Online Mammographic Images Database for Development and Comparison of CAD Schemes

Considering the difficulties in finding good-quality images for the development and test of computer-aided diagnosis (CAD), this paper presents a public online mammographic images database free for all interested viewers and aimed to help develop and evaluate CAD schemes. The digitalization of the mammographic images is made with suitable contrast and spatial resolution for processing purposes. The broad recuperation system allows the user to search for different images, exams, or patient characteristics. Comparison with other databases currently available has shown that the presented database has a sufficient number of images, is of high quality, and is the only one to include a functional search system.

Database technologies for l-system simulations in virtual plant applications on bioinformatics

One of the most important advantages of database systems is that the underlying mathematics is rich enough to specify very complex operations with a small number of statements in the database language. This research covers an aspect of biological informatics that is the marriage of information technology and biology, involving the study of real-world phenomena using virtual plants derived from L-systems simulation. L-systems were introduced by Aristid Lindenmayer as a mathematical model of multicellular organisms. Not much consideration has been given to the problem of persistent storage for these simulations. Current procedures for querying data generated by L-systems for scientific experiments, simulations and measurements are also inadequate. To address these problems the research in this paper presents a generic process for data-modeling tools (L-DBM) between L-systems and database systems. This paper shows how L-system productions can be generically and automatically represented in database schemas and how a database can be populated from the L-system strings. This paper further describes the idea of pre-computing recursive structures in the data into derived attributes using compiler generation. A method to allow a correspondence between biologists' terms and compiler-generated terms in a biologist computing environment is supplied. Once the L-DBM gets any specific L-systems productions and its declarations, it can generate the specific schema for both simple correspondence terminology and also complex recursive structure data attributes and relationships.

The integrated WRF/urban modelling system: development, evaluation, and applications to urban environmental problems

To bridge the gaps between traditional mesoscale modelling and microscale modelling, the National Center for Atmospheric Research, in collaboration with other agencies and research groups, has developed an integrated urban modelling system coupled to the weather research and forecasting (WRF) model as a community tool to address urban environmental issues. The core of this WRF/urban modelling system consists of the following: (1) three methods with different degrees of freedom to parameterize urban surface processes, ranging from a simple bulk parameterization to a sophisticated multi-layer urban canopy model with an indoor–outdoor exchange sub-model that directly interacts with the atmospheric boundary layer, (2) coupling to fine-scale computational fluid dynamic Reynolds-averaged Navier–Stokes and Large-Eddy simulation models for transport and dispersion (T&D) applications, (3) procedures to incorporate high-resolution urban land use, building morphology, and anthropogenic heating data using the National Urban Database and Access Portal Tool (NUDAPT), and (4) an urbanized high-resolution land data assimilation system. This paper provides an overview of this modelling system; addresses the daunting challenges of initializing the coupled WRF/urban model and of specifying the potentially vast number of parameters required to execute the WRF/urban model; explores the model sensitivity to these urban parameters; and evaluates the ability of WRF/urban to capture urban heat islands, complex boundary-layer structures aloft, and urban plume T&D for several major metropolitan regions. Recent applications of this modelling system illustrate its promising utility, as a regional climate-modelling tool, to investigate impacts of future urbanization on regional meteorological conditions and on air quality under future climate change scenarios. Copyright © 2010 Royal Meteorological Society

ICR water utility database system users' guide /

"EPA 814/B-96-004."

Dosage-dependent effects of Akt1/protein kinase Balpha (PKBalpha) and Akt3/PKBgamma on thymus, skin, and cardiovascular and nervous system development in mice.

Akt/protein kinase B (PKB) plays a critical role in the regulation of metabolism, transcription, cell migration, cell cycle progression, and cell survival. The existence of viable knockout mice for each of the three isoforms suggests functional redundancy. We generated mice with combined mutant alleles of Akt1 and Akt3 to study their effects on mouse development. Here we show that Akt1-/- Akt3+/- mice display multiple defects in the thymus, heart, and skin and die within several days after birth, while Akt1+/- Akt3-/- mice survive normally. Double knockout (Akt1-/-) Akt3-/-) causes embryonic lethality at around embryonic days 11 and 12, with more severe developmental defects in the cardiovascular and nervous systems. Increased apoptosis was found in the developing brain of double mutant embryos. These data indicate that the Akt1 gene is more essential than Akt3 for embryonic development and survival but that both are required for embryo development. Our results indicate isoform-specific and dosage-dependent effects of Akt on animal survival and development.

Online Community System Development, Case PROFCOM

The purpose of this bachelor's thesis is the development of online community. Nowadays Internet lets user to collaborate and share information online. Internet is also full of communities and the number of community users is continuously rising. Companies have also noticed this and want to make use of it. The result of the work was an online community for the use of PROFCOM research project. At the same time information was gathered about what kind of platforms are available as a backbone for an online community. Designing and developing of the online community provided experience about Drupal-environment. It also gave pros and cons of Drupal’s features. Drupal is a multifunctional software, which can handle big online communities, but its installation and maintenance is, however, reasonably simple.

Involving users in expert system development

The ultimate criterion of success for interactive expert systems is that they will be used, and used to effect, by individuals other than the system developers. A key ingredient of success in most systems is involving users in the specification and development of systems as they are being built. However, until recently, system designers have paid little attention to ascertaining user needs and to developing systems with corresponding functionality and appropriate interfaces to match those requirements. Although the situation is beginning to change, many developers do not know how to go about involving users, or else tackle the problem in an inadequate way. This paper discusses the need for user involvement and considers why many developers are still not involving users in an optimal way. It looks at the different ways in which users can be involved in the development process and describes how to select appropriate techniques and methods for studying users. Finally, it discusses some of the problems inherent in involving users in expert system development, and recommends an approach which incorporates both ethnographic analysis and formal user testing.

Student and teacher response system : development of an interactive anonymous real-timeformative feedback system

This paper is focusing IT-supported real-time formative feedback in a classroom context. The development of a Student and Teacher Response System (STRS) is described. Since there are a number of obstacles for effective interaction in large classes IT can be used to support the teachers aim to find out if students understand the lecture and accordingly adjust the content and design of the lecture. The system can be used for formative assessment before, during, and after a lecture. It is also possible for students to initiate interaction during lectures by posing questions anonymously. The main contributions of the paper are a) the description of the interactive real-time system and b) the development process behind it.

Use of a semantically grained database system for distribution and control within design environments

This paper presents a technique to share the data stored in an object-oriented database aimed at designing environments. This technique shares data between two related databases, called the Original and Product databases, and is composed of three processes: data separation, evolution and integration. Whenever a block of data needs to be shared, it is spread into both databases, resulting in a block on the original database, and another into the Product database, with special links between them controlled by the Object Manager. These blocks do not need to be maintained identical during the evolution phase of the sharing process. Six types of links were defined, and by choosing one, the designer control the evolution and reintegration of the block in both databases. This process uses the composite object concept as the unit of control. The presented concepts can be applied to any data model with support to composite objects.

Multi-level models and infrastructures for simulating biological system development

The hierarchical organisation of biological systems plays a crucial role in the pattern formation of gene expression resulting from the morphogenetic processes, where autonomous internal dynamics of cells, as well as cell-to-cell interactions through membranes, are responsible for the emergent peculiar structures of the individual phenotype. Being able to reproduce the systems dynamics at different levels of such a hierarchy might be very useful for studying such a complex phenomenon of self-organisation. The idea is to model the phenomenon in terms of a large and dynamic network of compartments, where the interplay between inter-compartment and intra-compartment events determines the emergent behaviour resulting in the formation of spatial patterns. According to these premises the thesis proposes a review of the different approaches already developed in modelling developmental biology problems, as well as the main models and infrastructures available in literature for modelling biological systems, analysing their capabilities in tackling multi-compartment / multi-level models. The thesis then introduces a practical framework, MS-BioNET, for modelling and simulating these scenarios exploiting the potential of multi-level dynamics. This is based on (i) a computational model featuring networks of compartments and an enhanced model of chemical reaction addressing molecule transfer, (ii) a logic-oriented language to flexibly specify complex simulation scenarios, and (iii) a simulation engine based on the many-species/many-channels optimised version of Gillespie’s direct method. The thesis finally proposes the adoption of the agent-based model as an approach capable of capture multi-level dynamics. To overcome the problem of parameter tuning in the model, the simulators are supplied with a module for parameter optimisation. The task is defined as an optimisation problem over the parameter space in which the objective function to be minimised is the distance between the output of the simulator and a target one. The problem is tackled with a metaheuristic algorithm. As an example of application of the MS-BioNET framework and of the agent-based model, a model of the first stages of Drosophila Melanogaster development is realised. The model goal is to generate the early spatial pattern of gap gene expression. The correctness of the models is shown comparing the simulation results with real data of gene expression with spatial and temporal resolution, acquired in free on-line sources.