A scalable and dynamic application-level secure communication framework for inter-cloud services Citation: Sajjad, A., Rajarajan, M., Zisman, A. and Dimitrakos, T. (2015). A scalable and dynamic application-level secure communication framework for inter-cloud services. Future generation computer systems: the international journal of grid computing and escience, 48(July), pp. 19-27. doi: 10.1016/j.future.2015.01.018 This is the accepted version of the paper.This version of the publication may differ from the final published version. PermanentMost of the current cloud computing platforms offer Infrastructure as a Service (IaaS) model, which aims to provision basic virtualized computing resources as on-demand and dynamic services. Nevertheless, a single cloud does not have limitless resources to offer to its users, hence the notion of an Inter-Cloud environment where a cloud can use the infrastructure resources of other clouds. However, there is no common framework in existence that allows the service owners to seamlessly provision even some basic services across multiple cloud service providers, albeit not due to any inherent incompatibility or proprietary nature of the foundation technologies on which these cloud platforms is built. In this paper we present a novel solution which aims to cover a gap in a subsection of this problem domain. Our solution offers a security architecture that enables service owners to provision a dynamic and service-oriented secure virtual private network on top of multiple cloud IaaS providers. It does this by leveraging the scalability, robustness and flexibility of peer-to-peer overlay techniques to eliminate the manual configuration, key management and peer churn problems encountered in setting up the secure communication channels dynamically, between different components of a typical service that is deployed on multiple clouds. We present the implementation details of our solution as well as experimental results carried out on two commercial clouds. Most of the currently available Cloud Computing solutions are mainly focused on providing functionalities and services at the infrastructure level, e.g., improved performance for virtualization of compute, storage and network resources, as well as necessary fundamental functionality such as virtual machine (VM) migrations and server consolidation etc. In the cases when higher-level and more abstract concerns need to be addressed, existing Infrastructure as a Service (IaaS) solutions tend to focus on functional aspects only. Furthermore, if a cloud's computational and storage infrastructure resources are overloaded due to increased workloads, its service towards it clients will degrade. The idea of an Inter-Cloud [1] has been gaining much traction to address such a situation, where a cloud can borrow the required infrastructure resources of other clouds. However, in order to progress from a basic cloud service infrastructure to a more adaptable cloud service ecosystem, there is a great need for tools and services that support and provide higher-level concerns and non-functional aspects in a comprehensive manner.. The OPTIMIS project [2] is an ongoing effort in this regard which strives to provide a holistic approach to cloud service provisioning by offering a single abstraction for multiple coexisting cloud architectures. Of the various highlevel concerns being addressed by the OPTIMIS project, a major concern of high importance is the provisioning of a secure communication framework to the services utilizing the resources of different cloud IaaS providers. The usage pattern of these services is usually quite flexible, i.e., on one hand they might be directly accessed by end-users or on the other hand they might be orchestrated by other Service Providers (SP) for their customers.. There are three fundamental steps in the life cycle of a service in the cloud computing ecosystem; the construction of the service, the deployment of the service to one or more IaaS clouds and lastly the operational management of the service. In the resulting scenarios, the presence of the multiple IaaS providers in the cloud ecosystem is the key issue that needs to be addressed by any inter-cloud security solution. A major goal of service owners is to select IaaS providers in an efficient way in order to host the different components of their services on appropriate clouds. In this respect, third-party cloud brokers [3] can play a major role in simplifying the use, performance and delivery of the cloud services. These brokers can also offer an intermediation layer spanning across multiple cloud providers to deliver a host of optimization and value-added services which take advantage of the myriad individual cloud services e.g., aggregation of different services or arbitration for a best-match service from multiple similar services. For the numerous interaction possibilities among these parties, whatever the usage scenarios maybe, the security of data and the communication between the consumers of the service and its multiple providers is of paramount importance.. In the light of the above discussion, it is clear that an inter-cloud security solution is highly desirable that would provide a framework enabling seamless and secure communication between the actors of a cloud ecosystem over multiple cloud platforms. Such a solution, however, has to overcome a number of challenges because of architectural limitations. This is because most of the current cloud service platforms, and the multi-tenants environments they offer, make it difficult to give the consumers of their services flexible and scalable control over the core security aspects of their services like encryption, communication isolation and key management. Secure communication is also challenged by lack of dynamic network configurability in most cloud providers, caused by the inherent limitations of the fixed network architectures offered by these providers.. In this work we address the secure, flexible and scalable communication concerns that in our view must be overcome in order to provide holistic provisioning of services to consumers from multiple cloud service providers. We present the architecture and design of an inter-cloud secure communication framework that offers the features of dynamic and scalable virtual network formation, efficient and scalable key management and minimal manual configuration all on top of secure and private communication between the components of the service across multiple cloud platforms. Our architecture provides a single virtual network to the service using resources from multiple cloud providers and offers the capability to efficiently and transparently run services on top of this network while catering for the dynamic growth and shrinkage of the components of the service.. The rest of the paper is organized as follows: In Section 2 we outline the key motivations for our approach. We elaborate on the detailed Inter-Cloud Virtual Private Network (ICVPN) architecture in Section 3. In Section 4 we present our experimental setup and the analysis of the performance results of our solution. In Section 5 we present the background and related works that address peer-to-peer overlays, virtual network connectivity and key manage-ment issue related to this domain. We conclude in Section 6 with the future directions of our work. In this paper, we present a scalable and robust secure communication framework for services deployed in an inter-cloud environment. We employ the flexibility and scalability afforded by structure peer-to-peer overlays to join virtual machines running on different cloud IaaS providers with each other using IPsec tunnels, hence providing confidentiality, authentication and integrity for all the data exchanged between different components of the service. Our solution needs minimal manual configuration as peers are automated to discover the information needed to perform their operations from the Universal Overlay. We also provide a distributed and scalable key management solution for the consumption of the virtual machines to setup the secure communication channels. Our solution supports the dynamic addition and removal of nodes from the VPN overlay as we use the peer-topeer DHT not just as a command and control channel for managing the VPN peers but also for the churn management of peers in the VPN overlay. We have evaluated a prototype implementation based on experiments conducted in realistic conditions, over multiple cloud infrastructure environments and found minimal latency and throughput overhead of creating and maintaining the ICVPN connections among the participating VMs of a service. The design and architecture of our inter-cloud secure communication framework is inspired by a collection of techniques like Virtual Private Networks [4] (VPN) and Peer-to-Peer (P2P) Overlays [5] . Network virtualization techniques like VPNs and P2P Overlays have been shown to provide their users legacy communication functionalities of their native network environments, despite the topology, configuration and management architecture of the actual underlying physical network. This fits perfectly with our goal of providing a secure virtual private network as a service to the consumers operating on top of multiple cloud providers. All complications and complexities of managing a physical network can be handled by the overlay network, enabling the services deployed on multiple clouds to benefit from a customized communication network typically only available in physical local-area environments. The central thrust of our architecture is the provisioning of a secure virtual private network over multi-cloud infrastructure. VPNs have been a mainstay for providing secure remote access over wide-area networks to resources in private organizational networks for a long time. Well-known tools and softwares like OpenVPN [34] are used to create secure point-to-point or site-to-site connections for authenticated remote access. However, the main problem in client/server based approaches is that they require centralized servers to manage the life cycle of all the secure connections for the participating clients, hence suffering from a single point-of-failure. Another issue is the quite complex and error prone configuration problems especially if you want to construct and manage a large-scale network not having a relatively simple topology, as it would require customized configuration on every client and even more elaborate management and routing configuration on the server-side. Another major drawback is the complexity of key distribution among all the participating clients in a VPN, as the software itself does not provide any key distribution service and all keys have to be manually transferred to individual hosts. In case of PKI model, an additional requirement of a trusted Certificate Authority exists that has to issue individual certificates to all the servers and clients constituting a VPN, which incurs an additional communication overhead when forming a virtual private network.. There have been some other VPN solutions for large-scale networks aimed at grid and cluster computing environments, such as VIOLIN [35] and VNET [36] , that do not follow a strict client/server model based approach. VNET is a layer 2 virtual networking tool that relies on a VNET server running on a Virtual Machine Monitor (VMM) hosting a virtual machine in a remote network which establishes an encrypted tunnel connection to a VNET server running on a machine (called Proxy) inside the users home network. All of the remote virtual machines communication goes through this tunnel and the goal of the Proxy is to emulate the remote virtual machine as a local host on the users home network, in effect presenting it as a member of the same LAN. The motivation of this approach is to tackle the users lack of administrative control at remote grid sites to manipulate network resources like routing and resource reservations etc. but it suffers from the previously discussing problem of complex and manual configuration though going for the simplicity of a private LAN. Also the scalability will be a big issue for the Proxy as the number of remote virtual machines grows as each will require a secure tunnel connection and corresponding virtual network interface mapped to the Proxys network interface by the VNET server software.. VIOLIN is a small-scale virtual network with virtual routers, switches and end hosts implemented in software and hosted by User-Mode Linux (UML) enabled machines as virtual appliances. It allows for the dynamic establishment of a private layer 3 virtual network among virtual machines, however, it does not offer dynamic or automatic network deployment or route management to setup the virtual network. Virtual links are established between the virtual appliances using encrypted UDP tunnels that have to be manually setup and are not self-configuring, making it cumbersome to establish inter-host connections in flexible and dynamic fashion.. P2P VPN solutions like Hamachi [37] and N2N [38] have come up as peer-to-peer alternatives to centralized and client/server model based VPNs. Hamachi is a shareware application that is capable of establishing direct links between computers that are behind NAT firewalls. A back-end cluster of servers are used to enable NAT traversal and establish direct peer-topeer connections among its clients. Each client establishes and maintains a control connection to the server cluster. It is mainly used for internet gaming and remote administration but suffers from scalability issues as each peer has to maintain the connection with the server as well as any other peers it wants to communicate with, ending up with the overhead of a meshtopology. It therefore offers limited number of peers (16 per virtual network) and limited number of concurrent clients (50 per virtual network). The keys used for connection encryption and authentication are also controlled by the vendors servers and individual users do not initially control who has access to their network. N2N is a layer 2 VPN solution which does not require a centralized back-end cluster of servers like Hamachi but it uses a peer-to-peer overlay network similar to Skype, where a number of dedicated super-nodes are used as relay agents for edge nodes that cannot communicate directly with each other due to firewall or NAT restrictions. The edge nodes connect to a super-node at start-up and pre-shared TwoFish [39] keys are used for link encryption. As it operates on layer 2, the users of the overlay have to configure their IP addresses etc. It also assumes node membership as relatively static with edge nodes rarely leaving or joining the network over their life cycle.. More recently, some commercial cloud computing services have been made available by different vendors that provide a virtual private network inside their public cloud offering and offering the customers some limited degree of control over this network, which is called a Virtual Private Cloud (VPC). Prime examples in this domain are Amazon Virtual Private Cloud [40] , Google Secure Data Connector [41] and CohsiveFT VPN-Cubed [42] . These are aimed at enterprise customers to allow them to access their resource deployed on the vendors cloud over an IPsec [22] based virtual private network. Although these products allow the possibility of leveraging the cloud providers APIs to flexibly grow and shrink their networks, the management and configuration is as complex as a traditional network as components of the VPC such as internet gateways, VPN servers, NAT instances and subnets have to be managed by the customers themselves. Furthermore, the customers are required to setup a hardware IPsec device on their premises that connects to an IPsec gateway in the VPC running as a virtual appliance which integrates the enterprises network with the VPC subnet in the cloud. Most importantly, with the exception of [42] , these solutions are locked to single cloud vendor and [42] provides use of a selective set of cloud providers by placing its virtual appliances as VPN gateways in these cloud infrastructures and allowing the customers to join these gateways in a mesh topology manually.

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Video Block Motion Estimation Based on Gray-Code Kernels Abstract-Motion in modern video coders is estimated using a block matching algorithm that calculates the distance and direction of motion on a block-by-block basis. In this paper, a novel fast block-based motion estimation algorithm is proposed. This algorithm uses an efficient projection framework that bounds the distance between a template block and candidate blocks. Fast projection is performed using a family of highly efficient filter kernels-the gray-code kernels-requiring only 2 operations per pixel per kernel. The projection framework is combined with a rejection scheme which allows rapid rejection of candidate blocks that are distant from the template block. The tradeoff between computational complexity and quality of results can be easily controlled in the proposed algorithm; thus, it enables adaptivity to image content to further improve the results. Experiments show that the proposed adaptive algorithm outperforms other popular fast motion estimation algorithms.

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A Dynamical Systems Approach for Static Evaluation in Go Abstract-In the paper arguments are given why the concept of static evaluation has the potential to be a useful extension to Monte Carlo tree search. A new concept of modeling static evaluation through a dynamical system is introduced and strengths and weaknesses are discussed. The general suitability of this approach is demonstrated.

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Current utilization of CASE technology: lessons from the field Abstract:S ince i t s inception, CAS E (computer-aided s of t war e engi neer i ng) tool s have been hailed as the s ilver bullet of applications development. Although thes e t ool s have failed t o live up t o s uch an advance billing ( as do mos t fix-all solutions), these pr oduct s remain a v i abl e opt i on for pr actitioner s of modern applications development. This study comments on the us e of CAS E in moder n I S installations, using the r es ul t s of an in-depth s ur vey completed by 226 I S professionals fr om over 30 Fortune 500-type com pani es . First, the s t udy identifies the mos t popular features pos s essed by respondents' CAS E toolsets. Next, it comments on the gap per cei v ed t o ex i s t between CAS E features actually possessed, and t hos e feat ur es needed by these pr ofes s i onal s in the per for mance of their job dut i es . Finally, implications for practice and r es ear ch ar e pr es ent ed. While certainly not the "silver bullet" to eradicate the information system (IS) organization's applications backlog, CASE (Computer-aided software engineering) technology remains a viable option for those responsible for the development and timely delivery of modern-day ISs. Like many other alternatives to the snail's pace of progress during the traditional systems development life-cycle (SDLC), such as prototyping, rapid application development, the use of canned software packages, or reusable code, CASE tools have great potential in alleviating (not necessarily eliminating) the applications backlog. Although the latest, greatest (or most publicized) advancement seems to be the proliferation of object-oriented analysis and design (OOAD) techniques (Freeman, 1997; Post et al., 1997) , it is still unclear as to whether these OOAD tools will become the final answer to the everincreasing problem of delivering application systems in a more timely manner (c.f. Johnson and Hardgrave, 1997; Wu and Wu, 1994 This study has reported on the use of CASE technology by 226 IS professionals from over 30 Fortune 500-type companies. The current inspection focused on the most popular CASE tool features possessed, as well as the perceived "gap" between features possessed, and those needed, by respondents. Considerable insight was obtained on the current utilization of CASE, especially in terms of which features seem to be the most popular. Furthermore, a dynamic relationship was uncovered between an existent "gap" of features needed versus those actually possessed. Future research into CASE should attempt, among other things, to determine the extent to which this gap has been bridged. Simply put, CASE is the automation of "anything a human does to software" (Stamps, 1987) . The broadest definition of a CASE tool is any software tool that provides automated assistance for software development, maintenance, or project management activities (McLure, 1989) . From its inception in the early to mid-1980s, CASE has evolved from simple "upper-CASE" tools such as screen and report painters, and "lower-CASE" tools such as code generators, to completely integrated CASE facilities that support the entire range of the SDLC. Integrated CASE (or ICASE) is a set of integrated CASE tools sharing a common user interface, data interface, life-cycle framework, and repository (du Plessis, 1993).. The following section outlines some common advantages and disadvantages associated with using CASE tools. The current study is part of an ongoing investigation into the use of CASE in IS development units. The researchers developed an in-depth survey instrument designed to capture the perceptions of those closest to the technology: the users, or applications developers, themselves. The questionnaire was designed using demonstrated research constructs with desirable psychometric properties. Specific questions pertaining to CASE features were adapted from the FCTM, developed by Henderson and Cooprider (1990) from an MIT study. The FCTM was refined through a Q-sort analysis, and extensive consultation, with vendors and practitioners of CASE technology.. The 226 respondents in this study come from a wide variety of backgrounds and experience. Table I shows that almost 30 percent were from the insurance industry, while just under one-quarter (23.5 percent) were from manufacturing concerns. Table II indicates that almost one-half (47.8 percent) of the respondents had between 8 and 17 years of experience in the IS field, while the average age was 38 years (table not shown) .. Thus, from the perspective of age and experience, the 226 respondents appear to be mature members of their profession. Therefore, the sample frame is (to the extent we can determine) representative of our target population: users of CASE tools. It is hoped that experienced IS developers, such as those that participated in this research, would respond conscientiously and responsibly to questions in the survey instrument.. In the Appendix, Tables AI and AII are used initially in the discussion of the FCTM. A key is provided following these tables that lists each of the 58 items, grouped by FCTM dimension. Afterwards, Table AIII lists the top ten features, grouped by FCTM dimension, of CASE technology possessed by the respondents.

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Reactive scheduling based on actual logistics data by applying simulation-based optimization Background: A reasonable management and monitoring of construction projects requires accurate construction schedules. Accuracy depends highly on availability of reliable actual logistics data. The efficient execution of construction projects depends highly on the accuracy of the underlying construction schedules. Here, construction scheduling means to sequence relevant activities based on certain interdependencies and resource availability. Finally, a schedule defines the starting and finishing time of each construction activity as well as the allocated resources needed for each activity. For project managers, such detailed schedules are the main basis to monitor the activities on construction sites. Due to planning modifications, construction delays, or unforeseen events, schedules are often not up-to-date and must be continuously adapted. However, in practice schedules are not updated as often as they should be. Furthermore, construction schedules often have to be modified due to delays or disturbances of logistics processes. In consequence, actual information about the current state of the construction progress needs to be collected. Actual logistics data contain information about available material, equipment and personnel as well as updated delivery dates and other data on site conditions. The quality of construction schedules highly depends on the availability of reliable actual data. However, actual data is often associated with different types of uncertainties due to infrequent collections, varying transport times, or manual assessments by engineers. Considering these uncertainties is very important for evaluating actual data regarding their impact on the overall construction progress. After analyzing the actual data, an updated or so-called actual schedule can be defined. This actual schedule should be compared to the target schedule to detect significant deviations. If crucial delays are identified, the existing target schedule needs to be adapted. This procedure is known as reactive scheduling. Currently, the adaptation of construction schedules is a manual, time consuming, error prone, and therefore poorly supported process (Song and Eldin 2012) . In practice, there exists a high demand for efficient and userfriendly concepts, which can integrate and evaluate actual data as well as compare and update schedules.. In the last few years, discrete-event simulations have increasingly supported the specification of realistic and efficient construction schedules. With the help of discrete-event simulations, it is possible to analyze construction activities and complex interdependencies under varying project conditions (AbouRizk 2010). Project modifications or construction delays can be evaluated by changing certain input parameters or by adding additional constrains. Another advantage of the application of discrete-event simulations is the possibility to couple them with optimization methods to generate good schedules. In this case, sequences and resource allocations are varied to find efficient schedules regarding different objectives, including short construction times, low costs, and high resource utilization. Updating a construction schedule can be defined as an optimization problem to find a new schedule considering new information by minimizing the deviations from existing project goals. In addition, so-called target schedule constraints need to be considered, such as fixed material delivery dates, on-site resources, contracted milestones and established sequences. This paper presents a novel and holistic framework for reactive construction scheduling based on actual data by applying simulation-based optimization. The focus lays on actual logistics data. However, other actual data can also be modeled and be investigated by using this approach. The proposed framework comprises three main contributions, which are not found in this combination in previous research:. Preparation of uncertain actual logistics data Analyzing actual data using construction simulation Modeling of target schedule constraints and adapting target schedules by applying simulationbased optimization.. In consequence, with the help of the proposed framework, project managers can monitor construction work more efficiently based on updated and more realistic schedules. The adaption of construction schedules based on current logistics data is an important aspect in the context of efficient project execution. Such current data can reveal disruptions in construction logistic processes, e.g. delayed material delivery or machine breakdowns among others. However, current logistics data is fraught with uncertainty, due to infrequent acquisition or inaccurate duration between recordings. Therefore, a reactive construction scheduling approach, which is composed of multiple parts, is presented. For one, the approach enables the processing of uncertain current logistics data, in order to investigate their impacts on the planned target schedule. A constraint-based simulation analysis is performed that considers the current logistics data, which results in an actual, updated schedule. Furthermore, a target-actual comparison is utilized to identify deviations between the planned target schedule and the actual schedule. Based on the comparison results, a simulationbased optimization is performed with the objective to minimize the deviations between the planned and actual schedule. This paper particularly emphasizes the simulation-based optimization of target schedules. In order to adapt the target schedule, information regarding this schedule can be modeled by additional soft constraints. Various target schedule constraints are classified and modeled. By considering these additional constraints in the simulation model, an efficiently adapted schedule can be calculated. To perform the simulationbased optimization, the NSGA II algorithm is utilized. The concept was verified by applying an established use case. The presented results show that solutions found by utilizing the reactive construction scheduling approach can be applied to support project execution. Findings in the conducted case study are that the simulation-based analysis is capable of identifying whether logistic related disruptions compromise a successful project realization. Furthermore, it has been shown that optimal solutions can be found which fulfill all hard constraints and additional target schedule restrictions. Still further research is required, such as modifying the definition of additional target schedule constraints. This paper already mentions some, but for various construction projects in different domains, like mechanized tunneling or transport infrastructure constructions other constraints could be necessary. Furthermore, stochastic optimization will be integrated to find adaptions that are both robust and reliable. Such a robust adaption should protect the adapted schedule against further disruptions as much as possible. Another optimization related aspect is to consider alternative activities for disrupted activities. For example, when it is not possible to realize column work with prefabricated elements, then consider whether in-situ work is adequate as a substitution. Another important aspect is the availability of current logistic data. Additional research work is required to improve the availability and accuracy of current data for construction management. A better availability of data allows the application of different methods to cope with uncertainty, i.e. portability-based approaches could be applied to investigate the impact of logistic related disturbances. Of course, more accurate current data improves the assessment of uncertainty. Possible research into a different adaption method could include knowledge-based approaches. However such approaches require a knowledge base with possible adaption or substitution rules for disrupted activities. In practice, some construction delays may have their origin in the unavailability of material, equipment, or personnel. Some of these delays can be identified proactively by analyzing the actual delivery states. Other delays are the result of unforeseen events like equipment breakdowns or lacking personnel. In the manufacturing industry, the acquisition of actual data is often performed by Auto-ID techniques such as biometrics or RFID. Due to fixed production lines, established and well-monitored supply chains, identifiable resources, and detailed schedules the recorded actual data can be clearly associated to the production activities. Furthermore, the measured data often contains only marginal uncertainties. Consequently, actual data can be directly used to update the planned schedule (Hotz et al. 2006) . In contrast, in civil engineering several concepts regarding the acquisition of actual data by Auto-ID techniques were proposed just recently. Only a few early applications were implemented in practice. For example, in Cho et al. (2011) and Yin et al. (2009) the authors propose RFID-based production management systems. The former investigates vertical resource transports while the latter one performs a construction yard tracking. In Kim et al. (2009) and Ren et al. (2011) RFID-based goods inward inspections are developed. RFID-based supply chain control and management system for construction projects is developed in Wang et al. (2007) . In Ergen et al. (2007) , the authors propose a concept regarding intelligent building components. These components are capable of holding information about their states, or assembly guide and maintenance information. In order to assess the progress of construction activities, an automated progress control using laser-scanning technology is presented in Zhang and Arditi (2013) . Laser-scanning technology is utilized to overcome unsatisfactory results by employing image processing and other techniques. Their system is able to assess progress control with minimum human input. In Cai et al. (2014) , Dzeng et al. (2014) , and Montaser and Moselhi (2014) different methodologies for RFID-based location and tracking are presented. These approaches enable the acquisition of data on a construction project status in almost realtime and detect the locations of workers and materials with very high accuracy. However, none of these researches considers the evaluation of uncertainties and their impact on schedules.. Few researchers are dealing with the adaption of target construction schedules in case of infeasibility or nonoptimality due to disturbances. In Koo et al. (2007) , a formal identification and re-sequencing process is presented. This approach supports fast development of sequencing alternatives in construction schedules. The approach is based on CPM without considering resources or working shifts. In Liu and Shih (2009) , another rescheduling approach is introduced which is based on Constraint Programming. Two rescheduling methods are presented: the complete regeneration and the partial rescheduling. However, these rescheduling approaches are based on mathematical models rather than simulation models and not applicable for the proposed approach in this paper.. The utilization of discrete-event simulation models is an established methodology for the analysis and planning of construction activities. CYCLONE by Halpin (1977) , STROBOSCOPE by Martinez and Ioannou (1994) and Simphony by Hajjar and AbouRizk (1999) are the first and important steps in the context of construction simulation. Domain specific construction activities, resource requirements, and technological dependencies can be described by applying different modeling concepts. These simulation frameworks are more flexible which allows the creation of more realistic simulation models. For example, special-purpose simulation-modeling tools are developed in Martinez (1998) and Ruwanpura and AbouRizk (2001) . Nevertheless, the effort to model realistic simulation models is very high and these simulation frameworks always model an explicit process chain. According to Wu et al. (2010) most construction processes consist of dynamic and spontaneous sequences of activities. Because of this, simulation is not often applied in practice. Therefore, recent research is investigating model driven simulation modeling. With the help of building information models (BIM) and knowledge-based methods, semi-automatic model generation can be implemented (Wu et al. 2010; Xu et al. 2003) . Moreover, by combining the Constraint Satisfaction Approach with discrete-event simulations, it is possible to guarantee that only valid construction schedules will be generated (Beißert et al. 2007) .. Regarding the optimization of real construction schedules, several research approaches exist. For detailed literature reviews, we refer to Hartmann and Kolisch (2006) and Liao et al. (2011) . Many optimization approaches utilizing genetic algorithms are proposed. To name only a few we refer to Leu and Yang (1999) , Chen and Weng (2009) , Ghoddousi et al. (2013) and Esthehardian et al. (2009) . These approaches contributed to resource allocation and resource leveling. In order to tackle multi-mode resource constraint project scheduling problems (MRCPSP) by considering resource allocation and resource leveling simultaneously, the utilization of the Non-dominated Sorting Genetic Algorithm (NSGA II) (Deb et al. 2002) has been proved successful. In particular, Esthehardian et al. (2009) applied fuzzy numbers in order to model uncertainties in activities concerning execution time and cost. A different optimization approach by Said and El-Rayes (2014) provides a holistic BIM-based framework to optimize material supply and site decisions to minimize total logistics costs. However, these optimization approaches neither applied actual logistics data nor simulation models regarding reactive construction scheduling.. To our best knowledge, there is no research work available, which deals with reactive construction scheduling using actual logistics data. Therefore, we purpose a novel and holistic concept for reactive construction scheduling for controlling and updating construction schedules. As already mentioned, one main benefit of the constraintbased construction simulation is that additional constraints can be easily integrated into an existing simulation model. However, defining a realistic and highly detailed simulation model for construction scheduling can be very time-consuming. Due to this fact, a user-friendly software tool has been developed to speed-up the simulation definition process. The so-called SiteSimEditor is a BIM-based tool to prepare input data for construction simulation (cf. Fig. 9 ). The SiteSimEditor can be used free of charge for non-commercial research projects (SimPlan 2015). By importing available project information like 3D building models, construction site layouts, bill of quantities and quantity take-off items, the construction activities and various constraints can be specified interactively. To keep the expenditure of time for data preparation as low as possible, reusable templates have been developed. Currently, several templates for activities, resources, technology dependencies, strategic executions sequences, and working shifts are available. Based on the prepared and generated input data simulation experiments can be directly executed by using the SiteSimEditor. These simulation experiments are performed by a constraint-based discrete-event simulation engine, which is implemented as a component of the SiteSimEditor. Afterwards, the results can be imported and visualized as Gantt charts, 4D animations or in form of different diagrams.. The SiteSimEditor has been extended to integrate target schedule constraints. For defining delivery dates and temporal equipment, an existing availability and shift management plugin can be used. In general, for each resource different partially overlapping shifts, which can be associated with duration limits, can be specified and considered within the simulation model. New components and user-interfaces have been developed to define constraints such as milestones or established sequences.. However, information about upper bounds or sequences between activities must be specified manually. Other important aspects are the definition of additional resources and modified shifts to relax existing constraints. In many cases, this has to be performed to find a realistic adaption of the target schedule and to satisfy constraints like milestones or project duration.

O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I I O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I I O O O O O O O O O O O O O B I I O O O O O O O O O O O O O B I I O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O


Evaluation of DOCK 6 as a pose generation and database enrichment tool Abstract In conjunction with the recent American Chemical Society symposium titled ''Docking and Scoring: A Review of Docking Programs'' the performance of the DOCK6 program was evaluated through (1) pose reproduction and (2) database enrichment calculations on a common set of organizer-specified systems and datasets (ASTEX, DUD, WOMBAT). Representative baseline grid score results averaged over five docking runs yield a relatively high pose identification success rate of 72.5 % (symmetry corrected rmsd) and sampling rate of 91.9 % for the multi site ASTEX set (N = 147) using organizer-supplied structures. Numerous additional docking experiments showed that ligand starting conditions, symmetry, multiple binding sites, clustering, and receptor preparation protocols all affect success. Encouragingly, in some cases, use of more sophisticated scoring and sampling methods yielded results which were comparable (Amber score ligand movable protocol) or exceeded (LMOD score) analogous baseline grid-score results. The analysis highlights the potential benefit and challenges associated with including receptor flexibility and indicates that different scoring functions have system dependent strengths and weaknesses. Enrichment studies with the DUD database prepared using the SB2010 preparation protocol and native ligand pairings yielded individual area under the curve (AUC) values derived from receiver operating characteristic curve analysis ranging from 0.29 (bad enrichment) to 0.96 (good enrichment) with an average value of 0.60 (27/38 have AUC C 0.5). Strong early enrichment was also observed in the critically important 1.0-2.0 % region. Somewhat surprisingly, an alternative receptor preparation protocol yielded comparable results. As expected, semirandom pairings yielded poorer enrichments, in particular, for unrelated receptors. Overall, the breadth and number of experiments performed provide a useful snapshot of current capabilities of DOCK6 as well as starting points to guide future development efforts to further improve sampling and scoring. Despite the many challenges [1, 2] computational docking has emerged to become a useful part of drug discovery and design [3] [4] [5] . And, with the advent of ever faster computers, publicly available databases of purchasable compounds [6] , and numerous software choices [7] , more and more research groups are embarking on virtual high throughput screening projects to identify potentially useful lead Scott R. Brozell and Sudipto Mukherjee contributed equally to this work. The primary goals of this study were to evaluate the performance of the DOCK6 program for (1) pose identification and (2) database enrichment. The reported results represent the combined effort of two DOCK development groups and were generated as a result of participating in the recent symposium titled ''Docking and Scoring: A Review of Docking Programs'' held at the Spring 2011 Meeting of the American Chemical Society.. Pose identification success was examined using the standard DOCK grid scoring function (Tables 3, 4 , 5), three variants of the Amber scoring function (Tables 6, 7, 8) , and the new LMOD scoring procedure (Tables 9, 10 ). Systems for docking and scoring were derived from the single site (N = 85) or multi site Astex database (N = 147) with structure preparation protocols employing organizer supplied coordinates (ASTEX SUP) or those downloaded from the protein data bank (ASTEX PDB). For select experiments, two different docking protocols (RU, SB) were employed. Not surprisingly, use of different docking protocols, preparation procedures, and in particular, different scoring functions, yield different results.. As a baseline, the SB/ASTEX SUP grid score results (five run average, multi site set, organizer supplied structures, Table 3e ) yields a symmetry corrected rmsd success rate of 72.5 % which should be comparable across different docking programs and platforms employed in the symposium. The analogous sampling success rate for the same docking runs is much higher at 91.9 % which indicates substantial room for improvement should a more accurate scoring function be used. Additional pose identification analysis includes evaluation of ligand starting conditions (Table 3) , the effects of ligand symmetry (Table 3 ; Fig. 5 ), multiple binding site analysis (Table S2) , rmsd statistics (Table 4) , rmsd spectrum plots (Fig. 6) , and the effects of clustering (Table 5) . A potential problem regarding pose identification statistics is the relatively small number of systems used (N = 85 pdb codes). To minimize noise the current results are based on averages obtained over five independent docking runs using different random seeds. A recommendation is that future work should make use of much larger publically available datasets such as SB2010 (N = 780 systems).. Rescoring grid-based results with potentially more accurate Amber scoring protocols yielded generally lower success rates (Table 6 ). However, use of the ligand only movable protocol yielded a slightly improved success rate (69.4 %) as the comparable grid results for the same ensemble (68.0 %). Interestingly, although the numerical value was similar, the group of sites ranked successfully was different suggesting that the grid and Amber score functions have system dependent strengths and weaknesses which should be explored. Immediate future work planned will address relaxation with the Amber force field by starting with the larger MD-ready SB2010 dataset, and the protocol and the general treatment of systems will be examined by employing the NAB atom expression feature for specifying movable receptor residues to a few specific targets. Alternatively, receptor flexibility could be introduced through use of multiple-docking grids which is currently under investigation.. Testing of a new scoring procedure based on low mode sampling (LMOD score) was also examined (Table 9, 10; Fig. 7) . Encouraging results were obtained with LMOD score (57.89 %) when compared to grid score (47.37 %) or Amber score (52.63 %) when using the same starting ensemble of structures for a subset of 19 Astex systems although given the relatively small dataset size employed more comprehensive studies should be performed. An important feature of LMOD is the ability to sample large regions of conformational space relatively quickly which can lead to improvements in both scoring and sampling.. Representative results for system 1sj0 shows the potential utility of the method for generating multiple low-energy poses, with native-like rmsds, starting from a single highenergy structure with a non-native-like rmsd (Fig. 7) . Additional LMOD studies are planned.. To evaluate the ability of DOCK6 to enrich actives versus decoy molecules, the standard DOCK grid scoring function was used to screen 38-40 systems (Table 11 ; Fig. 8, 9 ) contained in the DUD database using either organizer supplied receptor coordinates (DUD SUP) or the protein data bank (DUD PDB). In addition to the standard DUD sets a subset of 10 systems employing WOMBAT actives was studied. DUD PDB results ( Fig. 8a; Table 11 ) using native pairings yield AUC values obtained from ROC curve analysis (Fig. 11) ranging from 0.29 (bad enrichment) to 0.96 (good enrichment) with an average AUC of 0.60 (27/38 have AUC C 0.5). ROC curve analysis visually indicates good early enrichment for most systems which was quantified using several metrics including, %TPR, %FPR, %AUC, and FE, at 0.1, 1.0, and 2.0 % of the database examined (Table 12 ). In particular, at 1.0, and 2.0 % an order of magnitude improvement over random FE (1.0) is observed for the DUD PDB native pairing results. Overall, the early enrichment trends are encouraging and consistent with previous studies [1-3, 5, 11] in which DOCK was used to successfully identify active lead molecules through virtual screening.. As expected, analogous DUD PDB results for semirandom pairings show a lower average AUC (0.48). However, appreciable enrichment is observed among groups of related receptors (Fig. 9) . In contrast, the miscellaneous other enzyme group, comprised of unrelated receptors, shows only 1/11 systems with AUC [ 0.5. Some system specific analysis revealed possible contributors to differential enrichments according to which of the two receptor preparation protocols was used (DUD PDB vs. DUD SUP protocols). Observed differences include alternate side chain conformations, numbers of binding site waters, partial atomic charges, and protonation states.. In summary, the breadth and number of validation experiments presented here is notable and the results and analysis provide a useful starting point for future work to improve both sampling and scoring in DOCK. It is worth repeating that the baseline grid results were determined using only a simple two-term scoring function, and the same DOCK protocols were used for pose identification and enrichment. No fine tuning was performed to tweak parameters or scoring for any particular system or class of systems. Nevertheless, although such a simple function yields remarkably good results, there is clearly room for improvement. Community efforts are especially welcome in this regard since they attempt to provide a level field for comparing various production versions of docking software using a common set of validation tests. Participation provides an opportunity for development groups to share knowledge, thus facilitating the incorporation of new features, for example symmetry corrected rmsd which was previously missing from DOCK. While the best metrics for quantifying success and enrichment may continue to be debated, continued participation in activities such as these is important to help drive the field forward.

O O O O O O O O O O B O O O O O O O O O O O O B O B O O O B O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O B O O O O O B I O O O O O B O B O B O O O O O O O O O O O O O O O O O O B O O O O O O B O O O O O O O O O O O O O O O O O O O B O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I O O O B O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O B O O O O O O O O O O O O B I O O O O O O O O B O O O O O O O O O O O B O O O O O O O O O O B O O O O O O O B O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O B O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O O O O O B O O O O O O O O O B O O O O O B O O O O O O O O O O O O O O O O O B O O O O B I O O O O O O O O O O O O O O B O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O B I O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O O O O O O O O O O O O B O O O O O O O O O B I O B O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O B O B O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O


Wh-Fronting in a Two-Probe System Abstract. Prior work on wh-movement has distinguished among several types of wh-fronting languages that permit distinct patterns of overt and covert movement, instantiated for example by the Slavic languages, English, and German. This paper extends the cross-linguistic typology of multiple questions by arguing that Hebrew instantiates a new kind of wh-fronting language, unlike any that are discussed in the current literature. It will show that Hebrew distinguishes between two kinds of interrogative phrases: those that are headed by a wh-word (wh-headed phrases: what, who, [ DP which X], where, how ...) and those that contain a wh-word but are headed by some other element (wh-containing phrases: [ NP N of wh], [ PP P wh]). We observe the special status of wh-headed phrases when one occurs structurally lower in a question than a wh-containing phrase. In that case, the wh-headed phrase can be targeted by an Agree/Attract operation that ignores the presence of the c-commanding wh-containing phrase. The paper develops an account of the sensitivity of interrogative probing operations to the head of the interrogative phrase within Cable's (2010) Q-particle theory. It proposes that the Hebrew Q has an EPP feature which can trigger head-movement of wh to Q and that a wh-probe exists alongside the more familiar Q-probe, and shows how these two modifications to the theory can account for the intricate dataset that emerges from the paper. The emerging picture is one in which interrogative probing does not occur wholesale but rather can be sensitive to particular interrogative features on potential goals. Wh-phrases of different levels of complexity may sometimes have varying degrees of freedom in the movement operations that apply to them. In English, for example, superiority-violating multiple questions as in (1)b lead to ungrammaticality (Chomsky 1973) . may be attended to. An Attract operation may be triggered immediately following an Agree operation (Chomsky 1998 (Chomsky , 1999 . This paper introduced several novel observations regarding the behavior of Hebrew multiple whquestions. It established a correlation between the phenomena of superiority and intervention effects in Hebrew that is similar to the one found with D-linked interrogative phrases in English: Superiorityobeying questions never exhibit intervention effects; superiority-violating questions are grammatical but they are sensitive to intervention effects. These facts are captured within the theory of Q-particles under standard assumptions about superiority and intervention effects. The paper further argued that one additional factor correlates with superiority and intervention effects: superiority-obeying questions have pair-list as well as single-pair answers, but superiority-violating questions only have pair-list answers.. The main empirical contribution of this paper is in showing that Hebrew distinguishes between two kinds of interrogative phrases: those that are headed by a wh-word (wh-headed phrases: what, who, [ DP which X], where, how ...) and those that contain a wh-word but are headed by some other element (whcontaining phrases: [ NP N of wh], [ PP P wh]). Wh-headed phrases are privileged in that they can be targeted by more Agree/Attract operations than wh-containing phrases. The evidence supporting this claim came from intervention effects in multiple questions, and from possible readings of the questions. We observe the special status of the wh-headed phrase when it is positioned structurally lower in a question than a whcontaining phrase: we find that certain operations target the lower wh-headed phrase and appear not to notice the presence of the c-commanding wh-containing phrase in the same structure.. The sensitivity of interrogative probing operations to the head of the interrogative phrase is surprising and unexpected within current theories of interrogative probing. I proposed to capture the intricate behavior that this sensitivity gives rise to within Q-particle theory by making two modifications to the theory: first, the Hebrew Q has an EPP feature that can trigger movement of wh to Q when there is no intervening head between the two. This yields two kinds of interrogative phrases in Hebrew: those that are headed by Q alone (wh-containing phrases, QPs) and those that are headed by both wh and Q (whheaded phrases, whQPs). Moreover, although the only kind of interrogative movement in language is Qmovement, we must assume in our theory a wh-probe alongside the Q-probe. The Q-probe operates in the familiar way, targeting any kind of QP regardless of its head. The wh-probe, on the other hand, targets whQPs and bare wh-words and cannot detect the presence of "simple" QPs. The principle of parasitic agreement ensures that after the wh-probe Agrees with a whQP, the Q-probe can also Agree with the same phrase and move it to C. Interrogative probing is thus relativized to two kinds of interrogative features and does not happen wholesale. 40 As a reviewer notes, this is a transderivational constraint that must take into consideration not only the derivation at hand but also other potential derivations that could result in the same meaning. I refer the reader to Fox (2000) for extensive argumentation for this kind of economy constraint.

O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O B O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O


Magnetic Resonance Poroelastography: An Algorithm for Estimating the Mechanical Properties of Fluid-Saturated Soft Tissues Abstract-Magnetic resonance poroelastography (MRPE) is introduced as an alternative to single-phase model-based elastographic reconstruction methods. A 3-D finite element poroelastic inversion algorithm was developed to recover the mechanical properties of fluid-saturated tissues. The performance of this algorithm was assessed through a variety of numerical experiments, using synthetic data to probe its stability and sensitivity to the relevant model parameters. Preliminary results suggest the algorithm is robust in the presence of noise and capable of producing accurate assessments of the underlying mechanical properties in simulated phantoms. Furthermore, a 3-D time-harmonic motion field was recorded for a poroelastic phantom containing a single cylindrical inclusion and used to assess the feasibility of MRPE image reconstruction from experimental data. The elastograms obtained from the proposed poroelastic algorithm demonstrate significant improvement over linearly elastic MRE images generated using the same data. In addition, MRPE offers the opportunity to estimate the time-harmonic pressure field resulting from tissue excitation, highlighting the potential for its application in the diagnosis and monitoring of disease processes associated with changes in interstitial pressure.Index Terms-Finite element method, inverse problems, magnetic resonance elastography (MRE), poroelasticity. A 3-D finite element-based poroelastic inversion algorithm has been developed to estimate the mechanical properties of fluid-saturated media experiencing time-harmonic excitation.. MRPE has been introduced as a technique through which the mechanical properties of the solid matrix and the time-harmonic pore-pressure distribution of a porous medium can be estimated by modeling the complex mechanical interactions occurring between the solid and fluid phases. The performance of the algorithm was tested through numerical experiments using simulated data to probe its stability and sensitivity to the relevant model parameters. The results indicate that the algorithm is robust in the presence of noise and is capable of capturing accurate distributions of the underlying mechanical properties and time-harmonic pressure field resulting from material vibration. Phantom experiments were performed using soft silken tofu. The results show that linearly elastic assumptions are inadequate for assessing the mechanical properties of tofu, whereas the poroelastic algorithm is able to successfully characterize the shear modulus of both the background and inclusion.. The poroelastic reconstruction algorithm presented here is expected to facilitate the computation of mechanical property distributions representative of the underlying solid matrix in fluid-saturated tissue. Furthermore, the approach offers a unique opportunity to probe the relationship between tissue deformation and tissue pressure. While other mechanical characteristics of tissue such as viscoelasticity are also likely to influence tissue deformation, disease processes associated with cancer, hydrocephalus, and edema involve changes in fluid content and/or fluid pressure, which are likely to augment changes in tissue composition. Images obtained from the poroelastic reconstruction show good recovery of the shear modulus and pore-pressure amplitude across the simulated phantom. While the mean shear modulus value for the background was found to be accurate regardless of noise level, the mean value in each inclusion was slightly lower than the true value. In addition, variability in the reconstructed parameters was observed to increase with increasing noise level. While spatial filtering remains a factor that inhibits the development of sharp boundaries between regions of different moduli, increased accuracy and precision are likely to occur with enhanced data resolution.. A limitation of the poroelasticity reconstruction scheme implemented here is the need for an a priori estimate of the hydraulic conductivity distribution within the material being investigated. Characteristics of the response of the reconstruction algorithm over a range of assumed hydraulic conductivity values depend on the frequency at which the motion was generated and the extent of fluid-flow over a single excitation cycle. By assuming that the hydraulic conductivity is greater than the true value, the resistance to fluid-flow decreases and the calculated deformation behavior becomes dominated by the elastic matrix. Conversely, if the hydraulic conductivity is assumed to be smaller than the true value, the resistance to fluid-flow increases and the calculated deformation behavior is expected to emulate an incompressible elastic solid, which can lead to mechanical resonance or other numerical instabilities. Future studies are likely to explore the possibility of recovering hydraulic conductivity as an independent parameter. This will be done primarily by assessing the stability and sensitivity of an update equation of the form (15) in which the set of unknowns includes the parameter . While the success of such an approach remains uncertain, an algorithm of this type may offer additional clinical utility as interstitial hydraulic conductivity is known to vary between normal tissue and solid tumors, and is likely to be influenced by changes in fluid content.. The results from the tofu phantom show that the purely elastic reconstruction was unable to recover the linearly elastic properties of the tofu matrix or the stiffness inclusion, instead yielding an effective modulus distribution resulting from the complex interactions between the solid and fluid phases. This result was expected based on the evaluation in [27] that showed linearly elastic assumptions to be inadequate in describing the deformation behavior of poroelastic media under the time-harmonic conditions applied during MRE. While the inclusion itself is elastic, the measured displacements were likely influenced by the poroelastic background. In contrast, the poroelastic reconstruction was successful in recovering the expected spatial variation in shear modulus between the background and inclusion materials, though disagreement was observed between the recovered values and those determined via mechanical testing. The recovered Poisson ratio distribution from the linearly elastic algorithm suggests the bulk material is nearly incompressible; an interpretation that is expected for a linearly elastic assessment of a fluid-saturated porous medium. Variations observed which indicate more compressibility likely result from the data-model mismatch. The recovered Poisson ratio distribution from the poroelastic algorithm indicates an inherent compressibility of the matrix material. However, the algorithm also incorrectly identifies the gelatin inclusion as being more compressible than the matrix material. This finding can most likely be attributed to the invalid assumption of a uniform hydraulic conductivity across the tofu phantom and an attempt by the algorithm to fit the model to the measured data. In addition, while the exact variation in pore-pressure resulting from the external mechanical vibration cannot be measured, the algorithm produced a reasonable estimate for the internal time-harmonic pore-pressure distribution based on knowledge of the applied boundary conditions and excitation mode. Furthermore, only a relatively small increase in computation time was observed over the linearly elastic reconstruction despite the need to solve the forward problem on the entire domain at each global iteration.. Possible reasons for the observed differences between the estimated and measured mechanical parameters include effects from temperature (the small samples used in mechanical tests take less time to reach equilibrium), the assumption of a uniform hydraulic conductivity distribution, as well as the assumptions made regarding the boundary conditions on pressure. Furthermore, the values for the tofu background were determined from quasi-static stress-strain curves, yielding a linearly elastic modulus. These values were used for comparison since the linear poroelastic model assumes the matrix material to be purely elastic. However, real materials are expected to have some level of viscoelastic behavior. As a result, the linear poroelastic model is unable to account for all of the damping effects observed in the acquired MRE data, and thus the reconstructed properties reflect an apparent stiffness as interpreted by the underlying linear poroelastic model. Interestingly, the effect appears to be uniform across the background, suggesting homogeneous damping characteristics in the tofu. In spite of the required assumptions, the improvement in image quality over the linearly elastic property distribution is undeniable. The MRPE algorithm shows great promise for matrix stiffness as a more consistent measure of the mechanical properties in fluid saturated tissues. The findings presented here suggest that tissues exhibiting strong poroelastic characteristics are likely to be more appropriately described by model equations that account for both their solid and fluid compartments.. The results from this study demonstrate that the poroelastic inversion algorithm is robust in the presence of noise and able to provide reasonable, accurate estimates of the mechanical properties, and pore-pressure amplitude distributions in poroelastic media for an assumed hydraulic conductivity varying over several orders of magnitude. While preliminary results indicate hydraulic conductivity to the dominant parameter influencing the mechanical behavior under the prescribed conditions, future contributions are likely to include a detailed analysis of the algorithms sensitivity to a priori estimates of other experimentally derived parameters including porosity and the apparent mass density. Furthermore, given that MRPE provides a noninvasive method for estimating pore-pressure variation during mechanical excitation, future studies should investigate the effects of local changes in stiffness, hydraulic conductivity, fluid content, hydrostatic pressure and pressure gradient on the recovered pore-pressure distribution, and its potential clinical utility as a new diagnostic signature. One potential clinical application for this algorithm is in the differentiation of cerebral atrophy from hydrocephalus. Both disease processes can exhibit an enlarged ventricles, though cerebral atrophy is linked to degeneration of the periventricular white matter, while hydrocephalus is be attributed to an increase in cerebrospinal fluid (CSF) pressure. MRPE may offer the ability to distinguish between presentations by decoupling elastographic signals due to changes in tissue structure from those associated with increased CSF pressure and/or edema. The reconstructions performed on simulated data employed 16 processors for 60 global iterations resulting in an average runtime of approximately 5 h. Each global iteration was composed of approximately 250 individual iterative subzone calculations containing an average of 550-600 nodes/subzone, and a subsequent solution to the global forward problem. Fig. 5 contains images of the reconstructed shear modulus and pore-pressure amplitude distributions at various noise levels for a single horizontal slice passing through the center of the simulated poroelastic phantom described in Section II-F. The images labeled "Truth" refer to the shear modulus distribution used as input to the forward problem, and the pore-pressure distribution obtained from the solution to the forward problem under the prescribed boundary conditions on displacement and pressure. Fig. 6 compares the mean and standard deviation of the recovered shear modulus in the background and in each of the inclusions with the known values provided in Table I . The average reconstructed shear modulus for the background was found to differ from the true value by 2%-17% across all noise levels. In general, the average reconstructed shear modulus for an inclusion was found to be lower than the true value (0.7%-27%), with the most significant error observed in the 1 cm inclusion. This was expected as it had the smallest number of nodes comprising the inclusion volume, and therefore was affected to a greater extent by the spatial filtering process. Lastly, the variability in the reconstructed modulus values was observed to increase with noise level and inclusion volume. Fig. 7 contains interpolated shear modulus and pore-pressure results obtained for the same simulated phantom reconstructed over a range of assumed hydraulic conductivity values. Shear modulus distributions were clearly overestimated for reconstructions performed using hydraulic conductivities less than (m s)/kg. Some variability in the recovered modulus was observed for hydraulic conductivities greater than the true value, though the inclusions were still visibly apparent in the images. While reasonable estimates of the pore-pressure amplitude distribution were obtained for assumed hydraulic conductivities greater than the true value, the average pore-pressure amplitude was observed to be significantly higher than that of the true distribution when the assumed hydraulic conductivity was less than the true value. Fig. 8 contains an image of the real-part of the MRE recorded motion data for a representative coronal slice passing through a tofu phantom with a cylindrical stiffness inclusion in each of the orthogonal encoding directions. Fig. 9 contains representative shear modulus and Poisson's ratio distributions for the tofu phantom obtained from the linear elastic and poroelastic reconstruction algorithms. Also included is the estimated pore-pressure amplitude obtained from the poroelastic reconstruction for the same image slice. The elastic reconstruction shows significant variation in the recovered shear modulus and Poisson ratio across the tofu background and gelatin inclusion. The poroelastic reconstruction was found to provide smoothly varying modulus and Poisson ratio distributions for the tofu matrix representative of the material homogeneity. In addition, the gelatin stiffness inclusion was clearly defined in both images. Mechanical testing of soft tofu and gelatin samples via the procedure described in [27] have shown shear modulus values to vary between 500-600 Pa for tofu and 3-6 kPa for 10% gelatin, respectively. The estimated pore-pressure amplitude appears to be a reasonable assessment of the pressure variation given the nature of the applied boundary conditions on pressure and the major Fig. 8 . MRE recorded motion (real part) in each encoding direction for a single coronal slice passing through a tofu phantom containing a cylindrical gelatin inclusion. Note that M;P,andS refer to the frequency, phase, and slice encoding directions, respectively. mode of vibration (in and out of the image plane as described in Section II-G). Furthermore, the total reconstruction time was found to be approximately 2 h for the linearly elastic algorithm and approximately 2.8 h for the poroelastic inversion.

O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I B I I I B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O


Fairness in systems based on multiparty interactions In the context of the Multiparty Interaction Model, fairness is used to insure that an interaction that is enabled sufficiently often in a concurrent program will eventually be selected for execution. Unfortunately, this notion does not take conspiracies into account, i.e. situations in which an interaction never becomes enabled because of an unfortunate interleaving of independent actions; furthermore, eventual execution is usually too weak for practical purposes since this concept can only be used in the context of infinite executions. In this article, we present a new fairness notion, k-conspiracy-free fairness, that improves on others because it takes finite executions into account, alleviates conspiracies that are not inherent to a program, and k may be set a priori to control its goodness to address the above-mentioned problems. In this article, we focus on fairness in concurrent systems that use the Multiparty Interaction (MI) model. A multiparty interaction is an abstraction that allows several processes to synchronize and exchange information coordinately. Fairness becomes essential in MI-based systems since an MIbased process may offer to participate in several interactions, although it can execute only one at a time [1] . Intuitively, an execution of a program is fair iff every interaction that is ready for execution sufficiently often is executed sufficiently often, which avoids executions in which such interactions are neglected.. Notice that 'sufficiently often' is a vague term, which implies that there is not a single prevailing definition. However, many researchers agree in that so-called strong fairness deserves attention because it may induce desirable properties such as termination or eventual response to a request for service [1] [2] [3] . Unfortunately, this notion is not restrictive enough since it does not take finite executions into account, and an interaction might never get ready for execution because of an unfortunate interleaving of independent actions that might prevent some of the processes that need it to coordinate from engaging it at the right time. This has motivated several authors to work on stronger fairness notions, but none of them solves both problems simultaneously [4] [5] [6] [7] .. The main contribution we present in this article is a new fairness notion called k-conspiracy-free fairness that addresses the above-mentioned problems by fine-tuning the value we assign to k. We also present a framework we have devised to implement fair MI-based systems and report on the results of an experimental analysis we conducted to compare our proposal with others. From these results, we conclude that our proposal allows one to control conspiracies efficiently and it is easier to apply since our implementation is generic, i.e. it is not a transformational approach and thus needs not transform the source code of the systems to which it is applied.. The rest of the article is organized as follows. In Section 2, we report on some related work about multiparty interactions, fairness notions, and summarize how we improve other authors' work. The foundations of our framework are presented in Section 3 and in Section 4, we introduce our fairness notion and define it rigorously. We report on how to implement our fairness notion and on our experimental results in Sections 5 and 6, respectively. Finally, some conclusions are drawn from previous parts and summarized in Section 7. Fairness has been researched by many authors in the context of MI-based systems. They have devised several notions that attempt to avoid executions in which an interaction that is enabled sufficiently often is neglected. Strong fairness is quite an adequate notion, but it does not address fair finiteness and conspiracy problems.. In this article, we have shown that both problems may be addressed simultaneously by means of a new fairness notion that allows us to control to what extent conspiracies must be controlled and takes finite executions into account. We have defined our notion in the context of a framework we have designed and implemented to support MI-based systems. The experimental results show that our notion can deal with conspiracies while still performing comparably to other proposals that do not attempt to solve this problem. In this section, we first present the MI model. Later, we report on current fairness proposals and argue on their deficiencies. Finally we summarize our contributions.

B O O O O B I O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O B O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O B O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B I B O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O B I O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O O O O O O O O O O O O O O O O O O O B O O O O O O O O O O O