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Search Results: 1 - 10 of 174587 matches for " Peter B. Farmer "
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Environmental Exposure of the Mouse Germ Line: DNA Adducts in Spermatozoa and Formation of De Novo Mutations during Spermatogenesis
Ann-Karin Olsen,?shild Andreassen,Rajinder Singh,Richard Wiger,Nur Duale,Peter B. Farmer,Gunnar Brunborg
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0011349
Abstract: Spermatozoal DNA damage is associated with poor sperm quality, disturbed embryonic development and early embryonic loss, and some genetic diseases originate from paternal de novo mutations. We previously reported poor repair of bulky DNA-lesions in rodent testicular cells.
Polynomial Schur and Polynomial Dunford-Pettis Properties
Jeff Farmer,William B. Johnson
Mathematics , 1992,
Abstract: A Banach space is {\it polynomially Schur} if sequential convergence against analytic polynomials implies norm convergence. Carne, Cole and Gamelin show that a space has this property and the Dunford-Pettis property if and only if it is Schur. Herein is defined a reasonable generalization of the Dunford--Pettis property using polynomials of a fixed homogeneity. It is shown, for example, that a Banach space will has the $P_N$ Dunford--Pettis property if and only if every weakly compact $N-$homogeneous polynomial (in the sense of Ryan) on the space is completely continuous. A certain geometric condition, involving estimates on spreading models and implied by nontrivial type, is shown to be sufficient to imply that a space is polynomially Schur.
Male-Biased Autosomal Effect of 16p13.11 Copy Number Variation in Neurodevelopmental Disorders
Maria Tropeano, Joo Wook Ahn, Richard J. B. Dobson, Gerome Breen, James Rucker, Abhishek Dixit, Deb K. Pal, Peter McGuffin, Anne Farmer, Peter S. White, Joris Andrieux, Evangelos Vassos, Caroline Mackie Ogilvie, Sarah Curran, David A Collier
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0061365
Abstract: Copy number variants (CNVs) at chromosome 16p13.11 have been associated with a range of neurodevelopmental disorders including autism, ADHD, intellectual disability and schizophrenia. Significant sex differences in prevalence, course and severity have been described for a number of these conditions but the biological and environmental factors underlying such sex-specific features remain unclear. We tested the burden and the possible sex-biased effect of CNVs at 16p13.11 in a sample of 10,397 individuals with a range of neurodevelopmental conditions, clinically referred for array comparative genomic hybridisation (aCGH); cases were compared with 11,277 controls. In order to identify candidate phenotype-associated genes, we performed an interval-based analysis and investigated the presence of ohnologs at 16p13.11; finally, we searched the DECIPHER database for previously identified 16p13.11 copy number variants. In the clinical referral series, we identified 46 cases with CNVs of variable size at 16p13.11, including 28 duplications and 18 deletions. Patients were referred for various phenotypes, including developmental delay, autism, speech delay, learning difficulties, behavioural problems, epilepsy, microcephaly and physical dysmorphisms. CNVs at 16p13.11 were also present in 17 controls. Association analysis revealed an excess of CNVs in cases compared with controls (OR = 2.59; p = 0.0005), and a sex-biased effect, with a significant enrichment of CNVs only in the male subgroup of cases (OR = 5.62; p = 0.0002), but not in females (OR = 1.19, p = 0.673). The same pattern of results was also observed in the DECIPHER sample. Interval-based analysis showed a significant enrichment of case CNVs containing interval II (OR = 2.59; p = 0.0005), located in the 0.83 Mb genomic region between 15.49–16.32 Mb, and encompassing the four ohnologs NDE1, MYH11, ABCC1 and ABCC6. Our data confirm that duplications and deletions at 16p13.11 represent incompletely penetrant pathogenic mutations that predispose to a range of neurodevelopmental disorders, and suggest a sex-limited effect on the penetrance of the pathological phenotypes at the 16p13.11 locus.
Crystallization for a Brenner-like potential
Brittan Farmer,Selim Esedoglu,Peter Smereka
Physics , 2015,
Abstract: Graphene is a carbon molecule with the structure of a honeycomb lattice. We show how this structure can arise in two dimensions as the minimizer of an interaction energy with two-body and three-body terms. In the engineering literature, the Brenner potential is commonly used to describe the interactions between carbon atoms. We consider a potential of Stillinger-Weber type that incorporates certain characteristics of the Brenner potential: the preferred bond angles are 180 degrees and all interactions have finite range. We show that the thermodynamic limit of the ground state energy per particle is the same as that of a honeycomb lattice. We also prove that, subject to periodic boundary conditions, the minimizers are translated versions of the honeycomb lattice.
STrengthening the Reporting of OBservational studies in Epidemiology – Molecular Epidemiology (STROBE-ME): An Extension of the STROBE Statement
Valentina Gallo ,Matthias Egger,Valerie McCormack,Peter B. Farmer,John P. A. Ioannidis,Micheline Kirsch-Volders,Giuseppe Matullo,David H. Phillips,Bernadette Schoket,Ulf Stromberg,Roel Vermeulen,Christopher Wild,Miquel Porta,Paolo Vineis
PLOS Medicine , 2011, DOI: 10.1371/journal.pmed.1001117
Urinary Benzene Biomarkers and DNA Methylation in Bulgarian Petrochemical Workers: Study Findings and Comparison of Linear and Beta Regression Models
Wei Jie Seow, Angela Cecilia Pesatori, Emmanuel Dimont, Peter B. Farmer, Benedetta Albetti, Adrienne S. Ettinger, Valentina Bollati, Claudia Bolognesi, Paola Roggieri, Teodor I. Panev, Tzveta Georgieva, Domenico Franco Merlo, Pier Alberto Bertazzi, Andrea A. Baccarelli
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0050471
Abstract: Chronic occupational exposure to benzene is associated with an increased risk of hematological malignancies such as acute myeloid leukemia (AML), but the underlying mechanisms are still unclear. The main objective of this study was to investigate the association between benzene exposure and DNA methylation, both in repeated elements and candidate genes, in a population of 158 Bulgarian petrochemical workers and 50 unexposed office workers. Exposure assessment included personal monitoring of airborne benzene at work and urinary biomarkers of benzene metabolism (S-phenylmercapturic acid [SPMA] and trans,trans-muconic acid [t,t-MA]) at the end of the work-shift. The median levels of airborne benzene, SPMA and t,t-MA in workers were 0.46 ppm, 15.5 μg/L and 711 μg/L respectively, and exposure levels were significantly lower in the controls. Repeated-element DNA methylation was measured in Alu and LINE-1, and gene-specific methylation in MAGE and p15. DNA methylation levels were not significantly different between exposed workers and controls (P>0.05). Both ordinary least squares (OLS) and beta-regression models were used to estimate benzene-methylation associations. Beta-regression showed better model specification, as reflected in improved coefficient of determination (pseudo R2) and Akaike’s information criterion (AIC). In beta-regression, we found statistically significant reductions in LINE-1 (?0.15%, P<0.01) and p15 (?0.096%, P<0.01) mean methylation levels with each interquartile range (IQR) increase in SPMA. This study showed statistically significant but weak associations of LINE-1 and p15 hypomethylation with SPMA in Bulgarian petrochemical workers. We showed that beta-regression is more appropriate than OLS regression for fitting methylation data.
Random Coil to Globular Thermal Response of a Protein (H3.1) with Three Knowledge-Based Coarse-Grained Potentials
Ras B. Pandey, Barry L. Farmer
PLOS ONE , 2012, DOI: 10.1371/journal.pone.0049352
Abstract: The effect of temperature on the conformation of a histone (H3.1) is studied by a coarse-grained Monte Carlo simulation based on three knowledge-based contact potentials (MJ, BT, BFKV). Despite unique energy and mobility profiles of its residues, the histone H3.1 undergoes a systematic (possibly continuous) structural transition from a random coil to a globular conformation on reducing the temperature. The range over which such a systematic response in variation of the radius of gyration (Rg) with the temperature (T) occurs, however, depends on the potential, i.e. ΔTMJ ≈ 0.013–0.020, ΔTBT ≈ 0.018–0.026, and ΔTBFKV ≈ 0.006–0.013 (in reduced unit). Unlike MJ and BT potentials, results from the BFKV potential show an anomaly where the magnitude of Rg decreases on raising the temperature in a range ΔTA ≈ 0.015–0.018 before reaching its steady-state random coil configuration. Scaling of the structure factor, S(q) ∝ q?1/ν, with the wave vector, q = 2π/λ, and the wavelength, λ, reveals a systematic change in the effective dimension (De~1/ν) of the histone with all potentials (MJ, BT, BFKV): De~3 in the globular structure with De~2 for the random coil. Reproducibility of the general yet unique (monotonic) structural transition of the protein H3.1 with the temperature (in contrast to non-monotonic structural response of a similar but different protein H2AX) with three interaction sets shows that the knowledge-based contact potential is viable tool to investigate structural response of proteins. Caution should be exercise with the quantitative comparisons due to differences in transition regimes with these interactions.
Conformational Response to Solvent Interaction and Temperature of a Protein (Histone h3.1) by a Multi-Grained Monte Carlo Simulation
Ras B. Pandey, Barry L. Farmer
PLOS ONE , 2013, DOI: 10.1371/journal.pone.0076069
Abstract: Interaction with the solvent plays a critical role in modulating the structure and dynamics of a protein. Because of the heterogeneity of the interaction strength, it is difficult to identify multi-scale structural response. Using a coarse-grained Monte Carlo approach, we study the structure and dynamics of a protein (H3.1) in effective solvent media. The structural response is examined as a function of the solvent-residue interaction strength (based on hydropathy index) in a range of temperatures (spanning low to high) involving a knowledge-based (Miyazawa-Jernigan(MJ)) residue-residue interaction. The protein relaxes rapidly from an initial random configuration into a quasi-static structure at low temperatures while it continues to diffuse at high temperatures with fluctuating conformation. The radius of gyration (Rg) of the protein responds non-monotonically to solvent interaction, i.e., on increasing the residue-solvent interaction strength (fs), the increase in Rg (fs≤fsc) is followed by decay (fs≥fsc) with a maximum at a characteristic value (fsc) of the interaction. Raising the temperature leads to wider spread of the distribution of the radius of gyration with higher magnitude of fsc. The effect of solvent on the multi-scale (λ: residue to Rg) structures of the protein is examined by analyzing the structure factor (S(q),|q| = 2π/λ is the wave vector of wavelength, λ) in detail. Random-coil to globular transition with temperature of unsolvated protein (H3.1) is dramatically altered by the solvent at low temperature while a systematic change in structure and scale is observed on increasing the temperature. The interaction energy profile of the residues is not sufficient to predict its mobility in the solvent. Fine-grain representation of protein with two-node and three-node residue enhances the structural resolution; results of the fine-grained simulations are consistent with the finding described above of the coarse-grained description with one-node residue.
Factoring Hecke polynomials modulo a prime
J. Brian Conrey,David W. Farmer,Peter Jake Wallace
Mathematics , 1998,
Abstract: Let T^{N,chi}_{p,k}(x) be the characteristic polynomial of the Hecke operator T_p acting on the space of cusp forms S_k(N,chi). We describe the factorization of T^{N,chi}_{p,k}(x) mod l as k varies, and we explicitly calculate those factorizations for N=1 and small l. These factorizations are used to deduce the irreducibility of certain T^{1,1}_{q,k}(x) from the irreducibility of T^{1,1}_{2,k}(x).
To bail-out or to bail-in? Answers from an agent-based model
Peter Klimek,Sebastian Poledna,J. Doyne Farmer,Stefan Thurner
Quantitative Finance , 2014,
Abstract: Since beginning of the 2008 financial crisis almost half a trillion euros have been spent to financially assist EU member states in taxpayer-funded bail-outs. These crisis resolutions are often accompanied by austerity programs causing political and social friction on both domestic and international levels. The question of how to resolve failing financial institutions under which economic preconditions is therefore a pressing and controversial issue of vast political importance. In this work we employ an agent-based model to study the economic and financial ramifications of three highly relevant crisis resolution mechanisms. To establish the validity of the model we show that it reproduces a series of key stylized facts if the financial and real economy. The distressed institution can either be closed via a purchase & assumption transaction, it can be bailed-out using taxpayer money, or it may be bailed-in in a debt-to-equity conversion. We find that for an economy characterized by low unemployment and high productivity the optimal crisis resolution with respect to financial stability and economic productivity is to close the distressed institution. For economies in recession with high unemployment the bail-in tool provides the most efficient crisis resolution mechanism. Under no circumstances do taxpayer-funded bail-out schemes outperform bail-ins with private sector involvement.
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