletal phenome.

    Science.gov (United States)

    Groza, Tudor; Hunter, Jane; Zankl, Andreas

    2013-01-01

    Over the course of the last few years there has been a significant amount of research performed on ontology-based formalization of phenotype descriptions. The intrinsic value and knowledge captured within such descriptions can only be expressed by taking advantage of their inner structure that implicitly combines qualities and anatomical entities. We present a meta-model (the Phenotype Fragment Ontology) and a processing pipeline that enable together the automatic decomposition and conceptualization of phenotype descriptions for the human skeletal phenome. We use this approach to showcase the usefulness of the generic concept of phenotype decomposition by performing an experimental study on all skeletal phenotype concepts defined in the Human Phenotype Ontology.

  14. Transatlantic Regulatory Cooperation: Background and Analysis

    Science.gov (United States)

    2009-08-24

    than in chemicals. In this sector, the U.S. and EU have fundamentally different regulations on issues such as genetically modified organisms ( GMOs ...hormones, and the registration and restriction of chemical substances. In the case of GMOs , these differences have translated into longer...authorization times and stricter standards for approval, release, and marketing of GMOs in the EU than in the U.S. Moreover, GMOs have been the subject of a

  15. Background simulation for the GENIUS project

    International Nuclear Information System (INIS)

    Ponkratenko, O.A.; Tretyak, V.I.; Zdesenko, Yu.G.

    1999-01-01

    The background simulations for the GENIUS experiment were performed with the help of GEANT 3.21 package and event generator DECAY 4.Contributions from the cosmogenic activity produced in the Ge detectors and from its radioactive impurities as well as from contamination of the liquid nitrogen and other materials were calculated.External gamma and neutron background were taking into consideration also.The results of calculations evidently show feasibility of the GENIUS project,which can substantially promote development of modern astroparticle physics

  16. Electromagnetic wave collapse in a radiation background

    International Nuclear Information System (INIS)

    Marklund, Mattias; Brodin, Gert; Stenflo, Lennart

    2003-01-01

    The nonlinear interaction, due to quantum electrodynamical (QED) effects between an electromagnetic pulse and a radiation background, is investigated by combining the methods of radiation hydrodynamics with the QED theory for photon-photon scattering. For the case of a single coherent electromagnetic pulse, we obtain a Zakharov-like system, where the radiation pressure of the pulse acts as a driver of acoustic waves in the photon gas. For a sufficiently intense pulse and/or background energy density, there is focusing and the subsequent collapse of the pulse. The relevance of our results for various astrophysical applications are discussed

  17. Optimization of the ECT background coil

    International Nuclear Information System (INIS)

    Ballou, J.K.; Luton, J.N.

    1975-01-01

    This study was begun to optimize the Eccentric Coil Test (ECT) background coil. In the course of this work a general optimization code was obtained, tested, and applied to the ECT problem. So far this code has proven to be very satisfactory. The results obtained with this code and earlier codes have illustrated the parametric behavior of such a coil system and that the optimum for this type system is broad. This study also shows that a background coil with a winding current density of less than 3000 A/cm 2 is not feasible for the ECT models presented in this paper

  18. Elastic lattice in an incommensurate background

    International Nuclear Information System (INIS)

    Dickman, R.; Chudnovsky, E.M.

    1995-01-01

    We study a harmonic triangular lattice, which relaxes in the presence of an incommensurate short-wavelength potential. Monte Carlo simulations reveal that the elastic lattice exhibits only short-ranged translational correlations, despite the absence of defects in either lattice. Extended orientational order, however, persists in the presence of the background. Translational correlation lengths exhibit approximate power-law dependence upon cooling rate and background strength. Our results may be relevant to Wigner crystals, atomic monolayers on crystals surfaces, and flux-line and magnetic bubble lattices

  19. Cognitive psychology and depth psychology backgrounds

    International Nuclear Information System (INIS)

    Fritzsche, A.F.

    1986-01-01

    The sixth chapter gives an insight into the risk perception process which is highly determined by emotions, and, thus, deals with the psychological backgrounds of both the conscious cognitive and the subconscious intuitive realms of the human psyche. The chapter deals with the formation of opinion and the origination of an attitude towards an issue; cognitive-psychological patterns of thinking from the field of risk perception; the question of man's rationality; pertinent aspects of group behaviour; depth psychological backgrounds of the fear of technology; the collective subconscious; nuclear energy as a preferred object of projection for various psychological problems of modern man. (HSCH) [de

  20. Conserved quantities in background independent theories

    Energy Technology Data Exchange (ETDEWEB)

    Markopoulou, Fotini [Perimeter Institute for Theoretical Physics, 35 King Street North, Waterloo, Ontario N2J 2W9 (Canada); Department of Physics, University of Waterloo, Waterloo, Ontario N2L 3G1 (Canada)

    2007-05-15

    We discuss the difficulties that background independent theories based on quantum geometry encounter in deriving general relativity as the low energy limit. We follow a geometrogenesis scenario of a phase transition from a pre-geometric theory to a geometric phase which suggests that a first step towards the low energy limit is searching for the effective collective excitations that will characterize it. Using the correspondence between the pre-geometric background independent theory and a quantum information processor, we are able to use the method of noiseless subsystems to extract such coherent collective excitations. We illustrate this in the case of locally evolving graphs.

  1. Fermionic bound states in distinct kinklike backgrounds

    Energy Technology Data Exchange (ETDEWEB)

    Bazeia, D. [Universidade Federal da Paraiba, Departamento de Fisica, Joao Pessoa, Paraiba (Brazil); Mohammadi, A. [Universidade Federal de Campina Grande, Departamento de Fisica, Caixa Postal 10071, Campina Grande, Paraiba (Brazil)

    2017-04-15

    This work deals with fermions in the background of distinct localized structures in the two-dimensional spacetime. Although the structures have a similar topological character, which is responsible for the appearance of fractionally charged excitations, we want to investigate how the geometric deformations that appear in the localized structures contribute to the change in the physical properties of the fermionic bound states. We investigate the two-kink and compact kinklike backgrounds, and we consider two distinct boson-fermion interactions, one motivated by supersymmetry and the other described by the standard Yukawa coupling. (orig.)

  2. A low background pulsed neutron polyenergetic beam

    International Nuclear Information System (INIS)

    Adib, M.; Abdelkawy, A.; Habib, N.; abuelela, M.; Wahba, M.; kilany, M.; Kalebebin, S.M.

    1992-01-01

    A low background pulsed neutron polyenergetic thermal beam at ET-R R-1 is produced by a rotor and rotating collimator suspended in magnetic fields. Each of them is mounted on its mobile platform and whose centres are 66 cm apart, rotating synchronously at speeds up to 16000 rpm. It was found that the neutron burst produced by the rotor with almost 100% transmission passes through the collimator, when the rotation phase between them is 28.8 degree Moreover the background level achieved at the detector position is low, constant and free from peaks due to gamma rays and fast neutrons accompanying the reactor thermal beam.3 fig

  3. Noise correlations in cosmic microwave background experiments

    Science.gov (United States)

    Dodelson, Scott; Kosowsky, Arthur; Myers, Steven T.

    1995-01-01

    Many analysis of microwave background experiments neglect the correlation of noise in different frequency of polarization channels. We show that these correlations, should they be present, can lead to serve misinterpretation of an experiment. In particular, correlated noise arising from either electronics or atmosphere may mimic a cosmic signal. We quantify how the likelihood function for a given experiment varies with noise correlation, using both simple analytic models and actual data. For a typical microwave background anisotropy experiment, noise correlations at the level of 1% of the overall noise can seriously reduce the significance of a given detection.

  4. Cosmic microwave background probes models of inflation

    Science.gov (United States)

    Davis, Richard L.; Hodges, Hardy M.; Smoot, George F.; Steinhardt, Paul J.; Turner, Michael S.

    1992-01-01

    Inflation creates both scalar (density) and tensor (gravity wave) metric perturbations. We find that the tensor-mode contribution to the cosmic microwave background anisotropy on large-angular scales can only exceed that of the scalar mode in models where the spectrum of perturbations deviates significantly from scale invariance. If the tensor mode dominates at large-angular scales, then the value of DeltaT/T predicted on 1 deg is less than if the scalar mode dominates, and, for cold-dark-matter models, bias factors greater than 1 can be made consistent with Cosmic Background Explorer (COBE) DMR results.

  5. Cosmic microwave background at its twentieth anniversary

    International Nuclear Information System (INIS)

    Partridge, R.B.

    1986-01-01

    The role of cosmic microwave background radiation in cosmology is examined. The thermal spectrum, the large entropy in the universe, the large-scale isotropy of the radiation, and the small-scale isotropy or homogeneity of the radiation are analyzed in order to describe the properties of the universe. It is observed that the microwave background spectrum is thermal over a wide range, there is a significant detectable dipole anisotropy in the radiation, but no quadrupole anisotropy, and there is a high deree of radiation isotropy on angular scales between 1-5 degrees. 62 references

  6. Natural background radiation and oncologic disease incidence

    International Nuclear Information System (INIS)

    Burenin, P.I.

    1982-01-01

    Cause and effect relationships between oncologic disease incidence in human population and environmental factors are examined using investigation materials of Soviet and foreign authors. The data concerning US white population are adduced. The role and contribution of natural background radiation oncologic disease prevalence have been determined with the help of system information analysis. The probable damage of oncologic disease is shown to decrease as the background radiation level diminishes. The linear nature of dose-response relationspip has been established. The necessity to include the life history of the studied population along with environmental factors in epidemiological study under conditions of multiplicity of cancerogenesis causes is emphasized

  7. Socioeconomic and modifiable predictors of blood pressure control ...

    African Journals Online (AJOL)

    Background. Low socioeconomic status is associated with the risk of hypertension. There are few reports of the effect of socioeconomic and potentially modifiable factors on the control of hypertension in South Africa (SA). Objectives. To investigate associations between patients' socioeconomic status and characteristics of ...

  8. Host Genotype and Gut Microbiome Modulate Insulin Secretion and Diet-Induced Metabolic Phenotypes.

    Science.gov (United States)

    Kreznar, Julia H; Keller, Mark P; Traeger, Lindsay L; Rabaglia, Mary E; Schueler, Kathryn L; Stapleton, Donald S; Zhao, Wen; Vivas, Eugenio I; Yandell, Brian S; Broman, Aimee Teo; Hagenbuch, Bruno; Attie, Alan D; Rey, Federico E

    2017-02-14

    Genetic variation drives phenotypic diversity and influences the predisposition to metabolic disease. Here, we characterize the metabolic phenotypes of eight genetically distinct inbred mouse strains in response to a high-fat/high-sucrose diet. We found significant variation in diabetes-related phenotypes and gut microbiota composition among the different mouse strains in response to the dietary challenge and identified taxa associated with these traits. Follow-up microbiota transplant experiments showed that altering the composition of the gut microbiota modifies strain-specific susceptibility to diet-induced metabolic disease. Animals harboring microbial communities with enhanced capacity for processing dietary sugars and for generating hydrophobic bile acids showed increased susceptibility to metabolic disease. Notably, differences in glucose-stimulated insulin secretion between different mouse strains were partially recapitulated via gut microbiota transfer. Our results suggest that the gut microbiome contributes to the genetic and phenotypic diversity observed among mouse strains and provide a link between the gut microbiome and insulin secretion. Copyright © 2017 The Author(s). Published by Elsevier Inc. All rights reserved.

  9. Physical constraints in cell fate specification. A case in point: Microgravity and phenotypes differentiation.

    Science.gov (United States)

    Masiello, Maria Grazia; Verna, Roberto; Cucina, Alessandra; Bizzarri, Mariano

    2018-05-01

    Data obtained by studying mammalian cells in absence of gravity strongly support the notion that cell fate specification cannot be understood according to the current molecular model. A paradigmatic case in point is provided by studying cell populations growing in absence of gravity. When the physical constraint (gravity) is 'experimentally removed', cells spontaneously allocate into two morphologically different phenotypes. Such phenomenon is likely enacted by the intrinsic stochasticity, which, in turn, is successively 'canalized' by a specific gene regulatory network. Both phenotypes are thermodynamically and functionally 'compatibles' with the new, modified environment. However, when the two cell subsets are reseeded into the 1g gravity field the two phenotypes collapse into one. Gravity constraints the system in adopting only one phenotype, not by selecting a pre-existing configuration, but more precisely shaping it de-novo through the modification of the cytoskeleton three-dimensional structure. Overall, those findings highlight how macro-scale features are irreducible to lower-scale explanations. The identification of macroscale control parameters - as those depending on the field (gravity, electromagnetic fields) or emerging from the cooperativity among the field's components (tissue stiffness, cell-to-cell connectivity) - are mandatory for assessing boundary conditions for models at lower scales, thus providing a concrete instantiation of top-down effects. Copyright © 2018 Elsevier Ltd. All rights reserved.

  10. Developmental phenotypic plasticity helps bridge stochastic weather events associated with climate change.

    Science.gov (United States)

    Burggren, Warren

    2018-05-10

    The slow, inexorable rise in annual average global temperatures and acidification of the oceans are often advanced as consequences of global change. However, many environmental changes, especially those involving weather (as opposed to climate), are often stochastic, variable and extreme, particularly in temperate terrestrial or freshwater habitats. Moreover, few studies of animal and plant phenotypic plasticity employ realistic (i.e. short-term, stochastic) environmental change in their protocols. Here, I posit that the frequently abrupt environmental changes (days, weeks, months) accompanying much longer-term general climate change (e.g. global warming over decades or centuries) require consideration of the true nature of environmental change (as opposed to statistical means) coupled with an expansion of focus to consider developmental phenotypic plasticity. Such plasticity can be in multiple forms - obligatory/facultative, beneficial/deleterious - depending upon the degree and rate of environmental variability at specific points in organismal development. Essentially, adult phenotypic plasticity, as important as it is, will be irrelevant if developing offspring lack sufficient plasticity to create modified phenotypes necessary for survival. © 2018. Published by The Company of Biologists Ltd.

  11. Is rate of skin wound healing associated with aging or longevity phenotype?

    Science.gov (United States)

    Yanai, Hagai; Budovsky, Arie; Tacutu, Robi; Fraifeld, Vadim E

    2011-12-01

    Wound healing (WH) is a fundamental biological process. Is it associated with a longevity or aging phenotype? In an attempt to answer this question, we compared the established mouse models with genetically modified life span and also an altered rate of WH in the skin. Our analysis showed that the rate of skin WH in advanced ages (but not in the young animals) may be used as a marker for biological age, i.e., to be indicative of the longevity or aging phenotype. The ability to preserve the rate of skin WH up to an old age appears to be associated with a longevity phenotype, whereas a decline in WH-with an aging phenotype. In the young, this relationship is more complex and might even be inversed. While the aging process is likely to cause wounds to heal slowly, an altered WH rate in younger animals could indicate a different cellular proliferation and/or migration capacity, which is likely to affect other major processes such as the onset and progression of cancer. As a point for future studies on WH and longevity, using only young animals might yield confusing or misleading results, and therefore including older animals in the analysis is encouraged.

  12. Tensorial spacetime geometries and background-independent quantum field theory

    International Nuclear Information System (INIS)

    Raetzel, Dennis

    2012-01-01

    Famously, Einstein read off the geometry of spacetime from Maxwell's equations. Today, we take this geometry that serious that our fundamental theory of matter, the standard model of particle physics, is based on it. However, it seems that there is a gap in our understanding if it comes to the physics outside of the solar system. Independent surveys show that we need concepts like dark matter and dark energy to make our models fit with the observations. But these concepts do not fit in the standard model of particle physics. To overcome this problem, at least, we have to be open to matter fields with kinematics and dynamics beyond the standard model. But these matter fields might then very well correspond to different spacetime geometries. This is the basis of this thesis: it studies the underlying spacetime geometries and ventures into the quantization of those matter fields independently of any background geometry. In the first part of this thesis, conditions are identified that a general tensorial geometry must fulfill to serve as a viable spacetime structure. Kinematics of massless and massive point particles on such geometries are introduced and the physical implications are investigated. Additionally, field equations for massive matter fields are constructed like for example a modified Dirac equation. In the second part, a background independent formulation of quantum field theory, the general boundary formulation, is reviewed. The general boundary formulation is then applied to the Unruh effect as a testing ground and first attempts are made to quantize massive matter fields on tensorial spacetimes.

  13. Dirac fermions in nontrivial topology black hole backgrounds

    International Nuclear Information System (INIS)

    Gozdz, Marek; Nakonieczny, Lukasz; Rogatko, Marek

    2010-01-01

    We discuss the behavior of the Dirac fermions in a general spherically symmetric black hole background with a nontrivial topology of the event horizon. Both massive and massless cases are taken into account. We will conduct an analytical study of intermediate and late-time behavior of massive Dirac hair in the background of a black hole with a global monopole and dilaton black hole pierced by a cosmic string. In the case of a global monopole swallowed by a static black hole, the intermediate late-time behavior depends on the mass of the Dirac field, the multiple number of the wave mode, and the global monopole parameter. The late-time behavior is quite independent of these factors and has a decay rate proportional to t -5/6 . As far as the black hole pierced by a cosmic string is concerned, the intermediate late-time behavior depends only on the hair mass and the multipole number of the wave mode, while the late-time behavior dependence is the same as in the previous case. The main modification stems from the topology of the S 2 sphere pierced by a cosmic string. This factor modifies the eigenvalues of the Dirac operator acting on the transverse manifold.

  14. Advanced phenotyping and phenotype data analysis for the plant growth and development study

    Directory of Open Access Journals (Sweden)

    Md. Matiur eRahaman

    2015-08-01

    Full Text Available Due to increase in the consumption of food, feed, fuel and to ensure global food security for rapidly growing human population, there is need to breed high yielding crops that can adapt to future climate. To solve these global issues, novel approaches are required to provide quantitative phenotypes to elucidate the genetic basis of agriculturally import traits and to screen germplasm with super performance in function under resource-limited environment. At present, plant phenomics has offered and integrated suite technologies for understanding the complete set of phenotypes of plants, towards the progression of the full characteristics of plants with whole sequenced genomes. In this aspect, high-throughput phenotyping platforms have been developed that enables to capture extensive and intensive phenotype data from non-destructive imaging over time. These developments advance our view on plant growth and performance with responses to the changing climate and environment. In this paper, we present a brief review on currently developed high-throughput plant phenotyping infrastructures based on imaging techniques and corresponding principles for phenotype data analysis.

  15. ABO blood group phenotype frequency estimation using molecular phenotyping in rhesus and cynomolgus macaques.

    Science.gov (United States)

    Kanthaswamy, S; Ng, J; Oldt, R F; Valdivia, L; Houghton, P; Smith, D G

    2017-11-01

    A much larger sample (N = 2369) was used to evaluate a previously reported distribution of the A, AB and B blood group phenotypes in rhesus and cynomolgus macaques from six different regional populations. These samples, acquired from 15 different breeding and research facilities in the United States, were analyzed using a real-time quantitative polymerase chain reaction (qPCR) assay that targets single nucleotide polymorphisms (SNPs) responsible for the macaque A, B and AB phenotypes. The frequency distributions of blood group phenotypes of the two species differ significantly from each other and significant regional differentiation within the geographic ranges of each species was also observed. The B blood group phenotype was prevalent in rhesus macaques, especially those from India, while the frequencies of the A, B and AB phenotypes varied significantly among cynomolgus macaques from different geographic regions. The Mauritian cynomolgus macaques, despite having originated in Indonesia, showed significant (P ≪ .01) divergence from the Indonesian animals at the ABO blood group locus. Most Mauritian animals belonged to the B blood group while the Indonesian animals were mostly A. The close similarity in blood group frequency distributions between the Chinese rhesus and Indochinese cynomolgus macaques demonstrates that the introgression between these two species extends beyond the zone of intergradation in Indochina. This study underscores the importance of ABO blood group phenotyping of the domestic supply of macaques and their biospecimens. © 2017 John Wiley & Sons A/S. Published by John Wiley & Sons Ltd.

  16. Elucidating the genotype-phenotype map by automatic enumeration and analysis of the phenotypic repertoire.

    Science.gov (United States)

    Lomnitz, Jason G; Savageau, Michael A

    The gap between genotype and phenotype is filled by complex biochemical systems most of which are poorly understood. Because these systems are complex, it is widely appreciated that quantitative understanding can only be achieved with the aid of mathematical models. However, formulating models and measuring or estimating their numerous rate constants and binding constants is daunting. Here we present a strategy for automating difficult aspects of the process. The strategy, based on a system design space methodology, is applied to a class of 16 designs for a synthetic gene oscillator that includes seven designs previously formulated on the basis of experimentally measured and estimated parameters. Our strategy provides four important innovations by automating: (1) enumeration of the repertoire of qualitatively distinct phenotypes for a system; (2) generation of parameter values for any particular phenotype; (3) simultaneous realization of parameter values for several phenotypes to aid visualization of transitions from one phenotype to another, in critical cases from functional to dysfunctional; and (4) identification of ensembles of phenotypes whose expression can be phased to achieve a specific sequence of functions for rationally engineering synthetic constructs. Our strategy, applied to the 16 designs, reproduced previous results and identified two additional designs capable of sustained oscillations that were previously missed. Starting with a system's relatively fixed aspects, its architectural features, our method enables automated analysis of nonlinear biochemical systems from a global perspective, without first specifying parameter values. The examples presented demonstrate the efficiency and power of this automated strategy.

  17. In silico search for modifier genes associated with pancreatic and liver disease in Cystic Fibrosis.

    Directory of Open Access Journals (Sweden)

    Pascal Trouvé

    Full Text Available Cystic Fibrosis is the most common lethal autosomal recessive disorder in the white population, affecting among other organs, the lung, the pancreas and the liver. Whereas Cystic Fibrosis is a monogenic disease, many studies reveal a very complex relationship between genotype and clinical phenotype. Indeed, the broad phenotypic spectrum observed in Cystic Fibrosis is far from being explained by obvious genotype-phenotype correlations and it is admitted that Cystic Fibrosis disease is the result of multiple factors, including effects of the environment as well as modifier genes. Our objective was to highlight new modifier genes with potential implications in the lung, pancreatic and liver outcomes of the disease. For this purpose we performed a system biology approach which combined, database mining, literature mining, gene expression study and network analysis as well as pathway enrichment analysis and protein-protein interactions. We found that IFI16, CCNE2 and IGFBP2 are potential modifiers in the altered lung function in Cystic Fibrosis. We also found that EPHX1, HLA-DQA1, HLA-DQB1, DSP and SLC33A1, GPNMB, NCF2, RASGRP1, LGALS3 and PTPN13, are potential modifiers in pancreas and liver, respectively. Associated pathways indicate that immune system is likely involved and that Ubiquitin C is probably a central node, linking Cystic Fibrosis to liver and pancreatic disease. We highlight here new modifier genes with potential implications in Cystic Fibrosis. Nevertheless, our in silico analysis requires functional analysis to give our results a physiological relevance.

  18. Does Social Background Influence Political Science Grades?

    Science.gov (United States)

    Tiruneh, Gizachew

    2013-01-01

    This paper tests a hypothesized linear relationship between social background and final grades in several political science courses that I taught at the University of Central Arkansas. I employ a cross-sectional research design and ordinary least square (OLS) estimators to test the foregoing hypothesis. Relying on a sample of up to 204…

  19. Physiologic correlates to background noise acceptance

    Science.gov (United States)

    Tampas, Joanna; Harkrider, Ashley; Nabelek, Anna

    2004-05-01

    Acceptance of background noise can be evaluated by having listeners indicate the highest background noise level (BNL) they are willing to accept while following the words of a story presented at their most comfortable listening level (MCL). The difference between the selected MCL and BNL is termed the acceptable noise level (ANL). One of the consistent findings in previous studies of ANL is large intersubject variability in acceptance of background noise. This variability is not related to age, gender, hearing sensitivity, personality, type of background noise, or speech perception in noise performance. The purpose of the current experiment was to determine if individual differences in physiological activity measured from the peripheral and central auditory systems of young female adults with normal hearing can account for the variability observed in ANL. Correlations between ANL and various physiological responses, including spontaneous, click-evoked, and distortion-product otoacoustic emissions, auditory brainstem and middle latency evoked potentials, and electroencephalography will be presented. Results may increase understanding of the regions of the auditory system that contribute to individual noise acceptance.

  20. Egypt: Background and U.S. Relations

    Science.gov (United States)

    2013-06-27

    right to govern; the more the Brotherhood charges ahead, the more it confirms the others’ belief of its monopolistic designs over power. Even if...appropriate market -reform and economic growth activities.” Egypt: Background and U.S. Relations Congressional Research Service 18 according to the State