First-person science inquiry in virtual ambient environments Virtual ambients are a class of restricted simulations designed to support science inquiry learning among elementary school students. Virtual ambients employ large multi-user displays to support "first-person" collaborative exploration, data collection, and the construction of support for hypotheses in simulated environments. In order to reduce the cognitive load on learners, navigation--in space, time, and scale--is used instead of traditional learning simulations' direct control of independent model variables. Early experience with elementary school students at three grade levels is reported, employing a configurable virtual ambient named the Field.

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Acquiring engineering knowledge from design processes Knowledge management has recently become the focus of public attention in business and engineering. Because knowledge acquisition is situated in the upstream of knowledge management, capturing knowledge is an important step for enterprises to achieve successful knowledge management. We focus on how engineers solve their design problems under given design contexts and propose a novel model and methods to capture knowledge from engineering design processes. Our goal is to acquire know-how knowledge without disrupting the normal design process. A three-layer design process model is introduced to represent generic design processes, and a grammar and extended dynamic programming~GEDP! method is developed based on the process model. GEDP adopts the grammar approach and EDP to automatically identify meaningful clusters, called operations, from primitive design events. Our approach is evaluated through a case study of designing a double-reduction gear system. Engineering design is highly knowledge intensive in nature. In addition, in recent years, industrial design projects have grown larger in scale and more complex in content. In practice, a design task is usually divided into a number of highly coupled subtasks that require multiple designers to work together collaboratively. Some of the designers may be more skillful and have more experiences than the others.. To maintain the quality of the overall design, it is desirable for designers to clarify and share their knowledge. Developing ways to capture engineering knowledge from experienced designers without disturbing their normal design process is a key to achieving successful knowledge sharing.. Although the value of capturing, managing, and utilizing design knowledge has long been recognized and much research has been carried out, capturing engineering knowledge without disturbing the designers' normal design process is still a challenge. Design processes are often ill structured and ad hoc and vary greatly, depending on the design contexts. Although operation data recorded by CAD systems may contain valuable information, it is difficult to generalize ways of obtaining useful design knowledge directly from the operation data.. On the other hand, asking designers to record and share their design knowledge may also be problematic. There are several reasons:~1! a substantial time commitment is required for a designer to record his or her design knowledge; 2! design knowledge is tacit and embedded in the design process in most cases, so it will be difficult for a designer to express it fully and accurately; and~3! forcing designers to record their knowledge would interrupt their natural thinking process and become an unacceptable burden for them.. Our goal is to automatically capture engineering knowledge that can facilitate the understanding of a designer's design intent and provide guidance for designers to explore alternative designs, without disrupting the normal design process. There are several research questions that must be addressed to achieve this goal. What is engineering knowledge? What kind of knowledge should be acquired and accumulated in a design process? These questions are the crux of a knowledge system in engineering design. Furthermore, we must also understand what a design process is. This is a critical question for extracting design knowledge from design processes. To address these questions it is necessary to clarify knowledge structure in the engineering design field and develop a model of design processes. This paper categorizes design knowledge and emphasizes the importance of know-how knowledge. A generic design process model called a three-layer design process model is proposed. Based on this model, a novel method called grammar and extended dynamic programming~GEDP! is introduced to acquire know-how knowledge. Generally, design knowledge and design processes may both vary, depending on the structure of the design organization, whether it is a team's collaborative design or a single designer's design, because coordination and negotiation are indispensable to collaborative design. For simplicity, this paper focuses on a single designer's case. However, the proposed model and method can be extended to team collaborative design situations. We successfully tested our knowledge acquisition framework in a case study of designing a doublereduction gear system. This paper is organized as follows. Section 2 clarifies and categorizes engineering design knowledge and explains what knowledge on which we focus and why. Section 3 proposes a generic design process model called the three-layer design process model and describes the model in detail. In Section 4 we introduce the novel GEDP method for the acquisition of know-how knowledge and describe how it works. Section 5 presents a case study where the proposed model and methods are applied to a practical double-reduction gear system design problem. Sections 6 and 7 discuss the related work and makes concluding remarks, respectively. Our GEDP method based on the three-layer design process model was developed to extract know-how knowledge without disrupting a normal design process. Although the experiment discussed was only an example to evaluate this method, the results from the application of the GEDP method to the double-reduction gear system demonstrated the effectiveness of the method. Initially, design procedures were acquired by this bottom-up method. GEDP had several advantages. First, the captured operations shown in Table 6 were easy to understand for a user and the stream of operations represented sufficient content of a design context. Because 150 operations were captured from 472 events, the average abridging rate is 3.1. In addition to the trial mentioned above, several other experiments were carried out and the rate was similar: 43 operations from 139 events~abridging rate of 3.0! and 92 operations from 305 events~abridg-ing rate of 3.3!. Although the rate seems slightly small, it depends on the CAD system. Because Gear-CAD was developed to specialize in the double-reduction gear system problem, an event itself tended to represent specialized contents, for example, "Input the face width of gear." If this method is applied to a general CAD system, events represent more general actions and the abridging rate must be increased. Second, GEDP showed flexibility in pattern recognition. As mentioned in Section 5.2.2, GEDP allowed the deletion, insertion, or exchange of elements in a target sequence to some extent. Third, this method had the potential of wide application. In both the grammar ap- Further, procedure features were obtained. Three features identified as F1-F3 could never be acquired by means of a mediocre parameter analysis about product models, because they require the analysis of relationships between the tree structure and design operations generated by applying the GEDP. The procedure knowledge such as the examples in Table 6 contributed largely toward achieving the procedure features.. Know-how knowledge can be used in practical design. In practice, it is common for a group of designers to iteratively design different versions of the same artifacts such as cars and electrical appliances. Under these conditions, understanding other designers' know-how knowledge is important for managing the effectiveness and efficiency of collaboration. Furthermore, knowing expert designers' methods of design can help knowledge transfer. For instance, knowing the know-how of an expert or veteran designer may provide other designers with insights about designing and improve their design process. This knowledge transfer is important, especially when the new design- On the other hand, there are some limitations of our method. The first one relates to the types of design problems to which our method can be applied and the requirements that need to be imposed on the CAD systems. Generally, we need to develop specific rule sets used in GEDP for specific types of design problems. More rules will be needed to increase the applicability of GEDP. At the same time, the number of rules that need to be developed and how easily they can be developed depend on what events can be captured by the CAD system being used. Our approach requires that individual components and their parameters be recognizable and monitorable by the CAD system. Although the domain-specific rules would be sufficient for our method to operate, design task specific rules will be needed to capture more useful knowledge. In general, parametric design and routine design are most suitable for our method.. The second limitation is that the obtained know-how knowledge is usually domain specific and context specific. For example, we cannot apply know-how for a gear system as it is to a problem of designing a robot arm. To further generalize the know-how knowledge, we plan to deal with the problem of capturing know-why knowledge. Recently knowledge management are the key words in enterprises and business organizations to create value from an organization's intangible assets~Davenport, 1998; Liebowitz, 1999!. Generally speaking, knowledge management consists of knowledge capturing, securing, retrieving, and distributing steps, and a great deal of research on each step has been executed. We focus on the engineering and technology aspects of knowledge management and especially address the issue of knowledge capturing.. While many researchers in engineering and artificial intelligence focused their knowledge capturing research on documented domain knowledge~Bradshaw et al., 1997!, research on capturing know-how knowledge received little attention. That is because know-how knowledge seems domain specific and there is much difficulty in formalizing how to capture generic know-how knowledge. Despite the difficulty, some researchers point its importance out and struggle to capture and manage it; for example, Knowledge Infrastructure for Collaborative and Agent-Based Design was proposed for the agent system to use procedure knowledge and process knowledge in collaborative design~Jin & Zhou, 1999; !. However, the general way to capture know-how knowledge remains a research topic.. On the other hand, design rationale itself was studied from different point of views~Moran & Carroll, 1996!. There are three major models: argumentation-based design rationale, action-based design rationale, and modelbased design rationale. In the first approach the rationale is represented as a set of arguments~pros and cons! attached to issues, and the issues are interconnected. The Issue-Based Information System~IBIS!, developed by Rittel~Kunz & Rittel, 1970!, is an example of such methodologies. Various implementations of the IBIS concept were developed, for example, gIBIS~Conklin & Begeman, 1988 !, PHI~McCall, 1991 !, and DRL~Lee, 1990 !. However, the argumentation-based approach focused only on the design rationale; know-how knowledge is not considered.. Next the action-based rationale was developed. The claims are that actions can be explained by themselves~Lakin et al., 1989!. Although this approach includes know-how knowledge in its target, it creates a new problem in managing the large volume of information recorded.. Model-based design rationale was the last to be proposed. The Active Design Document system~Garcia & Howard, 1992! is based on a certain computational model of design rationale, which is developed for parametric design tasks. Although this system works effectively, its model and method are limited to a certain subject. In contrast, we propose a much more general model to apply to broad design problems. The Design History Tool~Chen et al., 1991! is proposed, which has both action-based and model-based features. The system stores structured and hierarchical representations of design based on what designers said and performed. Although their system can provide more information about design rationale, it interrupts the designers' design process and involves a huge analysis cost for each design case.. Recently several studies about action-and model-based design rationale were tackled with know-how and knowwhy knowledge capturing. Ganeshan et al.~1994! proposed the framework to capture how and why, in which the core idea is to model design as a selection from predefined transformation rules. When a rule is selected, the choice is recorded along with the rationale associated with that rule. In their approach, the designers' activities are constrained and they are translated into the predefined rules beforehand. They did not address the issues of capturing know-how knowledge from the bottom-level information such as events in CAD systems.. Myers et al.~1999! proposed the framework to capture design rationales from general CAD data. They developed an experimental system, the Rationale Construction Framework~RCF!, which automatically acquires rationale information for the detailed design process. It is valuable that they aim to develop a framework to apply to a general design problem. Although their research purpose is very similar to ours, there are some differences between us in both conceptualization and approach. In RCF they regarded design history as a conglomerate of detailed design rationales and focused on capturing many partly isolated design rationales in detail. Their focus is different from finding useful know-how, especially procedure features. On the other hand, our goal is to capture know-how knowledge, including procedure information and procedure features as mentioned above. Therefore, the approaches taken in Myers et al.'s research were different from ours. In their research, Acquiring engineering knowledge from design processessimple pattern matching is executed to detect design procedures using general predefined rules called design metaphors and qualitative reasoning is used to capture design rationale. In our research, complex pattern recognitioñ GEDP! is conducted to detect design procedures and a search based on rules derived from design principle knowledge is used to acquire procedure features.. In addition, some of the industrial Case-Based Reasoning~CBR! systems can be considered as capturing design process knowledge in terms of ways to fix problems. Several recent publications addressed specific issues of applying CBR to design~Maher & Pu, 1997!. The application of CBR to design domains that involve mechanical and other physical devices has extended the notion of design cases to include a representation of general knowledge in the form of causal or heuristic knowledge. Goel et al.~1997! directly addressed the representation of causal behavior through the use of structure-behavior-function~SBF! models. SBF models are useful to diagnose products. However, they focus on states of product models rather than design history.

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Clumps and collection description in the information environment in the UK with particular reference to Scotland The role, potential and interaction of networked catalogues and collection-level description have recently been given emphasis in order that efficient resource discovery mechanisms, and the effective organisation of such resources, be facilitated within the UK's developing JISC information environment (IE). This article describes the work of CC-interop, a JISC project, and related projects that inform the development of the IE and its ability to instantiate the functional model of online resource discovery to which JISC aspires. The article reviews the evolution of Z39.50 virtual union catalogue services and collection description services that preceded CCinterop. The paper also discusses how such work is informing regional information environments, with particular reference to Scotland, and reveals how such local arrangements will benefit the wider JISC IE. Services arising from the initiatives described in the previous section are, in the main, being created as separate entities, specifically defined by sector and domain. A more general information environment for London, and other regions, which integrates multiple clump and collection services will become possible if key deliverables of the CC-interop project are met. The ability to pass searches from one clump to another is as useful in creating regional catalogue networks from smaller components as creating national networks from regional ones. The use of interoperable collection description services will enhance the information environment by improving coherency and flexibility, giving the user greater control and better tools for surveying the landscape.. In Scotland, however, projects have tended to extend and expand CAIRNS and SCONE rather than create separate services. This allows us to fit the existing and planned services described in this paper into the functional model of the JISC 2.. The CAIRNS project report referred to "An embryonic Scottish national networked information service or Scottish Portal that continues to develop and offers the potential of integrated access to all publicly available research materials, learning and teaching r services in Scotland, whether digital or non that report poses the question: an embryonic cross information service for Scotland? allow us to respond, three years later, with an emphatic yes.

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Methodologies for assessing telemedicine: A systematic review of reviews Abstract Background and objectives Previous reviews have expressed concerns about the quality of telemedicine studies. There is debate about shortcomings and appropriate methodologies. The aim of this review of systematic reviews of telemedicine is to summarize methodologies used in telemedicine research, discuss knowledge gaps and recommendations and suggest methodological approaches for further research. Methods We conducted a review of systematic reviews of telemedicine according to a protocol listing explicit methods, selection criteria, data collection and quality assessment procedures. We included reviews where authors explicitly addressed and made recommendations for assessment methodologies. We did a qualitative analysis of the reviews included, sensitized by two broad methodological positions; positivist and naturalistic approaches. The analysis focused on methodologies used in the primary studies included in the reviews as reported by the review authors, and methodological recommendations made by the review authors. Results We identified 1593 titles/abstracts. We included 50 reviews that explicitly addressed assessment methodologies. One group of reviews recommended larger and more rigorously designed controlled studies to assess the impacts of telemedicine; a second group proposed standardisation of populations, and/or interventions and outcome measures to reduce heterogeneity and facilitate meta-analysis; a third group recommended combining quantitative and qualitative research methods; and others applying different naturalistic approaches including methodologies addressing mutual adaptations of services and users; politically driven action research and formative research aimed at collaboration to ensure capacity for improvement of services in natural settings. Conclusions Larger and more rigorous studies are crucial for the production of evidence of effectiveness of unambiguous telemedicine services for pre defined outcome measures. Summative methodologies acknowledging telemedicine as complex innovations and outcomes as partly contingent on values, meanings and contexts are also important. So are formative, naturalistic methodologies that acknowledge telemedicine as ongoing collaborative achievements and engage with stakeholders, including patients to produce and conceptualise new and effective telemedicine innovations. Many systematic reviews and primary studies addressing the impact of telemedicine have been criticized for low methodological quality [1] [2] . Previous reviews have also regularly expressed concerns about the quality of telemedicine studies [3] [4] [5] [6] [7] [8] and there is continuing debate about shortcomings and appropriate research methodologies. Examples include economic analysis of telemedicine which has not yet met accepted standards [7] ; concerns about a relative lack of exploration of the socio-economic impact of telemedicine [9] ; lack of evidence on factors promoting uptake of telemedicine [10] ; a relatively undeveloped use of qualitative methods [11] ; and claims that many existing studies have not been well-designed [3, 5, 8, 12] . The need for simulation modelling has also been expressed, given perceived difficulties of building a robust evidence base for recent innovations [13] . Telemedicine research exists at the crossroads of medical, technological and social/organisational research communities. These may differ in ways that reflect differences in the nature of the topics researched, norms for the conduct of research, and what they and their stakeholders would consider important outcomes [14] . Talmon et al have developed guidelines for the reporting of evaluations in Health Informatics, independent of the evaluation method used , the 'Statement on Reporting of Evaluation Studies in Health Informatics' (STARE-HI) [15] . They point to the gap between positivist and naturalistic approaches, express concerns that evaluation traditions do not collaborate sufficiently and state that a common language for evaluation is missing [16] .. These authors and critics raise questions about the quality of research evidence in terms not only of data collected and analysed and results produced, but also of the relevance of questions and approaches to assessments and evaluation. Basic axioms and methodologies used may create difficulties in researching all the questions that various stakeholders wish to address.. Methodology is concerned with how we know what we know, and the ways that science can help us to understand the world better. Methodology may refer to a set of methods or procedures, or it may refer to the rationale and the philosophical assumptions that underlie a particular study relative to the scientific method [19] . Positions and axioms on the nature of reality and knowing, which are set out in the philosophy of knowledge, are generally reflected in research questions and approaches.. Positivist and naturalistic approaches and their corresponding summative and formative research models may represent apparently different positions in scientific debates. These positions have been used to sensitize the presentation of qualitative results , the discussion and the conclusions in the paper.. Positivist traditions assert that the only authentic knowledge is that which is based on sense, experience and positive verification. Summative assessments, such as clinical trials and other controlled effect studies are derived from positivism. They address telemedicine as welldefined, preferably singular objects of study or interventions, and predefined outcomes.. Controlled experiments, preferably randomized controlled trials (RCTs) are applied to obtain evidence of causal relations and estimates of effects. Rigorous study designs are recommended to minimise risk of bias. Researchers are considered neutral observers of objective facts. Qualitative methods are not considered appropriate to examine effects of interventions, although they may be combined with quantitative evaluations and used for e.g. preliminary exploration, to assess unexpected results or the intervention process [20] [21] .. Naturalistic traditions view telemedicine as heterogeneous, multiple and developing in interaction with different stakeholders in natural settings. All entities involved in telemedicine development, including technologies, are considered to be in a state of mutual simultaneous influencing. Formative assessments are applied, where researchers interact with the object of study, and knowledge and "evidence" are context bound. That is, objectivity is only partly possible, as values are inherent in all inquiry. Formative assessments often seek to move beyond the objective/subjective dualism and apply both quantitative and qualitative methods. They focus on competing discourses, conflicting scripts, and the socially contingent nature of knowledge [22] [23] [24] . Table 1 , available as supplementary material, summarizes different axioms for positivist and naturalistic approaches, adapted from Lincoln and Guba [25] . It indicates that they differ in their perspectives on the nature of reality and what it is possible to know, the relationship of knower and known, on generalization and possible causation, and on the role of values in knowledge.. The paper is not concerned with the relative merits of quantitative or qualitative methods.. Their value has been widely substantiated in medical, medical informatics and social science research [26] [27] [28] . Our aim in this review of systematic reviews of telemedicine is to summarize methodologies used in telemedicine research, analyse knowledge gaps and suggest methodological recommendations for further research. This paper reports on research funded under EU SMART 2008/0064, which sought to review evidence of the effectiveness of telemedicine with reference to both outcomes and methodologies. An understanding of the positivist and naturalistic methodological positions and their underlying axioms regarding the nature of reality and knowing, the relationships of knower and known, the possibility of generalization and causal linkage and the role of contexts and values, assisted in making sense of the methodological attributes of the research reported in the reviews. Reviews including positivist and summative methodologies concluded that we need more controlled studies of better quality including standardisation of methodological aspects. Reviews that had included only summative primary studies also recommended that future research should address issues of subjectivity, needs, preferences, attitudes and knowledge of target populations and service providers. Reviews that had included both formative and summative methodologies noted that methodologies should also assume and address telemedicine interventions and achievements as complex and ongoing innovations in natural settings.. The included reviews also demonstrated that combinations of apparently opposing approaches like the positivist summative and naturalistic formative ones, gave valuable insights into the ways recent telemedicine assessments and evaluations can contribute to methodological debate. There is a clearly established need for further development of combinations of positivist and naturalist inquiry in the field of telemedicine, drawing on the limitations and strengths of both. Larger and more rigorous controlled studies, including standardisation of methodological aspects are recommended to produce evidence for the effectiveness of unambiguous telemedicine services on pre defined outcome measures. Summative methodologies that acknowledge telemedicine as complex innovations and outcomes as partly contingent on values meaning and changing contexts are also important. So are formative, naturalistic methodologies that acknowledge telemedicine as ongoing collaborative achievements and engage with stakeholders including patients, to ensure capacities and support processes to co-produce and conceptualise effective telemedicine innovations. What are larger studies, rigorous designs and standardisation producing?. The first knowledge gap presented was lack of evidence for effectiveness of telemedicine.. RCT's with more rigorous design and less risk of bias were required to get valid estimates of the effectiveness of telemedicine. Whilst many reviews identified large numbers of small studies and argued that larger studies are needed, there was little discussion of how large studies may be conducted in order to produce sufficient clinically relevant evidence for implementation of telemedicine. One might argue that well conducted small studies with low risk of bias may still provide useful and valid evidence, but they will usually lack power to detect clinically important effects of telemedicine. For the second group of reviews, the knowledge gap was also described as lack of evidence, and standardisation of interventions, population and outcome measures were recommended. Relevant for a discussion of methodologies, the authors assumed that control and standardisation were both possible and desirable. Patients as objects of the study of outcomes were implicitly expected to possess equal and measurable attributes possible for researchers to know objectively and generalise. We identified 1593 titles/abstracts. We included 50 reviews that explicitly addressed assessment methodologies. One group of reviews recommended larger and more rigorously designed controlled studies to assess the impacts of telemedicine; a second group proposed standardisation of populations, and/or interventions and outcome measures to reduce heterogeneity and facilitate meta-analysis; a third group recommended combining quantitative and qualitative research methods; and others applying different naturalistic approaches including methodologies addressing mutual adaptations of services and users;. We conducted a review of systematic reviews of telemedicine according to a protocol listing explicit methods, selection criteria, data collection and quality assessment procedures. We included reviews where authors explicitly addressed and made recommendations for assessment methodologies. We did a qualitative analysis of the reviews included, sensitized by two broad methodological positions; positivist and naturalistic approaches. The analysis focused on methodologies used in the primary studies included in the reviews as reported by the review authors, and methodological recommendations made by the review authors.. We searched for systematic reviews of research on the effects of telemedicine, and reviews describing or summarising methods used in studies assessing telemedicine. We included reviews published from 2005 and onwards. We searched these databases: British Nursing Index, Cochrane database of systematic reviews (CDSR), Database of reviews of effects The review adheres to the PRISMA checklist for preferred reporting items for systematic reviews, except for the items that are not relevant for a systematic review of reviews [17] .. The full account of methods, data collection and quality assessment of the reviews is presented in a companion paper which reviewed effectiveness and outcomes [18] . The inclusion criteria are presented in Table 2 and the PRISMA flow chart in Figure 1 . The full protocol (Appendix 1), the search criteria (Appendix 2), the Proforma used to extract data from the reviews (Appendix 3) and the PRISMA checklist (Appendix 4) are available as supplementary material.. A group of scientific experts assessed the systematic reviews identified and extracted data using the proforma developed for this project (Appendix 3). The review team (AGE, AB and SF) checked the data abstraction and assessments made. Based on the data extracted, we performed a qualitative summary and analysis of methodologies used in the studies included in the systematic reviews.. The preliminary results were presented for discussion in two feedback workshops involving service users, providers, policy makers and researchers. We asked the participants to comment on the usefulness of the results.

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


On the Numbers of Products in Prefix SOPs for Interval Functions †a) , Student Member and Tsutomu SASAO †b) , Member SUMMARY First, this paper derives the prefix sum-of-products expression (PreSOP) and the number of products in a PreSOP for an interval function. Second, it derives Ψ(n, τ p ), the number of n-variable interval functions that can be represented with τ p products. Finally, it shows that more than 99.9% of the n-variable interval functions can be represented with 3 2 n − 1 products, when n is sufficiently large. These results are useful for a fast PreSOP generator and for estimating the size of ternary content addressable memories (TCAMs) for packet classification. key words: prefix sum-of-products, number of products by PreSOP, distribution of interval functions, estimating the size of TCAM Packet classification [3] , [8] , [9] is a core function in computer network components, such as routers, firewalls, network address translators, and access control lists (ACL). A ternary content addressable memory (TCAM) [14] , [21] implements packet classification functions. Although a TCAM is fast, it is expensive and dissipates high power [1] . Table 1 shows an example of a packet classifier consisting of five fields: source IP, destination IP, source port, destination port, and protocol. In this example, both the source IP and the destination IP are represented by 32 bits, and they are specified by prefixes. Both the source port and the destination port are represented by 16 bits, and they are specified by intervals. The protocol is represented by a value of 8 bits or * (don't care). The action has two values: permit and deny. However, it can have more values such as deny and log or permit and log. When each of the port fields is specified by either * (don't care) or a single value, each rule corresponds to one word in a TCAM. However, when a port field is specified by an open interval such as (0, 7), then rule expansion occurs, i.e., each rule corresponds to many words in a TCAM [7] . If the packet header matches all the fields of a rule, then the rule is considered to be matched. If several rules match at the same time, the rule with the smallest number is applied.. To represent a port field, we use an interval function. An interval function can be represented as a sum of prefixes. The expression represented by a sum of prefixes is called a prefix sum-of-products expression (PreSOP). Note that each prefix corresponds to a word in a TCAM. To represent any interval function by a PreSOP, in the worst case, 2n − 2 products are necessary [24] . A sum-of-product expression (SOP) requires no more products than a PreSOP to represent the same function, and in many cases, the SOP requires fewer products than the Pre-SOP. For example to represent the interval (0, 2 n − 1), a Pre-SOP requires 2(n − 1) products, while an SOP requires only n products [17] . Although we can obtain an exact minimum SOP, it is often time consuming. In the design of integrated circuits for mass production, SOPs are routinely used [5] , [20] . Their minimization cost can be amortized by many integrated circuits. However, in the case of packet classification, PreSOPs are used instead of SOPs.. To reduce the number of words in a TCAM for ACL, minimization algorithms for SOPs, that are suitable for embedded microprocessors, have been developed [2] , [10] . It uses a ternary trie as a basic data structure. Such an algorithm is fast but produces solutions that require many more products than the exact minimum for some classes of functions [17] . Table 2 lists various methods to represent classification functions and their TCAM sizes. In [18] , [22] , the number of products needed to represent an interval function of n variables by a standard encoding in SOPs is analyzed. They show that any interval function can be represented with at most 2n − 4 products in an SOP. Especially, the paper [18] shows that only two interval functions require 2n − 4 products in SOPs. In the paper [19] , a 4-valued TCAM is proposed, where inputs are encoded with a 1-out-of-4 code. In this method, any interval function can be represented with at most n − 1 products by a 4-valued SOP. To use this method in packet classification, a special CAM and a 4-valued logic minimizer are necessary. In the paper [23] , a special TCAM that performs interval matching directly by hardware is proposed. In this case, each rule corresponds to just one word in a TCAM, but we need a special TCAM which would be expensive. In the paper [4] , Gray encoding is used to reduce the number of products. In the Gray encoding, any interval (A − 1, A + 2), where A is a non-negative integer, can be represented with a single product. The paper [4] showed that any interval function can be represented with at most 2n − 4 products in a PreSOP.. In a TCAM, a priority encoder is included to produce a unique address among the matched data [14] . By changing the order of rules stored in a TCAM, we can often reduce the number of products needed to represent the function [7] , Copyright c 2013 The Institute of Electronics, Information and Communication Engineers [19] non-prefixes TCAM with A direct interval 1 comparator circuit [23] [13]. In [12] , the authors presented a method to minimize the number of TCAM words. Although this method can find an exact minimum solution, it requires computation time that is impractically large. In [16] , an output encoding is used to reduce the number of products. To use this method in a real packet classification, a TCAM and an external memory are necessary.. In this paper, we show that 1) the minimum PreSOP (MPreSOP) and the number of products in a MPreSOP to represent an open interval (A, B) can be easily generated and calculated, and 2) the average number of products in MPreSOPs for interval functions is μ(n) ≈ n − 2, and the variance is σ 2 (n) ≈ n 2 + 1 † . Also, by numerical calculation, we show that 99.9% of the functions can be represented by PreSOPs with at most 3 2 n − 1 products when n > 12. An interval function can be represented by a product of a Greater-than (GT ) function and a Less-than (LT ) function.

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


The acquisition of novel N-glycosylation sites in conserved proteins during human evolution Background: N-linked protein glycosylation plays an important role in various biological processes, including protein folding and trafficking, and cell adhesion and signaling. The acquisition of a novel N-glycosylation site may have significant effect on protein structure and function, and therefore, on the phenotype. We have devised and applied a bioinformatics method to identify the acquisition of N-glycosylation sites during human evolution. We propose that the acquisition of novel N-glycosylation sites may play a role in the development of lineage-specific phenotypes during evolution. Thus, the cases identified in this study may provide a useful resource for molecular functional analyses in search of human traits acquired during evolution. Previously, it has been suggested that the gain of novel protein PTM sites such as ubiquitylation sites may be associated with the acquisition of novel phenotypes during human evolution by modulating the activity or network of proteins [16] . It is also highly probable that gains of novel N-glycosylation sites may result in functional modification of proteins and phenotypic changes in an organism. In this study, 1,027 human glycoproteins containing experimentally verified N-glycosylation sites and their orthologous mammalian proteins were systematically compared. As a result, 112 novel N-glycosylation sites were identified in 91 proteins that newly appeared during human evolution after the Euarchonta lineage diverged from the Glires lineage. It must be noted that most of these novel N-glycosylation sites were obtained by high-throughput mass spectrometry. The presence of these modifications must be further scrutinized by conventional molecular biology techniques.. Not all the novel N-glycosylation sites described in this study may have resulted in functional innovation. Some of them might have appeared as a result of random genetic drift and be functionally neutral. Nevertheless, some of them could have conferred selective advantage during human evolution and be fixed in the human genome. One such example identified in this study is the novel N-glycosylation site in UD19, which is involved in the elimination of potentially toxic xenobiotics and endogenous compounds. UD19 acquired the novel N-glycosylation site Asn-344 during the evolution of the common ancestor of apes and monkeys (see Figure 4C) . When the N-glycosylation at Asn-344 is abolished, folding is inhibited in UD19, and its glucuronidase activity is reduced [54] . Therefore, glycosylation at Asn-344 is required for proper folding and activity of UD19. It is possible that ancestral simian primates required better defense mechanisms against toxic compounds introduced into their systems by environmental or dietary shifts. The acquisition of a new N-glycosylation site in UD19 might have conferred improved xenobiotics metabolism to apes and monkeys, although there is no direct evidence for this hypothesis.. The three human-specific N-glycosylation sites are particularly interesting (see Table 1 and Figure 3) . The residue Asn-196 in APMAP is the first of the three human-specific N-glycosylation sites, which was inferred to be positively selected with an extremely high probability in humans (see Table 2 and Additional file 4). The human APMAP has been reported to be involved in a variety of biological processes including adipocyte differentiation, hepatic-specific metastasis in cancer, and inhibition of Aβ production [32] [33] [34] . The fact that APMAP is implicated in adipocyte differentiation is particularly interesting because humans and great apes exhibit large differences in adipose tissue and fatty acid storage, and these differences may be associated with the development of subcutaneous fat and even in brain development [58, 59] . Therefore, the molecular functional study of human-specific sequence changes in proteins such as APMAP, which are associated with adipose tissue and lipid metabolism, may reveal the molecular mechanisms for the evolution of these traits.. The human CD166 protein has two Ig-like V-type domains and three Ig-like C2-type domains ( Figure 5A ) and functions as a cell adhesion molecule. The humanspecific N-glycosylation site Asn-91, which was inferred to be positively selected (see Table 2 and Additional file 5), is located within the first Ig-like V-type domain, which is responsible for protein-protein interactions [35] [36] [37] . The addition of a bulky glycan moiety to this domain may change its structural profile and thus affect cell-cell adhesion activity or ligand specificity. The most interesting function of CD166 is its involvement in axon growth in neuronal cells [39, 40] . Of the 583 amino acid residues in CD166, only the residue at position 91 differs between humans and chimpanzees; therefore, the emergence of Asn-91 and its N-glycosylation might be associated with evolution of human-specific phenotypes, probably in the nervous system, which must be determined experimentally.. The human thyroglobulin, which serves as a precursor molecule for the thyroid hormones T4 and T3, has a human-specific N-glycosylation site Asn-76. The human thyroglobulin contains 11 thyroglobulin type-1 domains, which are involved in the control of proteolytic degradation [60] . The human-specific Asn-76 is located within the first thyroglobulin type-1 domain ( Figure 5B ). The Asn-76 was inferred to be positively selected during human evolution, along with the other 20 positions (see Table 2 and Additional file 6). Removal of the glycan group from the Asn-76 reduced thyroid hormone production, especially T4 production [44] ; thus, the gain of Asn-76 and its N-glycosylation, together with the other 20 putatively adaptive amino acid changes, may be implicated in the increased T4 concentration present in humans as compared to chimpanzees. It is possible that the additional glycan moiety may confer increased resistance to the proteolytic degradation of thyroglobulin proteins and thus lead to increased thyroid hormone production. It is very interesting that the T4 concentration in humans is higher than that in chimpanzees [45] , as elevated T4 production may have caused the modification of human physiology in response to selection pressures in a specific environment: specifically, it has been proposed that an altered thyroid hormone metabolism might have been beneficial for early humans in the savannah environment, as they practiced persistence hunting and thus had large energy requirements [46] .. Losses of N-glycosylation sites during human evolution are also very interesting. Some human diseases have been reported to be caused by the loss of N-glycosylation sites [61] . To find cases where ancestrally conserved N-glycosylation sites were lost during human evolution, a large amount of N-glycosylation data collected from animals distantly related to humans is required. The Nglycoproteome data obtained from mouse tissues and plasma using high-throughput mass spectrometry would be an ideal dataset for this analysis [62] . With a simple modification, the procedure described in this study could be used to analyze these data for the identification of N-glycosylation sites that were lost during human evolution and their possible phenotypic implications. Identification of novel N-glycosylation sites acquired during human evolution and determination of the timing of acquisition. We developed a bioinformatics procedure to identify the acquisition by proteins of the N-glycosylation motif Asn-X-Ser/Thr, where the Asn residue was experimentally verified to be N-glycosylated, during human evolution ( Figure 1) . A novel N-glycosylation site can arise by the emergence of not only an Asn residue but also a Ser or Thr residue to form the consensus motif [24] . The overall procedure devised in this study is similar to that used to identify novel ubiquitylation sites in a previous study [16] . Initially, there were 2,534 experimentally verified human N-glycosylation sites from 1,027 proteins in the UniProt database, and 57,289 orthologous protein sequence alignments from 62 mammalian species, including species from Euarchonta, Glires, Laurasiatheria, Afrotheria, Xenarthra, Marsupialia, and Monotremata, extracted from the UCSC "multiz100way" data [25] (see Additional file 1 for the list of mammalian species). These data were analyzed to collect N-glycosylation sites in human proteins that newly appeared during the evolution from the common ancestor, Euarchonta (primates and treeshrews); as the result, 112 novel N-glycosylation sites from 91 proteins were identified. A summary of the results are presented in Additional file 2, and detailed alignments are provided in Additional file 3. Of the 91 proteins, one protein (CFH) had acquired four N-glycosylation sites (Nos. 28 to 31 in Additional file 2 and Additional file 3; two proteins (PTPRC and PTPRJ) had acquired three sites each (Nos. 85 to 87, and 88 to 90, respectively); 14 proteins had acquired two sites each; and the remaining 74 proteins had acquired one site each. Figure 2 shows the number of the N-glycosylation sites that are shared by each of the Euarchonta clades along the human lineage: humans, three; ancestor of humans and chimpanzees, two; African great apes, 10; great apes, four; apes, 12; catarrhines, 16; simians, 45; primates, 15; and euarchonts, 5.. Most of the novel N-glycosylation sites were generated by the emergence of an Asn residue in an existing X-X-Ser/Thr motif. However, in some cases, the emergence of a Ser or a Thr residue in an Asn-X-X sequence created a novel N-glycosylation site: for example, a change from Asn-Glu-Ile to Asn-Glu-Thr generated a novel N-glycosylation site at Asn-911 in complement factor H (CFH) in apes (No. 30 in Additional file 3).. Of the 112 novel N-glycosylation sites, three sites in three proteins were human specific (Table 1 and Figure 3) ; therefore, these Asn residues subject to the N-glycosylation evolved and were fixed in human proteins after the Figure 1 Overall procedure for identifying gains of novel N-glycosylation sites during human evolution. Computational screening and manual inspection were employed to identify the acquisition of novel N-glycosylation sites in human proteins during human evolution.. divergence of humans and chimpanzees. The residues are Asn-196 in adipocyte plasma membrane-associated protein (APMAP), Asn-91 in cluster of differentiation 166 (CD166), and Asn-76 in thyroglobulin. N-linked glycosylation of the Asn residue in the consensus motif Asn-X-Ser/Thr, where X is any amino acid except Pro, is one of the most well-studied protein posttranslational modifications (PTMs) [1] . N-glycosylation, which mainly occurs in secreted or cell membrane proteins, plays important roles in protein folding, quality control, and trafficking [2] , as well as cell adhesion and signalling [3, 4] . The emergence of a new N-glycosylation site may alter protein function either positively or negatively. For example, missense mutations in factor VIII created novel N-glycosylation sites that cause severe hemophilia A [5] . Similarly, a missense mutation in the interferon γ receptor 2 induces novel N-glycosylation, which results in a Mendelian susceptibility to mycobacterial disease [6, 7] . The abolishment of N-glycosylation sites often causes disrupted protein folding, trafficking, or activity; thus, proper N-glycosylation is crucial for normal protein function [8, 9] . A proteome-wide analysis of nonsynonymous single-nucleotide variations in the N-glycosylation motifs of human genes showed that more than 1,000 human proteins had either lost or gained N-glycosylation sites due to missense substitutions, some of which may be implicated in diseases [10] .. The gain of new N-glycosylation sites during evolution may affect the structure and molecular function of proteins; when these novel modifications confer beneficial traits, they will be fixed during evolution. Previously, we identified a large variety of genetic changes that could have been involved in the acquisition of human traits, including gene inactivation [11, 12] , exon evolution [13, 14] , and gains of phosphorylation or ubiquitylation [15, 16] . Therefore, it would be of great interest to collect information on novel N-glycosylation sites that arose during human evolution, as the sites might have been involved in the development of some human phenotypes.. In order to study associations between the acquisition of an N-glycosylation site and its phenotypic outcome, a large amount of N-glycosylation site data and mammalian orthologous protein sequence data are required. Recent developments and advances in various highthroughput proteomics techniques for N-glycoproteome identification using immunoaffinity subtraction, hydrazide chemistry, and mass spectrometry have made it possible to access massive amounts of N-glycosylation site data from human proteomes [17] [18] [19] . These data are available at the UniProt database (http://www.uniprot.org), which is a universal protein sequence database, as well as some specialized PTM databases such as PHOSIDA (http:// www.phosida.com/) [20] .. Since human genome sequences were completed [21, 22] , a large amount of nucleotide and protein sequence data have become available not only from humans but also from many other organisms. Comparative sequence data, including alignments of mammalian orthologous protein sequences, are available at the University of California Santa Cruz (UCSC) Genome Browser Database (http:// genome.ucsc.edu) [23] .. In this study, a bioinformatics method was devised to identify novel N-glycosylated Asn residues that are located in the consensus motif Asn-X-Ser/Thr and arose during human evolution after the Euarchonta lineage diverged from the Glires lineage. Both a comprehensive literature survey and extensive data mining were conducted to examine the possible functional implications of novel N-glycosylation sites, especially in cases of human-specific gains.

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


Intra-subject elastic registration of 3D ultrasound images Abstract. 3D registration of ultrasound images is an important and fast-growing research area with various medical applications, such as image-guided radiotherapy and surgery. However, this registration process is extremely challenging due to the deformation of soft tissue and the existence of speckles in these images. This paper presents a novel intra-modality elastic registration technique for 3D ultrasound images. It uses the general concept of attribute vectors to find the corresponding voxels in the fixed and moving images. The method does not require any pre-segmentation and does not employ any numerical optimization procedure. Therefore, the computational requirements are very low and it has the potential to be used for real-time applications. The technique is implemented and tested for 3D ultrasound images of liver, captured by a 3D ultrasound transducer. The results show that the method is sufficiently accurate and robust and is not easily trapped with local minima. Ultrasound is an easy-to-use, inexpensive and real-time imaging tool with no ionizing radiation which is widely used for diagnosis applications. Recently, there has been major interest in the employment of this imaging technique for intraoperative registration in radiotherapy and image-guided surgery. Furthermore, ultrasound registration could be used for measuring tissue mechanics properties. However, due to speckles and shadowing effects, the registration of this imaging modality is a challenging process. Previous attempts include the development of techniques for registration of ultrasound to the other image modalities such as CT and MRI [1] [2] [3] [4] [5] , as well as intra-modality registration of these images [6] [7] [8] [9] .. Several methods have been used for elastic registration of ultrasound images. Shekhar et al. [6] investigated the registration of ultrasound volumes based on the mutual information measure. Median filter was found to be the proper smoothing filter for this method. The results of different transformation modes were presented. Krucker et al. [7] developed a subvolume-based algorithm for elastic ultrasound registration. The image was divided into subvolumes interactively and local rigid registrations were computed. Connectivity of the entire volume was ensured by global interpolation using thin-plate splines after each iteration. Xiao et al. [8] used a correlation-based approach for registration of 3D free-hand ultrasound images of the breast. Deformable registration of cardiac images has been investigated more specifically in [9, 10] . In this paper, we propose a novel technique for 3D elastic registration of ultrasound images. In our approach, the concept of attribute vector, introduced in [11] , is employed to find corresponding voxels in the ultrasound volumes. The elements of the attribute vector are revised to meet the requirements of ultrasound images. Using the attribute vectors, some leading points are automatically selected in the moving image, and their corresponding points in the fixed image are found. Finally, the moving image is warped into the fixed image.. This paper is organized as follows. Section 2 talks about the methodology and details of the implementation. Experimental results on 3D liver images are presented in Section 3. Section 4 concludes the paper and presents the future work. We have developed a new method for 3D elastic registration of ultrasound images, which is robust and flexible and is intended eventually for intra-operative surgical applications. The algorithm does not require any pre-segmentation or numerical optimization, and as a result, the running time is decreased. There are a number of parameters, such as the size of the search area, that should be set correctly for the algorithm to function properly. However, as long as the search area size is larger than the deformation between the two image data sets, the performance of the technique is not very sensitive to the changes in these parameters. Future work will include the optimization of the code to reduce the running time of the algorithm to within an acceptable range for intra-operative applications, as well as improving the normalization method of the elements of the attribute vector. The algorithm should also be tested for the registration of ultrasound images of other anatomical parts in addition to the liver. Ultrasound images were captured by a GE Voluson 730 3D/4D ultrasound machine. The RAB4-8P transducer was used to collect 3D images from two volunteers' livers, and the images were saved in Cartesian format. These images were captured at multiple locations under different forces applied to the abdomen by various operator's hand pressures on the transducer. The deformation in ultrasound volume data sets was also caused by respiration, heartbeat and changes in the physical position of the volunteers. For each volunteer, five sets of images were captured. Each set of images, consisted of two volumes at two different moments of the breathing cycle, were taken from one part of the volunteer's liver. For each set, one of the volumes was selected as the fixed image, and the other one (moving image) was registered to it. The average displacement between the images in each set was estimated to be 8.7 voxels with a maximum displacement of 20.8 voxels (the scale factor was set to 0.6 mm/voxel).. The code has been implemented using MATLAB TM . The matching and warping parts are written in C, and compiled with the C compiler of MATLAB TM to reduce the computation time. Figures 2(a,b,c) demonstrate one slice of the fixed, moving and registered data sets. The difference images shown in Figures 2(d,e) (a) depict the accuracy of the alignment of features after registration. It should be noted that the registration is performed in 3D, therefore some out-of-plane features, which may not exist in the demonstrated moving and fixed images, have been warped to the shown registered slice. Figure 3 shows the results of another experiment. Three slices in three orthogonal planes are demonstrated. The experiments show that the algorithm is robust, accurate and not sensitive to local minima, when the maximum displacement caused by deformation is less than the radius of the search area.. To evaluate the accuracy of the technique, two experiments were carried out. First, eight voxels on distinct features of the fixed and the registered volumes were manually selected. The distance between the corresponding voxels were then considered as the registration error. Using this method, the average error of registered images was about two voxels on average considering the uncertainties in the images and poor quality of them. In the second experiment, the matrices of displacement vectors generated in the previous experiments were used to simulate natural deformation. The original volumes were then registered to the deformed volumes, and the results were compared to the original displacement matrices. The average of mean error for 20 volumes deformed with this method was 1.50 voxels. For two 185x113x199 voxels volumes, the program took about 436 seconds to finalize registration on a Pentium 4 2.4GHz with 512MB RAM machine. Pre-filtering and calculating the attribute vectors took about 74 seconds; The time required for selection of leading points and registering them was about 203 seconds, and warping took the rest of time. The proposed algorithm is demonstrated in Figure 1 . At the first step, both fixed and moving images are passed through a Gaussian filter. This filter is used to generate more robust attribute vectors by reducing the effect of speckle, while providing different scales of images by adjusting its variance. In the next step, the elements of attribute vectors are calculated in two different scales for each voxel in both fixed and moving images. After this, the leading points with the highest magnitude attribute vectors are selected and registered, and finally the moving image is warped to the fixed image. The following paragraphs explain these steps in details.

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


Periodic Review, Push Inventory Policies for Remanufacturing Sustainability has become a major issue in most economies, causing many leading companies to focus on product recovery and reverse logistics. This research is focused on product recovery, and in particular on production control and inventory management in the remanufacturing context. We study a remanufacturing facility that receives a stream of returned products according to a Poisson process. Demand is uncertain and also follows a Poisson process. The decision problems for the remanufacturing facility are when to release returned products to the remanufacturing line and how many new products to manufacture. We assume that remanufactured products are as good as new. In this paper, we employ a "push" policy that combines these two decisions. It is well known that the optimal policy parameters are difficult to find analytically; therefore, we develop several heuristics based on traditional inventory models. We also investigate the performance of the system as a function of return rates, backorder costs and manufacturing and remanufacturing lead times; and we develop approximate lower and upper bounds on the optimal solution. We illustrate and explain some counter-intuitive results and we test the performance of the heuristics on a set of sample problems. We find that the average error of the heuristics is quite low. Sustainability has become a major issue for companies and countries as we enter the 21 st Century. Several European nations have mandated stringent laws for "product take back" after the product's useful life ends, forcing companies to respond with product redesign, changes in packaging, and creative solutions to the problem of product recovery. Efforts in all these areas can be seen in the automotive, computer, copier, and other industries (VROM (2002) ; EU (2002)).. Product recovery is an attempt to reuse as much of the product as economically worthwhile, and it takes many forms as highlighted in Figure 1 . Many companies currently can remanufacture their products, making them essentially as good as new. For these companies, the stream of returned products -also known as "carcasses" or "cores" -is uncertain. Therefore, they face a two-fold decision problem: First, should they remanufacture the carcasses they have in hand, and if so, when should these be released to the remanufacturing line? Second, should they manufacture new units because of low finished goods inventory and a trickle of carcasses, and if so, how many? In this paper, we utilize a particular policy -a periodic review, "push" policy -which addresses these two decisions. Breeze-Eastern is a U.S. company that serves a niche market by producing rescue hoists and cargo hooks for helicopters, construction, logging and other applications.. (Examples of rescue hoists can be seen in the movie "The Perfect Storm.") Rescue hoists are extremely sophisticated and expensive, ranging from $60,000 to $120,000 per system.. Cargo hooks are considerably less expensive, ranging from around $3000 to $20,000.. Both categories are remanufactured at their FAA certified repair center -the more expensive products generally by prearranged schedule, and the less expensive ones generally whenever they are returned for repair or upgrade. Because of the prearranged schedule of hoists, the remanufacturing facility at Breeze-Eastern builds an inventory of cargo hook carcasses, waiting to release them to the shop floor. Remanufactured cargo hooks are as good as new, and are held in finished goods inventory waiting for sale.. However, because the demand rate for finished goods is higher than the return rate of carcasses, Breeze-Eastern also manufactures new cargo hooks. Our analysis is focused on the Breeze-Eastern problem of remanufacturing inventory control. Specifically, we study a slightly simplified version of the remanufacturing of cargo hooks where we follow the Breeze-Eastern case in detail, except that, unlike the real case, we assume constant lead times for both remanufacturing and manufacturing, and we assume equal prices for products, regardless of their source. We explain these simplifying assumptions further in Section 3.. The form of the optimal policy is not known for the general problem we model.. Nevertheless, we restrict consideration to a periodic review, push policy for several reasons. First, the pervasiveness of MRP systems, including at Breeze-Eastern, suggests that periodic review is a good fit with the behavior of practitioners. One such example is described in Section 3. Second, van der Laan, Salomon, Dekker, & Van Wassenhove (1999) argues that push and pull systems are widely used in remanufacturing. And finally we build on analytical work by Inderfurth (1997) that addresses these policies.. Because the optimal policy parameters for our periodic review, push policy are difficult to find analytically, we develop heuristics based on traditional inventory policies. We also investigate the performance of the remanufacturing system as a function of return rates, backorder costs and manufacturing and remanufacturing lead times; and we develop approximate lower and upper bounds on the optimal solution. We illustrate and explain some counter-intuitive results and we test the performance of the heuristics on a set of sample problems.. This paper is organized as follows. In the next section, we review the relevant literature. In section 3, we describe the assumptions, notation and system in detail; then in section 4, we examine the behavior of the total cost function. In section 5, we develop three heuristics and then test them in section 6. Finally, we conclude and discuss future research in section 7.

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


The generalized assignment problem with minimum quantities We consider a variant of the generalized assignment problem (GAP) where the amount of space used in each bin is restricted to be either zero (if the bin is not opened) or above a given lower bound (a minimum quantity). We provide several complexity results for different versions of the problem and give polynomial time exact algorithms and approximation algorithms for restricted cases. For the most general version of the problem, we show that it does not admit a polynomial time approximation algorithm (unless P = NP), even for the case of a single bin. This motivates to study dual approximation algorithms that compute solutions violating the bin capacities and minimum quantities by a constant factor. When the number of bins is fixed and the minimum quantity of each bin is at least a factor δ > 1 larger than the largest size of an item in the bin, we show how to obtain a polynomial time dual approximation algorithm that computes a solution violating the minimum quantities and bin capacities by at most a factor 1 − 1 δ and 1 + 1 δ , respectively, and whose profit is at least as large as the profit of the best solution that satisfies the minimum quantities and bin capacities strictly. In particular, for δ = 2, we obtain a polynomial time (1, 2)-approximation algorithm. The generalized assignment problem (cf., for example, [1, 2] ) is a classical generalization of both the (multiple) knapsack problem and the bin packing problem. In the classical version of GAP, one is given m bins, a capacity B j for each bin j, and n items such that each item i has size s i,j and yields profit p i,j when packed into bin j. The goal is to find a feasible packing of the items into the bins that maximizes the total profit. Applications of GAP include fixed charge location problems, grouping and loading for flexible manufacturing systems, vehicle routing, scheduling projects, allocating storage space, scheduling payments on accounts, designing communication networks, assigning software development tasks to programmers, assigning jobs to computers in networks, scheduling variable length TV commercials, and assigning ships to overhaul facilities. For details on these applications, we refer to [2] and the references therein.. In this paper, we consider a variation of the problem where the amount of space used in each bin is restricted to be either zero (if the bin is not opened) or above a given lower bound (a minimum quantity). This additional restriction is motivated from many practical packing problems where it does often not make sense to open an additional container (bin) if not at least a certain amount of space in it will be used. For example, in the classical application of GAP where the bins correspond to workers and the items correspond to jobs that can be assigned to them, it may be unreasonable to hire an additional worker if not at least a certain amount of work will be assigned to him.. Another motivation for adding minimum quantities to GAP is its application in unrelated machine scheduling [3] . Here, the bins correspond to machines and the items to jobs. In practice, it may be that running a machine is only feasible if a prescribed minimum load is attained on the machine. In a foundry or steel works, for example, a machine can only be used if it has a certain minimum amount of metal to process.. Formally, the generalized assignment problem with minimum quantities (GAP-MQ) is defined as follows: The classical GAP is well-studied in literature. A comprehensive introduction to the problem can be found in [1] . A survey of algorithms for GAP is given in [2] . For a survey on different variants of assignment problems studied in literature, we refer to [4] .. GAP is known to be APX-hard [5] , but there exists a 2-approximation algorithm [3, 5] . Cohen et al. [6] showed how any polynomial time α-approximation algorithm for the knapsack problem can be translated into a polynomial time (1 + α)-approximation algorithm for GAP. A (1, 2)-approximation algorithm for the equivalent minimization version of GAP, assigning item i to bin j causes a cost c i,j , was provided by Shmoys and Tardos [3] : For every feasible instance of GAP, their algorithm computes a solution that violates the bin capacities by at most a factor of 2 and whose cost is at most as large as the cost of the best solution that satisfies the bin capacities strictly.. GAP is a generalization of both the (multiple) knapsack problem (cf. [1, 5, 7] ) and the bin packing problem (cf. [8, 9, 10] ). The multiple knapsack problem is the special case of GAP where the size and profit of an item are independent of the bin (knapsack) it is packed into. The bin packing problem can be seen as the special case of the decision version of GAP in which all bins have the same capacity and all profits are one. The question of deciding whether a packing of total profit equal to the number of items exists is then equivalent to asking whether all items can be packed into the given number of bins.. A dual version of bin packing (often called bin covering) in which minimum quantities are involved was introduced in [11, 12] . Here, the problem is to pack a given set of items with sizes that do not depend on the bins so as to maximize the number of bins used, subject to the constraint that each bin contains items of total size at least a given threshold T (upper bin capacities are not considered due to the nature of the objective function). Hence, the bin covering problem can be seen as a variant of GAP-MQ in which the minimum quantity is the same for each bin and the objective is to maximize the number of bins used. Since any approximation algorithm with approximation ratio strictly smaller than 2 would have to solve the NP-complete partition problem when applied to instances in which the sizes of the items sum up to two, it follows that (unless P = NP) no polynomial time (2−ǫ)-approximation for bin covering exists for any ǫ > 0. In contrast, the main result of Assmann et al. [12] is an O(n log 2 n) time algorithm that yields an asymptotic approximation ratio of 4/3 for bin covering, while easier algorithms based on next fit and first fit decreasing are shown to yield asymptotic approximation ratios of 2 and 3/2, respectively. Later, an asymptotic PTAS [13] and an asymptotic FPTAS [14] for bin covering were developed.. Minimum quantities have recently been studied for minimum cost network flow problems [15, 16, 17] . In this setting, minimum quantities for the flow on each arc are considered, which results in the minimum cost flow problem becoming strongly NP-complete [16] . Moreover, it was shown in [16] that (unless P = NP) no polynomial time g(|I|)-approximation for the problem exists for any polynomially computable function g : N + → N + , where |I| denotes the encoding length of the given instance.

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