Sequence-specific reconstruction from fragmentary databases using seed sequences: implementation and validation on SAGE, proteome and generic sequencing data

Motivation: DNA assembly programs classically perform an all-against-all comparison of reads to identify overlaps, followed by a multiple sequence alignment and generation of a consensus sequence. If the aim is to assemble a particular segment, instead of a whole genome or transcriptome, a target-specific assembly is a more sensible approach. GenSeed is a Perl program that implements a seed-driven recursive assembly consisting of cycles comprising a similarity search, read selection and assembly. The iterative process results in a progressive extension of the original seed sequence. GenSeed was tested and validated on many applications, including the reconstruction of nuclear genes or segments, full-length transcripts, and extrachromosomal genomes. The robustness of the method was confirmed through the use of a variety of DNA and protein seeds, including short sequences derived from SAGE and proteome projects.

The assessment of change in rural landscape and the analysis of the driving forces. Proposal of a spatial model for the rural built environment

The presented study carried out an analysis on rural landscape changes. In particular the study focuses on the understanding of driving forces acting on the rural built environment using a statistical spatial model implemented through GIS techniques. It is well known that the study of landscape changes is essential for a conscious decision making in land planning. From a bibliography review results a general lack of studies dealing with the modeling of rural built environment and hence a theoretical modelling approach for such purpose is needed. The advancement in technology and modernity in building construction and agriculture have gradually changed the rural built environment. In addition, the phenomenon of urbanization of a determined the construction of new volumes that occurred beside abandoned or derelict rural buildings. Consequently there are two types of transformation dynamics affecting mainly the rural built environment that can be observed: the conversion of rural buildings and the increasing of building numbers. It is the specific aim of the presented study to propose a methodology for the development of a spatial model that allows the identification of driving forces that acted on the behaviours of the building allocation. In fact one of the most concerning dynamic nowadays is related to an irrational expansion of buildings sprawl across landscape. The proposed methodology is composed by some conceptual steps that cover different aspects related to the development of a spatial model: the selection of a response variable that better describe the phenomenon under study, the identification of possible driving forces, the sampling methodology concerning the collection of data, the most suitable algorithm to be adopted in relation to statistical theory and method used, the calibration process and evaluation of the model. A different combination of factors in various parts of the territory generated favourable or less favourable conditions for the building allocation and the existence of buildings represents the evidence of such optimum. Conversely the absence of buildings expresses a combination of agents which is not suitable for building allocation. Presence or absence of buildings can be adopted as indicators of such driving conditions, since they represent the expression of the action of driving forces in the land suitability sorting process. The existence of correlation between site selection and hypothetical driving forces, evaluated by means of modeling techniques, provides an evidence of which driving forces are involved in the allocation dynamic and an insight on their level of influence into the process. GIS software by means of spatial analysis tools allows to associate the concept of presence and absence with point futures generating a point process. Presence or absence of buildings at some site locations represent the expression of these driving factors interaction. In case of presences, points represent locations of real existing buildings, conversely absences represent locations were buildings are not existent and so they are generated by a stochastic mechanism. Possible driving forces are selected and the existence of a causal relationship with building allocations is assessed through a spatial model. The adoption of empirical statistical models provides a mechanism for the explanatory variable analysis and for the identification of key driving variables behind the site selection process for new building allocation. The model developed by following the methodology is applied to a case study to test the validity of the methodology. In particular the study area for the testing of the methodology is represented by the New District of Imola characterized by a prevailing agricultural production vocation and were transformation dynamic intensively occurred. The development of the model involved the identification of predictive variables (related to geomorphologic, socio-economic, structural and infrastructural systems of landscape) capable of representing the driving forces responsible for landscape changes.. The calibration of the model is carried out referring to spatial data regarding the periurban and rural area of the study area within the 1975-2005 time period by means of Generalised linear model. The resulting output from the model fit is continuous grid surface where cells assume values ranged from 0 to 1 of probability of building occurrences along the rural and periurban area of the study area. Hence the response variable assesses the changes in the rural built environment occurred in such time interval and is correlated to the selected explanatory variables by means of a generalized linear model using logistic regression. Comparing the probability map obtained from the model to the actual rural building distribution in 2005, the interpretation capability of the model can be evaluated. The proposed model can be also applied to the interpretation of trends which occurred in other study areas, and also referring to different time intervals, depending on the availability of data. The use of suitable data in terms of time, information, and spatial resolution and the costs related to data acquisition, pre-processing, and survey are among the most critical aspects of model implementation. Future in-depth studies can focus on using the proposed model to predict short/medium-range future scenarios for the rural built environment distribution in the study area. In order to predict future scenarios it is necessary to assume that the driving forces do not change and that their levels of influence within the model are not far from those assessed for the time interval used for the calibration.

Randomization in clinical trials in orthodontics: its significance in research design and methods to achieve it

Randomization is a key step in reducing selection bias during the treatment allocation phase in randomized clinical trials. The process of randomization follows specific steps, which include generation of the randomization list, allocation concealment, and implementation of randomization. The phenomenon in the dental and orthodontic literature of characterizing treatment allocation as random is frequent; however, often the randomization procedures followed are not appropriate. Randomization methods assign, at random, treatment to the trial arms without foreknowledge of allocation by either the participants or the investigators thus reducing selection bias. Randomization entails generation of random allocation, allocation concealment, and the actual methodology of implementing treatment allocation randomly and unpredictably. Most popular randomization methods include some form of restricted and/or stratified randomization. This article introduces the reasons, which make randomization an integral part of solid clinical trial methodology, and presents the main randomization schemes applicable to clinical trials in orthodontics.

Tools for better SLM knowledge management and informed decision-making in addressing land degradation at different scales: the WOCAT–LADA–DESIRE methodology

Desertification research conventionally focuses on the problem – that is, degradation – while neglecting the appraisal of successful conservation practices. Based on the premise that Sustainable Land Management (SLM) experiences are not sufficiently or comprehensively documented, evaluated, and shared, the World Overview of Conservation Approaches and Technologies (WOCAT) initiative (www.wocat.net), in collaboration with FAO’s Land Degradation Assessment in Drylands (LADA) project (www.fao.org/nr/lada/) and the EU’s DESIRE project (http://www.desire-project.eu/), has developed standardised tools and methods for compiling and evaluating the biophysical and socio-economic knowledge available about SLM. The tools allow SLM specialists to share their knowledge and assess the impact of SLM at the local, national, and global levels. As a whole, the WOCAT–LADA–DESIRE methodology comprises tools for documenting, self-evaluating, and assessing the impact of SLM practices, as well as for knowledge sharing and decision support in the field, at the planning level, and in scaling up identified good practices. SLM depends on flexibility and responsiveness to changing complex ecological and socioeconomic causes of land degradation. The WOCAT tools are designed to reflect and capture this capacity of SLM. In order to take account of new challenges and meet emerging needs of WOCAT users, the tools are constantly further developed and adapted. Recent enhancements include tools for improved data analysis (impact and cost/benefit), cross-scale mapping, climate change adaptation and disaster risk management, and easier reporting on SLM best practices to UNCCD and other national and international partners. Moreover, WOCAT has begun to give land users a voice by backing conventional documentation with video clips straight from the field. To promote the scaling up of SLM, WOCAT works with key institutions and partners at the local and national level, for example advisory services and implementation projects. Keywords: Sustainable Land Management (SLM), knowledge management, decision-making, WOCAT–LADA–DESIRE methodology.

Quantitative multi-slice computed tomography assessment of the mitral valvular complex for transcatheter mitral valve interventions part 1: systematic measurement methodology and inter-observer variability

AIMS Transcatheter mitral valve replacement (TMVR) is an emerging technology with the potential to treat patients with severe mitral regurgitation at excessive risk for surgical mitral valve surgery. Multimodal imaging of the mitral valvular complex and surrounding structures will be an important component for patient selection for TMVR. Our aim was to describe and evaluate a systematic multi-slice computed tomography (MSCT) image analysis methodology that provides measurements relevant for transcatheter mitral valve replacement. METHODS AND RESULTS A systematic step-by-step measurement methodology is described for structures of the mitral valvular complex including: the mitral valve annulus, left ventricle, left atrium, papillary muscles and left ventricular outflow tract. To evaluate reproducibility, two observers applied this methodology to a retrospective series of 49 cardiac MSCT scans in patients with heart failure and significant mitral regurgitation. For each of 25 geometrical metrics, we evaluated inter-observer difference and intra-class correlation. The inter-observer difference was below 10% and the intra-class correlation was above 0.81 for measurements of critical importance in the sizing of TMVR devices: the mitral valve annulus diameters, area, perimeter, the inter-trigone distance, and the aorto-mitral angle. CONCLUSIONS MSCT can provide measurements that are important for patient selection and sizing of TMVR devices. These measurements have excellent inter-observer reproducibility in patients with functional mitral regurgitation.

A qualitative analysis of leadership styles and the selection of quality improvement in primary care practice

In the Practice Change Model, physicians act as key stakeholders, people who have both an investment in the practice and the capacity to influence how the practice performs. This leadership role is critical to the development and change of the practice. Leadership roles and effectiveness are an important factor in quality improvement in primary care practices.^ The study conducted involved a comparative case study analysis to identify leadership roles and the relationship between leadership roles and the number and type of quality improvement strategies adopted during a Practice Change Model-based intervention study. The research utilized secondary data from four primary care practices with various leadership styles. The practices are located in the San Antonio region and serve a large Hispanic population. The data was collected by two ABC Project Facilitators from each practice during a 12-month period including Key Informant Interviews (all staff members), MAP (Multi-method Assessment Process), and Practice Facilitation field notes. This data was used to evaluate leadership styles, management within the practice, and intervention tools that were implemented. The chief steps will be (1) to analyze if the leader-member relations contribute to the type of quality improvement strategy or strategies selected (2) to investigate if leader-position power contributes to the number of strategies selected and the type of strategy selected (3) and to explore whether the task structure varies across the four primary care practices.^ The research found that involving more members of the clinic staff in decision-making, building bridges between organizational staff and clinical staff, and task structure are all associated with the direct influence on the number and type of quality improvement strategies implemented in primary care practice.^ Although this research only investigated leadership styles of four different practices, it will offer future guidance on how to establish the priorities and implementation of quality improvement strategies that will have the greatest impact on patient care improvement. ^

Consciousness, Action Selection, Meaning and Phenomenic Anticipation

Phenomenal states are generally considered the ultimate sources of intrinsic motivation for autonomous biological agents. In this article, we will address the issue of the necessity of exploiting these states for the design and implementation of robust goal-directed artificial systems. We will provide an analysis of consciousness in terms of a precise definition of how an agent "understands" the informational flows entering the agent and its very own action possibilities. This abstract model of consciousness and understanding will be based in the analysis and evaluation of phenomenal states along potential future trajectories in the state space of the agents. This implies that a potential strategy to follow in order to build autonomous but still customer-useful systems is to embed them with the particular, ad hoc phenomenality that captures the system-external requirements that define the system usefulness from a customer-based, requirements-strict engineering viewpoint.

Real time optimization in chemical process: evaluation of strategies, improvements and industrial application.

The increasing economic competition drives the industry to implement tools that improve their processes efficiencies. The process automation is one of these tools, and the Real Time Optimization (RTO) is an automation methodology that considers economic aspects to update the process control in accordance with market prices and disturbances. Basically, RTO uses a steady-state phenomenological model to predict the process behavior, and then, optimizes an economic objective function subject to this model. Although largely implemented in industry, there is not a general agreement about the benefits of implementing RTO due to some limitations discussed in the present work: structural plant/model mismatch, identifiability issues and low frequency of set points update. Some alternative RTO approaches have been proposed in literature to handle the problem of structural plant/model mismatch. However, there is not a sensible comparison evaluating the scope and limitations of these RTO approaches under different aspects. For this reason, the classical two-step method is compared to more recently derivative-based methods (Modifier Adaptation, Integrated System Optimization and Parameter estimation, and Sufficient Conditions of Feasibility and Optimality) using a Monte Carlo methodology. The results of this comparison show that the classical RTO method is consistent, providing a model flexible enough to represent the process topology, a parameter estimation method appropriate to handle measurement noise characteristics and a method to improve the sample information quality. At each iteration, the RTO methodology updates some key parameter of the model, where it is possible to observe identifiability issues caused by lack of measurements and measurement noise, resulting in bad prediction ability. Therefore, four different parameter estimation approaches (Rotational Discrimination, Automatic Selection and Parameter estimation, Reparametrization via Differential Geometry and classical nonlinear Least Square) are evaluated with respect to their prediction accuracy, robustness and speed. The results show that the Rotational Discrimination method is the most suitable to be implemented in a RTO framework, since it requires less a priori information, it is simple to be implemented and avoid the overfitting caused by the Least Square method. The third RTO drawback discussed in the present thesis is the low frequency of set points update, this problem increases the period in which the process operates at suboptimum conditions. An alternative to handle this problem is proposed in this thesis, by integrating the classic RTO and Self-Optimizing control (SOC) using a new Model Predictive Control strategy. The new approach demonstrates that it is possible to reduce the problem of low frequency of set points updates, improving the economic performance. Finally, the practical aspects of the RTO implementation are carried out in an industrial case study, a Vapor Recompression Distillation (VRD) process located in Paulínea refinery from Petrobras. The conclusions of this study suggest that the model parameters are successfully estimated by the Rotational Discrimination method; the RTO is able to improve the process profit in about 3%, equivalent to 2 million dollars per year; and the integration of SOC and RTO may be an interesting control alternative for the VRD process.

Manager Training and Development Strategy: A Methodology to Link Strategic Initiatives at Washington and Lee University

Washington and Lee University has developed and implemented a strategic plan and performance development initiative for 2007-2017. In concert with the strategic plan and performance development initiative, supportive manager core competencies have been identified. The deliverable for this capstone project is a documented methodology that supports the strategy for the design and implementation of a manager training and development program that ensures needed competencies are available. The author uses survey data to determine training needs and priorities and, through a review of literature, investigates effective strategies to arrive at a successful implementation methodology. The author presents findings and conclusions regarding design implementation methodology for manager training and development.

Decision support system for project selection

The evaluation and selection of industrial projects before investment decision is customarily done using marketing, technical, and financial information. Subsequently, environmental impact assessment and social impact assessment are carried out mainly to satisfy the statutory agencies. Because of stricter environment regulations in developed and developing countries, quite often impact assessment suggests alternate sites, technologies, designs, and implementation methods as mitigating measures. This causes considerable delay to complete project feasibility analysis and selection as complete analysis requires to be taken up again and again until the statutory regulatory authority approves the project. Moreover, project analysis through the above process often results in suboptimal projects as financial analysis may eliminate better options as more environment friendly alternative will always be cost intensive. In this circumstance, this study proposes a decision support system which analyses projects with respect to market, technicalities, and social and environmental impact in an integrated framework using analytic hierarchy process, a multiple attribute decision-making technique. This not only reduces duration of project evaluation and selection, but also helps select an optimal project for the organization for sustainable development. The entire methodology has been applied to a cross-country oil pipeline project in India and its effectiveness has been demonstrated. © 2008, IGI Global.

The DRAMA methodology for analysing strategy and its links with production system design

This paper describes a methodology: 'decision rules for analyzing manufacturing activities', which is designed to be a practical system of enquiry linking a strategic analysis to the design of production systems. The paper describes the development of the system, an industry specific design methodology, into DRAMA II which is a model that serves as an analytical tool for studying decision processes and implementation of production systems.

Developing and evaluating a methodology for business process improvement

Purpose – There appears to be an ever-insatiable demand from markets for organisations to improve their products and services. To meet this, there is a need to provide business process improvement (BPI) methodologies that are holistic, structured and procedural. Therefore, this paper describes research that has formed and tested a generic and practical methodology termed model-based and integrated process improvement (MIPI) to support the implementation of BPI; and to validate its effectiveness in organisations. This methodology has been created as an aid for practitioners within organisations. Design/methodology/approach – The research objectives were achieved by: reviewing and analysing current methodologies, and selecting a few frameworks against key performance indicators. Using a refined Delphi approach and semi-structured interview with the “experts” in the field. Intervention, case study and process research approach to evaluating a methodology. Findings – The BPI methodology was successfully formed and applied by the researcher and directly by the companies involved against the criteria of feasibility, usability and usefulness. Research limitations/implications – The paper has demonstrated a new knowledge on how to systematically assess a BPI methodology in practice. Practical implications – Model-based and integrated process improvement methodology (MIPI) methodology offers the practitioner (experienced and novice) a set of step-by-step aids necessary to make informed, consistent and efficient changes to business processes. Originality/value – The novelty of this research work is the creation of a holistic workbook-based methodology with relevant tools and techniques. It extends the capabilities of existing methodologies.

An analysis of the role of soft systems methodology in the change process and the contribution of the facilitator within this process

This research aims to examine the effectiveness of Soft Systems Methodology (SSM) to enable systemic change within local goverment and local NHS environments and to examine the role of the facilitator within this process. Checkland's Mode 2 variant of Soft Systems Methodology was applied on an experimental basis in two environments, Herefordshire Health Authority and Sand well Health Authority. The Herefordshire application used SSM in the design of an Integrated Care Pathway for stroke patients. In Sandwell, SSM was deployed to assist in the design of an Infonnation Management and Technology (IM&T) Strategy for the boundary-spanning Sandwell Partnership. Both of these environments were experiencing significant organisational change as the experiments unfurled. The explicit objectives of the research were: To examine the evolution and development of SSM and to contribute to its further development. To apply the Soft Systems Methodology to change processes within the NHS. To evaluate the potential role of SSM in this wider process of change. To assess the role of the researcher as a facilitator within this process. To develop a critical framework through which the impact of SSM on change might be understood and assessed. In developing these objectives, it became apparent that there was a gap in knowledge relating to SSM. This gap concerns the evaluation of the role of the approach in the change process. The case studies highlighted issues in stakeholder selection and management; the communicative assumptions in SSM; the ambiguous role of the facilitator; and the impact of highly politicised problem environments on the effectiveness of the methodology in the process of change. An augmented variant on SSM that integrates an appropriate (social constructivist) evaluation method is outlined, together with a series of hypotheses about the operationalisation of this proposed method.

Understanding the dynamics of information technology implementation: The case of clinical information systems

The ultimate intent of this dissertation was to broaden and strengthen our understanding of IT implementation by emphasizing research efforts on the dynamic nature of the implementation process. More specifically, efforts were directed toward opening the "black box" and providing the story that explains how and why contextual conditions and implementation tactics interact to produce project outcomes. In pursuit of this objective, the dissertation was aimed at theory building and adopted a case study methodology combining qualitative and quantitative evidence. Precisely, it examined the implementation process, use and consequences of three clinical information systems at Jackson Memorial Hospital, a large tertiary care teaching hospital.^ As a preliminary step toward the development of a more realistic model of system implementation, the study proposes a new set of research propositions reflecting the dynamic nature of the implementation process.^ Findings clearly reveal that successful implementation projects are likely to be those where key actors envision end goals, anticipate challenges ahead, and recognize the presence of and seize opportunities. It was also found that IT implementation is characterized by the systems theory of equifinality, that is, there are likely several equally effective ways to achieve a given end goal. The selection of a particular implementation strategy appears to be a rational process where actions and decisions are largely influenced by the degree to which key actors recognize the mediating role of each tactic and are motivated to action. The nature of the implementation process is also characterized by the concept of "duality of structure," that is, context and actions mutually influence each other. Another key finding suggests that there is no underlying program that regulates the process of change and moves it form one given point toward a subsequent and already prefigured end. For this reason, the implementation process cannot be thought of as a series of activities performed in a sequential manner such as conceived in stage models. Finally, it was found that IT implementation is punctuated by a certain indeterminacy. Results suggest that only when substantial efforts are focused on what to look for and think about, it is less likely that unfavorable and undesirable consequences will occur. ^

A methodology to select an enterprise resource planning system for a small or medium sized enterprise

Enterprise Resource Planning (ERP) systems are software programs designed to integrate the functional requirements, and operational information needs of a business. Pressures of competition and entry standards for participation in major manufacturing supply chains are creating greater demand for small business ERP systems. The proliferation of new offerings of ERP systems introduces complexity to the selection process to identify the right ERP business software for a small and medium-sized enterprise (SME). The selection of an ERP system is a process in which a faulty conclusion poses a significant risk of failure to SME’s. The literature reveals that there are still very high failure rates in ERP implementation, and that faulty selection processes contribute to this failure rate. However, the literature is devoid of a systematic methodology for the selection process for an ERP system by SME’s. This study provides a methodological approach to selecting the right ERP system for a small or medium-sized enterprise. The study employs Thomann’s meta-methodology for methodology development; a survey of SME’s is conducted to inform the development of the methodology, and a case study is employed to test, and revise the new methodology. The study shows that a rigorously developed, effective methodology that includes benchmarking experiences has been developed and successfully employed. It is verified that the methodology may be applied to the domain of users it was developed to serve, and that the test results are validated by expert users and stakeholders. Future research should investigate in greater detail the application of meta-methodologies to supplier selection and evaluation processes for services and software; additional research into the purchasing practices of small firms is clearly needed.^