Towards operational cost minimization for cloud bursting with deadline constraints in hybrid clouds

In hybrid clouds, there is a technique named cloud bursting which can allow companies to expand their capacity to meet the demands of peak workloads in a low-priced manner. In this work, a cost-aware job scheduling approach based on queueing theory in hybrid clouds is proposed. The job scheduling problem in the private cloud is modeled as a queueing model. A genetic algorithm is applied to achieve optimal queues for jobs to improve the utilization rate of the private cloud. Then, the task execution time is predicted by back propagation neural network. The max–min strategy is applied to schedule tasks according to the prediction results in hybrid clouds. Experiments show that our cost-aware job scheduling algorithm can reduce the average job waiting time and average job response time in the private cloud. In additional, our proposed job scheduling algorithm can improve the system throughput of the private cloud. It also can reduce the average task waiting time, average task response time and total costs in hybrid clouds.     

An Efficient Two-Tier Causal Protocol for Mobile Distributed Systems

Causal ordering is a useful tool for mobile distributed systems (MDS) to reduce the non-determinism induced by three main aspects: host mobility, asynchronous execution, and unpredictable communication delays. Several causal protocols for MDS exist. Most of them, in order to reduce the overhead and the computational cost over wireless channels and mobile hosts (MH), ensure causal ordering at and according to the causal view of the Base Stations. Nevertheless, these protocols introduce certain disadvantage, such as unnecessary inhibition at the delivery of messages. In this paper, we present an efficient causal protocol for groupware that satisfies the MDS''s constraints, avoiding unnecessary inhibitions and ensuring the causal delivery based on the view of the MHs. One interesting aspect of our protocol is that it dynamically adapts the causal information attached to each message based on the number of messages with immediate dependency relation, and this is not directly proportional to the number of MHs.     

Evaluation of quantitative and qualitative aspects of mitochondrial function in human skeletal and cardiac muscles

Techniques and protocols of assessment of mitochondrial properties are of physiological and physiopathological important significance. A precise knowledge of the advantages and limitations of the different protocols used to investigate the mitochondrial function, is therefore necessary. This report presents examples of how the skinned (or permeabilized) fibers technique could be applied for the polarographic determination of the actual quantitative and qualitative aspects of mitochondrial function in human muscle samples. We described and compared the main available respiration protocols in order to sort out which protocol seems more appropriate for the characterization of mitochondrial properties according to the questions under consideration: quantitative determination of oxidative capacities of a given muscle, characterization of the pattern of control of mitochondrial respiration, or assessment of a mitochondrial defect at the level of the respiratory chain complexes. We showed that while protocol A, using only two levels of the phosphate acceptor adenosine diphosphate (ADP) concentration and the adjunction of creatine, could be used for the determination of quantitative changes in very small amount of muscle samples, the ADP sensitivity of mitochondrial respiration was underestimated by this protocol in muscles with high oxidative capacities. The actual apparent Km for ADP and the role of functional activation of miCK in ATP production and energy transfer in oxidative muscles, are well-assessed by protocol B (in the absence of creatine) together with protocol C (in the presence of creatine) that use increasing concentrations of ADP ranging from 2.5-2000 microM. Protocol D is well-adapted to investigate the potential changes at different levels of the respiratory chain, by the use of specific substrates and inhibitors. As can be seen from the present data and the current review of previous reports in the literature, a standardization of the respiration protocols is needed for useful comparisons between studies.     

Exploiting application buffer reuse to improve MPI small message transfer protocols over RDMA-enabled networks

To avoid the memory registration cost for small messages in MPI implementations over RDMA-enabled networks, message transfer protocols involve a copy to intermediate buffers at both sender and receiver. In this paper, we propose to eliminate the send-side copy when an application buffer is reused frequently. We show that it is more efficient to register the application buffer and use it for data transfer. The idea is examined for small message transfer protocols in MVAPICH2, including RDMA Write and Send/Receive based communications, one-sided communications and collectives. The proposed protocol adaptively falls back to the current protocol when the application does not frequently use its buffers. The performance results over InfiniBand indicate up to 14% improvement for single message latency, close to 20% improvement for one-sided operations and up to 25% improvement for collectives. In addition, the communication time in MPI applications with high buffer reuse is improved using this technique.     

Lifetime extension based on residual energy for receiver-driven multi-hop wireless network

An important research topic in wireless sensor networking is the extension of operating time by controlling the power consumption of individual nodes. In a receiver-driven communication protocol, a receiver node periodically transmits its ID to the sender node, and in response the sender node sends an acknowledgment, after which data transmission starts. By applying such a receiver-driven protocol to wireless sensor networks, the average power consumption of the network can be controlled, but there still remains the problem of unbalanced load distribution among nodes. Therefore, part of the network shuts down when the battery of the node that consumes the most power is completely discharged. To extend the network lifetime, we propose a method where information about the residual energy level is exchanged through ID packets in order to balance power consumption. Simulation results show that the network lifetime can be extended by about 70–100 % while maintaining high network performance in terms of packet collection ratio and delay.     

Glycan characterization of the NIST RM monoclonal antibody using a total analytical solution: From sample preparation to data analysis

Glycosylation is an important attribute of biopharmaceutical products to monitor from development through production. However, glycosylation analysis has traditionally been a time-consuming process with long sample preparation protocols and manual interpretation of the data. To address the challenges associated with glycan analysis, we developed a streamlined analytical solution that covers the entire process from sample preparation to data analysis. In this communication, we describe the complete analytical solution that begins with a simplified and fast N-linked glycan sample preparation protocol that can be completed in less than 1 hr. The sample preparation includes labelling with RapiFluor-MS tag to improve both fluorescence (FLR) and mass spectral (MS) sensitivities. Following HILIC-UPLC/FLR/MS analyses, the data are processed and a library search based on glucose units has been included to expedite the task of structural assignment. We then applied this total analytical solution to characterize the glycosylation of the NIST Reference Material mAb 8761. For this glycoprotein, we confidently identified 35 N-linked glycans and all three major classes, high mannose, complex, and hybrid, were present. The majority of the glycans were neutral and fucosylated; glycans featuring N-glycolylneuraminic acid and those with two galactoses connected via an α1,3-linkage were also identified.     

SpeQuloS: a QoS service for hybrid and elastic computing infrastructures

The large choice of Distributed Computing Infrastructures (DCIs) available allows users to select and combine their preferred architectures amongst Clusters, Grids, Clouds, Desktop Grids and more. In these hybrid DCIs, elasticity is emerging as a key property. In elastic infrastructures, resources available to execute application continuously vary, either because of application requirements or because of constraints on the infrastructure, such as node volatility. In the former case, there is no guarantee that the computing resources will remain available during the entire execution of an application. In this paper, we show that Bag-of-Tasks (BoT) execution on these “Best-Effort” infrastructures suffer from a drop of the task completion rate at the end of the execution. The SpeQuloS service presented in this paper improves the Quality of Service (QoS) of BoT applications executed on hybrid and elastic infrastructures. SpeQuloS monitors the execution of the BoT, and dynamically supplies fast and reliable Cloud resources when the critical part of the BoT is executed. SpeQuloS offers several features to hybrid DCIs users, such as estimating completion time and execution speedup. Performance evaluation shows that BoT executions can be accelerated by a factor 2, while offloading less than 2.5 % of the workload to the Cloud. We report on several scenarios where SpeQuloS is deployed on hybrid infrastructures featuring a large variety of infrastructures combinations. In the context of the European Desktop Grid Initiative (EDGI), SpeQuloS is operated to improve QoS of Desktop Grids using resources from private Clouds. We present a use case where SpeQuloS uses both EC2 regular and spot instances to decrease the cost of computation while preserving a similar QoS level. Finally, in the last scenario SpeQuloS allows to optimize Grid5000 resources utilization.     

A Comparison of Protocols for Updating Location Information

Detailed location information of mobile objects, for example that of a user with a mobile computer or phone, is an important input for many location-aware applications. However, constantly updating the location information for thousands of mobile objects is not feasible. Therefore, special update protocols for location information are required that transmit the information as efficiently as possible, that is requiring only few update messages, while still being effective in returning the location information with the desired accuracy. Different classes of such update protocols are described in this paper and a new combined protocol is proposed. To be able to compare their effectiveness and efficiency, we present an analysis for the minimum and average resulting accuracy of the location information in comparison with the number of messages transmitted. We also present the results of simulations that we have performed to back up our analysis.     

Incremental energy supply for microalgae culture in a photobioreactor

A model was developed for any PBR, based on mixing requirement per unit of biomass production rather than constant amount of mixing energy. The model assumes constant biomass concentration throughout the culture time which means the volume of the culture would increase over time; the mixing energy will also increase over time according to the volume of the culture. Such incremental energy supply (IES) consumes much less energy compared to constant energy supply (CES); higher the culture time in the PBR, more is the savings in the IES compared to CES. In addition to mixing energy, light energy can also be applied using IES scheme. The model was validated with the algae Nannochloropsis sp.; 44% of the energy input of CES was saved by adopting IES with equal biomass productivities for a culture period of 60 h.     

Efficient chameleon hashing-based privacy-preserving auditing in cloud storage

Cloud storage is an important application service in cloud computing, it allows data users to store and access their files anytime, from anywhere and with any device. To ensure the security of the outsourced data, data user needs to periodically check data integrity. In some cases, the identity privacy of data user must be protected. However, in the existing preserving identity privacy protocols, data tag generation is mainly based on complex ring signature or group signature. It brings a heavy burden to data user. To ensure identity privacy of data user, in this paper we propose a novel identity privacy-preserving public auditing protocol by utilizing chameleon hash function. It can achieve the following properties: (1) the identity privacy of data user is preserved for cloud server; (2) the validity of the outsourced data is verified; (3) data privacy can be preserved for the auditor in auditing process; (4) computation cost to produce data tag is very low. Finally, we also show that our scheme is provably secure in the random oracle model, the security of the proposed scheme is related to the computational Diffie–Hellman problem and hash function problem.     

Asymmetrically reliable caches for multicore architectures under performance and energy constraints

Cache structures in a multicore system are more vulnerable to soft errors due to high transistor density. Protecting all caches unselectively has notable overhead on performance and energy consumption. In this study, we propose asymmetrically reliable caches to supply reliability need of the system using sufficient additional hardware under the performance and energy constraints. In our framework, a chip multiprocessor is composed of a high reliability core which has ECC protection, and a set of low reliability cores which have no protection on their data caches. Between two types of cores, there is also a middle-level reliability core which has only parity check. Application threads are mapped on the different cores in terms of reliability based on their critical data usage. The experimental results for selected applications show that our proposed techniques improve reliability with considerable performance and energy overhead on the average compared to traditional unsafe caches.     

Efficient TPA-based auditing scheme for secure cloud storage

In recent years, how to design efficient auditing protocol to verify the integrity of users’ data, which is stored in cloud services provider (CSP), becomes a research focus. Homomorphic message authentication code (MAC) and homomorphic signature are two popular techniques to respectively design private and public auditing protocols. On the one hand, it is not suitable for the homomorphic-MAC-based auditing protocols to be outsourced to third-party auditor (TPA), who has more professional knowledge and computational abilities, although they have high efficiencies. On the other hand, the homomorphic-signature-based ones are very suitable for employing TPA without compromising user’s signing key but have very low efficiency (compared to the former case). In this paper, we propose a new auditing protocol, which perfectly combines the advantages of above two cases. In particular, it is almost as efficient as a homomorphic-MAC-based protocol proposed by Zhang et al. recently. Moreover, it is also suitable for outsourcing to TPA because it does not compromise the privacy of users’ signing key, which can be seen from our security analysis. Finally, numerical analysis and experimental results demonstrate the high-efficiency of our protocol.

     

Direct vs. Indirect Benefits of Caching by Gray Squirrels (Sciurus carolinensis)

Individuals of many species cache food to gain direct benefits from consuming their own caches, but individuals of a few species also gain indirect benefits by sharing caches with kin. We investigated whether gray squirrels cache primarily to gain direct benefits or if they also gain indirect benefits by sharing caches with kin. If squirrels share caches with kin, then genetically related squirrels should live near one another and cache near one another to facilitate cache sharing. In contrast, if squirrels cache primarily for direct benefits, then they should clump their caches near the center of their ranges to facilitate cache defense. This study was conducted with 140 squirrels in a 10 ha forest. DNA was extracted from blood samples taken from squirrels, and genetic similarity scores from randomly amplified polymorphic DNA (RAPD) loci were used to measure relatedness. Squirrels were given piles of pecans for caching at six sites and observed from a blind. We recorded the direction squirrels took nuts from piles and at one site determined the location of caches. For male–female comparisons, related squirrels lived significantly closer to one another than unrelated squirrels, but this was not the case for female–female and male–male comparisons. The genetic similarity of neighboring squirrels did not influence the location of caches or the direction that squirrels took nuts from piles. Squirrels clumped their own caches and moved nuts toward their own home range centers. These results suggest that gray squirrels cache primarily to gain direct benefits rather than indirect benefits.     

Finding scalable configurations for AEDB broadcasting protocol using multi-objective evolutionary algorithms

Energy consumption is one of the main concerns in mobile ad hoc networks (or MANETs). The lifetime of its devices highly depends on the energy consumption as they rely on batteries. The adaptive enhanced distance based broadcasting algorithm, AEDB, is a message dissemination protocol for MANETs that uses cross-layer technology to highly reduce the energy consumption of devices in the process, while still providing competitive performance in terms of coverage and time. We use two different multi-objective evolutionary algorithms to optimize the protocol on three network densities, and we evaluate the scalability of the best found AEDB configurations on larger networks and different densities.     

Effects of food value, predation risk, and pilferage on the caching decisions of Dipodomys merriami

Animals that scatter cache their food face a trade-off betweenthe benefits of protecting caches from pilferers and the costsassociated with caching. Placing food into a large number ofwidely spaced caches helps to protect it from pilferage butalso involves costs such as greater exposure to predators. Ipredicted that animals would disperse food into a larger numberof more widely spaced caches when caching (1) a preferred foodversus a less preferred food and (2) under conditions of lowpredation risk versus high predation risk. To test these predictions,I examined the scatter-caching decisions of Merriam's kangaroorats (Dipodomys merriami). D. merriami distributed caches inclumped patterns, regardless of food preference, but they showeda tendency to invest more in a preferred food by distributingcaches more widely. Under the relative safety of the new moon,they did not disperse caches more widely, rather they partitionedthe same amount of food into a larger number of caches thanthey did under the full moon, when predation risk is higher.To examine whether their cache spacing decisions had a significantimpact on the success of cache pilferers, I measured discoveryby pilferers of artificial caches of two food types at differentcaching distances. Results indicate that the cache spacing behaviorof D. merriami functions to protect caches from pilferers, becauseincreased spacing of artificial caches decreased the probabilityof pilferage for both types of food.     

Impact of Library Preparation on Downstream Analysis and Interpretation of RNA-Seq Data: Comparison between Illumina PolyA and NuGEN Ovation Protocol

Objectives

The sequencing by the PolyA selection is the most common approach for library preparation. With limited amount or degraded RNA, alternative protocols such as the NuGEN have been developed. However, it is not yet clear how the different library preparations affect the downstream analyses of the broad applications of RNA sequencing.

Methods and Materials

Eight human mammary epithelial cell (HMEC) lines with high quality RNA were sequenced by Illumina’s mRNA-Seq PolyA selection and NuGEN ENCORE library preparation. The following analyses and comparisons were conducted: 1) the numbers of genes captured by each protocol; 2) the impact of protocols on differentially expressed gene detection between biological replicates; 3) expressed single nucleotide variant (SNV) detection; 4) non-coding RNAs, particularly lincRNA detection; and 5) intragenic gene expression.

Results

Sequences from the NuGEN protocol had lower (75%) alignment rate than the PolyA (over 90%). The NuGEN protocol detected fewer genes (12–20% less) with a significant portion of reads mapped to non-coding regions. A large number of genes were differentially detected between the two protocols. About 17–20% of the differentially expressed genes between biological replicates were commonly detected between the two protocols. Significantly higher numbers of SNVs (5–6 times) were detected in the NuGEN samples, which were largely from intragenic and intergenic regions. The NuGEN captured fewer exons (25% less) and had higher base level coverage variance. While 6.3% of reads were mapped to intragenic regions in the PolyA samples, the percentages were much higher (20–25%) for the NuGEN samples. The NuGEN protocol did not detect more known non-coding RNAs such as lincRNAs, but targeted small and “novel” lincRNAs.

Conclusion

Different library preparations can have significant impacts on downstream analysis and interpretation of RNA-seq data. The NuGEN provides an alternative for limited or degraded RNA but it has limitations for some RNA-seq applications.     

Dynamic changes in brain functional connectivity during concurrent dual-task performance

This study investigated the spatial, spectral, temporal and functional proprieties of functional brain connections involved in the concurrent execution of unrelated visual perception and working memory tasks. Electroencephalography data was analysed using a novel data-driven approach assessing source coherence at the whole-brain level. Three connections in the beta-band (18-24 Hz) and one in the gamma-band (30-40 Hz) were modulated by dual-task performance. Beta-coherence increased within two dorsofrontal-occipital connections in dual-task conditions compared to the single-task condition, with the highest coherence seen during low working memory load trials. In contrast, beta-coherence in a prefrontal-occipital functional connection and gamma-coherence in an inferior frontal-occipitoparietal connection was not affected by the addition of the second task and only showed elevated coherence under high working memory load. Analysis of coherence as a function of time suggested that the dorsofrontal-occipital beta-connections were relevant to working memory maintenance, while the prefrontal-occipital beta-connection and the inferior frontal-occipitoparietal gamma-connection were involved in top-down control of concurrent visual processing. The fact that increased coherence in the gamma-connection, from low to high working memory load, was negatively correlated with faster reaction time on the perception task supports this interpretation. Together, these results demonstrate that dual-task demands trigger non-linear changes in functional interactions between frontal-executive and occipitoparietal-perceptual cortices.     

The Everyday Life Context of Increasing Energy Demands: Time Use Survey Data in a Decomposition Analysis

Industrial ecologists have modeled with precision the material foundations of industrial systems, but given less attention to the demand for products and the drivers of structural changes in these systems. This article suggests that time use data complement data on monetary expenditure and can be used to elucidate the everyday life context in which the changes in the economy take place. It builds upon the claim that goods are not direct sources of utility, but enter specific household activities as inputs. A second argument for the proposed approach is that it can be used to introduce and foster human agency in analyses of production systems. The article uses Finnish time use survey data, consumption expenditure data, and data on the sectoral energy intensities of financial output in the Finnish economy. First, a measure of the energy intensity of activities is derived by relating consumer time use and the required direct and indirect energy requirements. Second, the results include a decomposition of changes in the energy requirements of private consumption in Finland during the 1990s. It is shown that although the same activities on average require increasing energy inputs per unit of time, Finns have simultaneously changed the structure of their everyday life toward less energy-intensive activities.     

Gossip-Style Failure Detection and Distributed Consensus for Scalable Heterogeneous Clusters

Gossip protocols provide a means by which failures can be detected in large, distributed systems in an asynchronous manner without the limits associated with reliable multicasting for group communications. However, in order to be effective with application recovery and reconfiguration, these protocols require mechanisms by which failures can be detected with system-wide consensus in a scalable fashion. This paper presents three new gossip-style protocols supported by a novel algorithm to achieve consensus in scalable, heterogeneous clusters. The round-robin protocol improves on basic randomized gossiping by distributing gossip messages in a deterministic order that optimizes bandwidth consumption. Redundant gossiping is completely eliminated in the binary round-robin protocol, and the round-robin with sequence check protocol is a useful extension that yields efficient detection times without the need for system-specific optimization. The distributed consensus algorithm works with these gossip protocols to achieve agreement among the operable nodes in the cluster on the state of the system featuring either a flat or a layered design. The various protocols are simulated and evaluated in terms of consensus time and scalability using a high-fidelity, fault-injection model for distributed systems comprised of clusters of workstations connected by high-performance networks.     

Microwave ablation of the atrioventricular junction in open-chest dogs

The use of microwave energy for ablation of the atrioventricular (AV) junction was examined in open-chest dogs. Using a specially designed microwave catheter and a 2450 MHz generator, microwave energy was delivered to the AV junction according to one of two protocols. In protocol 1, increasing amounts of energy were delivered until irreversible AV block occurred. In protocol 2, only two applications of energy were used, one at low energy and the other at an energy found to be high enough to cause irreversible AV block. Each dog received between one and six applications of microwave energy. The amount of energy delivered per application ranged from 25.6 to 311.4 J. No AV block was seen at 59.4 ± 28.3 J. Reversible AV block was seen with an energy of 120.6 ± 58 J. Irreversible AV block was seen at 188.1 ± 75.9 J. Irreversible AV block could be achieved in each animal. There was no difference in the energy required to cause irreversible AV block between the two protocols. The tissue temperature measured near the tip of the microwave catheter was correlated with both the amount of energy delivered and the extent of AV block caused. Histologic examination demonstrated coagulation necrosis of the conduction system. Microwave energy is a feasible alternative energy source for myocardial ablation. Since tissue damage is due exclusively to heating and the resulting rise in temperature can be measured, microwave energy may have advantages over currently existing energy sources in terms of both titrating delivered energy and monitoring the extent of tissue destruction. © 1995 Wiley-Liss, Inc.