Safe Compositional Specification of Network Systems With Polymorphic, Constrained Types

In the framework of iBench research project, our previous work created a domain specific language TRAFFIC [6] that facilitates specification, programming, and maintenance of distributed applications over a network. It allows safety property to be formalized in terms of types and subtyping relations. Extending upon our previous work, we add Hindley-Milner style polymorphism [8] with constraints [9] to the type system of TRAFFIC. This allows a programmer to use for-all quantifier to describe types of network components, escalating power and expressiveness of types to a new level that was not possible before with propositional subtyping relations. Furthermore, we design our type system with a pluggable constraint system, so it can adapt to different application needs while maintaining soundness. In this paper, we show the soundness of the type system, which is not syntax-directed but is easier to do typing derivation. We show that there is an equivalent syntax-directed type system, which is what a type checker program would implement to verify the safety of a network flow. This is followed by discussion on several constraint systems: polymorphism with subtyping constraints, Linear Programming, and Constraint Handling Rules (CHR) [3]. Finally, we provide some examples to illustrate workings of these constraint systems.National Science Foundation (CCR-0205294

Simple, safe, and efficient memory management using linear pointers

Efficient and safe memory management is a hard problem. Garbage collection promises automatic memory management but comes with the cost of increased memory footprint, reduced parallelism in multi-threaded programs, unpredictable pause time, and intricate tuning parameters balancing the program's workload and designated memory usage in order for an application to perform reasonably well. Existing research mitigates the above problems to some extent, but programmer error could still cause memory leak by erroneously keeping memory references when they are no longer needed. We need a methodology for programmers to become resource aware, so that efficient, scalable, predictable and high performance programs may be written without the fear of resource leak. Linear logic has been recognized as the formalism of choice for resource tracking. It requires explicit introduction and elimination of resources and guarantees that a resource cannot be implicitly shared or abandoned, hence must be linear. Early languages based on linear logic focused on Curry-Howard correspondence. They began by limiting the expressive powers of the language and then reintroduced them by allowing controlled sharing which is necessary for recursive functions. However, only by deviating from Curry-Howard correspondence could later development actually address programming errors in resource usage. The contribution of this dissertation is a simple, safe, and efficient approach introducing linear resource ownership semantics into C++ (which is still a widely used language after 30 years since inception) through linear pointer, a smart pointer inspired by linear logic. By implementing various linear data structures and a parallel, multi-threaded memory allocator based on these data structures, this work shows that linear pointer is practical and efficient in the real world, and that it is possible to build a memory management stack that is entirely leak free. The dissertation offers some closing remarks on the difficulties a formal system would encounter when reasoning about a concurrent linear data algorithm, and what might be done to solve these problems

Safe Compositional Specification of Networking Systems: A Compositional Analysis Approach

We present a type inference algorithm, in the style of compositional analysis, for the language TRAFFIC—a specification language for flow composition applications proposed in [2]—and prove that this algorithm is correct: the typings it infers are principal typings, and the typings agree with syntax-directed type checking on closed flow specifications. This algorithm is capable of verifying partial flow specifications, which is a significant improvement over syntax-directed type checking algorithm presented in [3]. We also show that this algorithm runs efficiently, i.e., in low-degree polynomial time.National Science Foundation (ITR ANI-0205294, ANI-0095988, ANI-9986397, EIA-0202067

Localization of BEN1-LIKE protein and nuclear degradation during development of metaphloem sieve elements in Triticum aestivum L.

Metaphloem sieve elements (MSEs) in the developing caryopsis of Triticum aestivum L. undergo a unique type of programmed cell death (PCD); cell organelles gradually degrade with the MSE differentiation while mature sieve elements keep active. This study focuses on locating BEN1-LIKE protein and nuclear degradation in differentiating MSEs of wheat. Transmission electron microscopy (TEM) showed that nuclei degraded in MSE development. First, the degradation started at 2–3 days after flowering (DAF). The degraded fragments were then swallowed by phagocytic vacuoles at 4 DAF. Finally, nuclei almost completely degraded at 5 DAF. We measured the BEN1-LIKE protein expression in differentiating MSEs. In situ hybridization showed that BEN1-LIKE mRNA was a more obvious hybridization signal at 3–4 DAF at the microscopic level. Immuno-electron microscopy further revealed that BEN1-LIKE protein was mainly localized in MSE nuclei. Furthermore, MSE differentiation was tested using a TSQ Zn2+ fluorescence probe which showed that the dynamic change of Zn2+ accumulation was similar to BEN1-LIKE protein expression. These results suggest that nucleus degradation in wheat MSEs is associated with BEN1-LIKE protein and that the expression of this protein may be regulated by Zn2+ accumulation variation

High-resolution QTL mapping for grain appearance traits and co-localization of chalkiness-associated differentially expressed candidate genes in rice

Table S4. Annotated function of differentially expressed genes identified between parents. (XLSX 1232 kb

Towards increased concentration sensitivity for continuous wave EPR investigations of spin-labeled biological macromolecules at high fields

This work was performed at the National High Magnetic Field Laboratory (NHMFL), which is supported by the National Science Foundation (DMR-1157490) and the State of Florida. L.S. acknowledges support from the National Institutes of Health (AI091693) and the NHMFL User Collaboration Grants Program (Award No. 5080). G.E.F. acknowledges support from the National Science Foundation (MCB-1329467) and the National Institutes of Health (GM105409 and S10RR031603). S.H. acknowledges support from the National Science Foundation (DMR-1309463). J.M.E acknowledges support from the National Science Foundation (DGE-0802270).High-field, high-frequency electron paramagnetic resonance (EPR) spectroscopy at W- (∼95 GHz) and D-band (∼140 GHz) is important for investigating the conformational dynamics of flexible biological macromolecules because this frequency range has increased spectral sensitivity to nitroxide motion over the 100 ps to 2 ns regime. However, low concentration sensitivity remains a roadblock for studying aqueous samples at high magnetic fields. Here, we examine the sensitivity of a non-resonant thin-layer cylindrical sample holder, coupled to a quasi-optical induction-mode W-band EPR spectrometer (HiPER), for continuous wave (CW) EPR analyses of: (i) the aqueous nitroxide standard, TEMPO; (ii) the unstructured to α-helical transition of a model IDP protein; and (iii) the base-stacking transition in a kink-turn motif of a large 232 nt RNA. For sample volumes of ∼50 μL, concentration sensitivities of 2-20 μM were achieved, representing a ∼10-fold enhancement compared to a cylindrical TE011 resonator on a commercial Bruker W-band spectrometer. These results therefore highlight the sensitivity of the thin-layer sample holders employed in HiPER for spin-labeling studies of biological macromolecules at high fields, where applications can extend to other systems that are facilitated by the modest sample volumes and ease of sample loading and geometry.PostprintPeer reviewe