Pattern of Amino Acid Substitutions in Transmembrane Domains of β-Barrel Membrane Proteins for Detecting Remote Homologs in Bacteria and Mitochondria

-barrel membrane proteins play an important role in controlling the exchange and transport of ions and organic molecules across bacterial and mitochondrial outer membranes. They are also major regulators of apoptosis and are important determinants of bacterial virulence. In contrast to -helical membrane proteins, their evolutionary pattern of residue substitutions has not been quantified, and there are no scoring matrices appropriate for their detection through sequence alignment. Using a Bayesian Monte Carlo estimator, we have calculated the instantaneous substitution rates of transmembrane domains of bacterial -barrel membrane proteins. The scoring matrices constructed from the estimated rates, called bbTM for -barrel Transmembrane Matrices, improve significantly the sensitivity in detecting homologs of -barrel membrane proteins, while avoiding erroneous selection of both soluble proteins and other membrane proteins of similar composition. The estimated evolutionary patterns are general and can detect -barrel membrane proteins very remote from those used for substitution rate estimation. Furthermore, despite the separation of 2–3 billion years since the proto-mitochondrion entered the proto-eukaryotic cell, mitochondria outer membrane proteins in eukaryotes can also be detected accurately using these scoring matrices derived from bacteria. This is consistent with the suggestion that there is no eukaryote-specific signals for translocation. With these matrices, remote homologs of -barrel membrane proteins with known structures can be reliably detected at genome scale, allowing construction of high quality structural models of their transmembrane domains, at the rate of 131 structures per template protein. The scoring matrices will be useful for identification, classification, and functional inference of membrane proteins from genome and metagenome sequencing projects. The estimated substitution pattern will also help to identify key elements important for the structural and functional integrity of -barrel membrane proteins, and will aid in the design of mutagenesis studies

SpreadCluster: Recovering Versioned Spreadsheets through Similarity-Based Clustering

Version information plays an important role in spreadsheet understanding, maintaining and quality improving. However, end users rarely use version control tools to document spreadsheet version information. Thus, the spreadsheet version information is missing, and different versions of a spreadsheet coexist as individual and similar spreadsheets. Existing approaches try to recover spreadsheet version information through clustering these similar spreadsheets based on spreadsheet filenames or related email conversation. However, the applicability and accuracy of existing clustering approaches are limited due to the necessary information (e.g., filenames and email conversation) is usually missing. We inspected the versioned spreadsheets in VEnron, which is extracted from the Enron Corporation. In VEnron, the different versions of a spreadsheet are clustered into an evolution group. We observed that the versioned spreadsheets in each evolution group exhibit certain common features (e.g., similar table headers and worksheet names). Based on this observation, we proposed an automatic clustering algorithm, SpreadCluster. SpreadCluster learns the criteria of features from the versioned spreadsheets in VEnron, and then automatically clusters spreadsheets with the similar features into the same evolution group. We applied SpreadCluster on all spreadsheets in the Enron corpus. The evaluation result shows that SpreadCluster could cluster spreadsheets with higher precision and recall rate than the filename-based approach used by VEnron. Based on the clustering result by SpreadCluster, we further created a new versioned spreadsheet corpus VEnron2, which is much bigger than VEnron. We also applied SpreadCluster on the other two spreadsheet corpora FUSE and EUSES. The results show that SpreadCluster can cluster the versioned spreadsheets in these two corpora with high precision.Comment: 12 pages, MSR 201

Electrodynamic Response and Stability of Molecular Crystals

We show that electrodynamic dipolar interactions, responsible for long-range fluctuations in matter, play a significant role in the stability of molecular crystals. Density functional theory calculations with van der Waals interactions determined from a semilocal "atom-in-a-molecule" model result in a large overestimation of the dielectric constants and sublimation enthalpies for polyacene crystals from naphthalene to pentacene, whereas an accurate treatment of non-local electrodynamic response leads to an agreement with the measured values for both quantities. Our findings suggest that collective response effects play a substantial role not only for optical excitations, but also for cohesive properties of non-covalently bound molecular crystals

Joint Task Assignment and Wireless Resource Allocation for Cooperative Mobile-Edge Computing

This paper studies a multi-user cooperative mobile-edge computing (MEC) system, in which a local mobile user can offload intensive computation tasks to multiple nearby edge devices serving as helpers for remote execution. We focus on the scenario where the local user has a number of independent tasks that can be executed in parallel but cannot be further partitioned. We consider a time division multiple access (TDMA) communication protocol, in which the local user can offload computation tasks to the helpers and download results from them over pre-scheduled time slots. Under this setup, we minimize the local user's computation latency by optimizing the task assignment jointly with the time and power allocations, subject to individual energy constraints at the local user and the helpers. However, the joint task assignment and wireless resource allocation problem is a mixed-integer non-linear program (MINLP) that is hard to solve optimally. To tackle this challenge, we first relax it into a convex problem, and then propose an efficient suboptimal solution based on the optimal solution to the relaxed convex problem. Finally, numerical results show that our proposed joint design significantly reduces the local user's computation latency, as compared against other benchmark schemes that design the task assignment separately from the offloading/downloading resource allocations and local execution.Comment: 6 pages, 4 figures, accepted by IEEE International Conference on Communications (ICC), Kansas City, MO, USA, 201

Adaptive Fog Configuration for the Industrial Internet of Things

Industrial Fog computing deploys various industrial services, such as automatic monitoring/control and imminent failure detection, at the Fog Nodes (FNs) to improve the performance of industrial systems. Much effort has been made in the literature on the design of fog network architecture and computation offloading. This paper studies an equally important but much less investigated problem of service hosting where FNs are adaptively configured to host services for Sensor Nodes (SNs), thereby enabling corresponding tasks to be executed by the FNs. The problem of service hosting emerges because of the limited computational and storage resources at FNs, which limit the number of different types of services that can be hosted by an FN at the same time. Considering the variability of service demand in both temporal and spatial dimensions, when, where, and which services to host have to be judiciously decided to maximize the utility of the Fog computing network. Our proposed Fog configuration strategies are tailored to battery-powered FNs. The limited battery capacity of FNs creates a long-term energy budget constraint that significantly complicates the Fog configuration problem as it introduces temporal coupling of decision making across the timeline. To address all these challenges, we propose an online distributed algorithm, called Adaptive Fog Configuration (AFC), based on Lyapunov optimization and parallel Gibbs sampling. AFC jointly optimizes service hosting and task admission decisions, requiring only currently available system information while guaranteeing close-to-optimal performance compared to an oracle algorithm with full future information