PDB-Explorer: a web-based interactive map of the protein data bank in shape space

Background The RCSB Protein Data Bank (PDB) provides public access to experimentally determined 3D-structures of biological macromolecules (proteins, peptides and nucleic acids). While various tools are available to explore the PDB, options to access the global structural diversity of the entire PDB and to perceive relationships between PDB structures remain very limited. Methods A 136-dimensional atom pair 3D-fingerprint for proteins (3DP) counting categorized atom pairs at increasing through-space distances was designed to represent the molecular shape of PDB-entries. Nearest neighbor searches examples were reported exemplifying the ability of 3DP-similarity to identify closely related biomolecules from small peptides to enzyme and large multiprotein complexes such as virus particles. The principle component analysis was used to obtain the visualization of PDB in 3DP-space. Results The 3DP property space groups proteins and protein assemblies according to their 3D-shape similarity, yet shows exquisite ability to distinguish between closely related structures. An interactive website called PDB-Explorer is presented featuring a color-coded interactive map of PDB in 3DP-space. Each pixel of the map contains one or more PDB-entries which are directly visualized as ribbon diagrams when the pixel is selected. The PDB-Explorer website allows performing 3DP-nearest neighbor searches of any PDB-entry or of any structure uploaded as protein-type PDB file. All functionalities on the website are implemented in JavaScript in a platform-independent manner and draw data from a server that is updated daily with the latest PDB additions, ensuring complete and up-to-date coverage. The essentially instantaneous 3DP-similarity search with the PDB-Explorer provides results comparable to those of much slower 3D-alignment algorithms, and automatically clusters proteins from the same superfamilies in tight groups. Conclusion A chemical space classification of PDB based on molecular shape was obtained using a new atom-pair 3D-fingerprint for proteins and implemented in a web-based database exploration tool comprising an interactive color-coded map of the PDB chemical space and a nearest neighbor search tool. The PDB-Explorer website is freely available at www.​cheminfo.​org/​pdbexplorer and represents an unprecedented opportunity to interactively visualize and explore the structural diversity of the PDB.

Improving Pediatric Basic Life Support Performance Through Blended Learning With Web-Based Virtual Patients: Randomized Controlled Trial

BACKGROUND E-learning and blended learning approaches gain more and more popularity in emergency medicine curricula. So far, little data is available on the impact of such approaches on procedural learning and skill acquisition and their comparison with traditional approaches. OBJECTIVE This study investigated the impact of a blended learning approach, including Web-based virtual patients (VPs) and standard pediatric basic life support (PBLS) training, on procedural knowledge, objective performance, and self-assessment. METHODS A total of 57 medical students were randomly assigned to an intervention group (n=30) and a control group (n=27). Both groups received paper handouts in preparation of simulation-based PBLS training. The intervention group additionally completed two Web-based VPs with embedded video clips. Measurements were taken at randomization (t0), after the preparation period (t1), and after hands-on training (t2). Clinical decision-making skills and procedural knowledge were assessed at t0 and t1. PBLS performance was scored regarding adherence to the correct algorithm, conformance to temporal demands, and the quality of procedural steps at t1 and t2. Participants' self-assessments were recorded in all three measurements. RESULTS Procedural knowledge of the intervention group was significantly superior to that of the control group at t1. At t2, the intervention group showed significantly better adherence to the algorithm and temporal demands, and better procedural quality of PBLS in objective measures than did the control group. These aspects differed between the groups even at t1 (after VPs, prior to practical training). Self-assessments differed significantly only at t1 in favor of the intervention group. CONCLUSIONS Training with VPs combined with hands-on training improves PBLS performance as judged by objective measures.

Evaluation of web-based resources for pregnant and parenting teens

Current teen pregnancy and repeat pregnancy rates reveal that there is a pressing need for comprehensive care for pregnant and parenting teens to address their unique needs. The Internet has become a source of various types of information and as a result, several efforts have begun to assess the quality of health information provided on websites. The objective of this study was to assess the functionality and quality of websites containing health information and resources for pregnant and parenting teens. The three most widely used search engines currently: Google, MSN, and Yahoo were searched using three general search terms “teen pregnancy”, “pregnant teen”, and “teen parent”. The first 5 pages of each search were reviewed and categorized to yield 12 websites which met inclusion criteria for content evaluation. The 12 websites were rated using a pre-existing instrument encompassing two domains: functionality and content analysis. Within the functionality domain, this sample highlighted the need to improve accessibility and credibility for the target population. The content analysis revealed that among the topics which are recommended for pregnant and parenting teens, the topics most commonly covered were mental health and primary and preventive health care. The majority of websites neglected sexual health topics including STI’s and family planning. This study provides the first glimpse into health information and resources for pregnant and parenting teens on the Internet. Researchers, health care providers, social workers, health educators, and website sponsors can use these results to maintain and recommend websites which offer easily accessible, accurate, and practical information for pregnant and parenting teens.^

Air Force web-based preventive health assessement alcohol screening effectiveness using the Alcohol Use Disorders Identification Tool (AUDIT)

Alcohol consumption has a long-standing tradition in the United States Air Force (USAF). From squadron bars to officers and enlisted clubs, alcohol has been used in social settings to increase morale and also as a way to help decrease the stress of military operations. Surveys have demonstrated that the USAF has more than double the percentage of heavy drinkers than the US population. More than one-third of the Air Force reports binge drinking in the last month while only six percent of the nation reports the same consumption pattern.^ However, alcohol has a significant harmful health effect if consumed in excess. As part of an overall prevention and treatment program aimed at curbing the harmful effects of alcohol consumption, the USAF uses the Alcohol Use Disorder Identification Test (AUDIT) to screen for high-risk alcohol consumption patterns before alcohol disorder and disability occur. All Air Force active-duty members are required to complete a yearly Preventive Health Assessment questionnaire. Various health topics are included in this questionnaire including nutrition, exercise, tobacco use, family history, mental health and alcohol use. While this questionnaire has been available in a web-based format for several years, mandatory use was not implemented until 2009.^ Although the AUDIT was selected due to its effectiveness in assessing high-risk alcohol consumption in other populations, its effectiveness in the Air Force population had not been studied previously. In order to assess the sensitivity, specificity, and positive predictive value of this screening tool, the Air Force Web-based Preventive Health Assessment alcohol screening results were compared to whether any alcohol-related diagnosis was made from January 1, 2009 to March 31, 2010.^ While the AUDIT has previously been shown to have a high sensitivity and specificity, the Air Force screening values were 27.9% and 93.0% respectively. Positive predictive value was only 4.9%. With the screening statistics found, less than one-third of those having an alcohol disorder will be found with this screening tool and only 1 out of 20 Airmen who require further evaluation actually have an alcohol-related diagnosis.^

Evaluation of web-based resources for HIV+ youth

Given current rates of the Human Immunodeficiency Virus (HIV) in youth ages 15–24, comprehensive care is imperative in order to manage the virus and to prevent further transmission. In the past decade, the Internet has become an immensely popular source for information, including health information. Due to the increase in Internet use for this purpose, the assessment of the quality, accuracy, and timeliness of health information on the Internet is necessary since the information delivered may not be current or accurate. The purpose of this study was to determine the quantity and quality of websites containing health information and resources directed specifically towards HIV positive youth. Three general search terms, “HIV + teens”, “HIV teens info”, and “HIV infected teens,” were searched using the current top three search engines: Google, Yahoo!, and MSN/Bing. The first hundred hits of each search were then categorized by type of website. The examination of the search results yielded 7 sites that met the inclusion criteria. These sites were consequently evaluated on functionality and content using an adapted version of a pre-existing instrument. The functionality analysis revealed that no websites that contained self management information were dedicated specifically to HIV positive youth. The content analysis showed that the sites chosen for evaluation were mostly consistent with the guidelines provided by the Department of Health and Human Services. The most discussed topics in the sites included the importance of safer sexual behavior, HIV counseling, partner notification, safer behavior choices, such as condom use, and mental health. These results highlight the need for the development of accessible websites that contain accurate information targeting youth infected with HIV. This study provides a snapshot of the available web-based resources and health information for HIV positive youth, and is relevant for health educators, care providers, researchers, and others intervening with HIV+ youth. ^

Implementing and evaluating a Web -based close call reporting system at an urban hospital

Medical errors and close calls are pervasive in health care. It is hypothesized that the causes of close calls are the same as for medical errors; therefore learning about close calls can help prevent errors and increase patient safety. Yet despite efforts to encourage close call reporting, close calls as well as medical errors are under-reported in health care. The purpose of this dissertation was to implement and evaluate a web-based anonymous close call reporting system in three units at an urban hospital. ^ The study participants were physicians, nurses and medical technicians (N = 187) who care for patients in the Medical Intermediate Care Unit, the Surgical Intermediate Care Unit, and the Coronary Catheterization Laboratory in the hospital. We provided educational information to the participants on how to use the system and e-mailed and delivered paper reminders to report to the participants throughout the 19-month project. We surveyed the participants at the beginning and at the end of the study to assess their attitudes and beliefs regarding incident reporting. We found that the majority of the health care providers in our study are supportive of incident reporting in general but in practice very few had actually reported an error or a close call, semi-structured interview 20 weeks after we made the close call reporting system available. The purpose of the interviews was to further assess the participants' attitudes regarding incident reporting and the reporting system. Our findings suggest that the health care providers are supportive of medical error reporting in general, but are not convinced of the benefit of reporting close calls. Barriers to close call reporting cited include lack of time, heavy workloads, preferring to take care of close calls "on the spot", and not seeing the benefits of close call reporting. Consequently only two = close calls were reported via the system by two separate caregivers during the project. ^ The findings suggest that future efforts to increase close call reporting must address barriers to reporting, especially the belief among care givers that it is not worth taking time from their already busy schedules to report close calls. ^

Web-based Biodiversity Citizen Science Database (assembled 2012)

The collective impact of humans on biodiversity rivals mass extinction events defining Earth's history, but does our large population also present opportunities to document and contend with this crisis? We provide the first quantitative review of biodiversity-related citizen science to determine whether data collected by these projects can be, and are currently being, effectively used in biodiversity research. We find strong evidence of the potential of citizen science: within projects we sampled (n = 388), ~1.3 million volunteers participate, contributing up to US Dollar 2.5 billion in-kind annually. These projects exceed most federally-funded studies in spatial and temporal extent, and collectively they sample a breadth of taxonomic diversity. However, only 12% of the 388 projects surveyed obviously provide data to peer-reviewed scientific articles, despite the fact that a third of these projects have verifiable, standardized data that are accessible online. Factors influencing publication included project spatial scale and longevity and having publically available data, as well as one measure of scientific rigor (taxonomic identification training). Because of the low rate at which citizen science data reach publication, the large and growing citizen science movement is likely only realizing a small portion of its potential impact on the scientific research community. Strengthening connections between professional and non-professional participants in the scientific process will enable this large data resource to be better harnessed to understand and address global change impacts on biodiversity.

Competence Monitoring in Project Teams by using Web based portfolio management systems

This paper reports a learning experience related to the acquisition of project management competences. Students from three different universities and backgrounds, cooperate in a common project that drives the learning-teaching process. Previous related works on this initiative have already evaluated the goodness of this multidisciplinary, project-based learning approach in the context of a new educative paradigm. Yet the innovative experience has allowed the authors to define a rubric in order to measure specific competences in project management. The study shows the rubric’s main aspects as well as competence acquisition evaluation alternatives, based in the metrics defined. Key indicators and specific reports obtained from data base fields in the web tool will support this work. As a result, new competences can be assessed, such ones like teamwork, problem solving, communication and leadership. Final goal is to provide an overall competence map to the students at the same time they improve their skills.

Web-based education in Spanish Universities. A Comparison of Open Source E-Learning Platforms

Web-based education or „e-learning‟ has become a critical component in higher education for the last decade, replacing other distance learning methods, such as traditional computer training or correspondence learning. The number of university students who take on-line courses is continuously increasing all over the world. In Spain, nearly a 90% of the universities have an institutional e-learning platform and over 60% of the traditional on-site courses use this technology as a supplement to the traditional face-to-face classes. This new form of learning allows the disappearance of geographical barriers and enables students to schedule their own learning process, among some other advantages. On-line education is developed through specific software called „e-learning platform‟ or „virtual learning environment‟ (VLE). A considerable number of web-based tools to deliver distance courses are currently available. Open source software packages such as Moodle, Sakai, dotLRN or Dokeos are the most commonly used in the virtual campuses of Spanish universities. This paper analyzes the possibilities that virtual learning environments provide university teachers and learners and offers a technical comparison among some of the most popular e-learning learning platforms.

A Multingual Web-based Educational System for Professional Musicians

This paper presents the main results of the eContent HARMOS project. The project has developed a webbased educational system for professional musicians. The main idea of the project consists of recording master classes taught by highly recognised maestros and annotate this multimedia material using an educational musical taxonomy and automatic annotation tools. Users of the system access a multi-criteria search engine that allows them to find and play video segments according to a combination of criteria, which include instrument, teacher, composer, composition, movement and pedagogical concept. In order to preserve teachers and students rights, a DRM and protection system has been developed. The system is being publicly exploited. This model preserves musical heritage, since these valuable master classes are usually not recorded and it also provides a sustainable model for musical institutions.

A Web-based Support System for Providing Effective Monitoring, Feedback and Evaluation in Project Management Education

This work introduces a web-based learning environment to facilitate learning in Project Management. The proposed web-based support system integrates methodological procedures and information systems, allowing to promote learning among geographically-dispersed students. Thus, students who are enrolled in different universities at different locations and attend their own project management courses, share a virtual experience in executing and managing projects. Specific support systems were used or developed to automatically collect information about student activities, making it possible to monitor the progress made on learning and assess learning performance as established in the defined rubric.

Web based interactive educational software introducing semiconductor laser dynamics: Sound Of Lasers (SOL)

In this work, educational software for intuitive understanding of the basic dynamic processes of semiconductor lasers is presented. The proposed tool is addressed to the students of optical communication courses, encouraging self consolidation of the subjects learned in lectures. The semiconductor laser model is based on the well known rate equations for the carrier density, photon density and optical phase. The direct modulation of the laser is considered with input parameters which can be selected by the user. Different options for the waveform, amplitude and frequency of thpoint. Simulation results are plotted for carrier density and output power versus time. Instantaneous frequency variations of the laser output are numerically shifted to the audible frequency range and sent to the computer loudspeakers. This results in an intuitive description of the “chirp” phenomenon due to amplitude-phase coupling, typical of directly modulated semiconductor lasers. In this way, the student can actually listen to the time resolved spectral content of the laser output. By changing the laser parameters and/or the modulation parameters,consequent variation of the laser output can be appreciated in intuitive manner. The proposed educational tool has been previously implemented by the same authors with locally executable software. In the present manuscript, we extend our previous work to a web based platform, offering improved distribution and allowing its use to the wide audience of the web.

Evaluating a web-based clinical decision support system for language disorders screening in a nursery school

Background: Early and effective identification of developmental disorders during childhood remains a critical task for the international community. The second highest prevalence of common developmental disorders in children are language delays, which are frequently the first symptoms of a possible disorder. Objective: This paper evaluates a Web-based Clinical Decision Support System (CDSS) whose aim is to enhance the screening of language disorders at a nursery school. The common lack of early diagnosis of language disorders led us to deploy an easy-to-use CDSS in order to evaluate its accuracy in early detection of language pathologies. This CDSS can be used by pediatricians to support the screening of language disorders in primary care. Methods: This paper details the evaluation results of the ?Gades? CDSS at a nursery school with 146 children, 12 educators, and 1 language therapist. The methodology embraces two consecutive phases. The first stage involves the observation of each child?s language abilities, carried out by the educators, to facilitate the evaluation of language acquisition level performed by a language therapist. Next, the same language therapist evaluates the reliability of the observed results. Results: The Gades CDSS was integrated to provide the language therapist with the required clinical information. The validation process showed a global 83.6% (122/146) success rate in language evaluation and a 7% (7/94) rate of non-accepted system decisions within the range of children from 0 to 3 years old. The system helped language therapists to identify new children with potential disorders who required further evaluation. This process will revalidate the CDSS output and allow the enhancement of early detection of language disorders in children. The system does need minor refinement, since the therapists disagreed with some questions from the CDSS knowledge base (KB) and suggested adding a few questions about speech production and pragmatic abilities. The refinement of the KB will address these issues and include the requested improvements, with the support of the experts who took part in the original KB development. Conclusions: This research demonstrated the benefit of a Web-based CDSS to monitor children?s neurodevelopment via the early detection of language delays at a nursery school. Current next steps focus on the design of a model that includes pseudo auto-learning capacity, supervised by experts.