Minimal information for chemosensitivity assays (MICHA): a next-generation pipeline to enable the FAIRification of drug screening experiments

Chemosensitivity assays are commonly used for preclinical drug discovery and clinical trial optimization. However, data from independent assays are often discordant, largely attributed to uncharacterized variation in the experimental materials and protocols. We report here the launching of Minimal Information for Chemosensitivity Assays (MICHA), accessed via https://micha-protocol.org. Distinguished from existing efforts that are often lacking support from data integration tools, MICHA can automatically extract publicly available information to facilitate the assay annotation including: 1) compounds, 2) samples, 3) reagents and 4) data processing methods. For example, MICHA provides an integrative web server and database to obtain compound annotation including chemical structures, targets and disease indications. In addition, the annotation of cell line samples, assay protocols and literature references can be greatly eased by retrieving manually curated catalogues. Once the annotation is complete, MICHA can export a report that conforms to the FAIR principle (Findable, Accessible, Interoperable and Reusable) of drug screening studies. To consolidate the utility of MICHA, we provide FAIRified protocols from five major cancer drug screening studies as well as six recently conducted COVID-19 studies. With the MICHA web server and database, we envisage a wider adoption of a community-driven effort to improve the open access of drug sensitivity assays.Peer reviewe

Transgenerational Trauma and the Figure of the Perpetrator: Holocaust Fiction in “Micha” by Rachel Seiffert.

This essay aims to study the figure of the perpetrator and how trauma can be transmitted through several generations in the long short story “Micha” by Rachel Seiffert. This is the third and last story in a volume entitled The Dark Room (2001), which deals with three different generations that are connected indirectly to Germans who participated in the genocide. In “Micha”, entitled after its protagonist’s name, we observe the third generation: Micha is the grandchild of Askan Boell, a Waffen-SS member. Through the long short story, Micha will try to discover his grandfather’s dark past. I will first contextualize the story within Holocaust fiction and Trauma literature before I focus on the transgenerational transmission of trauma and the perpetrator.<br /

A Supergravity Dual of a (1,0) Field Theory in Six Dimensions

We suggest a supergravity dual for the $(1,0)$ superconformal field theory in six dimensions which has $E_8$ global symmetry. Compared to the description of the (2,0) field theory, the 4-sphere is replaced by a 4-hemisphere, or by orbifolding the 4-sphere.Comment: 5 pages, Harvmac. Typos corrected, References correcte

From SYM Perturbation Theory to Closed Strings in Matrix Theory

For the purpose of better understanding the AdS/CFT correspondence it is useful to have a description of the theory for all values of the 't Hooft coupling, and for all $N$. We discuss such a description in the framework of Matrix theory for SYM on D4-branes, which is given in terms of quantum mechanics on the moduli space of solutions of the Nahm equations. This description reduces to both SYM perturbation theory and to closed string perturbation theory, each in its appropriate regime of validity, suggesting a way of directly relating the variables in the two descriptions. For example, it shows explicitly how holes in the world-sheets of the 't Hooft expansion close to give closed surfaces.Comment: 19 page

Relational Width of First-Order Expansions of Homogeneous Graphs with Bounded Strict Width

Solving the algebraic dichotomy conjecture for constraint satisfaction problems over structures first-order definable in countably infinite finitely bounded homogeneous structures requires understanding the applicability of local-consistency methods in this setting. We study the amount of consistency (measured by relational width) needed to solve CSP(?) for first-order expansions ? of countably infinite homogeneous graphs ? := (A; E), which happen all to be finitely bounded. We study our problem for structures ? that additionally have bounded strict width, i.e., for which establishing local consistency of an instance of CSP(?) not only decides if there is a solution but also ensures that every solution may be obtained from a locally consistent instance by greedily assigning values to variables, without backtracking. Our main result is that the structures ? under consideration have relational width exactly (2, ?_?) where ?_? is the maximal size of a forbidden subgraph of ?, but not smaller than 3. It beats the upper bound: (2 m, 3 m) where m = max(arity(?)+1, ?, 3) and arity(?) is the largest arity of a relation in ?, which follows from a sufficient condition implying bounded relational width given in [Manuel Bodirsky and Antoine Mottet, 2018]. Since ?_? may be arbitrarily large, our result contrasts the collapse of the relational bounded width hierarchy for finite structures ?, whose relational width, if finite, is always at most (2,3)

Equidimensional Isometric Extensions

Let $\Sigma$ be a hypersurface in an $n$-dimensional Riemannian manifold $M$, $n\geqslant 2$. We study the isometric extension problem for isometric immersions $f:\Sigma\to\mathbb R^n$, where $\mathbb R^n$ is equipped with the Euclidean standard metric. Using a weak form of convex integration suggested by Sz\'ekelyhidi, we construct "one-sided" isometric Lipschitz-extensions and obtain an accompanying density result.Comment: 15 page

hh-Principle for Curves with Prescribed Curvature

We prove that every immersed $C^2$-curve $\gamma$ in $\mathbb R^n$, $n\geqslant 3$ with curvature $k_{\gamma}$ can be $C^1$-approximated by immersed $C^2$-curves having prescribed curvature $k>k_{\gamma}$. The approximating curves satisfy a $C^1$-dense $h$-principle. As an application we obtain the existence of $C^2$-knots of arbitrary positive curvature in each isotopy class, which generalizes a similar result by McAtee for $C^2$-knots of constant curvature.Comment: Final version, to appear in Geometriae Dedicata, 9 pages, 1 figur