Code Documentation Research Articles

A Content Analysis of Images of Novice Teacher Induction: First-Semester Themes

The powerful nature of novice teachers’ experiences in their first years of teaching has been well documented. However, the variance in novices’ initial immersion in the school environment is largely dependent on perceived personal and professional support as well as the environmental inducements that lend to novice teachers’ success in the classroom. For the purposes of this study, 72 participating novices, who were participants in an alternative certification program, drew representations of their current teaching environments. Of the 72 initial participants’ pictures, 58 were used in this content analysis. The interrater analysis involving multiple documentation of codes between and among researches, revealed five themes from the novices’ pictures: (a) concerns about students, (b) overwhelmed and struggling, (c) relationships with others, (d) concerns about education quality and excessive accountability, and (e) issues with administration. Implications are provided.

How to put plant root uptake into a soil water flow model: A documentation with complete computer code.

The need for improved crop water use efficiency calls for flexible modelingplatforms to implement new ideas in plant root uptake and its regulation mechanisms. Thispaper documents the details of modifying a soil infiltration and redistribution model to include(a) dynamic root growth, (b) non-uniform root distribution and water uptake, (c) the effect ofwater stress on plant water uptake, and (d) soil evaporation. The paper also demonstratesstrategies of using the modified model to simulate soil water dynamics and plant transpirationconsidering different sensitivity of plants to soil dryness and different mechanisms of rootwater uptake. In particular, the flexibility of simulating various degrees of compensateduptake (whereby plants tend to maintain potential transpiration under mild water stress)is emphasized. The paper also describes how to estimate unknown root distributionand rooting depth parameters by the use of a simulation-based searching method. Thefull documentation of the computer code will allow further applications and new development.

Atrial Fibrillation and Colonic Neoplasia in African Americans.

BackgroundColorectal cancer (CRC) and atrial fibrillation/flutter (AF) share several risk factors including increasing age and obesity. However, the association between CRC and AF has not been thoroughly examined, especially in African Americans. In this study we aimed to assess the prevalence of AF and its risk factors in colorectal neoplasia in an African American.MethodsWe reviewed records of 527 African American patients diagnosed with CRC and 1008 patients diagnosed with benign colonic lesions at Howard University Hospital from January 2000 to December 2012. A control group of 731 hospitalized patients without any cancer or colonic lesion were randomly selected from the same time and age range, excluding patients who had diagnosis of both CRC and/or adenoma. The presence or absence of AF was based upon ICD-9 code documentation. The prevalence of AF in these three groups was compared by multivariate logistic regression.ResultsThe prevalence of AF was highest among CRC patients (10%) followed by adenoma patients (7.2%) then the control group (5.4%, P for trend = 0.002). In the three groups of participants, older age (P<0.008) and heart failure (P<0.001) were significantly associated with higher risk of AF. After adjusting for these risk factors, CRC (OR: 1.4(95%CI):0.9–2.2, P = 0.2) and adenoma (OR: 1.1(95%CI):0.7–1.6, P = 0.7) were not significantly associated AF compared to control group.ConclusionsAF is highly prevalent among CRC patients; 1 in 10 patients had AF in our study. The predictors of AF in CRC was similar to that in adenoma and other patients after adjustment for potential confounders suggesting that the increased AF risk in CRC is explained by higher prevalence of AF risk factors.

Event Documentation and Transfer of Care After Severe Contrast Reactions

PurposeRadiology residencies are increasingly using clinical simulation to teach contrast reaction management. The aim of this study was to evaluate resident documentation of management and transfer of care in severe contrast reactions after a clinical simulation. MethodsAfter a high-fidelity mannequin simulation of contrast-induced anaphylactic shock, residents (n = 18) were asked to document the event in a progress note and transfer care to a receiving medical team. A total of 22 prospectively determined criteria were selected, and notes were analyzed by a blinded reviewer. ResultsNotes contained between 12 and 21 of the prospectively determined 22 criteria (54%-95%). The median number of criteria contained in a note was 16. None of the notes fulfilled all 22 criteria. However, consistent deficiencies were found in documenting prior reaction to contrast (28%) and transfer-of-care criteria (22%-44%). ConclusionsAlthough standards for the documentation of advanced cardiovascular life support codes and other emergencies have been devised, no such standards exist for documentation in the management of contrast reactions. The results of this study suggest the need to develop a standardized documentation system for severe contrast-induced reactions. Education regarding transfer of care and documentation should be emphasized during clinical simulation.

Collaborating to Create a Comprehensive Neonatal Resuscitation Form

Poster Presentation Purpose for the Program High‐quality care of the newborn at birth is critically important in obstetrics. To assess response to newborns who require extra assistance at birth, a newborn code review committee was formed in July 2012. Newborn resuscitation documentation was audited for 3 months, and it was determined the current form was a barrier to accurate documentation and care. Of the 16 indicators audited, documentation was found to be 0% to 67% complete in seven categories. The code committee searched the literature, Internet, and area hospitals to find a better documentation form. Forms found were either equal to or less comprehensive than the current form. Proposed Change To create a new form that follows the guidelines of the American Academy of Pediatrics (AAP) Neonatal Resuscitation Program to increase documentation adherence and provide documentation prompts to perform correct actions during a newborn code. The American Heart Association (AHA) Get with the Guidelines neonatal resuscitation form was used as a starting point. Content was added and removed based on team experience with newborn codes and AAP guidelines. Implementation, Outcomes, and Evaluation The new form, completed in October 2012, was taken to delivery team nurses and neonatologists for review. After suggested changes were made, the code team approved the final form, and staff members involved in newborn resuscitation were taught to use it. Health care providers began using the new form in May 2013. Neonatal resuscitation records from July through October 2013 were reviewed to identify trends and improvements after implementation of the new form. Of 16 categories audited, adherence scores increased from 88% to 100%. Nursing and medical staff expressed satisfaction and acceptance of the new form, noting ease of use and guidance through code documentation and prompts for needed actions. Audits continue to show improvement in documentation after the implementation of the form. Implications for Nursing Practice Teams should review current neonatal resuscitation forms for documentation accuracy and adherence. Revisions may be necessary to help guide practitioners through resuscitation and assist with accurate documentation.

Reimplementation and reuse of the Canegro model: From sugarcane to giant reed

Model reuse can be limited by software design, which often forces third parties to completely rewrite new versions of existing models before adapting them to new needs. This tendency removes resources from the improvement of models and from the extension of their domain, leading to the proliferation of software tools representing a variety of different implementations of the same algorithms. The component-oriented paradigm allows these limitations to be overcome, facilitating model reuse and extension. This study presents the application of component-oriented principles to the reimplementation of the sugarcane (Saccharum officinarum L.) model Canegro (DSSAT v4.5) in a framework-independent component following the BioMA architecture. The potential for reuse and extension of the component (UNIMI.Cassandra.CaneML.Canegro) is here demonstrated by its straightforward adaptation to the simulation of giant reed (Arundo donax L.), a promising energy crop that shares several morphological and physiological features with sugarcane. The new component, named UNIMI.Cassandra.CaneML.Arungro, extends UNIMI.Cassandra.CaneML.Canegro, and was effectively developed by inheriting about 70% of the sugarcane model code. The development, calibration and evaluation of the giant reed model were performed using field data collected in two experimental sites in Northern Italy between 2009 and 2012. Model performances were satisfactory, with average relative root mean square error and modelling efficiency for aboveground biomass simulation of 34.33% and 0.57, respectively. The Canegro component is distributed via a Software Development Kit that includes documentation of code and algorithms, and the source code of sample applications illustrating how to use it.

A New Graphical User Interface Generator for Economic Models and its Comparison to Existing Approaches

The paper discusses the role of Graphical User Inter-faces in economic modelling and specifically the de-velopment of a new Graphical User Interface Genera-tor for applications realized in GAMS (General Alge-braic Modelling System), a widely used Algebraic Modelling Language for (bio-)economic simulation models. It motivates the development of GGIG (Gams Graphical Interface Generator) by reviewing existing approaches. In opposite to frameworks available for environmental and Agent Based Modelling, GUI ge-nerators for more classical economic models seem to be scarce. GGIG aims at a fast development process not requiring programming skills where simple user operable controls are defined in an XML file such that GAMS based projects can add easily a GUI. It com-prises quite versatile exploitation tools for interactive reporting (tables, graphs and maps) including a ma-chine learning package plus useful utilities, e.g. to generate a HTML based GAMS code documentation or batch execution. In opposite to other approaches, GGIG strictly separates the GUI and GAMS code, but does not offer IDE functionality. Applications to CAPRI, a rather complex model, and some smaller projects seem to show that researchers without formal programming training are able to develop and modify a GUI for their models, while model users can be quickly trained in GGIG based GUIs.

Automatic Lens Distortion Correction Using One-Parameter Division Models

We present a method to automatically correct the radial distortion caused by wide-angle lenses using the distorted lines generated by the projection of 3D straight lines onto the image. Lens distortion is estimated by the division model using one parameter, which allows to state the problem into the Hough transform scheme by adding a distortion parameter to better extract straight lines from the image. This paper describes an algorithm which applies this technique, providing all the details of the design of an improved Hough transform. We perform experiments using calibration patterns and real scenes showing a strong distortion to illustrate the performance of the proposed method. Source Code The source code, the code documentation, and the online demo are accessible at the IPOL web page of this article 1 . In this page, an implementation is available for download. Compilation and usage instructions are included in the README.txt file of the archive.

An empirical study of the textual similarity between source code and source code summaries

Source code documentation often contains summaries of source code written by authors. Recently, automatic source code summarization tools have emerged that generate summaries without requiring author intervention. These summaries are designed for readers to be able to understand the high-level concepts of the source code. Unfortunately, there is no agreed upon understanding of what makes up a "good summary." This paper presents an empirical study examining summaries of source code written by authors, readers, and automatic source code summarization tools. This empirical study examines the textual similarity between source code and summaries of source code using Short Text Semantic Similarity metrics. We found that readers use source code in their summaries more than authors do. Additionally, this study finds that accuracy of a human written summary can be estimated by the textual similarity of that summary to the source code.

What's new in GSAS-II

The General Structure and Analysis Software II (GSAS-II) package is an all-new crystallographic analysis package written to replace and extend the capabilities of the universal and widely used GSAS and EXPGUI packages. GSAS-II was described in a 2013 article, but considerable work has been completed since then. This paper describes the advances, which include: rigid body fitting and structure solution modules; improved treatment for parametric refinements and equation of state fitting; and small-angle scattering data reduction and analysis. GSAS-II offers versatile and extensible modules for import and export of data and results. Capabilities are provided for users to select any version of the code. Code documentation has reached 150 pages and 17 web-tutorials are offered.

In-Hospital Cardiopulmonary Arrests in Patients With Left Ventricular Assist Devices

BackgroundBasic and advanced cardiac life support guidelines do not address resuscitation of patients with continuous-flow (CF) left ventricular assist devices (LVADs). As the population of LVAD patients increases, it becomes important to understand how to provide emergency care to such patients. Methods and ResultsWe retrospectively reviewed a consecutive series of patients with an implanted CF-LVAD who had an in-hospital cardiopulmonary arrest at our medical center from January 2011 to October 2013. We compared them with a matched cohort of patients without LVADs who had an in-hospital cardiopulmonary arrest during the same time period. Code documentation was used to determine arrest characteristics, perfusion assessment techniques, and time to cardiopulmonary resuscitation (CPR) initiation. There were 415 in-hospital arrests during the study period, and 4% (n = 16) occurred in patients with CF-LVADs. Response teams used various approaches to assess arterial perfusion, including palpation or Doppler of the arterial pulse and measurement of blood pressure by Doppler or arterial line. Nine of the 16 patients required CPR, but only 5 (56%) received CPR in <2 minutes. In the control group (n = 32) of patients without an LVAD, 22 received CPR, which was initiated within 2 minutes in all (100%) of the patients. ConclusionsCardiopulmonary arrests in LVAD patients accounted for 4% of all arrests in our center. We identified important time delays in CPR initiation, highlighting the need to develop resuscitation guidelines for this patient population.

COMENTE+: A TOOL FOR IMPROVING SOURCE CODE DOCUMENTATION USING INFORMATION RETRIEVAL

Document source code is seen as a boring time consuming task by several developers. However, a well-documented source code, allow developers to have a better visibility into what was and is being developed, helping, for example, the reuse of the code. This study presents a semi-automatic method for documentation of source code from the existing artifacts in a software project under development. The method aims to reduce developer’s workload, allowing them to work on other tasks of the project and/or ensure that the project deadlines will be met. The method, implemented in a tool, called Comente+, is capable of creating or updating comments into a source code from gathered information recovered from the project artifacts. To implement Comente+, we used an information retrieval approach. We performed some experiments with real data to validate this approach. For that, we created a special measure that estimates how well documented a source code is.

A software component implementing a library of models for the simulation of pre-harvest rice grain quality

Despite the availability of a variety of models to simulate crop growth and development, few operational approaches have been developed to assess pre-harvest quality of agricultural productions as a function of the conditions actually explored by the crop during the season. This represents a clear gap of knowledge researchers are trying to fill, in light of the evidences of a climate change-driven decline in the nutritional properties of important food crops. Rice represents the staple food for half of the world’s population, and this explains the noticeable interest in rice grain quality, because of the direct implications on the economic value of productions, on their market destination, and on food security issues. This paper presents a framework-independent .NET software library, i.e., UNIMI.CropQuality, implementing models to simulate various aspects of rice quality: amylose, protein, lipids and starch content, viscosity profile, chalkiness, cracking and head rice yield. Alternate approaches for the simulation of the same quality property are included, to allow users to select the most suitable for specific modelling studies. A case study is also presented where the library was linked to the WARM rice model and used to simulate head rice yield and the percentage incidence of cracked and milky white kernels (severely chalky) for two rice varieties in the main European rice district. RRMSE ranged between 4.33% and 6.47% for head rice yield, 21.88% and 32.18% for cracking percentage, 35.92% and 55.01% for milky white chalkiness; modelling efficiency were always positive. The component, developed according to the state-of-the-art of component-oriented software development, is released with a Software Development Kit containing help and code documentation files, as well as sample applications showing how to use the library with different crop simulators.

Clinical Challenges in Diagnosis and Management of Diabetic Kidney Disease

Diabetic kidney disease (DKD) is a major and increasing worldwide public health issue. There is a great need for implementing treatments that either prevent or significantly slow the progression of DKD. Although there have been significant improvements in management, the increasing numbers of patients with DKD illustrate that current management is not wholly adequate. The reasons for suboptimal management include the lack of early diagnosis, lack of aggressive interventions, and lack of understanding about which interventions are most successful. There are a number of challenges and controversies regarding the current management of patients with DKD. Understanding of these issues is needed in order to provide the best care to patients with DKD. This article describes some of the clinically important challenges associated with DKD: the current epidemiology and cost burden and the role of biopsy in the diagnosis of DKD. Treatment controversies regarding current pharmacologic and nonpharmacologic approaches are reviewed and recommendations based on the published literature are made.

Verifiable source code documentation in controlled natural language

Writing documentation about software internals is rarely considered a rewarding activity. It is highly time-consuming and the resulting documentation is fragile when the software is continuously evolving in a multi-developer setting. Unfortunately, traditional programming environments poorly support the writing and maintenance of documentation. Consequences are severe as the lack of documentation on software structure negatively impacts the overall quality of the software product. We show that using a controlled natural language with a reasoner and a query engine is a viable technique for verifying the consistency and accuracy of documentation and source code. Using ACE, a state-of-the-art controlled natural language, we present positive results on the comprehensibility and the general feasibility of creating and verifying documentation. As a case study, we used automatic documentation verification to identify and fix severe flaws in the architecture of a non-trivial piece of software. Moreover, a user experiment shows that our language is faster and easier to learn and understand than other formal languages for software documentation.

Reading between the lines: Source code documentation as a conservation strategy for software-based art

Conservation expertise required for software-based art varies depending on the nature and function of its components. Our focus in this study is technology, specifically related to the impact of changes and upgrades to the operating environment that can adversely impact future exhibition of software-based art. In our research to date, we found that each specific work requires individual analysis and conservation strategies due to unique technical risks. We also concluded that artist-generated source code is a primary risk for software-based works. We then devoted the next phase of our research to a closer examination of risks associated with source code. The purpose of the research reported in this article is to investigate whether examining and documenting the source code can inform conservation practice. A corollary second goal is to define relevant best practices for documenting source code for software-based art. In order to address these questions, we selected two artworks at the Museum of Modern Art for a collaborative study using students and faculty from both the Museum Studies and Computer Science departments at New York University. This collaboration helped ensure that technology skills complemented a deep understanding of art history in the museum context. We based the methodology for our study on current software engineering practices and composed diagrams and narrative documents to reflect what we found in the source code. We also relied on artist interviews to explore the requirements and goals of the system, and user manuals to assist in understanding the implementation and physical installation of the works. It was our hypothesis that once the behavior of software-based art is understood by combining a standard software engineering approach with considerations specific to artist and museum needs, conservators and programmers will be better prepared to address changes in the operating environment. Based on our experience, we found this to be true. We conclude this paper with plans for our next phase of research.

Robust Optical Flow Estimation

In this work, we describe an implementation of the variational method proposed by Brox et al. in 2004, which yields accurate optical flows with low running times. It has several benefits with respect to the method of Horn and Schunck: it is more robust to the presence of outliers, produces piecewise-smooth flow fields and can cope with constant brightness changes. This method relies on the brightness and gradient constancy assumptions, using the information of the image intensities and the image gradients to find correspondences. It also generalizes the use of continuous L 1 functionals, which help mitigate the effect of outliers and create a Total Variation (TV) regularization. Additionally, it introduces a simple temporal regularization scheme that enforces a continuous temporal coherence of the flow fields. Source Code The source code, the code documentation, and the online demo are accessible at the IPOL web page of this article 1 . In this page an implementation is available for download. This file contains two directories: one for the spatial method and another for the temporal method. The spatial method is suitable for general image sequences, while the temporal method should be used when the flow fields are known to be very continuous.

Selective Contrast Adjustment by Poisson Equation

Poisson Image Editing is a new technique permitting to modify the gradient vector field of an image, and then to recover an image with a gradient approaching this modified gradient field. This amounts to solve a Poisson equation, an operation which can be efficiently performed by Fast Fourier Transform (FFT). This paper describes an algorithm applying this technique, with two different variants. The first variant enhances the contrast by increasing the gradient in the dark regions of the image. This method is well adapted to images with back light or strong shadows, and reveals details in the shadows. The second variant of the same Poisson technique enhances all small gradients in the image, thus also sometimes revealing details and texture. Source Code The source code, the code documentation, and the online demo are accessible at the IPOL web page of this article 1 . In this page an implementation is available for download. Compilation and usage instruction are included in the README.txt file of the archive.

Analysis of Risks in Re-Engineering Software Systems

ABSTRACT Software re-engineering has become a vital field of computer science and an active research area. The nature of software re-engineering is to improve or transform existing software so it can be understood, controlled and reused as new software. Re-engineering is frequently challenged, because certain risks will threaten the project success. In this article we have described some risks and their classification what we believe to be the most important. From the analysis of risks, some mitigation techniques have been suggested from the existing literature that helps to make the re-engineering projects more beneficial. Keywords Software re-engineering, risks, mitigation, analysis. 1. INTRODUCTION Software Re-engineering is the examination, reorganization, analysis and alteration of an existing software system. It helps to system. The process of restructuring,make them more maintainable and to reconstitute it in a new form and the subsequent implementation of the modified system. This process involves in order to get the target system according to the new the restructuring or recoding of a component or all parts of legacy system without affecting its functionality [1]. Re-engineering is a combination of other processes such as reverse engineering, re-documentation, translation, and forward engineering. The main purpose is to understand the specification, design, implementation of the legacy system and then to implement its modernize form to improve its overall functionality and performance. The difficulty lies in the conceptual understanding of the legacy system. Usually requirements, design and documentation of programming code is no longer available, or is out of date, so it is not clear to the software engineer that what types of functions are to be shifted. Often the software system contains major functions that are not needed anymore, and those should not be re-coded to the new system [2]. The re-engineering process is not risk free and faces various types of risks as software engineering other approaches face. The risk identification is crucial in development and evolution of a legacy system. Risk identification is very important for effective risk assessment, risk analysis, and management and mitigation of risks. In our proposed work, the potential challenges and risks during transformation are analyzed and then categorized on the basis of severity and nature. A well monitoring technique has been described for the categorized risks. It will help a re-engineering system towards successful and easy maintenance and cost benefit with reduced risk.

Djeen (Database for Joomla!’s Extensible Engine): a research information management system for flexible multi-technology project administration

BackgroundWith the advance of post-genomic technologies, the need for tools to manage large scale data in biology becomes more pressing. This involves annotating and storing data securely, as well as granting permissions flexibly with several technologies (all array types, flow cytometry, proteomics) for collaborative work and data sharing. This task is not easily achieved with most systems available today.FindingsWe developed Djeen (Database for Joomla!’s Extensible Engine), a new Research Information Management System (RIMS) for collaborative projects. Djeen is a user-friendly application, designed to streamline data storage and annotation collaboratively. Its database model, kept simple, is compliant with most technologies and allows storing and managing of heterogeneous data with the same system. Advanced permissions are managed through different roles. Templates allow Minimum Information (MI) compliance.ConclusionDjeen allows managing project associated with heterogeneous data types while enforcing annotation integrity and minimum information. Projects are managed within a hierarchy and user permissions are finely-grained for each project, user and group.Djeen Component source code (version 1.5.1) and installation documentation are available under CeCILL license from http://sourceforge.net/projects/djeen/files and supplementary material.