Trace Properties from Separation Logic Specifications

We propose a formal approach for relating abstract separation logic library specifications with the trace properties they enforce on interactions between a client and a library. Separation logic with abstract predicates enforces a resource discipline that constrains when and how calls may be made between a client and a library. Intuitively, this can enforce a protocol on the interaction trace. This intuition is broadly used in the separation logic community but has not previously been formalised. We provide just such a formalisation. Our approach is based on using wrappers which instrument library code to induce execution traces for the properties under examination. By considering a separation logic extended with trace resources, we prove that when a library satisfies its separation logic specification then its wrapped version satisfies the same specification and, moreover, maintains the trace properties as an invariant. Consequently, any client and library implementation that are correct with respect to the separation logic specification will satisfy the trace properties

Modular termination verification for non-blocking concurrency

© Springer-Verlag Berlin Heidelberg 2016.We present Total-TaDA, a program logic for verifying the total correctness of concurrent programs: that such programs both terminate and produce the correct result. With Total-TaDA, we can specify constraints on a thread’s concurrent environment that are necessary to guarantee termination. This allows us to verify total correctness for nonblocking algorithms, e.g. a counter and a stack. Our specifications can express lock- and wait-freedom. More generally, they can express that one operation cannot impede the progress of another, a new non-blocking property we call non-impedance. Moreover, our approach is modular. We can verify the operations of a module independently, and build up modules on top of each other

First-principles study of ternary fcc solution phases from special quasirandom structures

In the present work, ternary Special Quasirandom Structures (SQSs) for a fcc solid solution phase are generated at different compositions, $x_A=x_B=x_C=\tfrac{1}{3}$ and $x_A=\tfrac{1}{2}$, $x_B=x_C=\tfrac{1}{4}$, whose correlation functions are satisfactorily close to those of a random fcc solution. The generated SQSs are used to calculate the mixing enthalpy of the fcc phase in the Ca-Sr-Yb system. It is observed that first-principles calculations of all the binary and ternary SQSs in the Ca-Sr-Yb system exhibit very small local relaxation. It is concluded that the fcc ternary SQSs can provide valuable information about the mixing behavior of the fcc ternary solid solution phase. The SQSs presented in this work can be widely used to study the behavior of ternary fcc solid solutions.Comment: 20 pages, 7 figure

DEDD regulates degradation of intermediate filaments during apoptosis

Apoptosis depends critically on regulated cytoskeletal reorganization events in a cell. We demonstrate that death effector domain containing DNA binding protein (DEDD), a highly conserved and ubiquitous death effector domain containing protein, exists predominantly as mono- or diubiquitinated, and that diubiquitinated DEDD interacts with both the K8/18 intermediate filament network and pro–caspase-3. Early in apoptosis, both cytosolic DEDD and its close homologue DEDD2 formed filaments that colocalized with and depended on K8/18 and active caspase-3. Subsequently, these filamentous structures collapsed into intracellular inclusions that migrated into cytoplasmic blebs and contained DEDD, DEDD2, active caspase-3, and caspase-3–cleaved K18 late in apoptosis. Biochemical studies further confirmed that DEDD coimmunoprecipitated with both K18 and pro–caspase-3, and kinetic analyses placed apoptotic DEDD staining prior to caspase-3 activation and K18 cleavage. In addition, both caspase-3 activation and K18 cleavage was inhibited by expression of DEDDΔNLS1-3, a cytosolic form of DEDD that cannot be ubiquitinated. Finally, siRNA mediated DEDD knockdown cells exhibited inhibition of staurosporine-induced DNA degradation. Our data suggest that DEDD represents a novel scaffold protein that directs the effector caspase-3 to certain substrates facilitating their ordered degradation during apoptosis

The impact of transfer learning on 3D deep learning convolutional neural network segmentation of the hippocampus in mild cognitive impairment and Alzheimer disease subjects

Research on segmentation of the hippocampus in magnetic resonance images through deep learning convolutional neural networks (CNNs) shows promising results, suggesting that these methods can identify small structural abnormalities of the hippocampus, which are among the earliest and most frequent brain changes associated with Alzheimer disease (AD). However, CNNs typically achieve the highest accuracy on datasets acquired from the same domain as the training dataset. Transfer learning allows domain adaptation through further training on a limited dataset. In this study, we applied transfer learning on a network called spatial warping network segmentation (SWANS), developed and trained in a previous study. We used MR images of patients with clinical diagnoses of mild cognitive impairment (MCI) and AD, segmented by two different raters. By using transfer learning techniques, we developed four new models, using different training methods. Testing was performed using 26% of the original dataset, which was excluded from training as a hold-out test set. In addition, 10% of the overall training dataset was used as a hold-out validation set. Results showed that all the new models achieved better hippocampal segmentation quality than the baseline SWANS model (ps <.001), with high similarity to the manual segmentations (mean dice [best model] = 0.878 ± 0.003). The best model was chosen based on visual assessment and volume percentage error (VPE). The increased precision in estimating hippocampal volumes allows the detection of small hippocampal abnormalities already present in the MCI phase (SD = [3.9 ± 0.6]%), which may be crucial for early diagnosis

Ordering variable for parton showers

The parton splittings in a parton shower are ordered according to an ordering variable, for example the transverse momentum of the daughter partons relative to the direction of the mother, the virtuality of the splitting, or the angle between the daughter partons. We analyze the choice of the ordering variable and conclude that one particular choice has the advantage of factoring softer splittings from harder splittings graph by graph in a physical gauge.Comment: 28 pages, 5 figure

On-shell recursion relations for all Born QCD amplitudes

We consider on-shell recursion relations for all Born QCD amplitudes. This includes amplitudes with several pairs of quarks and massive quarks. We give a detailed description on how to shift the external particles in spinor space and clarify the allowed helicities of the shifted legs. We proof that the corresponding meromorphic functions vanish at z --> infinity. As an application we obtain compact expressions for helicity amplitudes including a pair of massive quarks, one negative helicity gluon and an arbitrary number of positive helicity gluons.Comment: 30 pages, minor change

Modular termination veri cation for non-blocking concurrency (extended version)

We present Total-TaDA, a program logic for verifying the total correctness of concurrent programs: that such programs both terminate and produce the correct result. With Total-TaDA, we can specify constraints on a thread's concurrent environment that are necessary to guarantee termination. This allows us to verify total correctness for nonblocking algorithms, e.g. a counter and a stack. Our speci cations can express lock- and wait-freedom. More generally, they can express that one operation cannot impede the progress of another, a new non-blocking property we call non-impedance. Moreover, our approach is modular. We can verify the operations of a module independently, and build up modules on top of each other

Substrate Type Determines Metagenomic Profiles from Diverse Chemical Habitats

Environmental parameters drive phenotypic and genotypic frequency variations in microbial communities and thus control the extent and structure of microbial diversity. We tested the extent to which microbial community composition changes are controlled by shifting physiochemical properties within a hypersaline lagoon. We sequenced four sediment metagenomes from the Coorong, South Australia from samples which varied in salinity by 99 Practical Salinity Units (PSU), an order of magnitude in ammonia concentration and two orders of magnitude in microbial abundance. Despite the marked divergence in environmental parameters observed between samples, hierarchical clustering of taxonomic and metabolic profiles of these metagenomes showed striking similarity between the samples (>89%). Comparison of these profiles to those derived from a wide variety of publically available datasets demonstrated that the Coorong sediment metagenomes were similar to other sediment, soil, biofilm and microbial mat samples regardless of salinity (>85% similarity). Overall, clustering of solid substrate and water metagenomes into discrete similarity groups based on functional potential indicated that the dichotomy between water and solid matrices is a fundamental determinant of community microbial metabolism that is not masked by salinity, nutrient concentration or microbial abundance.</p