Recursos de colección

DSpace at MIT (91.223 recursos)

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MIT Open Access Articles

Mostrando recursos 1 - 20 de 20.708

  1. Computing Néron–Severi groups and cycle class groups

    Testa, Damiano; van Luijk, Ronald; Poonen, Bjorn
    Assuming the Tate conjecture and the computability of étale cohomology with finite coefficients, we give an algorithm that computes the Néron–Severi group of any smooth projective geometrically integral variety, and also the rank of the group of numerical equivalence classes of codimension p cycles for any p.

  2. Index theory of the de Rham complex on manifolds with periodic ends

    Ruberman, Daniel; Saveliev, Nikolai; Mrowka, Tomasz S
    We study the de Rham complex on a smooth manifold with a periodic end modeled on an infinite cyclic cover [tilde over X]→X. The completion of this complex in exponentially weighted L² norms is Fredholm for all but finitely many exceptional weights determined by the eigenvalues of the covering translation map H[subscript ∗] ([tilde over X])→H[subscript ∗] ([tilde over X]). We calculate the index of this weighted de Rham complex for all weights away from the exceptional ones.

  3. Improvement of DNA minicircle production by optimization of the secondary structure of the 5′-UTR of ParA resolvase

    Brito, Liliana; Alves, Cláudia P. A.; Monteiro, Gabriel A.; Simcikova, Michaela; Jones, Kristala L; Prazeres, Duarte Miguel; Jones, Kristala L.
    The use of minicircles in gene therapy applications is dependent on the availability of high-producer cell systems. In order to improve the performance of minicircle production in Escherichia coli by ParA resolvase-mediated in vivo recombination, we focus on the 5′ untranslated region (5′-UTR) of parA messenger RNA (mRNA). The arabinose-inducible P[subscript BAD]/araC promoter controls ParA expression and strains with improved arabinose uptake are used. The 27-nucleotide-long 5′-UTR of parA mRNA was optimized using a predictive thermodynamic model. An analysis of original and optimized mRNA subsequences predicted a decrease of 8.6–14.9 kcal/mol in the change in Gibbs free energy upon assembly...

  4. Evidence that the insertion events of IS2 transposition are biased towards abrupt compositional shifts in target DNA and modulated by a diverse set of culture parameters

    Gonçalves, Geisa A. L.; Oliveira, Pedro H.; Gomes, Ana G.; Lewis, Leslie A.; Monteiro, Gabriel A.; Jones, Kristala L.; Prazeres, Duarte Miguel
    Insertion specificity of mobile genetic elements is a rather complex aspect of DNA transposition, which, despite much progress towards its elucidation, still remains incompletely understood. We report here the results of a meta-analysis of IS2 target sites from genomic, phage, and plasmid DNA and find that newly acquired IS2 elements are consistently inserted around abrupt DNA compositional shifts, particularly in the form of switch sites of GC skew. The results presented in this study not only corroborate our previous observations that both the insertion sequence (IS) minicircle junction and target region adopt intrinsically bent conformations in IS2, but most interestingly,...

  5. Biosynthesis of poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P(HB-co-HHx)) from butyrate using engineered Ralstonia eutropha

    Jeon, Jong-Min; Kim, Yong-Hyun; Kim, Hyun-Joong; Yi, Da-Hye; Kim, Hyungsup; Rha, ChoKyun; Yang, Yung-Hun; Brigham, Christopher J.; Sinskey, Anthony J
    Polyhydroxyalkanoates (PHAs), a promising family of bio-based polymers, are considered to be alternatives to traditional petroleum-based plastics. Copolymers like poly(3-hydroxybutyrate-co-3-hydroxyhexanoate) (P(HB-co-HHx)) have been shown to exhibit favorable physical and mechanical properties, due to decreased crystallinity resulting from the presence of medium-chain-length 3-hydroxyhexanoate (3HHx) monomers. In this study, we produced P(HB-co-HHx) using engineered Ralstonia eutropha strains containing deletions of the acetoacetyl-CoA reductase (phaB) genes and replacing the native PHA synthase with phaC2 from Rhodococcus aetherivorans I24 and by using butyrate, a short-chain organic acid, as the carbon source. Although the wild-type R. eutropha did not produce P(HB-co-HHx) when grown on mixed...

  6. Relative trace formulae toward Bessel and Fourier–Jacobi periods on unitary groups

    Liu, Yifeng
    We propose an approach, via relative trace formulae, toward the global restriction problem involving Bessel or Fourier–Jacobi periods on unitary groups U[subscript n] × U[subscript m], generalizing the work of Jacquet–Rallis for m = n − 1 (which is a Bessel period). In particular, when m = 0, we recover a relative trace formula proposed by Flicker concerning Kloosterman/Fourier integrals on quasi-split unitary groups. As evidences for our approach, we prove the vanishing part of the fundamental lemmas in all cases, and the full lemma for U[subscript n] × U[subscript n].

  7. The singular set of mean curvature flow with generic singularities

    Colding, Tobias; Minicozzi, William
    A mean curvature flow starting from a closed embedded hypersurface in R[superscript n+1] must develop singularities. We show that if the flow has only generic singularities, then the space-time singular set is contained in finitely many compact embedded (n−1)-dimensional Lipschitz submanifolds plus a set of dimension at most n−2. If the initial hypersurface is mean convex, then all singularities are generic and the results apply. In R³ and R[superscript 4], we show that for almost all times the evolving hypersurface is completely smooth and any connected component of the singular set is entirely contained in a time-slice. For 2 or...

  8. Determining thresholds using adaptive procedures and psychometric fits: evaluating efficiency using theory, simulations, and human experiments

    Karmali, Faisal; Yi, Yongwoo; Merfeld, Daniel M.; Chaudhuri, Shomesh Ernesto
    When measuring thresholds, careful selection of stimulus amplitude can increase efficiency by increasing the precision of psychometric fit parameters (e.g., decreasing the fit parameter error bars). To find efficient adaptive algorithms for psychometric threshold (“sigma”) estimation, we combined analytic approaches, Monte Carlo simulations, and human experiments for a one-interval, binary forced-choice, direction-recognition task. To our knowledge, this is the first time analytic results have been combined and compared with either simulation or human results. Human performance was consistent with theory and not significantly different from simulation predictions. Our analytic approach provides a bound on efficiency, which we compared against the...

  9. Spectral Theory for Interacting Particle Systems Solvable by Coordinate Bethe Ansatz

    Borodin, Alexei; Corwin, Ivan; Petrov, Leonid; Sasamoto, Tomohiro
    We develop spectral theory for the q-Hahn stochastic particle system introduced recently by Povolotsky. That is, we establish a Plancherel type isomorphism result that implies completeness and biorthogonality statements for the Bethe ansatz eigenfunctions of the system. Owing to a Markov duality with the q-Hahn TASEP (a discrete-time generalization of TASEP with particles’ jump distribution being the orthogonality weight for the classical q-Hahn orthogonal polynomials), we write down moment formulas that characterize the fixed time distribution of the q-Hahn TASEP with general initial data. The Bethe ansatz eigenfunctions of the q-Hahn system degenerate into eigenfunctions of other (not necessarily stochastic)...

  10. From Alternating Sign Matrices to the Gaussian Unitary Ensemble

    Gorin, Vadim
    The aim of this note is to prove that fluctuations of uniformly random alternating sign matrices (equivalently, configurations of the 6-vertex model with domain wall boundary conditions) near the boundary are described by the Gaussian Unitary Ensemble and the GUE-corners process.

  11. Minimizers of Anisotropic Surface Tensions Under Gravity: Higher Dimensions via Symmetrization

    Baer, Eric
    We consider a variational model describing the shape of liquid drops and crystals under the influence of gravity, resting on a horizontal surface. Making use of anisotropic symmetrization techniques, we establish the existence, convexity and symmetry of minimizers for a class of surface tensions admissible to the symmetrization procedure. In the case of smooth surface tensions, we obtain the uniqueness of minimizers via an ODE characterization.

  12. Higher order hydrodynamic interaction between two slender bodies in potential flow

    Kadri, Usama; Weihs, Daniel
    In this paper, we apply the slender body theory to study the effect of higher order hydrodynamic interactions between two slender bodies of revolution moving in close proximity, in an unbounded, inviscid, and incompressible fluid. We compare between leading and second-order approximations, as well as approximate and exact separation distances. The total solution is found to be valid for both small and large lateral separation distances. The contribution of the higher order forces is found to be relatively small for large separation distances, though significant for small separation distances. Comparisons with measurements and simulations are satisfactory.

  13. Occurrence and genetic diversity of human cosavirus in influent and effluent of wastewater treatment plants in Arizona, United States

    Kitajima, Masaaki; Haramoto, Eiji; Rachmadi, Andri T.; Iker, Brandon C.; Pepper, Ian L.; Gerba, Charles P.
    Human cosavirus (HCoSV) is a novel member of the family Picornaviridae. We investigated the prevalence and genetic diversity of HCoSV in influent and effluent wastewater in Arizona over a 12-month period, from August 2011 to July 2012. HCoSV sequences were identified in six (25 %) influent samples and one (4 %) effluent sample, with the highest concentration of 3.24 x 10[superscript 5] and 1.54 x 10³ copies/liter in influent and effluent, respectively. The strains were characterized based on their 5’ untranslated region and classified into species A and D, demonstrating that genetically heterogeneous HCoSV were circulating with a clear temporal...

  14. Characterization of a genetic and antigenic variant of avian paramyxovirus 6 isolated from a migratory wild bird, the red-necked stint (Calidris ruficollis)

    Mizutani, Tetsuya; Yamamoto, Yu; Nakamura, Kikuyasu; Saito, Keisuke; Watanabe, Yukiko; Runstadler, Jonathan; Huettmann, Falk; Ogawa, Haruko; Imai, Kunitoshi; Bui, Vuong Nghia; Nguyen, Tung Hoang; Trinh, Dai Quang; Awad, Sanaa S. A.; Minoungou, Germaine L.
    A hemagglutinating virus (8KS0813) was isolated from a red-necked stint. Hemagglutination inhibition and neutralization tests indicated that 8KS0813 was antigenically related to a prototype strain, APMV-6/duck/Hong Kong/18/199/77, but with an 8- and 16-fold difference, respectively, in their titers. The full genome sequence of 8KS0813 showed 98.6 % nucleotide sequence identity to that of APMV-6/duck/Italy/4524-2/07, which has been reported to belong to an APMV-6 subgroup, and showed less similarity to that of the prototype strain (70.6 % similarity). The growth of 8KS0813 and the prototype strain in four different cell cultures was greatly enhanced by adding trypsin. Interestingly, this virus induced...

  15. Population dynamics of DENV-1 genotype V in Brazil is characterized by co-circulation and strain/lineage replacement

    Mondini, Adriano; Bosch, Irene; Drumond, Betânia Paiva; Schmidt, Diane J.; Nogueira, Maurício Lacerda
    Following successive outbreaks of dengue fever caused predominantly by dengue virus (DENV) 2 and 3, DENV-1 is now the primary serotype circulating in Brazil. We sequenced and analyzed Brazilian DENV-1 genomes and found that all isolates belong to genotype V and are subdivided into three lineages, which were introduced during four different events. The first introduction occurred in 1984-85, the second in 1997-99, and the third and fourth occurred from 2004 to 2007. These events were associated with an increase in genetic diversity but not with positive selection. Moreover, a potential new recombinant strain derived from two distinct lineages was...

  16. Bertini irreducibility theorems over finite fields

    Charles, François; Poonen, Bjorn; Charles, Francois
    Given a geometrically irreducible subscheme $ X \subseteq \mathbb{P}^n_{\mathbb{F}_q}$ of dimension at least $ 2$, we prove that the fraction of degree $ d$ hypersurfaces $ H$ such that $ H \cap X$ is geometrically irreducible tends to $ 1$ as $ d \to \infty $. We also prove variants in which $ X$ is over an extension of $ \mathbb{F}_q$, and in which the immersion $ X \to \mathbb{P}^n_{\mathbb{F}_q}$ is replaced by a more general morphism.

  17. Toric Actions on b-Symplectic Manifolds

    Guillemin, Victor W; Miranda, Eva; Pires, Ana Rita; Scott, Geoffrey
    We study Hamiltonian actions on b-symplectic manifolds with a focus on the effective case of half the dimension of the manifold. In particular, we prove a Delzant-type theorem that classifies these manifolds using polytopes that reside in a certain enlarged and decorated version of the dual of the Lie algebra of the torus.

  18. Sensing and inactivation of Bacillus anthracis Sterne by polymer–bromine complexes

    D’Angelo, Paola A.; Bromberg, Lev E; Hatton, Trevor Alan; Wilusz, Eugene
    We report on the performance of brominated poly(N-vinylpyrrolidone) (PVP-Br), brominated poly(ethylene glycol) (PEG-Br), and brominated poly(allylamine-co-4-aminopyridine) (PAAm-APy-Br) for their ability to decontaminate Bacillus anthracis Sterne spores in solution while also allowing for the sensing of the spores. The polymers were brominated by bromine using carbon tetrachloride or potassium tribromide as solvents, with bromine loadings ranging from 1.6 to 4.2 mEq/g of polymer. B. anthracis Sterne spores were exposed to increasing concentrations of brominated polymers for 5 min, while the kinetics of the sporicidal activity was assessed. All brominated polymers demonstrated spore log-kills of 8 within 5 min of exposure at 12 mg/mL aqueous polymer...

  19. Biomarkers and diagnostic tools for detection of Helicobacter pylori

    Khalilpour, Akbar; Kazemzadeh-Narbat, Mehdi; Tamayol, Ali; Oklu, Rahmi; Khademhosseini, Alireza
    Helicobacter pylori is responsible for worldwide chronic bacterial infection in humans affecting approximately half of the world’s population. H. pylori is associated with significant morbidity and mortality including gastric cancer. The infection has both direct and indirect impacts on economic and overall well-being of patients; hence, there is a great need for diagnostic markers that could be used in the development of diagnostic kits. Here, we briefly review general aspects of H. pylori infection and the diagnostic biomarkers used in laboratory tests today with a focus on the potential role of microfluidic systems in future immunodiagnosis platforms.

  20. Experimental design-aided systematic pathway optimization of glucose uptake and deoxyxylulose phosphate pathway for improved amorphadiene production

    Zhang, Congqiang; Zou, Ruiyang; Chen, Xixian; Stephanopoulos, Gregory; Too, Heng-Phon
    Artemisinin is a potent antimalarial drug; however, it suffers from unstable and insufficient supply from plant source. Here, we established a novel multivariate-modular approach based on experimental design for systematic pathway optimization that succeeded in improving the production of amorphadiene (AD), the precursor of artemisinin, in Escherichia coli. It was initially found that the AD production was limited by the imbalance of glyceraldehyde 3-phosphate (GAP) and pyruvate (PYR), the two precursors of the 1-deoxy-d-xylulose-5-phosphate (DXP) pathway. Furthermore, it was identified that GAP and PYR could be balanced by replacing the phosphoenolpyruvate (PEP)-dependent phosphotransferase system (PTS) with the ATP-dependent galactose permease...

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