The eICU Collaborative Research Database, a freely available multi-center database for critical care research.
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ABSTRACT:
SUBMITTER: Pollard TJ
PROVIDER: S-EPMC6132188 | biostudies-literature | 2018 Sep
REPOSITORIES: biostudies-literature
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Project description:MIMIC-III ('Medical Information Mart for Intensive Care') is a large, single-center database comprising information relating to patients admitted to critical care units at a large tertiary care hospital. Data includes vital signs, medications, laboratory measurements, observations and notes charted by care providers, fluid balance, procedure codes, diagnostic codes, imaging reports, hospital length of stay, survival data, and more. The database supports applications including academic and industrial research, quality improvement initiatives, and higher education coursework.
| S-EPMC4878278 | biostudies-literature
Project description:Background: Acute respiratory distress syndrome (ARDS) is a common cause of respiratory failure in patients in intensive care unit (ICU). The therapeutic value of glucocorticoids (GCs) in the prognosis of ARDS remains controversial. The aim of this research is studying the impacts of GCs treatment on ARDS patients in ICU. Methods: We retrospectively studied 2,167 ARDS patients whose data were collected from the public eICU Collaborative Research Database, among which 254 patients who received glucocorticoid (GCs) treatment were 1:1 matched by propensity matching analysis (PSM). The primary outcome was ICU mortality. Every oxygenation index (PaO2/FiO2) measurement before death or ICU discharge was recorded. A joint model (JM) which combined longitudinal sub-model (mixed-effect model) and time-to-event sub-model (Cox regression model) by trajectory functions of PaO2/FiO2 was conducted to determine the effects of GCs treatment on both ICU mortality and PaO2/FiO2 level and further PaO2/FiO2's effect on event status. The marginal structural cox model (MSCM) adjusted the overall PaO2/FiO2 of patients to further validate the results. Results: The result of the survival sub-model showed that GCs treatment was significantly associated with reduced ICU mortality in ARDS patients [HR (95% CI) = 0.642 (0.453, 0.912)], demonstrating that GCs treatment was a protective factor of ICU mortality. In the longitudinal sub-model, GCs treatment was not correlated to the PaO2/FiO2. After adjusted by the JM, the HR of GCs treatment was 0.602 while GCs was still not significantly related to PaO2/FiO2 level. The JM-induced association showed that higher PaO2/FiO2 was a significant protective factor of mortality in ARDS patients and the HR was 0.991 which demonstrated that one level increase of PaO2/FiO2 level decreased 0.9% risk of ICU mortality. MSCM results also show that GCs can improve the prognosis of patients. Conclusion: Rational use of GCs can reduce the ICU mortality of ARDS patients in ICU. In addition to the use of GCs treatment, clinicians should also focus on the shifting trend of PaO2/FiO2 level to provide better conditions for patients' survival.
| S-EPMC8350484 | biostudies-literature
Project description:Background and purposeResearch electives are commonly offered in doctor of pharmacy programs but are typically limited to one faculty member mentoring individual students at a single site for a semester long self-study experience. The purpose of this paper is to describe pharmacy student experiences and perceptions of the research process after completing a multi-campus, multi-investigator critical care research elective.Educational activity and settingThe Research in Critical Care Pharmacotherapy elective was launched in spring 2019 and implemented a novel approach to the pharmacy research elective that promoted collaborative research across four campuses that may be continued for up to four semesters of credit.FindingsSix second- and third-year doctor of pharmacy students enrolled in the course during the first offering. Three students were located on the main campus with one student on each of the extended campuses. Students completed a median of five unique research activities with at least one student participating in 15 of the 19 activities evaluated. Students were asked to complete a pre- and post-course survey assessing perceived research abilities using the Dreyfus model. There was a significant decrease in the number of novice responses in the post-course survey (pre- 10 vs. post- 2, p = 0.043).SummaryA multi-campus, multi-investigator critical care research elective provided broad research experiences and increased student confidence related to numerous research skills.
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Project description:ICU telemedicine uses audiovisual conferencing technology to provide critical care from a remote location. Research is needed to best define the optimal use of ICU telemedicine, but efforts are hindered by methodological challenges and the lack of an organized delivery approach. We convened an interdisciplinary working group to develop a research agenda in ICU telemedicine, addressing both methodological and knowledge gaps in the field. To best inform clinical decision-making and health policy, future research should be organized around a conceptual framework that enables consistent descriptions of both the study setting and the telemedicine intervention. The framework should include standardized methods for assessing the preimplementation ICU environment and describing the telemedicine program. This framework will facilitate comparisons across studies and improve generalizability by permitting context-specific interpretation. Research based on this framework should consider the multidisciplinary nature of ICU care and describe the specific program goals. Key topic areas to be addressed include the effect of ICU telemedicine on the structure, process, and outcome of critical care delivery. Ideally, future research should attempt to address causation instead of simply associations and elucidate the mechanism of action in order to determine exactly how ICU telemedicine achieves its effects. ICU telemedicine has significant potential to improve critical care delivery, but high-quality research is needed to best inform its use. We propose an agenda to advance the science of ICU telemedicine and generate research with the greatest potential to improve patient care.
| S-EPMC3130530 | biostudies-literature
Project description:3D-e-Chem-VM is an open source, freely available Virtual Machine ( http://3d-e-chem.github.io/3D-e-Chem-VM/ ) that integrates cheminformatics and bioinformatics tools for the analysis of protein-ligand interaction data. 3D-e-Chem-VM consists of software libraries, and database and workflow tools that can analyze and combine small molecule and protein structural information in a graphical programming environment. New chemical and biological data analytics tools and workflows have been developed for the efficient exploitation of structural and pharmacological protein-ligand interaction data from proteomewide databases (e.g., ChEMBLdb and PDB), as well as customized information systems focused on, e.g., G protein-coupled receptors (GPCRdb) and protein kinases (KLIFS). The integrated structural cheminformatics research infrastructure compiled in the 3D-e-Chem-VM enables the design of new approaches in virtual ligand screening (Chemdb4VS), ligand-based metabolism prediction (SyGMa), and structure-based protein binding site comparison and bioisosteric replacement for ligand design (KRIPOdb).
| S-EPMC5342320 | biostudies-literature
Project description:The foundation for integrating mass spectrometry (MS)-based proteomics into systems medicine is to develop standardized start-to-finish and fit-for-purpose workflows for clinical specimens. An essential step in this pursuit is to highlight common ground in a diverse landscape of different sample preparation techniques and LC-MS setups with the aim to explore differences and potential confounding factors as well as to identify areas for improvement with a direct practical benefit. With the aim to benchmark and improve current best practices among the proteomics MS laboratories of the CLINSPECT-M consortium we performed two consecutive round robin studies with full freedom to operate in terms of sample preparation and MS measurements. The six participating study partners were provided with two clinically relevant sample matrices: plasma, and cerebrospinal fluid (CSF). In the first round each laboratory applied their current best practice protocol for the respective matrix, covering laboratory-specific sample proteolysis, liquid chromatography, and MS measurement procedure. All resulting MS files were analyzed centrally by a standardized pipeline. Based on the achieved results and following a fully transparent exchange of all lab-specific protocols within the consortium, each laboratory could improve their methods before measuring the same samples in a second acquisition round. The results of both measurement time points are compared with respect to identifications (IDs), data completeness, retention time and quantitative precision as well as inter-laboratory reproducibility. For instance, the number of identified protein groups was increased on average by 14% for CSF and 5% for plasma from first to second measurement round across participants resulting in a median overlap number of 579 protein groups for CSF and 246 IDs for plasma across setups. The individual performances of participating study centers and the inter-laboratory reproducibility were improved in the second measurement, emphasizing the effect and importance of expert-driven exchange of best practices. In total, the study not only clearly demonstrates the beneficial effect of sharing knowledge and expertise for direct practical improvements but also highlights tendencies such as common limits of detection or preferable preparation strategies.
2024-01-02 | PXD044053 | Pride
Project description:BackgroundAnalysis of ciliary function for assessment of patients suspected of primary ciliary dyskinesia (PCD) and for research studies of respiratory and ependymal cilia requires assessment of both ciliary beat pattern and beat frequency. While direct measurement of beat frequency from high-speed video recordings is the most accurate and reproducible technique it is extremely time consuming. The aim of this study was to develop a freely available automated method of ciliary beat frequency analysis from digital video (AVI) files that runs on open-source software (ImageJ) coupled to Microsoft Excel, and to validate this by comparison to the direct measuring high-speed video recordings of respiratory and ependymal cilia. These models allowed comparison to cilia beating between 3 and 52 Hz.MethodsDigital video files of motile ciliated ependymal (frequency range 34 to 52 Hz) and respiratory epithelial cells (frequency 3 to 18 Hz) were captured using a high-speed digital video recorder. To cover the range above between 18 and 37 Hz the frequency of ependymal cilia were slowed by the addition of the pneumococcal toxin pneumolysin. Measurements made directly by timing a given number of individual ciliary beat cycles were compared with those obtained using the automated ciliaFA system.ResultsThe overall mean difference (± SD) between the ciliaFA and direct measurement high-speed digital imaging methods was -0.05 ± 1.25 Hz, the correlation coefficient was shown to be 0.991 and the Bland-Altman limits of agreement were from -1.99 to 1.49 Hz for respiratory and from -2.55 to 3.25 Hz for ependymal cilia.ConclusionsA plugin for ImageJ was developed that extracts pixel intensities and performs fast Fourier transformation (FFT) using Microsoft Excel. The ciliaFA software allowed automated, high throughput measurement of respiratory and ependymal ciliary beat frequency (range 3 to 52 Hz) and avoids operator error due to selection bias. We have included free access to the ciliaFA plugin and installation instructions in Additional file 1 accompanying this manuscript that other researchers may use.
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Project description:ObjectivesTo describe the epidemiology of sepsis in critical care by applying the Sepsis-3 criteria to electronic health records.DesignRetrospective cohort study using electronic health records.SettingTen ICUs from four U.K. National Health Service hospital trusts contributing to the National Institute for Health Research Critical Care Health Informatics Collaborative.PatientsA total of 28,456 critical care admissions (14,332 emergency medical, 4,585 emergency surgical, and 9,539 elective surgical).Measurements and main resultsTwenty-nine thousand three hundred forty-three episodes of clinical deterioration were identified with a rise in Sequential Organ Failure Assessment score of at least 2 points, of which 14,869 (50.7%) were associated with antibiotic escalation and thereby met the Sepsis-3 criteria for sepsis. A total of 4,100 episodes of sepsis (27.6%) were associated with vasopressor use and lactate greater than 2.0 mmol/L, and therefore met the Sepsis-3 criteria for septic shock. ICU mortality by source of sepsis was highest for ICU-acquired sepsis (23.7%; 95% CI, 21.9-25.6%), followed by hospital-acquired sepsis (18.6%; 95% CI, 17.5-19.9%), and community-acquired sepsis (12.9%; 95% CI, 12.1-13.6%) (p for comparison less than 0.0001).ConclusionsWe successfully operationalized the Sepsis-3 criteria to an electronic health record dataset to describe the characteristics of critical care patients with sepsis. This may facilitate sepsis research using electronic health record data at scale without relying on human coding.
| S-EPMC8508729 | biostudies-literature
Project description:IntroductionThe field of metabolomics has expanded greatly over the past two decades, both as an experimental science with applications in many areas, as well as in regards to data standards and bioinformatics software tools. The diversity of experimental designs and instrumental technologies used for metabolomics has led to the need for distinct data analysis methods and the development of many software tools.ObjectivesTo compile a comprehensive list of the most widely used freely available software and tools that are used primarily in metabolomics.MethodsThe most widely used tools were selected for inclusion in the review by either ? 50 citations on Web of Science (as of 08/09/16) or the use of the tool being reported in the recent Metabolomics Society survey. Tools were then categorised by the type of instrumental data (i.e. LC-MS, GC-MS or NMR) and the functionality (i.e. pre- and post-processing, statistical analysis, workflow and other functions) they are designed for.ResultsA comprehensive list of the most used tools was compiled. Each tool is discussed within the context of its application domain and in relation to comparable tools of the same domain. An extended list including additional tools is available at https://github.com/RASpicer/MetabolomicsTools which is classified and searchable via a simple controlled vocabulary.ConclusionThis review presents the most widely used tools for metabolomics analysis, categorised based on their main functionality. As future work, we suggest a direct comparison of tools' abilities to perform specific data analysis tasks e.g. peak picking.
| S-EPMC5550549 | biostudies-literature
Project description:PurposeSince the introduction of the first prosthetic mesh for abdominal hernia repair, there has been a search for the "ideal mesh." The use of preclinical or animal models for assessment of necessary characteristics of new and existing meshes is an indispensable part of hernia research. Unfortunately, in our experience there is a lack of consensus among different research groups on which model to use. Therefore, we hypothesized that there is a lack of comparability within published animal research on hernia surgery due to wide range in experimental setup among different research groups.MethodsA systematic search of the literature was performed to provide a complete overview of all animal models published between 2000 and 2014. Relevant parameters on model characteristics and outcome measurement were scored on a standardized scoring sheet.ResultsDue to the wide range in different animals used, ranging from large animal models like pigs to rodents, we decided to limit the study to 168 articles concerning rat models. Within these rat models, we found wide range of baseline animal characteristics, operation techniques, and outcome measurements. Making reliable comparison of results among these studies is impossible.ConclusionThere is a lack of comparability among experimental hernia research, limiting the impact of this experimental research. We therefore propose the establishment of guidelines for experimental hernia research by the EHS.
| S-EPMC5608772 | biostudies-literature