Addition Of New Features Research Articles

Computer aided classification of diagnostic terms in spanish

The goal of this paper is to classify Medical Records (MRs) by their diagnostic terms (DTs) according to the International Classification of Diseases Clinical Modification (ICD-9-CM). The challenge we face is twofold: (i) to treat the natural and non-standard language in which doctors express their diagnostics and (ii) to perform a large-scale classification problem.We propose the use of Finite-State Transducers (FSTs) that, for their underlying topology, constrain the allowed input DT string while synchronously produce the output ICD-9-CM class. It is outstanding their versatility to efficiently implement soft-matching operations between terms expressed in natural language to standard terms and, hence, to the final ICD-9-CM code. The FSTs were built up from a corpora and standard resources such as the ICD-9-CM and SNOMED CT amongst others. Our corpora count on a big-data comprising more than 20,000 DTs from MRs from the Basque Hospital System so as to model natural language in this domain. An F1-measure of 91.2 was achieved on a test-set of 2850 randomly selected DTs, and a random 5-fold cross validation on a training set served to double-check the stability of the provided results. Real MRs were of much help to adapt the system to natural language. Misspellings, colloquial and specific language and abbreviations made the classification process difficult. The FSTs were proven efficient in this large-scale classification task. Moreover, the composition operation for FSTs made it easy the addition of new features to the system.

FASTER: Facilitating Analysis and Synthesis Technologies for Effective Reconfiguration

The FASTER (Facilitating Analysis and Synthesis Technologies for Effective Reconfiguration) EU FP7 project, aims to ease the design and implementation of dynamically changing hardware systems. Our motivation stems from the promise reconfigurable systems hold for achieving high performance and extending product functionality and lifetime via the addition of new features that operate at hardware speed. However, designing a changing hardware system is both challenging and time-consuming.FASTER facilitates the use of reconfigurable technology by providing a complete methodology enabling designers to easily specify, analyze, implement and verify applications on platforms with general-purpose processors and acceleration modules implemented in the latest reconfigurable technology. Our tool-chain supports both coarse- and fine-grain FPGA reconfiguration, while during execution a flexible run-time system manages the reconfigurable resources. We target three applications from different domains. We explore the way each application benefits from reconfiguration, and then we asses them and the FASTER tools, in terms of performance, area consumption and accuracy of analysis.

Learning from optimization: A case study with Apache Ant

ContextSoftware architecture degrades when changes violating the design-time architectural intents are imposed on the software throughout its life cycle. Such phenomenon is called architecture erosion. When changes are not controlled, erosion makes maintenance harder and negatively affects software evolution. ObjectiveTo study the effects of architecture erosion on a large software project and determine whether search-based module clustering might reduce the conceptual distance between the current architecture and the design-time one. MethodTo run an exploratory study with Apache Ant. First, we characterize Ant’s evolution in terms of size, change dispersion, cohesion, and coupling metrics, highlighting the potential introduction of architecture and code-level problems that might affect the cost of changing the system. Then, we reorganize the distribution of Ant’s classes using a heuristic search approach, intending to re-emerge its design-time architecture. ResultsIn characterizing the system, we observed that its original, simple design was lost due to maintenance and the addition of new features. In optimizing its architecture, we found that current models used to drive search-based software module clustering produce complex designs, which maximize the characteristics driving optimization while producing class distributions that would hardly be acceptable to developers maintaining Ant. ConclusionThe structural perspective promoted by the coupling and cohesion metrics precludes observing the adequate software module clustering from the perspective of software engineers when considering a large open source system. Our analysis adds evidence to the criticism of the dogma of driving design towards high cohesion and low coupling, at the same time observing the need for better models to drive design decisions. Apart from that, we see SBSE as a learning tool, allowing researchers to test Software Engineering models in extreme situations that would not be easily found in software projects.

The Big Effects of Short-term Efforts: Mentorship and Code Integration in Open Source Scientific Software

Scientific progress relies crucially on software, yet in practice there are significant challenges to scientific software production and maintenance. We conducted a case study of a bioinformatics software library called Biopython to investigate the promise of Google Summer of Code (GSoC), a program that pays students to work on open-source projects for the summer, for addressing these challenges. We find three positive outcomes of GSoC in the Biopython community: the addition of new features to the Biopython codebase, training, and personal development. We also find, however, that mentors face several challenges related to GSoC project selection and ranking. We believe that because GSoC provides an occasion to extend the software with capabilities that can be used to produce new knowledge, and to train successive generations of potential contributors to the software, it can play a vital role in the sustainability of open-source scientific software.

Predicting the complexity of code changes using entropy based measures

Changes in software source codes are inevitable. The source codes of software are frequently changed to meet the user’s enormous requirements. These changes are occurring due to bug repairs (BR), enhancement/modification (EM) and the addition of new features (NF). The maintenance task becomes quite difficult if these changes are not properly recorded. The versions of these frequent changes are being maintained using the software configuration management repository. These continuous changes in the software source code make the code complex and negatively affect the quality of the product. In the literature, the complexity of the code changes has been quantified using entropy based measures (Hassan, in: Proceedings of the 31st international conference on software engineering, pp. 78–88, 2009). In this paper, we have proposed a model to predict the potential complexity of code changes using entropy based measures. The predicted potential complexity of code changes helps in determining the remaining code changes yet to be diffused in the software. The proposed model has been validated using seven components of web browser Mozilla. The model has been evaluated using goodness of fit criteria namely R squared, bias, mean squared error, variation, and root mean squared prediction error (RMSPE).The statistical significance of the proposed model has been tested using χ2 and Kolmogorov–Smirnov (K–S) test. The proposed model is found statistically significant based on the associated p value of the K–S test. Further, we conclude that the rate of complexity diffusion due to BR is found higher in four cases namely Bonsai, Mozbot, tables and XUL. The other components of Mozilla namely AUS, MXR and Tinderbox show increase in complexity due to EM and NF.

A Brief History of the NSREC

This is the 50 year anniversary of the annual IEEE Nuclear and Space Radiation Effect Conference (NSREC). The first official IEEE NSREC was held at the University of Washington, Seattle, WA in 1964. Although the NSREC started primarily as a forum for the reporting of U.S. research on nuclear weapons effects in electronics it has grown to be primarily an international conference on the effect of space radiation on microelectronics. In this paper the history of NSREC will be discussed in terms of changes in technical content, change in mix of papers between industry, government labs and universities, change in venue, growth in number of authors per paper and the addition of new features in the conference.

SuperIDR: A Tool for Fish Identification and Information Retrieval

ABSTRACTStudents, fisheries professionals, and the general public may value computer‐facilitated assistance for fish identification and access to ecological and life history information. We developed SuperIDR, a software package supporting such applications, by utilizing the search and data retrieval capabilities of digital libraries, as well as key features of tablet PCs. We demonstrated SuperIDR utilizing a database with information on 207 freshwater fishes of Virginia. A user may annotate fish images and identify fishes by using a dichotomous key; searching for key words, similar images, subimages, or annotations on images; or combinations of these approaches. Students using the software demonstrated enhanced ability to correctly identify specimens. Their comments led to improvements, including the addition of new features. The PC‐based system for identifying freshwater fishes of Virginia may be downloaded and modified. SuperIDR is a prototype for PC‐based species identification applications—the system architecture and the open‐source software that we developed are applicable to other fish faunas and to a broader range of species identification tasks.

MANTA—an open-source, high density electrophysiology recording suite for MATLAB

The distributed nature of nervous systems makes it necessary to record from a large number of sites in order to decipher the neural code, whether single cell, local field potential (LFP), micro-electrocorticograms (μECoG), electroencephalographic (EEG), magnetoencephalographic (MEG) or in vitro micro-electrode array (MEA) data are considered. High channel-count recordings also optimize the yield of a preparation and the efficiency of time invested by the researcher. Currently, data acquisition (DAQ) systems with high channel counts (>100) can be purchased from a limited number of companies at considerable prices. These systems are typically closed-source and thus prohibit custom extensions or improvements by end users. We have developed MANTA, an open-source MATLAB-based DAQ system, as an alternative to existing options. MANTA combines high channel counts (up to 1440 channels/PC), usage of analog or digital headstages, low per channel cost (<$90/channel), feature-rich display and filtering, a user-friendly interface, and a modular design permitting easy addition of new features. MANTA is licensed under the GPL and free of charge. The system has been tested by daily use in multiple setups for >1 year, recording reliably from 128 channels. It offers a growing list of features, including integrated spike sorting, PSTH and CSD display and fully customizable electrode array geometry (including 3D arrays), some of which are not available in commercial systems. MANTA runs on a typical PC and communicates via TCP/IP and can thus be easily integrated with existing stimulus generation/control systems in a lab at a fraction of the cost of commercial systems. With modern neuroscience developing rapidly, MANTA provides a flexible platform that can be rapidly adapted to the needs of new analyses and questions. Being open-source, the development of MANTA can outpace commercial solutions in functionality, while maintaining a low price-point.

Effects of laboratory data exchange in the care of patients with HIV

BackgroundElectronic health record (EHR) systems are often modified through the addition of new features over time. Few studies have examined the specific effects of such changes. We examined whether implementation of a bidirectional laboratory interface for order entry and data reporting within an existing ambulatory EHR would result in more prompt responses to laboratory indications for antiretroviral therapy (ART) changes or in improved communication with HIV+ patients about relevant laboratory results. MethodsWe conducted a single-arm intervention study comparing the timeliness of ART regimen changes, HIV viral load (VL) outcomes and patient-reported assessments of care before and after implementation of a laboratory data exchange interface within an existing EHR, without changing the EHR ordering or results reporting user interface. Patient data was extracted from the EHR covering the period from 1 year before to 2 years after the intervention for a cohort of 1181 patients who had received care during the baseline year. The timeliness of ART changes was represented by the days from a laboratory-result “signal” (CD4 dropping below 350 or 200 or VL increasing by a half-log or to a value over 100,000) to an ART-change “response”. Patient assessments of care were collected by interviewing 100 anonymous patients at baseline and another 125 at 2 years post-intervention. ResultsA total of 171 laboratory “signal” events were followed within 80 days by a change in ART therapy. The mean time from signal to therapy change (adjusted for clustering by patient) initially increased, from 37.7 days during the pre-intervention year to 48.2 days during the quarter immediately following activation of the lab intervention. It then declined to a mean of 31.4 days over the remaining 21 months of observation (P=0.03 for the 6-day improvement from the pre-period). A majority of patients (65%) achieved undetectable VL values by the end of the observation period; faster signal–response times were not associated with greater achievement of undetectable VL. Patients rated communication about laboratory tests more highly after implementation of the interface (91 vs. 83 on a 100-point scale, P=0.01); ratings were not higher for other aspects of care. ConclusionsAdding laboratory data exchange interfaces within existing EHRs holds promise for improving HIV care, both in the timeliness of responses to important laboratory results and in the quality of provider communication about lab tests. However, the benefits from this incremental change may be modest unless more extensive redesign of laboratory follow-up workflows is undertaken, with support from enhanced user interfaces that take advantage of the laboratory information delivered. Providers should also consider increased staffing to compensate for dips in follow-up performance during the initial post-implementation months.

An Open-Standards Grammar for Outline-Style Radiology Report Templates

Structured reporting uses consistent ordering of results and standardized terminology to improve the quality and reduce the complexity of radiology reports. We sought to define a generalized approach for radiology reporting that produces flexible outline-style reports, accommodates structured information and named reporting elements, allows reporting terms to be linked to controlled vocabularies, uses existing informatics standards, and allows structured report data to be extracted readily. We applied the Regular Language for XML-Next Generation (RELAX NG) schema language to create templates for 110 reporting templates created as part of the Radiological Society of North America reporting initiative. We evaluated how well this approach addressed the project's goals. The RELAX NG schema language expressed the cardinality and hierarchical relationships of reporting concepts, and allowed reporting elements to be mapped to terms in controlled medical vocabularies, such as RadLex®, Systematized Nomenclature of Medicine Clinical Terms®, and Logical Observation Identifiers Names and Codes®. The approach provided extensibility and accommodated the addition of new features. Overall, the approach has proven to be useful and will form the basis for a supplement to the Digital Imaging and Communication in Medicine Standard.

CrossQuery: A Web Tool for Easy Associative Querying of Transcriptome Data

Enormous amounts of data are being generated by modern methods such as transcriptome or exome sequencing and microarray profiling. Primary analyses such as quality control, normalization, statistics and mapping are highly complex and need to be performed by specialists. Thereafter, results are handed back to biomedical researchers, who are then confronted with complicated data lists. For rather simple tasks like data filtering, sorting and cross-association there is a need for new tools which can be used by non-specialists. Here, we describe CrossQuery, a web tool that enables straight forward, simple syntax queries to be executed on transcriptome sequencing and microarray datasets. We provide deep-sequencing data sets of stem cell lines derived from the model fish Medaka and microarray data of human endothelial cells. In the example datasets provided, mRNA expression levels, gene, transcript and sample identification numbers, GO-terms and gene descriptions can be freely correlated, filtered and sorted. Queries can be saved for later reuse and results can be exported to standard formats that allow copy-and-paste to all widespread data visualization tools such as Microsoft Excel. CrossQuery enables researchers to quickly and freely work with transcriptome and microarray data sets requiring only minimal computer skills. Furthermore, CrossQuery allows growing association of multiple datasets as long as at least one common point of correlated information, such as transcript identification numbers or GO-terms, is shared between samples. For advanced users, the object-oriented plug-in and event-driven code design of both server-side and client-side scripts allow easy addition of new features, data sources and data types.

Body plan innovation in treehoppers through the evolution of an extra wing-like appendage

Body plans, which characterize the anatomical organization of animal groups of high taxonomic rank, often evolve by the reduction or loss of appendages (limbs in vertebrates and legs and wings in insects, for example). In contrast, the addition of new features is extremely rare and is thought to be heavily constrained, although the nature of the constraints remains elusive. Here we show that the treehopper (Membracidae) 'helmet' is actually an appendage, a wing serial homologue on the first thoracic segment. This innovation in the insect body plan is an unprecedented situation in 250 Myr of insect evolution. We provide evidence suggesting that the helmet arose by escaping the ancestral repression of wing formation imparted by a member of the Hox gene family, which sculpts the number and pattern of appendages along the body axis. Moreover, we propose that the exceptional morphological diversification of the helmet was possible because, in contrast to the wings, it escaped the stringent functional requirements imposed by flight. This example illustrates how complex morphological structures can arise by the expression of ancestral developmental potentials and fuel the morphological diversification of an evolutionary lineage.

Biometrics and identity management for homeland security applications in Saudi Arabia

Identity is the collection of all characteristics related to an entity, be it a person, enterprise or an object. Identities allow entities to be distinguished from each other. This is what makes an identity a key component in several administrative, social and economic transactions. Identity management is important for government, communication, commerce and just about any significant societal activity. Government identity management systems are not usually static and are frequently changed with the change of time and situation. A flexible approach is needed towards the addition of new features in identity management systems. This paper analyzes different identity cards used for different purposes in the Kingdom of Saudi Arabia as a case study followed by their deficiencies. Finally, a biometric based identity management system is proposed referring to the successful and extendible identity management system of developed countries. Key words: Biometrics, security, privacy, identity management, e-ID

Main-Group and Transition-Element IRMOF Homologues

A simple two-component procedure was developed to synthesize not only classical zinc-based IRMOFs represented by MOF-5 but also the cobalt and beryllium homologues of this most prominent MOF. The procedure is the first manifestation of mirroring the IRMOF series with other metal centers taken from main-group as well as transition-metal elements. Because of the existence of many suitable precursors, the procedure promises the generation of a large number of IRMOF homologues. Since the IRMOF series together with the MIL series is the MOF group with the largest number of representatives, the possibility of choosing the metal centers of the secondary building units from an extended set will tremendously expand the number of obtainable structures in a predictive, crystal-engineering-type way. Use of metal centers other than zinc will allow the addition of new features to the existing IRMOF structures, such as magnetic properties in the example of cobalt.

An improved method for voice pathology detection by means of a HMM-based feature space transformation

This paper presents new a feature transformation technique applied to improve the screening accuracy for the automatic detection of pathological voices. The statistical transformation is based on Hidden Markov Models, obtaining a transformation and classification stage simultaneously and adjusting the parameters of the model with a criterion that minimizes the classification error. The original feature vectors are built up using classic short-term noise parameters and mel-frequency cepstral coefficients. With respect to conventional approaches found in the literature of automatic detection of pathological voices, the proposed feature space transformation technique demonstrates a significant improvement of the performance with no addition of new features to the original input space. In view of the results, it is expected that this technique could provide good results in other areas such as speaker verification and/or identification.

Effort modeling and programmer participation in open source software projects

This paper develops models for programmer participation and effort estimation in open source software projects and employs the results to assess the efficiency of open source software creation. Successful development of such models will be important for decision makers of various kinds. We propose hypotheses based on a prior case study on manpower function and effort modeling. A large data set retrieved from a project repository is used to test these hypotheses. The main results are that if Norden–Rayleigh-based approaches are used, they need to be complemented in order to account for the addition of new features during a product life cycle, and that programmer-participation based effort models result in distinctly lower estimations of effort than those based on output metrics, such as lines of code.

Dynamic Optimization of Software Enhancement Effort

As the competition in the software development business grows fiercer, the features provided in the software become more and more important. With the growing popularity of open source software and the advent of new software delivery models, such as software-as-a-service, the traditional software vendors cannot compete on price in the long run. Therefore, they need to compete by increasing the number of features provided to customers. Moreover, the new entrants and the open source software vendors also need to provide increased number of features continuously in order to penetrate the market. Hence, these software firms need to invest judiciously in the software enhancement effort such that their revenue is maximized at the minimum possible cost. In addition, this strategy should be dynamic in order to capture the dynamic nature of the market. Therefore, we propose a dynamic optimization approach to obtain the optimal software enhancement effort over time. In this paper, we consider the value of adding more features as well as the impact of more bugs introduced while adding new features. Most of the past literature ignore the fact that the value of adding more features is not realized immediately by users. Therefore, we consider that there is a lag between the addition of new features and the increase in system's value. We also present several interesting managerial insights that can be used by software vendors to efficiently allocate resources based on the values of related parameters.

E-Portfolios for Developing Transferable Skills in a Freshman Engineering Course

Reflective thinking and learning skills are essential for engineers in the knowledge economy. This paper describes an approach to develop these and other transferable skills through individual and collaborative reflective learning using open-source software. The learning activities and an open-source e-portfolio system called Dotfolio were tested by freshman engineering students. Findings from a survey-based study, which investigated students' beliefs about reflective learning and their expectations and experiences related to the task and open-source tool, are reported. From the beginning of the semester the students understood the significance of reflective learning and chose to work with the tool. However, they were less positive about the collaboration with peers during this activity. At the end of the semester, students were significantly more positive about the tool, but even more negative about the collaboration. The main problems encountered by the tutors and learners were plagiarism and a tension between the privacy of students' reflections and knowledge sharing. The open-source modular architecture allowed for the use of student and tutor feedback for the addition of new features that addressed their concerns.

An Introduction to XBRL

XBRL, the eXtensible Business Reporting Language, is an open standards-based reporting system being built to accommodate the electronic preparation and exchange of business reports around the world. XBRL is all about the electronic tagging of data. It has been compared to the introduction of bar-coding and to the introduction of the ISBN number for books. While financial data is an obvious choice for electronic tagging, all data can be tagged. XBRL is an extension of XML, the eXtensible Markup Language. An extensible language means one that is designed to easily allow the addition of new features at a later date. As might be expected, the rules, or specifications, for these languages need to be managed so as to allow consistency in their development. The goal of XBRL is to develop a standard set of XML-type tags that can be used to create instance documents that can be then presented in a variety of formats. XBRL is not trying to set new accounting standards; it is attempting to standardise the XML-based tags that are used in business reporting so that the business reports prepared by organisations can be more easily compared and collated for regulatory and other purposes.

A Rule-Based Approach to Framework Evolution.

Framework development is very expensive, not only because of the intrinsic difficulty related to capturing the domain knowledge, but also because of the lack of appropriate methods and techniques to support the evolution of the framework architecture. In this context, we introduce the concept of extension rules. Extension rules allow the addition of new features into the framework design, making sure the consistency with the applications previously instantiated. We propose the use of extension rules in combination with the refactoring approach to support framework evolution. In addition, we propose a methodology to prove the correctness of evolution processes. The approach is illustrated through Avestruz, a framework for web searching.