Property-driven benchmark generation: synthesizing programs of realistic structure

We present a systematic approach to the automatic generation of platform-independent benchmarks of realistic structure and tailored complexity for evaluating verification tools for reactive systems. The idea is to mimic a systematic constraint-driven software development process by automatically transforming randomly generated temporal-logic-based requirement specifications on the basis of a sequence of property-preserving, randomly generated structural design decisions into executable source code of a chosen target language or platform. Our automated transformation process steps through dedicated representations in terms of Büchi automata, Mealy machines, decision diagram models, and code models. It comprises LTL synthesis, model checking, property-oriented expansion, path condition extraction, theorem proving, SAT solving, and code motion. This setup allows us to address different communities via a growing set of programming languages, tailored sets of programming constructs, different notions of observation, and the full variety of LTL properties—ranging from mere reachability over general safety properties to arbitrary liveness properties. The paper illustrates the corresponding tool chain along accompanying examples, emphasizes the current state of development, and sketches the envisioned potential and impact of our approach.     

Temporally graded retrograde amnesia of contextual fear after hippocampal damage in rats: within-subjects examination

We have shown previously that electrolytic lesions of the dorsal hippocampus (DH) produce a severe deficit in contextual fear if made 1 d, but not 28 d, after fear conditioning (). As such, the hippocampus seems to play a time-limited role in the consolidation of contextual fear conditioning. Here, we examine retrograde amnesia of contextual fear produced by DH lesions in a within-subjects design. Unlike our previous reports, rats had both a remote and recent memory at the time of the lesion. Rats were given 10 tone-shock pairings in one context (remote memory) and 10 tone-shock pairings in a distinct context (with a different tone) 50 d later (recent memory), followed by DH or sham lesions 1 d later. Relative to controls, DH-lesioned rats exhibited no deficit in remote contextual fear, but recent contextual fear memory was severely impaired. They also did not exhibit deficits in tone freezing. This highly specific deficit in recent contextual memory demonstrated in a within-subjects design favors mnemonic over performance accounts of hippocampal involvement in fear. These findings also provide further support for a time-limited role of the hippocampus in memory storage.     

Fungal infections of fresh-cut fruit can be detected by the gas chromatography-mass spectrometric identification of microbial volatile organic compounds

There is a large and rapidly growing market for fresh-cut fruit. Microbial volatile organic compounds indicate the presence of fungal or bacterial contamination in fruit. In order to determine whether microbial volatile organic compounds can be used to detect contamination before fruit becomes unmarketable, pieces of cantaloupe, apple, pineapple, and orange were inoculated with a variety of fungal species, incubated at 25 degrees C, then sealed in glass vials. The volatiles were extracted by headspace solid-phase microextraction and analyzed by gas chromatography-mass spectrometry. Forty-five compounds were identified that might serve as unique identifiers of fungal contamination. Fungal contamination can be detected as early as 24 h after inoculation.     

Structure and biosynthesis of myxochromides S1-3 in Stigmatella aurantiaca: evidence for an iterative bacterial type I polyketide synthase and for module skipping in nonribosomal peptide biosynthesis

The myxobacterium Stigmatella aurantiaca DW4/3-1 harbours an astonishing variety of secondary metabolic gene clusters, at least two of which were found by gene inactivation experiments to be connected to the biosynthesis of previously unknown metabolites. In this study, we elucidate the structures of myxochromides S1-3, novel cyclic pentapeptide natural products possessing unsaturated polyketide side chains, and identify the corresponding biosynthetic gene locus, made up of six nonribosomal peptide synthetase modules. By analyzing the deduced substrate specificities of the adenylation domains, it is shown that module 4 is most probably skipped during the biosynthetic process. The polyketide synthase MchA harbours only one module and is presumably responsible for the formation of the variable complete polyketide side chains. These data indicate that MchA is responsible for an unusual iterative polyketide chain assembly.     

Hippocampus and Pavlovian Fear Conditioning in Rats: Muscimol Infusions Into the Ventral, but Not Dorsal, Hippocampus Impair the Acquisition of Conditional Freezing to an Auditory Conditional Stimulus.

The authors compared the effects of pharmacological inactivation of the dorsal hippocampus (DH) or ventral hippocampus (VH) on Pavlovian fear conditioning in rats. Freezing behavior served as the measure of fear. Pretraining infusions of muscimol, a GABAA receptor agonist, into the VH disrupted auditory, but not contextual, fear conditioning; DH infusions did not affect fear conditioning. Pretesting inactivation of the VH or DH did not affect the expression of conditional freezing. Pretraining electrolytic lesions of the VH reproduced the effects of muscimol infusions, whereas posttraining VH lesions disrupted both auditory and contextual freezing. Hence, neurons in the VH are importantly involved in the acquisition of auditory fear conditioning and the expression of auditory and contextual fear under some conditions. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Layer‐by‐Layer Fabrication of Covalently Crosslinked and Reactive Polymer Multilayers Using Azlactone‐Functionalized Copolymers: A Platform for the Design of Functional Biointerfaces

We report a method for modulating the physicochemical properties of surfaces that is based on the reactive layer‐by‐layer fabrication of covalently crosslinked thin films using azlactone‐functionalized copolymers. We demonstrate that copolymers containing different molar ratios of methyl methacrylate (MMA) and 2‐vinyl‐4,4‐dimethylazlactone (VDMA) can be alternately deposited with poly(ethyleneimine) to assemble covalently crosslinked thin films. Characterization using ellipsometry demonstrates that, in general, film growth and thickness decrease as the content of reactive, azlactone functionality in the copolymer used to assemble the film decreases. Reflective infrared spectroscopy experiments demonstrate that films fabricated from MMA:VDMA copolymers contain residual azlactone functionality and that these reactive groups can be exploited to modify film‐coated surfaces. Fabricating films from MMA:VDMA copolymers containing different compositions permitted modulation of the density of reactive groups within the films and, thus, the extent to which the films are functionalized by exposure to small molecule amines. For example, functionalization of MMA:VDMA copolymer films with the small molecule D ‐glucamine resulted in films with water contact angles that varied with the composition of the copolymer used to fabricate the film (e.g., as the azlactone content in the film increased, glucamine‐modified films became more hydrophilic). We demonstrate further that treatment of copolymer‐containing films with glucamine resulted in changes in the numbers of mammalian cells that grow on the surfaces of the films. Our results suggest the basis of methods that could be used to modulate or tune the density of chemical and biological functionality presented on surfaces of interest in a variety of fundamental and applied contexts.