PDNAsite:identification of DNA-binding site from protein sequence by incorporating spatial and sequence context

Protein-DNA interactions are involved in many fundamental biological processes essential for cellular function. Most of the existing computational approaches employed only the sequence context of the target residue for its prediction. In the present study, for each target residue, we applied both the spatial context and the sequence context to construct the feature space. Subsequently, Latent Semantic Analysis (LSA) was applied to remove the redundancies in the feature space. Finally, a predictor (PDNAsite) was developed through the integration of the support vector machines (SVM) classifier and ensemble learning. Results on the PDNA-62 and the PDNA-224 datasets demonstrate that features extracted from spatial context provide more information than those from sequence context and the combination of them gives more performance gain. An analysis of the number of binding sites in the spatial context of the target site indicates that the interactions between binding sites next to each other are important for protein-DNA recognition and their binding ability. The comparison between our proposed PDNAsite method and the existing methods indicate that PDNAsite outperforms most of the existing methods and is a useful tool for DNA-binding site identification. A web-server of our predictor (http://hlt.hitsz.edu.cn:8080/PDNAsite/) is made available for free public accessible to the biological research community.

Conclusion : on multiple levels of analysis, context, contingency and capital

In this concluding chapter, we bring together the threads and reflections on the chapters contained in this text and show how they relate to multi-level issues. The book has focused on the world of Human Resource Management (HRM) and the systems and practices it must put in place to foster innovation. Many of the contributions argue that in order to bring innovation about, organisations have to think carefully about the way in which they will integrate what is, in practice, organisationally relevant — but socially distributed — knowledge. They need to build a series of knowledge-intensive activities and networks, both within their own boundaries and across other important external inter-relationships. In so doing, they help to co-ordinate important information structures. They have, in effect, to find ways of enabling people to collaborate with each other at lower cost, by reducing both the costs of their co-ordination and the levels of unproductive search activity. They have to engineer these behaviours by reducing the risks for people that might be associated with incorrect ideas and help individuals, teams and business units to advance incomplete ideas that are so often difficult to codify. In short, a range of intangible assets must flow more rapidly throughout the organisation and an appropriate balance must be found between the rewards and incentives associated with creativity, novelty and innovation, versus the risks that innovation may also bring.

The role of enduring involvement in the relationship between reference price and price acceptance in the context of multichannel choice

Understanding online price acceptance and its determining factors can be essential if the companies try to manage different type of channels. The paper aimed to reveal the role of enduring involvement in price acceptance in a multichannel (online and offline) context. The study revealed that the hedonic value of shopping can increase the negative intention of price acceptance in the online channel, but also explored that for the segment without shopping motivations a similar price level can be applied both in the online and in the offline environment.

Creating Responsive Information Systems with the Help of SSADM

In this paper, a program for a research is outlined. Firstly, the concept of responsive information systems is defined and then the notion of the capacity planning and software performance engineering is clarified. Secondly, the purpose of the proposed methodology of capacity planning, the interface to information systems analysis and development methodologies (SSADM), the advantage of knowledge-based approach is discussed. The interfaces to CASE tools more precisely to data dictionaries or repositories (IRDS) are examined in the context of a certain systems analysis and design methodology (e.g. SSADM).

Hogyan kezeljük a „közösségi ügyfeleket”? – Social CRM marketing és IT megközelítésben (How to manage social customer? Social CRM in marketing and IT context.)

Van egy szó, ami egyre fontosabb lesz a társadalom és a vállalatok számára is, ez a szó a közösség. A közösséghez tevékenységek tartoznak, és ezen a ponton kapcsolódik be a vállalat. A vállalkozások az elmúlt években a közösségi igényeket a CRM-(Customer Relationship Management) megoldásokkal szolgálták ki. Informatikailag a közösségi hálózatok, már nemcsak vállalkozási folyamatot, hanem ehhez kapcsoltan az emberek társadalmi igényét is megpróbálják lefedni az elektronika lehetőségeivel. Egyre inkább a közösségi vállalkozások korát éljük, melyben a folyamathoz tartozó közösségek megosztják, egymás rendelkezésére bocsátják az információkat. A korábbi klasszikus CRM-rendszerek csak begyűjtötték az információkat, ezzel ellenben a közösségi CRM-rendszerek kétirányú kommunikációt folytatnak, párbeszédet kezdeményeznek az ügyfelekkel, buzdítják őket, hogy mondják el a véleményüket. Vajon ez az új stratégia,egy teljesen új világot hoz el a vállalatok számára, vagy csak a CRM fejlődésének egy újabb fokát jelenti? A szerzők erre a kérdésre keresik a választ gyakorlati esetek és szakirodalmi publikációk feldolgozásával. ______ There is a word that begins to be more and more important for the society and the companies, and this word is community. We can talk about social networks, people seek the social demand they already had as a part of their lives for a long time, and this means that it appears in the electronic society as an essential need too. The community is not enough, activities are also needed and this is the point where the companies link in, who promote their goods and facilities to the outside world and with this they use the next stage of customer relationship management, the fulfilment of social needs. We live in the age of social shopping, communities are everywhere and everyone shares information, and up to the present classic CR M systems ran from static databases. On the contrary social CR M systems perform a two-way communication, start a conversation with customers and encourage them to tell their opinions, which always changes on social media, so they build a dynamic database and communicate with customers through response-reactions. Does this new strategy bring a whole new world to companies or is it only another step in the development and another channel of CRM?

Section I: Institutional setting; Background Information about the School

Document detailing the Institutional Setting of the FLorida International University College of Medicine. Part of the Medical Education Database for Preliminary Accreditation, 2006-2007.

Office of Information Technology

Outline detailing the planning and implementation process for the establishment of the College of Medicine's Office of Information Technology. Includes a timeline of the Office of IT's development, a strategic roadmap, and a technology analysis.

Consequences of interorganizational information systems: An empirical investigation of the effects of EDI use on interorganizational relationships in the retail industry

This dissertation examines the consequences of Electronic Data Interchange (EDI) use on interorganizational relations (IR) in the retail industry. EDI is a type of interorganizational information system that facilitates the exchange of business documents in structured, machine processable form. The research model links EDI use and three IR dimensions--structural, behavioral, and outcome. Based on relevant literature from organizational theory and marketing channels, fourteen hypotheses were proposed for the relationships among EDI use and the three IR dimensions.^ Data were collected through self-administered questionnaires from key informants in 97 retail companies (19% response rate). The hypotheses were tested using multiple regression analysis. The analysis supports the following hypothesis: (a) EDI use is positively related to information intensity and formalization, (b) formalization is positively related to cooperation, (c) information intensity is positively related to cooperation, (d) conflict is negatively related to performance and satisfaction, (e) cooperation is positively related to performance, and (f) performance is positively related to satisfaction. The results support the general premise of the model that the relationship between EDI use and satisfaction among channel members has to be viewed within an interorganizational context.^ Research on EDI is still in a nascent stage. By identifying and testing relevant interorganizational variables, this study offers insights for practitioners managing boundary-spanning activities in organizations using or planning to use EDI. Further, the thesis provides avenues for future research aimed at understanding the consequences of this interorganizational information technology. ^

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. ^

Managing conflict in user-oriented development environments: Effects on information systems success

Today, many organizations are turning to new approaches to building and maintaining information systems (I/S) to cope with a highly competitive business environment. Current anecdotal evidence indicates that the approaches being used improve the effectiveness of software development by encouraging active user participation throughout the development process. Unfortunately, very little is known about how the use of such approaches enhances the ability of team members to develop I/S that are responsive to changing business conditions.^ Drawing from predominant theories of organizational conflict, this study develops and tests a model of conflict among members of a development team. The model proposes that development approaches provide the relevant context conditioning the management and resolution of conflict in software development which, in turn, are crucial for the success of the development process.^ Empirical testing of the model was conducted using data collected through a combination of interviews with I/S executives and surveys of team members and business users at nine organizations. Results of path analysis provide support for the model's main prediction that integrative conflict management and distributive conflict management can contribute to I/S success by influencing differently the manifestation and resolution of conflict in software development. Further, analyses of variance indicate that object-oriented development, when compared to rapid and structured development, appears to produce the lowest levels of conflict management, conflict resolution, and I/S success.^ The proposed model and findings suggest academic implications for understanding the effects of different conflict management behaviors on software development outcomes, and practical implications for better managing the software development process, especially in user-oriented development environments. ^

Estimation of average annual daily traffic (AADT) using geographically weighted regression (GWR) method and geographic information system (GIS)

Annual average daily traffic (AADT) is important information for many transportation planning, design, operation, and maintenance activities, as well as for the allocation of highway funds. Many studies have attempted AADT estimation using factor approach, regression analysis, time series, and artificial neural networks. However, these methods are unable to account for spatially variable influence of independent variables on the dependent variable even though it is well known that to many transportation problems, including AADT estimation, spatial context is important. ^ In this study, applications of geographically weighted regression (GWR) methods to estimating AADT were investigated. The GWR based methods considered the influence of correlations among the variables over space and the spatially non-stationarity of the variables. A GWR model allows different relationships between the dependent and independent variables to exist at different points in space. In other words, model parameters vary from location to location and the locally linear regression parameters at a point are affected more by observations near that point than observations further away. ^ The study area was Broward County, Florida. Broward County lies on the Atlantic coast between Palm Beach and Miami-Dade counties. In this study, a total of 67 variables were considered as potential AADT predictors, and six variables (lanes, speed, regional accessibility, direct access, density of roadway length, and density of seasonal household) were selected to develop the models. ^ To investigate the predictive powers of various AADT predictors over the space, the statistics including local r-square, local parameter estimates, and local errors were examined and mapped. The local variations in relationships among parameters were investigated, measured, and mapped to assess the usefulness of GWR methods. ^ The results indicated that the GWR models were able to better explain the variation in the data and to predict AADT with smaller errors than the ordinary linear regression models for the same dataset. Additionally, GWR was able to model the spatial non-stationarity in the data, i.e., the spatially varying relationship between AADT and predictors, which cannot be modeled in ordinary linear regression. ^

Data partitioning and replication management in distributed geographic information system (GIS) database

This research presents several components encompassing the scope of the objective of Data Partitioning and Replication Management in Distributed GIS Database. Modern Geographic Information Systems (GIS) databases are often large and complicated. Therefore data partitioning and replication management problems need to be addresses in development of an efficient and scalable solution. ^ Part of the research is to study the patterns of geographical raster data processing and to propose the algorithms to improve availability of such data. These algorithms and approaches are targeting granularity of geographic data objects as well as data partitioning in geographic databases to achieve high data availability and Quality of Service(QoS) considering distributed data delivery and processing. To achieve this goal a dynamic, real-time approach for mosaicking digital images of different temporal and spatial characteristics into tiles is proposed. This dynamic approach reuses digital images upon demand and generates mosaicked tiles only for the required region according to user's requirements such as resolution, temporal range, and target bands to reduce redundancy in storage and to utilize available computing and storage resources more efficiently. ^ Another part of the research pursued methods for efficient acquiring of GIS data from external heterogeneous databases and Web services as well as end-user GIS data delivery enhancements, automation and 3D virtual reality presentation. ^ There are vast numbers of computing, network, and storage resources idling or not fully utilized available on the Internet. Proposed "Crawling Distributed Operating System "(CDOS) approach employs such resources and creates benefits for the hosts that lend their CPU, network, and storage resources to be used in GIS database context. ^ The results of this dissertation demonstrate effective ways to develop a highly scalable GIS database. The approach developed in this dissertation has resulted in creation of TerraFly GIS database that is used by US government, researchers, and general public to facilitate Web access to remotely-sensed imagery and GIS vector information. ^

Secure information flow via stripping and fast simulation

Type systems for secure information flow aim to prevent a program from leaking information from H (high) to L (low) variables. Traditionally, bisimulation has been the prevalent technique for proving the soundness of such systems. This work introduces a new proof technique based on stripping and fast simulation, and shows that it can be applied in a number of cases where bisimulation fails. We present a progressive development of this technique over a representative sample of languages including a simple imperative language (core theory), a multiprocessing nondeterministic language, a probabilistic language, and a language with cryptographic primitives. In the core theory we illustrate the key concepts of this technique in a basic setting. A fast low simulation in the context of transition systems is a binary relation where simulating states can match the moves of simulated states while maintaining the equivalence of low variables; stripping is a function that removes high commands from programs. We show that we can prove secure information flow by arguing that the stripping relation is a fast low simulation. We then extend the core theory to an abstract distributed language under a nondeterministic scheduler. Next, we extend to a probabilistic language with a random assignment command; we generalize fast simulation to the setting of discrete time Markov Chains, and prove approximate probabilistic noninterference. Finally, we introduce cryptographic primitives into the probabilistic language and prove computational noninterference, provided that the underling encryption scheme is secure.