
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.

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.

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 highproducer cell systems. In order to improve the performance of minicircle production in Escherichia coli by ParA resolvasemediated in vivo recombination, we focus on the 5′ untranslated region (5′UTR) of parA messenger RNA (mRNA). The arabinoseinducible P[subscript BAD]/araC promoter controls ParA expression and strains with improved arabinose uptake are used. The 27nucleotidelong 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...

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 metaanalysis 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,...

Jeon, JongMin; Kim, YongHyun; Kim, HyunJoong; Yi, DaHye; Kim, Hyungsup; Rha, ChoKyun; Yang, YungHun; Brigham, Christopher J.; Sinskey, Anthony J
Polyhydroxyalkanoates (PHAs), a promising family of biobased polymers, are considered to be alternatives to traditional petroleumbased plastics. Copolymers like poly(3hydroxybutyrateco3hydroxyhexanoate) (P(HBcoHHx)) have been shown to exhibit favorable physical and mechanical properties, due to decreased crystallinity resulting from the presence of mediumchainlength 3hydroxyhexanoate (3HHx) monomers. In this study, we produced P(HBcoHHx) using engineered Ralstonia eutropha strains containing deletions of the acetoacetylCoA reductase (phaB) genes and replacing the native PHA synthase with phaC2 from Rhodococcus aetherivorans I24 and by using butyrate, a shortchain organic acid, as the carbon source. Although the wildtype R. eutropha did not produce P(HBcoHHx) when grown on mixed...

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 quasisplit 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].

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 spacetime 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 timeslice. For 2 or...

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 oneinterval, binary forcedchoice, directionrecognition 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...

Borodin, Alexei; Corwin, Ivan; Petrov, Leonid; Sasamoto, Tomohiro
We develop spectral theory for the qHahn 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 qHahn TASEP (a discretetime generalization of TASEP with particles’ jump distribution being the orthogonality weight for the classical qHahn orthogonal polynomials), we write down moment formulas that characterize the fixed time distribution of the qHahn TASEP with general initial data. The Bethe ansatz eigenfunctions of the qHahn system degenerate into eigenfunctions of other (not necessarily stochastic)...

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

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.

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 secondorder 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.

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 12month 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...

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 rednecked stint. Hemagglutination inhibition and neutralization tests indicated that 8KS0813 was antigenically related to a prototype strain, APMV6/duck/Hong Kong/18/199/77, but with an 8 and 16fold difference, respectively, in their titers. The full genome sequence of 8KS0813 showed 98.6 % nucleotide sequence identity to that of APMV6/duck/Italy/45242/07, which has been reported to belong to an APMV6 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...

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, DENV1 is now the primary serotype circulating in Brazil. We sequenced and analyzed Brazilian DENV1 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 198485, the second in 199799, 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...

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.

Guillemin, Victor W; Miranda, Eva; Pires, Ana Rita; Scott, Geoffrey
We study Hamiltonian actions on bsymplectic manifolds with a focus on the effective case of half the dimension of the manifold. In particular, we prove a Delzanttype 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.

D’Angelo, Paola A.; Bromberg, Lev E; Hatton, Trevor Alan; Wilusz, Eugene
We report on the performance of brominated poly(Nvinylpyrrolidone) (PVPBr), brominated poly(ethylene glycol) (PEGBr), and brominated poly(allylamineco4aminopyridine) (PAAmAPyBr) 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 logkills of 8 within 5 min of exposure at 12 mg/mL aqueous polymer...

Khalilpour, Akbar; KazemzadehNarbat, 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 wellbeing 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.

Zhang, Congqiang; Zou, Ruiyang; Chen, Xixian; Stephanopoulos, Gregory; Too, HengPhon
Artemisinin is a potent antimalarial drug; however, it suffers from unstable and insufficient supply from plant source. Here, we established a novel multivariatemodular 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 3phosphate (GAP) and pyruvate (PYR), the two precursors of the 1deoxydxylulose5phosphate (DXP) pathway. Furthermore, it was identified that GAP and PYR could be balanced by replacing the phosphoenolpyruvate (PEP)dependent phosphotransferase system (PTS) with the ATPdependent galactose permease...