The Crystal Structure of Monovalent Streptavidin.

The strong interaction between streptavidin (SA) and biotin is widely utilized in biotechnological applications. A SA variant, monovalent SA, was developed with a single and high affinity biotin-binding site within the intact tetramer. However, its structural characterization remains undetermined. Here, we seek to determine the crystal structure of monovalent SA at 1.7-Å resolution. We show that, in contrast to its 'close-state' in the only wild-type subunit, the L3,4 loops of three Dead SA subunits are free from crystal packing and remain in an 'open state', stabilized by a consistent H-bonding network involving S52. This H-bonding network also applies to the previously reported open state of the wild-type apo-SA. These results suggest that specific substitutions (N23A/S27D/S45A) at biotin-binding sites stabilize the open state of SA L3,4 loop, thereby further reducing biotin-binding affinity. The general features of the 'open state' SA among different SA variants may facilitate its rational design. The structural information of monovalent SA will be valuable for its applications across a wide range of biotechnological areas

DNAD, a Simple Tool for Automatic Differentiation of Fortran Codes Using Dual Numbers

DNAD (dual number automatic differentiation) is a simple, general-purpose tool to automatically differentiate Fortran codes written in modern Fortran (F90/95/2003) or legacy codes written in previous version of the Fortran language. It implements the forward mode of automatic differentiation using the arithmetic of dual numbers and the operator overloading feature of F90/95/2003. Very minimum changes of the source codes are needed to compute the first derivatives of Fortran programs. The advantages of DNAD in comparison to other existing similar computer codes are its programming simplicity, extensibility, and computational efficiency. Specifically, DNAD is more accurate and efficient than the popular complex-step approximation. Several examples are used to demonstrate its applications and advantages

Assess the Accuracy of the Variational Asymptotic Plate and Shell Analysis Using the Generalized Uni

The accuracy of the Variational Asymptotic Plate and Shell Analysis (VAPAS) is assessed against several higher order, zig zag and layerwise theories generated by using the invariant axiomatic framework denoted as Generalized Unified Formulation (GUF). These theories are also compared against the elasticity solution developed for the case of a sandwich structure with high Face to Core Stiffness Ratio. GUF allows to use an infinite number of axiomatic theories (Equivalent Single Layer theories with or without zig zag effects and Layerwise theories as well) with any combination of orders of the displacements and it is an ideal tool to precisely assess the range of applicability of the Variational Asymptotic Plate and Shell Analysis or other theories in general. In fact, all the axiomatic theories generated by GUF are obtained from the kernels or fundamental nuclei of the Generalized Unified Formulation and changing the order of the variables is “naturally” and systematically done with GUF. It is demonstrated that VAPAS achieves accuracy comparable to a fourth (or higher) order zig-zag theory or lower-order layerwise theories with the least number degrees of freedom. The differences between the axiomatic Zig-zag models and VAPAS are also assessed. Range of applicability of VAPAS will be discussed in detail and guidelines for new developments based on GUF and VAPAS are provided

Linking Aboveground Traits to Root Traits and Local Environment: Implications of the Plant Economics Spectrum.

The plant economics spectrum proposes that ecological traits are functionally coordinated and adapt along environmental gradients. However, empirical evidence is mixed about whether aboveground and root traits are consistently linked and which environmental factors drive functional responses. Here we measure the strength of relationships between aboveground and root traits, and examine whether community-weighted mean trait values are adapted along gradients of light and soil fertility, based on the seedling censuses of 57 species in a subtropical forest. We found that aboveground traits were good predictors of root traits; specific leaf area, dry matter, nitrogen and phosphorus content were strongly correlated with root tissue density and specific root length. Traits showed patterns of adaptation along the gradients of soil fertility and light; species with fast resource-acquisitive strategies were more strongly associated with high soil phosphorus, potassium, openness, and with low nitrogen, organic matter conditions. This demonstrates the potential to estimate belowground traits from known aboveground traits in seedling communities, and suggests that soil fertility is one of the main factors driving functional responses. Our results extend our understanding of how ecological strategies shape potential responses of plant communities to environmental change

A New Framework for Online Testing of Heterogeneous Treatment Effect

We propose a new framework for online testing of heterogeneous treatment effects. The proposed test, named sequential score test (SST), is able to control type I error under continuous monitoring and detect multi-dimensional heterogeneous treatment effects. We provide an online p-value calculation for SST, making it convenient for continuous monitoring, and extend our tests to online multiple testing settings by controlling the false discovery rate. We examine the empirical performance of the proposed tests and compare them with a state-of-art online test, named mSPRT using simulations and a real data. The results show that our proposed test controls type I error at any time, has higher detection power and allows quick inference on online A/B testing.Comment: 8 pages, no figures. To be published on AAAI 2020 proceeding

Quantum forgery attacks on COPA,AES-COPA and marble authenticated encryption algorithms

The classic forgery attacks on COPA, AES-COPA and Marble authenticated encryption algorithms need to query about 2^(n/2) times, and their success probability is not high. To solve this problem, the corresponding quantum forgery attacks on COPA, AES-COPA and Marble authenticated encryption algorithms are presented. In the quantum forgery attacks on COPA and AES-COPA, we use Simon's algorithm to find the period of the tag generation function in COPA and AES-COPA by querying in superposition, and then generate a forged tag for a new message. In the quantum forgery attack on Marble, Simon's algorithm is used to recover the secret parameter L, and the forged tag can be computed with L. Compared with classic forgery attacks on COPA, AES-COPA and Marble, our attack can reduce the number of queries from O(2^(n/2)) to O(n) and improve success probability close to 100%.Comment: 21 pages, 11 figure