Technical development of PubMed Interact: an improved interface for MEDLINE/PubMed searches

BACKGROUND: The project aims to create an alternative search interface for MEDLINE/PubMed that may provide assistance to the novice user and added convenience to the advanced user. An earlier version of the project was the 'Slider Interface for MEDLINE/PubMed searches' (SLIM) which provided JavaScript slider bars to control search parameters. In this new version, recent developments in Web-based technologies were implemented. These changes may prove to be even more valuable in enhancing user interactivity through client-side manipulation and management of results. RESULTS: PubMed Interact is a Web-based MEDLINE/PubMed search application built with HTML, JavaScript and PHP. It is implemented on a Windows Server 2003 with Apache 2.0.52, PHP 4.4.1 and MySQL 4.1.18. PHP scripts provide the backend engine that connects with E-Utilities and parses XML files. JavaScript manages client-side functionalities and converts Web pages into interactive platforms using dynamic HTML (DHTML), Document Object Model (DOM) tree manipulation and Ajax methods. With PubMed Interact, users can limit searches with JavaScript slider bars, preview result counts, delete citations from the list, display and add related articles and create relevance lists. Many interactive features occur at client-side, which allow instant feedback without reloading or refreshing the page resulting in a more efficient user experience. CONCLUSION: PubMed Interact is a highly interactive Web-based search application for MEDLINE/PubMed that explores recent trends in Web technologies like DOM tree manipulation and Ajax. It may become a valuable technical development for online medical search applications

Some mechanisms leading to underdispersion : Old and new proposals

Altres ajuts: acords transformatius de la UABIn statistical modeling, it is important to know the mechanisms that cause underdispersion. Several mechanisms that lead to underdispersed count distributions are revisited from new perspectives, and new ones are introduced. These include procedures based on the number of arrivals in arrival processes, such as renewal and pure birth processes and steady-state distributions of birth-death processes, like queues with state-dependent service rates. Weighted Poisson and other well-known underdispersed distributions are also related to birth-death processes. Classical and variable binomial thinning mechanisms are also viewed as important procedures for generating underdispersed distributions, which can also generate bivariate count distributions with negative correlation. Some example applications are shown, one of which is related to Biodosimetry

SLIM: an alternative Web interface for MEDLINE/PubMed searches – a preliminary study

BACKGROUND: With the rapid growth of medical information and the pervasiveness of the Internet, online search and retrieval systems have become indispensable tools in medicine. The progress of Web technologies can provide expert searching capabilities to non-expert information seekers. The objective of the project is to create an alternative search interface for MEDLINE/PubMed searches using JavaScript slider bars. SLIM, or Slider Interface for MEDLINE/PubMed searches, was developed with PHP and JavaScript. Interactive slider bars in the search form controlled search parameters such as limits, filters and MeSH terminologies. Connections to PubMed were done using the Entrez Programming Utilities (E-Utilities). Custom scripts were created to mimic the automatic term mapping process of Entrez. Page generation times for both local and remote connections were recorded. RESULTS: Alpha testing by developers showed SLIM to be functionally stable. Page generation times to simulate loading times were recorded the first week of alpha and beta testing. Average page generation times for the index page, previews and searches were 2.94 milliseconds, 0.63 seconds and 3.84 seconds, respectively. Eighteen physicians from the US, Australia and the Philippines participated in the beta testing and provided feedback through an online survey. Most users found the search interface user-friendly and easy to use. Information on MeSH terms and the ability to instantly hide and display abstracts were identified as distinctive features. CONCLUSION: SLIM can be an interactive time-saving tool for online medical literature research that improves user control and capability to instantly refine and refocus search strategies. With continued development and by integrating search limits, methodology filters, MeSH terms and levels of evidence, SLIM may be useful in the practice of evidence-based medicine

Inspiring students to pursue science: a program evaluation of Pitt summer science outreach

Elementary and middle school children in low-income communities often do not receive engaging science curriculum and also role models for careers in science, resulting in a lack of interest in science and lower rates of students who pursue scientific careers. Pitt Summer Science Outreach is a summer camp that brings science education to students in grades 4 through 6 at various underserved YMCA/YWCA locations in the city of Pittsburgh. The camp is offered by the Clinical and Translational Science Institute at the University of Pittsburgh and brings together scientists, college student mentors, and uses sustained experiments to provide a positive, engaging, and memorable experience with science. For 2013, the camp had two curricula: Science of Nutrition and Exercise and Laboratory in Your Bedroom. The goal of the summer program is to inspire a lifelong interest in science in the elementary school students who attend. The program was evaluated using semi-structured interviews with all students who attended to measure participants’ comfort with science. In addition, the evaluation team used a social networking activity to measure with whom the participants were discussing camp, and an art activity inspired by the creative painting and writing “Visual Voices” methodology to assess participants’ favorite activities. Several themes emerged from the evaluation. We documented that the students were engaged in camp activities, enjoyed hands-on learning, and desired to return to the camp the following year. The social networking activity showed that participants were discussing camp with family and friends who did not attend camp. Finally, participants enthusiastically enjoyed the curricula as determined by the evaluation. A number of the students expressed that they felt more confident in their ability to do science and may have an interest in pursuing career in a scientific field. The public health significance of Pitt Summer Science Outreach is its effect on the social determinants of health. By providing engaging science education in underserved communities, the program enables participants the means to improve their health outcomes and impact the conditions in which they live

An exact goodness-of-fit test based on the occupancy problems to study zero-inflation and zero-deflation in biological dosimetry data

The goal in biological dosimetry is to estimate the dose of radiation that a suspected irradiated individual has received. For that, the analysis of aberrations (most commonly dicentric chromosome aberrations) in scored cells is performed and dose response calibration curves are built. In whole body irradiation (WBI) with X- and gamma-rays, the number of aberrations in samples is properly described by the Poisson distribution, although in partial body irradiation (PBI) the excess of zeros provided by the non-irradiated cells leads, for instance, to the Zero-Inflated Poisson distribution. Different methods are used to analyse the dosimetry data taking into account the distribution of the sample. In order to test the Poisson distribution against the Zero-Inflated Poisson distribution, several asymptotic and exact methods have been proposed which are focused on the dispersion of the data. In this work, we suggest an exact test for the Poisson distribution focused on the zero-inflation of the data developed by Rao and Chakravarti (Some small sample tests of significance for a Poisson distribution. Biometrics 1956;12 : 264–82.), derived from the problems of occupancy. An approximation based on the standard Normal distribution is proposed in those cases where the computation of the exact test can be tedious. A Monte Carlo Simulation study was performed in order to estimate empirical confidence levels and powers of the exact test and other tests proposed in the literature. Different examples of applications based on in vitro data and also data recorded in several radiation accidents are presented and discussed. A Shiny application which computes the exact test and other interesting goodness-of-fit tests for the Poisson distribution is presented in order to provide them to all interested researchers

Estimating the real burden of disease under a pandemic situation: The SARS-CoV2 case

The present paper introduces a new model used to study and analyse the severe acute respiratory syndrome coronavirus 2 (SARS-CoV2) epidemic-reported-data from Spain. This is a Hidden Markov Model whose hidden layer is a regeneration process with Poisson immigration, Po-INAR(1), together with a mechanism that allows the estimation of the under-reporting in non-stationary count time series. A novelty of the model is that the expectation of the unobserved process's innovations is a time-dependent function defined in such a way that information about the spread of an epidemic, as modelled through a Susceptible-Infectious-Removed dynamical system, is incorporated into the model. In addition, the parameter controlling the intensity of the under-reporting is also made to vary with time to adjust to possible seasonality or trend in the data. Maximum likelihood methods are used to estimate the parameters of the model

Evaluation of txt2MEDLINE and Development of Short Messaging Service–Optimized, Clinical Practice Guidelines in Botswana

Objective: Currently clinicians in sub-Saharan Africa have limited access to the Internet, whereas mobile phone access and use is extensive. The University of Pennsylvania in collaboration with the National Library of Medicine launched txt2MEDLINE, a short messaging service (SMS) query of PubMed/MEDLINE, and SMS-optimized clinical guidelines in Botswana. The objective of this project was to establish and evaluate the utility of these tools for clinicians in Botswana. Materials and Methods: A local server was established at the University of Botswana that allowed clinicians to send queries and receive results via local (in-country) SMS text messaging on any type of cellular phone. The queries sent via txt2MEDLINE were returned as abbreviated “the bottom line” summaries of abstracts. The 2007 Botswana Treatment Guide was converted into a format that can be queried by SMS. Various types of healthcare workers were recruited to use and evaluate these services. Results: Seventy-six healthcare workers attended training sessions for these services. In the preusage survey, most said they would use the services daily or weekly. During a 4-week trial period, use of these services dropped off dramatically. Participant feedback was collected and indicated that improvements in ease of use would increase the usage. Conclusions: This pilot project enables clinicians to query and receive PubMed abstract summaries and country-specific clinical guidelines using mobile phones. Feedback offers insight on how to improve this technology so that it can be adopted for long-term use. With further adjustments, these resources may provide an effective working model for other countries where limited Internet access impedes upon patient care

Estimated Covid-19 burden in Spain: ARCH underreported non-stationary time series

Background The problem of dealing with misreported data is very common in a wide range of contexts for different reasons. The current situation caused by the Covid-19 worldwide pandemic is a clear example, where the data provided by official sources were not always reliable due to data collection issues and to the high proportion of asymptomatic cases. In this work, a flexible framework is proposed, with the objective of quantifying the severity of misreporting in a time series and reconstructing the most likely evolution of the process. Methods The performance of Bayesian Synthetic Likelihood to estimate the parameters of a model based on AutoRegressive Conditional Heteroskedastic time series capable of dealing with misreported information and to reconstruct the most likely evolution of the phenomenon is assessed through a comprehensive simulation study and illustrated by reconstructing the weekly Covid-19 incidence in each Spanish Autonomous Community. Results Only around 51% of the Covid-19 cases in the period 2020/02/23–2022/02/27 were reported in Spain, showing relevant differences in the severity of underreporting across the regions. Conclusions The proposed methodology provides public health decision-makers with a valuable tool in order to improve the assessment of a disease evolution under different scenarios.Research funded by Fundación MAPFRE. This work was partially supported by grant RTI2018-096072-B-I00 from the Spanish Ministry of Science and Innovation and by the Spanish State Research Agency, through the Severo Ochoa and María de Maeztu Program for Centers and Units of Excellence in R&D (CEX2020–001084-M). A.F-F acknowledges Agencia Estatal de Investigación for the financial support IJC2020-045188I/AEI/10.13039/501100011033. AC was partially financed by PID2021-123733NB-I00 (Ministerio de Ciencia e Innovación, Spain). AC and AA were partially supported by Project “EcoDep” CY-AAP2020-0000000013 (“Investissements d’Avenir” ANR-16-IDEX-0008, France).Peer ReviewedPostprint (published version