Framework Of Ab Research Articles

D2ABS: A Framework for Dynamic Dependence Analysis of Distributed Programs

As modern software systems are increasingly developed for running in distributed environments, it is crucial to provide fundamental techniques such as dependence analysis for checking, diagnosing, and evolving those systems. However, traditional dependence analysis is either inapplicable or of very limited utility for distributed programs due to the decoupled components of these programs that run in concurrent processes at physically separated machines. Motivated by the need for dependence analysis of distributed software and the diverse cost-effectiveness needs of dependence-based applications, this paper presents D$^2$ABS, a framework of dynamic dependence abstraction for distributed programs. By partial-ordering distributed method-execution events and inferring causality from the ordered events, D$^2$ABS abstracts method-level dependencies both within and across process boundaries. Further, by exploiting message-passing semantics across processes, and incorporating static dependencies and statement coverage within individual components, we present three additional instantiations of D$^2$ABS that trade efficiency for better precision. We present the design of the D$^2$ABS framework and evaluate the four instantiations of D$^2$ABS on distributed systems of various architectures and scales using our implementation for Java. Our empirical results show that D$^2$ABS is significantly more effective than existing options while offering varied levels of cost-effectiveness tradeoffs. As our framework essentially computes whole-system run-time dependencies, it naturally empowers a range of other dependence-based applications.

Discovery of Marburg virus neutralizing antibodies from virus-naïve human antibody repertoires using large-scale structural predictions

Marburg virus (MARV) disease is lethal, with fatality rates up to 90%. Neutralizing antibodies (Abs) are promising drug candidates to prevent or treat the disease. Current efforts are focused in part on vaccine development to induce such MARV-neutralizing Abs. We analyzed the antibody repertoire from healthy unexposed and previously MARV-infected individuals to assess if naïve repertoires contain suitable precursor antibodies that could become neutralizing with a limited set of somatic mutations. We computationally searched the human Ab variable gene repertoire for predicted structural homologs of the neutralizing Ab MR78 that is specific to the receptor binding site (RBS) of MARV glycoprotein (GP). Eight Ab heavy-chain complementarity determining region 3 (HCDR3) loops from MARV-naïve individuals and one from a previously MARV-infected individual were selected for testing as HCDR3 loop chimeras on the MR78 Ab framework. Three of these chimerized antibodies bound to MARV GP. We then tested a full-length native Ab heavy chain encoding the same 17-residue-long HCDR3 loop that bound to the MARV GP the best among the chimeric Abs tested. Despite only 57% amino acid sequence identity, the Ab from a MARV-naïve donor recognized MARV GP and possessed neutralizing activity against the virus. Crystallization of both chimeric and full-length native heavy chain-containing Abs provided structural insights into the mechanism of binding for these types of Abs. Our work suggests that the MARV GP RBS is a promising candidate for epitope-focused vaccine design to induce neutralizing Abs against MARV.

Antibodies VRC01 and 10E8 Neutralize HIV-1 with High Breadth and Potency Even with Ig-Framework Regions Substantially Reverted to Germline

Abs capable of effectively neutralizing HIV-1 generally exhibit very high levels of somatic hypermutation, both in their CDR and framework-variable regions. In many cases, full reversion of the Ab-framework mutations back to germline results in substantial to complete loss of HIV-1-neutralizing activity. However, it has been unclear whether all or most of the observed framework mutations would be necessary or whether a small subset of these mutations might be sufficient for broad and potent neutralization. To address this issue and to explore the dependence of neutralization activity on the level of somatic hypermutation in the Ab framework, we applied a computationally guided framework-reversion procedure to two broadly neutralizing anti-HIV-1 Abs, VRC01 and 10E8, which target two different HIV-1 sites of vulnerability. Ab variants in which up to 78% (38 of 49 for VRC01) and 89% (31 of 35 for 10E8) of framework mutations were reverted to germline retained breadth and potency within 3-fold of the mature Abs when evaluated on a panel of 21 diverse viral strains. Further, a VRC01 variant with an ∼50% framework-reverted L chain showed a 2-fold improvement in potency over the mature Ab. Our results indicate that only a small number of Ab-framework mutations may be sufficient for high breadth and potency of HIV-1 neutralization by Abs VRC01 and 10E8. Partial framework revertants of HIV-1 broadly neutralizing Abs may present advantages over their highly mutated counterparts as Ab therapeutics and as targets for immunogen design.

Nuclear magnetic moments for J π = 2 1 + state of 10Be with ab initio Monte Carlo shell model calculation

The magnetic moment of 2 1 + state for 10Be are calculated and investigated in terms of single particle orbits for protons and neutrons under the framework of ab initio Monte Carlo shell model method in an e max = 3 model space. The reduced matrix elements of orbital and spin angular momentum are evaluated. It is found that the orientations of orbital angular momentum in different single particle orbits are consistent. Conversely, the orientations of spin in different single particle orbits tend to be chaotic. The nuclear magnetic moment of 2 1 + state for 10Be is obtained as 1.006 µ N and is discussed in regards to the contribution of orbital and spin angular momentum both for protons and neutrons. The corresponding g-factor is also given.

Synthesis of an A′B′ Precursor to Angelmicin B: Product Diversification in the Suárez Lactol Fragmentation

We describe a synthetic strategy for the angelimicin family of anthraquinoid natural products that involves converting a central highly oxygenated decalin intermediate to the AB and A'B' subunits. Herein, we report the synthesis of the bicyclic A'B' subunit that complements our earlier route to the tricyclic AB framework. The differentiating tact in the two syntheses focused on controlling the Suárez radical fragmentation of lactol precursors by modulating the substrate's structural rigidity. A more flexible lactol gave the tricyclic AB framework, whereas a more rigid substrate led to the bicyclic A'B' precursor, presumably through divergent pathways from the radical produced in the initial fragmentation step. These results establish a versatile advanced synthetic precursor for the angelimicins, and on a more general note, illustrate strategies for applying the Suárez fragmentation to diverse and complex molecular frameworks.

Phase Transition and Energy Spectra of Some Ferroelectrics-Ferroelastics

We report the results of electronic structure calculations for several types of MoO4-clusters in the Gd2(MoO4)3 structure in ferroelectric and paraelectric phase by using cluster ab initio restricted Hartree Fock method. The results give a variational approximation to the ground state electron densities of these clusters within the framework of ab initio restricted Hartree Fock (RHF) MO LCAO method.

A class of ABS algorithms for Diophantine linear systems

Systems of integer linear (Diophantine) equations arise from various applications. In this paper we present an approach, based upon the ABS methods, to solve a general system of linear Diophantine equations. This approach determines if the system has a solution, generalizing the classical fundamental theorem of the single linear Diophantine equation. If so, a solution is found along with an integer Abaffian (rank deficient) matrix such that the integer combinations of its rows span the integer null space of the cofficient matrix, implying that every integer solution is obtained by the sum of a single solution and an integer combination of the rows of the Abaffian. We show by a counterexample that, in general, it is not true that any set of linearly independent rows of the Abaffian forms an integer basis for the null space, contrary to a statement by Egervary. Finally we show how to compute the Hermite normal form for an integer matrix in the ABS framework.

Analytical second derivatives in ab initio Hartree–Fock crystal orbital theory of polymers

In the framework of ab initio Hartree–Fock crystal orbital theory of polymers, the formulas for the analytical second derivatives of energy with respect to in-phase ( k=0) nuclear coordinates are derived. The coupled perturbed Hartree–Fock (CPHF) equation is iteratively solved by using the direct (recomputation of two-electron integrals) atomic-orbital-based algorithm. Frequencies of the Brillouin zone center ( k=0) vibrations of all- trans polyethylene are calculated by using the STO-3G, 3-21G and 6-31G* basis sets. The dependence of the frequencies on the number of neighbors included in the lattice summations, on the number of momentum sampling points in the first Brillouin zone, and on the convergence criterion for the CPHF solutions is examined. In our implementation, the use of analytical second derivatives is more efficient than the use of the finite differences of analytical first derivatives.

Fragment interaction analysis of structural problems in the framework ofAb initio SCF-MO computations

Fragment interaction analysis of structural problems in the framework ofAb initio SCF-MO computations

Fragment interaction analysis of structural problems in the framework ofAb initio SCF-MO computations

We describe here a procedure which allows to extend the application of the quantitative orbital interaction analysis at theab initio SCF-MO level to any kind of orbital interaction. In this new procedure a localization scheme is applied to the fragment MOs obtained with the procedure suggested by Wolfe et al. (JACS99, 1296 (1977)): in this way also the resulting σ-type fragment localized MOs have correct orbital occupancies and can be used for a PMO analysis. In addition the availability of quantitative expressions for the fragment localized MOs allows also to compute the total energy of the system in the absence of the orbital interactions under examination. For illustrative purposes the procedure is applied to the analysis of the factors which determine the preferential stability oftrans overcis diimide.