Is there any sense in antisense editing?

A number of recent studies have hypothesized that sense-antisense RNA transcript pairs create dsRNA duplexes that undergo extensive A-to-I RNA editing. Here we studied human and mouse genomic antisense regions, and found that the editing level in these areas is negligible. This observation puts in question the scope of sense-antisense duplexes formation in-vivo, which is the basis for a number of proposed regulatory mechanisms

Gorenstein homological algebra and universal coefficient theorems

We study criteria for a ring—or more generally, for a small category—to be Gorenstein and for a module over it to be of finite projective dimension. The goal is to unify the universal coefficient theorems found in the literature and to develop machinery for proving new ones. Among the universal coefficient theorems covered by our methods we find, besides all the classic examples, several exotic examples arising from the KK-theory of C*-algebras and also Neeman’s Brown–Adams representability theorem for compactly generated categories

The Baum-Connes Conjecture via Localisation of Categories

We redefine the Baum-Connes assembly map using simplicial approximation in the equivariant Kasparov category. This new interpretation is ideal for studying functorial properties and gives analogues of the assembly maps for all equivariant homology theories, not just for the K-theory of the crossed product. We extend many of the known techniques for proving the Baum-Connes conjecture to this more general setting

Nano-sized SQUID-on-tip for scanning probe microscopy

We present a SQUID of novel design, which is fabricated on the tip of a pulled quartz tube in a simple 3-step evaporation process without need for any additional processing, patterning, or lithography. The resulting devices have SQUID loops with typical diameters in the range 75–300 nm. They operate in magnetic fields up to 0.6 T and have flux sensitivity of 1.8 μΦ0/Hz1/2 and magnetic field sensitivity of 10−7 T/Hz1/2, which corresponds to a spin sensitivity of 65 μB/Hz1/2 for aluminum SQUIDs. The shape of the tip and the small area of the SQUID loop, together with its high sensitivity, make our device an excellent tool for scanning SQUID microscopy: With the SQUID-on-tip glued to a tine of a quartz tuning fork, we have succeeded in obtaining magnetic images of a patterned niobium film and of vortices in a superconducting film in a magnetic field.Physic

Stratifying derived categories of cochains on certain spaces

In recent years, Benson, Iyengar and Krause have developed a theory of stratification for compactly generated triangulated categories with an action of a graded commutative Noetherian ring. Stratification implies a classification of localizing and thick subcategories in terms of subsets of the prime ideal spectrum of the given ring. In this paper two stratification results are presented: one for the derived category of a commutative ring-spectrum with polynomial homotopy and another for the derived category of cochains on certain spaces. We also give the stratification of cochains on a space a topological content.Comment: 27 page

Worldline Superfield Actions for N=2 Superparticles

We propose doubly supersymmetric actions in terms of n=2(D-2) worldline superfields for N=2 superparticles in D=3,4 and Type IIA D=6 superspaces. These actions are obtained by dimensional reduction of superfield actions for N=1 superparticles in D=4,6 and 10, respectively. We show that in all these models geometrodynamical constraints on target superspace coordinates do not put the theory on the mass shell, so the actions constructed consistently describe the dynamics of the corresponding N=2 superparticles. We also find that in contrast to the IIA D=6 superparticle a chiral IIB D=6 superparticle, which is not obtainable by dimensional reduction from N=1, D=10, is described by superfield constraints which produce dynamical equations. This implies that for the IIB D=6 superparticle the doubly supersymmetric action does not exist in the conventional form.Comment: Latex, 20 pp. Minor corrections, acknowledgements adde

Response to COVID-19 vaccination in patients on cancer therapy:Analysis in a SARS-CoV-2-naïve population

Background: Cancer patients have increased morbidity and mortality from COVID-19, but may respond poorly to vaccination. The Evaluation of COVID-19 Vaccination Efficacy and Rare Events in Solid Tumors (EVEREST) study, comparing seropositivity between cancer patients and healthy controls in a low SARS-CoV-2 community-transmission setting, allows determination of vaccine response with minimal interference from infection. Methods: Solid tumor patients from The Canberra Hospital, Canberra, Australia, and healthy controls who received COVID-19 vaccination between March 2021 and January 2022 were included. Blood samples were collected at baseline, pre-second vaccine dose and at 1, 3 (primary endpoint), and 6 months post-second dose. SARS-CoV-2 anti-spike-RBD (S-RBD) and anti-nucleocapsid IgG antibodies were measured. Results: Ninety-six solid tumor patients and 20 healthy controls were enrolled, with median age 62 years, and 60% were female. Participants received either AZD1222 (65%) or BNT162b2 (35%) COVID-19 vaccines. Seropositivity 3 months post vaccination was 87% (76/87) in patients and 100% (20/20) in controls (p =.12). Seropositivity was observed in 84% of patients on chemotherapy, 80% on immunotherapy, and 96% on targeted therapy (differences not satistically significant). Seropositivity in cancer patients increased from 40% (6/15) after first dose, to 95% (35/37) 1 month after second dose, then dropped to 87% (76/87) 3 months after second dose. Conclusion: Most patients and all controls became seropositive after two vaccine doses. Antibody concentrations and seropositivity showed a decrease between 1 and 3 months post vaccination, highlighting need for booster vaccinations. SARS-CoV-2 infection amplifies S-RBD antibody responses; however, cannot be adequately identified using nucleocapsid serology. This underlines the value of our COVID-naïve population in studying vaccine immunogenicity.</p

The Universality of Einstein Equations

It is shown that for a wide class of analytic Lagrangians which depend only on the scalar curvature of a metric and a connection, the application of the so--called ``Palatini formalism'', i.e., treating the metric and the connection as independent variables, leads to ``universal'' equations. If the dimension $n$ of space--time is greater than two these universal equations are Einstein equations for a generic Lagrangian and are suitably replaced by other universal equations at bifurcation points. We show that bifurcations take place in particular for conformally invariant Lagrangians $L=R^{n/2} \sqrt g$ and prove that their solutions are conformally equivalent to solutions of Einstein equations. For 2--dimensional space--time we find instead that the universal equation is always the equation of constant scalar curvature; the connection in this case is a Weyl connection, containing the Levi--Civita connection of the metric and an additional vectorfield ensuing from conformal invariance. As an example, we investigate in detail some polynomial Lagrangians and discuss their bifurcations.Comment: 15 pages, LaTeX, (Extended Version), TO-JLL-P1/9

Comparative Study for Inference of Hidden Classes in Stochastic Block Models

Inference of hidden classes in stochastic block model is a classical problem with important applications. Most commonly used methods for this problem involve na\"{\i}ve mean field approaches or heuristic spectral methods. Recently, belief propagation was proposed for this problem. In this contribution we perform a comparative study between the three methods on synthetically created networks. We show that belief propagation shows much better performance when compared to na\"{\i}ve mean field and spectral approaches. This applies to accuracy, computational efficiency and the tendency to overfit the data.Comment: 8 pages, 5 figures AIGM1

Triangle-generation in topological D-brane categories

Tachyon condensation in topological Landau-Ginzburg models can generally be studied using methods of commutative algebra and properties of triangulated categories. The efficiency of this approach is demonstrated by explicitly proving that every D-brane system in all minimal models of type ADE can be generated from only one or two fundamental branes.Comment: 34 page