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Supporting clinical practice at the bedside using wireless technology.

OBJECTIVES: Despite studies that show improvements in both standards of care and outcomes with the judicious application of clinical practice guidelines (CPGs), their clinical utilization remains low. This randomized controlled trial examined the use of a wirelessly networked mobile computer (MC) by physicians at the bedside with access to an emergency department information system, decision support tools (DSTs), and other software options. METHODS: Each of ten volunteer emergency physicians was randomized using a matched-pair design to work five shifts in standard fashion (desktop computer [DC] access) and five shifts with a wirelessly networked MC. Work pattern issues and electronic CPG/DST use were compared using end-of-shift satisfaction questionnaires and review of a CPG/DST database. Repeated-measures analysis of variance was used to examine between-shift differences. RESULTS: A total of 100 eight-hour shifts were evaluated; 99% compliance with postshift questionnaires was achieved. Using a seven-point Likert scale (MC values first), MCs were rated as being as fast (5.04 vs. 4.54; p=0.13) and convenient (5.08 vs. 4.14; p=0.07) as DCs. Overall, physicians rated MCs to be less efficient (3.18 vs. 4.30; p=0.02) but encouraged more frequent use of DSTs (4.10 vs. 3.47; p=0.03) without impacting doctor-patient communication (2.78 vs. 2.96; p=0.51). During the study period, physician use of an intranet Web application (eCPG) was more frequent during shifts assigned to the MC when compared with the DC (eCPG uses/shift, 3.6 vs. 2.0; p=0.033). CONCLUSIONS: The MC technology permitted physicians to access information at the bedside and increased the use of CPG/DST tools. According to physicians, patients appeared to accept their use of information technology to assist in decision making. Development of improved computer technology may address the major limitation of MC portability.

Computers↗

BayesFold: rational 2 degrees folds that combine thermodynamic, covariation, and chemical data for aligned RNA sequences.

BayesFold is a Web application that folds an alignment of closely related sequences and evaluates hypotheses about their shared structure. It uses Bayes's Theorem to combine information from several sources, including chemical mapping (if available), thermodynamic folding, and observed sequence variations. Its method provides a rational basis for integrating results, even when these methods conflict. On a gapped alignment of 86 tRNAPhe sequences each 77 bases long, BayesFold takes 31 sec to perform the calculations; the best structure contained 95% of the base pairs in the true structure, and the true structure was ranked second. Notably, similar results come from random samples of only 10 sequences from the alignment (running time 3 sec), suggesting that remarkably few sequences are required for good results. In contrast, folding single sequences with BayesFold produced structures 9.6 bp different, or with the Vienna package, 13.4 bp different, from the true structure. Similar results were obtained for other families of tRNAs. We especially recommend BayesFold for alignments of 3-50 closely related sequences, such as the sequence families frequently found in SELEX. In addition to providing a convenient way to explore the effects of each of the criteria on the plausibility of different structures, BayesFold also makes it easy to produce publication-quality secondary-structure graphics. The Web interface, available at http://bayes.colorado.edu/fold/, includes the flexibility to thread any of the sequences (or the consensus sequence) through any of the structures, including the one judged most probable.

Algorithms↗

Chemical effects in biological systems (CEBS) object model for toxicology data, SysTox-OM: design and application.

MOTIVATION: The CEBS data repository is being developed to promote a systems biology approach to understand the biological effects of environmental stressors. CEBS will house data from multiple gene expression platforms (transcriptomics), protein expression and protein-protein interaction (proteomics), and changes in low molecular weight metabolite levels (metabolomics) aligned by their detailed toxicological context. The system will accommodate extensive complex querying in a user-friendly manner. CEBS will store toxicological contexts including the study design details, treatment protocols, animal characteristics and conventional toxicological endpoints such as histopathology findings and clinical chemistry measures. All of these data types can be integrated in a seamless fashion to enable data query and analysis in a biologically meaningful manner. RESULTS: An object model, the SysBio-OM (Xirasagar et al., 2004) has been designed to facilitate the integration of microarray gene expression, proteomics and metabolomics data in the CEBS database system. We now report SysTox-OM as an open source systems toxicology model designed to integrate toxicological context into gene expression experiments. The SysTox-OM model is comprehensive and leverages other open source efforts, namely, the Standard for Exchange of Nonclinical Data (http://www.cdisc.org/models/send/v2/index.html) which is a data standard for capturing toxicological information for animal studies and Clinical Data Interchange Standards Consortium (http://www.cdisc.org/models/sdtm/index.html) that serves as a standard for the exchange of clinical data. Such standardization increases the accuracy of data mining, interpretation and exchange. The open source SysTox-OM model, which can be implemented on various software platforms, is presented here. AVAILABILITY: A universal modeling language (UML) depiction of the entire SysTox-OM is available at http://cebs.niehs.nih.gov and the Rational Rose object model package is distributed under an open source license that permits unrestricted academic and commercial use and is available at http://cebs.niehs.nih.gov/cebsdownloads. Currently, the public toxicological data in CEBS can be queried via a web application based on the SysTox-OM at http://cebs.niehs.nih.gov CONTACT: xirasagars@saic.com SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Computational Biology↗

Communication in science.

Science must have a common language. For centuries, Latin language carried out this job, but the progress in computer technology and internet world through the last 20 years, began to produce a new language with the new century; the computer language. The information masses, which need data language standardization, are the followings; Digital libraries and medical education systems, Consumer health informatics, Medical education systems, World Wide Web Applications, Database systems, Medical language processing, Automatic indexing systems, Image processing units, Telemedicine, New Generation Internet (NGI).

Communication↗

[New communication media for ophthalmology].

BACKGROUND: The use of high-tech communication is undoubtedly growing and has become established in almost all sciences and research fields. This article surveys the possibilities for scientific data-exchange via the Internet, the world's largest computer network. METHODS: An introduction is given to network as a whole, its history and structure, and the hardware and software required. Examples are provided to describe the basic services on the Internet with special emphasis on World wide web applications. CONCLUSIONS: The paper indicates that the Internet has a vast potential for providing almost unlimited information of relevance to users. By using the Internet and its resources, modern ophthalmological research will become more effective and successful.

Computer Communication Networks↗

CONCOR, an initiative towards a national registry and DNA-bank of patients with congenital heart disease in the Netherlands: rationale, design, and first results.

INTRODUCTION: Survival of patients with congenital heart disease has dramatically improved after surgical repair became available 40 years ago. Instead of a mortality of 85% during childhood following the natural course, over 85% of these infants are now expected to reach adulthood. However, data on long-term outcome is scarce due to the lack of large, national registries. Moreover, little is known about the genetic basis of congenital heart defects. In 2000, the Interuniversity Cardiology Institute of the Netherlands and the Netherlands Heart Foundation have taken the initiative to develop a national registry and DNA-bank of patients with congenital heart disease in the Netherlands named CONCOR. OBJECTIVES: The aims of the CONCOR project are to facilitate investigation of the prevalence and long-term outcome of specific congenital heart defects and their treatment, to develop an efficient organisational structure for the improvement of healthcare for patients with congenital heart disease, and to allow investigation of the molecular basis of congenital heart defects. METHODS: After informed consent, research nurses enter data of participating patients into the CONCOR database using a web application. Data is transferred over the Internet via a secure connection. About 20 ml blood is withdrawn from the patient, and the DNA is isolated and stored. From each participating patient family history on congenital heart disease is obtained. RESULTS: Within two and a half years more than 4200 patients have agreed to participate. More than 99% of the patients that were asked have given their consent to participate in CONCOR. From 60% of these patients DNA has already been obtained. Mean age of the patients included is 34 years; more than 85% of the patients are younger than 45 years. Late complications occur frequently and the incidence increases with advancing age. 18% of the patients are known with supraventricular or ventricular arrhythmias. 2% of the included patients suffered a cerebrovascular accident, 139 (3%) had endocarditis. 6% of the patients has pulmonary hypertension or Eisenmenger syndrome. More than 15% of the patients reported an affected family member with congenital heart disease in the first, second, or third degree. 6% has an affected first-degree relative, and 4% a second-degree relative. Already 10 research projects have started using the CONCOR data and DNA. CONCLUSION: The population of patients with congenital heart disease is young and rapidly growing. Late complications occur frequently and the incidence increases with advances age. The CONCOR registry and DNA-bank facilitates research on prevalence and long-term outcome and allows investigation of the molecular basis of congenital heart disease.

Academies and Institutes↗

Interactive simulation system for artificial ventilation on the internet: virtual ventilator.

OBJECTIVE: To develop an interactive simulation system "virtual ventilator" that demonstrates the dynamics of pressure and flow in the respiratory system under the combination of spontaneous breathing, ventilation modes, and ventilator options. The simulation system was designed to be used by unexperienced health care professionals as a self-training tool. METHODS: The system consists of a simulation controller and three modules: respiratory, spontaneous breath, and ventilator. The respiratory module models the respiratory system by three resistances representing the main airway, the right and left lungs, and two compliances also representing the right and left lungs. The spontaneous breath module generates inspiratory negative pressure produced by a patient. The ventilator module generates driving force of pressure or flow according to the combination of the ventilation mode and options. These forces are given to the respiratory module through the simulation controller. RESULTS: The simulation system was developed using HTML, VBScript (3000 lines, 100 kB) and ActiveX control (120 kB), and runs on Internet Explorer (5.5 or higher). The spontaneous breath is defined by a frequency, amplitude and inspiratory patterns in the spontaneous breath module. The user can construct a ventilation mode by setting a control variable, phase variables (trigger, limit, and cycle), and options. Available ventilation modes are: controlled mechanical ventilation (CMV), continuous positive airway pressure, synchronized intermittent mandatory ventilation (SIMV), pressure support ventilation (PSV), SIMV + PSV, pressure-controlled ventilation (PCV), pressure-regulated volume control (PRVC), proportional assisted ventilation, mandatory minute ventilation (MMV), bilevel positive airway pressure (BiPAP). The simulation system demonstrates in a graph and animation the airway pressure, flow, and volume of the respiratory system during mechanical ventilation both with and without spontaneous breathing. CONCLUSIONS: We developed a web application that demonstrated the respiratory mechanics and the basic theory of ventilation mode.

Computer Simulation↗

Electronic clinical path system based on semistructured data model using personal digital assistant for onsite access.

Clinical Paths (Paths) have been introduced by different hospitals for patient care management. An Electronic Clinical Path (ECP) with onsite access provision seems to improve the efficiency of medical staffs because they can share vast medical information about patients at a time and also can reuse accumulated data easily, which is impossible with paper-based Path. Data model is the basis for implementing ECP. However, there is no established model for ECP. The purpose of this study is to introduce a model for ECP and implement an ECP with onsite access system. We introduced a Semistructured Data Model (SSDM) for ECP, and implemented a Web application system based on this model using Personal Digital Assistant (PDA) as inputting device. Our system functioned as expected with wireless LAN, and users handled the data on bedside using PDA. By introducing SSDM, we showed the correspondence between schema of Paths and implementation of ECP.

Access to Information↗

Systematic Review and Transcriptomic Meta-analysis of Environmental Enrichment Reveal Core Molecular Programs of Brain Plasticity.

Environmental enrichment (EE) paradigms in rodents have long demonstrated that enhanced sensory, cognitive, social, and motor stimulation positively impacts brain function, improving learning, memory, and neuroplasticity. These effects have significant implications for understanding cognitive development and mitigating cognitive decline and brain aging. While numerous transcriptomic studies have explored EE-induced molecular changes, a unified view of the genes and pathways consistently modulated remains lacking. To address this gap, we performed a systematic review and meta-analysis. We conducted a comprehensive PubMed search for all studies published up to February 2025 that matched all the following inclusion criteria: (1) employed EE paradigms; (2) were conducted on rodents; (3) utilized genome-wide transcriptomic methods; (4) examined brain regions or neuronal populations. The 323 retrieved articles were manually screened for relevance to the study aims and data availability. Datasets from 20 eligible RNA-seq reports were reprocessed using a unified analysis pipeline and subjected to a meta-analysis with three complementary statistical methods. Despite considerable heterogeneity across studies, our integrative analysis identified consistent gene expression signatures linked to synaptic function, plasticity and their transcriptional regulation. In particular, our findings highlight the upregulation of the activity-dependent transcriptional program, including Fos and Jun family members. These molecular insights advance our understanding of how EE impacts on neuronal and behavioral outcomes, and may inform therapeutic strategies aimed at replicating or enhancing EE benefits. To promote open science and foster further research, we developed an accessible web application, mEEtaBrain, that enables the neuroscience community to navigate and interrogate our meta-analysis results. Substantial methodological heterogeneity across source studies increased variability in the meta-analysis outcomes. The use of stressors or disease models, particularly in rat studies, introduced a major confounding factor and limited reliable interspecies comparison. Overall, the studies exhibited a low to moderate risk of bias.

Neuronal Plasticity↗

A research synthesis of humans, animals, and environmental compartments exposed to PFAS: A systematic evidence map and bibliometric analysis of secondary literature.

BACKGROUND: Per- and polyfluoroalkyl substances (PFAS) are a class of widely used anthropogenic chemicals. Concerns regarding their persistence and potential adverse effects have led to multiple secondary research publications. Here, we aim to assess the resulting evidence base in the systematic secondary literature by examining research gaps, evaluating the quality of reviews, and exploring interdisciplinary connections. METHODS: This study employed a systematic evidence-mapping approach to assess the secondary literature on the biological, environmental, and medical aspects of exposure to 35 fluorinated compounds. The inclusion criteria encompassed systematic reviews published in peer-reviewed journals, pre-prints, and theses. Comprehensive searches across electronic databases and grey literature identified relevant reviews. Data extraction and synthesis involved mapping literature content and narrative descriptions. We employed a modified version of the AMSTAR2 checklist to evaluate the methodological rigour of the reviews. A bibliometric data analysis uncovered patterns and trends in the academic literature. A research protocol for this study was previously pre-registered (osf.io/2tpn8) and published (Vendl et al., Environment International 158 (2022) 106973). The database is freely accessible through the interactive and user-friendly web application of this systematic evidence map at https://hi-this-is-lorenzo.shinyapps.io/PFAS_SEM_Shiny_App/. RESULTS: Our map includes a total of 175 systematic reviews. Over the years, there has been a steady increase in the annual number of publications, with a notable surge in 2021. Most reviews focused on human exposure, whereas environmental and animal-related reviews were fewer and often lacked a rigorous systematic approach to literature search and screening. Review outcomes were predominantly associated with human health, particularly with reproductive and children's developmental health. Animal reviews primarily focused on studies conducted in controlled laboratory settings, and wildlife reviews were characterised by an over-representation of birds and fish species. Recent reviews increasingly incorporated quantitative synthesis methodologies. The methodological strengths of the reviews included detailed descriptions of study selection processes and disclosure of potential conflicts of interest. However, weaknesses were observed in the critical lack of detail in reporting methods. A bibliometric analysis revealed that the most productive authors collaborate within their own country, leading to limited and clustered international collaborations. CONCLUSIONS: In this overview of the available systematic secondary literature, we map literature content, assess reviews' methodological quality, highlight data gaps, and draw research network clusters. We aim to facilitate literature reviews, guide future research initiatives, and enhance opportunities for cross-country collaboration. Furthermore, we discuss how this systematic evidence map and its publicly available database benefit scientists, regulatory agencies, and other stakeholders by providing access to current systematic secondary literature on PFAS exposure.

Bibliometrics↗

Characterization and prediction of alternative splice sites.

Human alternative isoform, cryptic, skipped, and constitutive splice sites from the ALTEXTRON database were analysed regarding splice site strength, composition, GC content, position and binding site strength of polypyrimidine tract and branch site. Several features were identified which distinguish alternative isoform and cryptic splice sites, but not skipped splice sites from constitutive ones. These include splice site strength, introns GC content, U2AF35 binding site score, and oligonucleotide frequencies. For the predictive classification of splice sites, pattern recognition models for different splicing factor binding sites and oligonucleotide frequency models (OFMs) were combined using backpropagation networks. 67.45% of acceptor sites and 71.23% of donor sites are correctly classified by networks trained for classification of constitutive and alternative isoform/cryptic splice sites. A web-application for the prediction of alternative splice sites is available at http://es.embnet.org/~mwang/assp.html .

Alternative Splicing↗

PropeR revisited.

INTRODUCTION: The PropeR EHR system (PropeRWeb) is a multidisciplinary electronic health record (EHR) system for multidisciplinary use in extramural patient care for stroke patients. DESIGN: The system is built using existing open source components and is based on open standards. It is implemented as a web application using servlets and Java Server Pages (JSP's) with a CORBA connection to the database servers, which are based on the OMG HDTF specifications. PropeRWeb is a generic system which can be readily customized for use in a variety of clinical domains. EVALUATION: The system proved to be stable and flexible, although some aspects (a.o. user friendliness) could be improved. These improvements are currently under development in a second version.

Computer Systems↗

TFinder: A Python Web Tool for Predicting Transcription Factor Binding Sites.

Transcription is a key cell process that consists of synthesizing several copies of RNA from a gene DNA sequence. This process is highly regulated and closely linked to the ability of transcription factors to bind specifically to DNA. TFinder is an easy-to-use Python web portal allowing the identification of Individual Motifs (IM) such as Transcription Factor Binding Sites (TFBS). Using the NCBI API, TFinder extracts either promoter or gene terminal regulatory regions, through a simple query of NCBI gene name or ID. It enables simultaneous analysis across five different species for an unlimited number of genes. TFinder searches for Individual Motifs in different formats, including IUPAC codes and JASPAR entries. Moreover, TFinder also allows de novo generations of a Position Weight Matrix (PWM) and the use of already established PWM. Finally, the data are provided in a tabular and a graph format showing the relevance and the P-value of the Individual Motifs found as well as their location relative to the Transcription Start Site (TSS) or the terminal region of the gene. The results are then sent by email to users facilitating the subsequent data analysis and sharing. TFinder is written in Python and freely available on GitHub under the MIT license: https://github.com/Jumitti/TFinder. It can be accessed as a web application implemented in Streamlit at https://tfinder-ipmc.streamlit.app. Resources are available on Streamlit "Resources" tab. TFINDER strength is that it relies on an all-in-one intuitive tool allowing users inexperienced with bioinformatics tools to retrieve gene regulatory regions sequences in multiple species and to search for individual motifs in a huge number of genes.

Transcription Factors↗

[Surveillance of antimicrobial resistance and antimicrobial use in a university-affiliated hospital: implementation of a computerized system].

UNLABELLED: After half a century of antibiotic use, the increasing problem of the emergence and spread of antimicrobial-resistant pathogens has created a problem of public health. The causes of this problem are multifactorial, but the excessive and inappropriate use of antimicrobials is the principal cause. The current guidelines for the control of antimicrobial resistance in hospitals recommend the implementation of a surveillance system of antimicrobial use and antimicrobial resistance data. AIM OF THE STUDY: The objective of our project was to develop a computerised tool to survey the antibiotic consumption data and the antimicrobial resistance. MATERIALS AND METHODS: We have collected antimicrobial resistance data from the software of the bacteriology laboratory, antibiotic use data from the pharmacy and demographical data from the hospital's admission department. These data were integrated in a database server and available with a web application. Antimicrobial resistance data of 15 major microorganisms were extracted and expressed as a frequency with elimination of repeats by using time criteria (7, 14 or 28 days). Antibiotic use data were converted into defined daily doses (DDD) and expressed per 1000 patient-days. RESULTS: Data are available for consultation in the form of tables or graphs per unit, type of units (medicine, surgery, pediatrics, intensive care units) or in the whole hospital. The system allows the confrontation on the same graph of antimicrobial resistance and antibiotic use data. CONCLUSION: Our surveillance system constitutes a needed prerequisite to the implementation of a global strategy of antibiotic use improvement in our hospital.

Anti-Infective Agents↗

The Synthetic Gene Designer: a flexible web platform to explore sequence manipulation for heterologous expression.

"Codon optimization" is a general approach to improving heterologous expression where genes are moved from their native genomes into alternatives that exhibit different patterns of codon usage. However, despite reports of successful manipulations and the existence of stand-alone codon optimization software packages or commercial services that offer to redesign genes, the scientific community lacks any systematic understanding of what exactly it means to optimize codon usage. Thus we present a bona fide web application, the "Synthetic Gene Designer," which contrasts with existing software by providing a centralized, free, and transparent platform for the broader scientific community to develop knowledge about synthetic gene design. Consistent with this goal, our software is associated with a moderated e-forum that promotes discussion of synthetic gene design and offers technical support. In addition, the Synthetic Gene Designer presents enhanced functionality over existing software options: for example, it enables users to work with non-standard genetic codes, with user-defined patterns of codon usage and an expanded range of methods for codon optimization. The Synthetic Gene Designer, together with on-line tutorials and the forum, is available at .

Animals↗

Detecting false expression signals in high-density oligonucleotide arrays by an in silico approach.

High-density oligonucleotide arrays have become a popular assay for concurrent measurement of mRNA expression at the genome scale. Much effort has been devoted to the development of statistical analysis tools aimed at reducing experimental noise and normalizing experimental variation in gene expression analysis. However, these investigations do not detect or catalog systematic problems associated with specific oligonucleotide probes. Here, we present an investigation of problematic probes that yield consistent but inaccurate signals across multiple experiments. By evaluating data integrity among gene, probe sequence, and genomic structure we identified a total of 20,696 (10.5%) nonspecific probes that could cross-hybridize to multiple genes and a total of 18,363 (9.3%) probes that miss the target transcript sequences on the Affymetrix GeneChip U95A/Av2 array. The numbers of nonspecific and mistargeted probes on the U133A array are 29,405 (12.1%) and 19,717 (8.0%), respectively. The poor performance of the mistargeted probes was confirmed in two GeneChip experiments, in which these probes showed a 20-30% decrease in detecting present signals compared with normal probes. Comparison of qualitative expression signals obtained from SAGE and EST data with those from GeneChip arrays showed that the consistency of the two platforms is 30% lower in problematic probes than in normal probes. A Web application was developed to apply our results for improving the accuracy of expression analysis.

Expressed Sequence Tags↗

A web-based self-monitoring system for people living with HIV/AIDS.

Available evidence indicates that the internet is becoming the main source for delivering information on the prevention, control and treatment of HIV/AIDS. This paper presents a further step in the use of the internet to meet the new challenge of managing HIV as a chronic illness. It describes a work carried out under the SEAHORSE EU project to build and test a Web-based self-monitoring system for HIV/AIDS patient care. The user interface has been carefully designed to provide a high-level of interaction and therefore improve some of the current limitations of Web applications. The system comprises three modules: (1) a patient self-monitoring personal diary, to create a follow-up patient record; (2) a data analysis and visualisation tool; and (3) a section to allow patients to ask for advising and remote doctor support. One of the crucial system design issues has been the system security and users anonymity features required in this clinical domain. A feasibility pilot has been carried out to test the system in three organisations involved in the research project: the Immune Development Trust (London), the Lambeth, Southwark and Lewisham Health Authority (London) and Apoyo Positivo in Madrid. The preliminary results of the system evaluation show the potential validity and usefulness of the tool for helping people living with HIV/AIDS to promote and manage their health and for providing health professionals with new means for tele-monitoring and tele-caring patients.

Acquired Immunodeficiency Syndrome↗

Scalable near-real-time Bayesian phylogenetics for outbreaks with Delphy.

Pathogen genomic analysis is central to tracking, understanding and containing outbreaks1-13, but the complexity and cost of state-of-the-art phylogenetic tools limit global access and impact. Here we introduce Delphy, an exact reformulation of Bayesian phylogenetics14-17 designed to transform its speed, scalability and accessibility while retaining Bayesian state-of-the-art accuracy. Delphy's central data structure, an explicit mutation-annotated tree, takes advantage of the high sequence similarity of large-scale epidemic datasets18-20 for efficient tree exploration and convergence. By reproducing key analyses from recent major epidemics, including Ebola1,21, Zika2, SARS-CoV-2 (ref. 22), mpox3,4 and H5N1 (refs. 23,24), we demonstrate state-of-the-art accuracy with up to 2-3 orders of magnitude improvements in speed. Assessing Delphy's scalability, we show that a simulated dataset of 100,000 sequences can be analysed within a day. We distribute Delphy as a client-side web application that enables local, interactive analysis of raw data on the user's machine. Delphy automatically identifies key viral lineages and mutations, as well as their emergence and prevalence through time, with quantified uncertainties grounded in Bayesian theory. Delphy establishes Bayesian phylogenetics as a fast, accessible frontline tool for future outbreak response.

Journal Article↗