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Journal articles on the topic 'Querying clinical database'

Author: Grafiati

Published: 11 March 2023

Last updated: 31 July 2025

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1

Giardine, Belinda M., Philippe Joly, Serge Pissard, et al. "Clinically relevant updates of the HbVar database of human hemoglobin variants and thalassemia mutations." Nucleic Acids Research 49, no. D1 (2020): D1192—D1196. http://dx.doi.org/10.1093/nar/gkaa959.

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Abstract HbVar (http://globin.bx.psu.edu/hbvar) is a widely-used locus-specific database (LSDB) launched 20 years ago by a multi-center academic effort to provide timely information on the numerous genomic variants leading to hemoglobin variants and all types of thalassemia and hemoglobinopathies. Here, we report several advances for the database. We made clinically relevant updates of HbVar, implemented as additional querying options in the HbVar query page, allowing the user to explore the clinical phenotype of compound heterozygous patients. We also made significant improvements to the HbVa

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Nigrin, D. J., and I. S. Kohane. "Temporal Expressiveness in Querying a Time-stamp--based Clinical Database." Journal of the American Medical Informatics Association 7, no. 2 (2000): 152–63. http://dx.doi.org/10.1136/jamia.2000.0070152.

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Tradigo, G., P. Veltri, and S. Greco. "Geomedica: managing and querying clinical data distributions on geographical database systems." Procedia Computer Science 1, no. 1 (2010): 979–86. http://dx.doi.org/10.1016/j.procs.2010.04.108.

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d’Acierno, Antonio, Angelo Facchiano, and Anna Marabotti. "GALT Protein Database: Querying Structural and Functional Features of GALT Enzyme." Human Mutation 35, no. 9 (2014): 1060–67. http://dx.doi.org/10.1002/humu.22613.

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Hurdle, J. F., S. C. Haroldsen, A. Hammer, et al. "Identifying clinical/translational research cohorts: ascertainment via querying an integrated multi-source database." Journal of the American Medical Informatics Association 20, no. 1 (2013): 164–71. http://dx.doi.org/10.1136/amiajnl-2012-001050.

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Mudaranthakam, Dinesh Pal, Jeffrey Thompson, Jinxiang Hu, et al. "A Curated Cancer Clinical Outcomes Database (C3OD) for accelerating patient recruitment in cancer clinical trials." JAMIA Open 1, no. 2 (2018): 166–71. http://dx.doi.org/10.1093/jamiaopen/ooy023.

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Abstract Data used to determine patient eligibility for cancer clinical trials often come from disparate sources that are typically maintained by different groups within an institution, use differing technologies, and are stored in different formats. Collecting data and resolving inconsistencies across sources increase the time it takes to screen eligible patients, potentially delaying study completion. To address these challenges, the Biostatistics and Informatics Shared Resource at The University of Kansas Cancer Center developed the Curated Cancer Clinical Outcomes Database (C3OD). C3OD mer

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Huot, Mathieu, Matin Ghavami, Alexander K. Lew, et al. "GenSQL: A Probabilistic Programming System for Querying Generative Models of Database Tables." Proceedings of the ACM on Programming Languages 8, PLDI (2024): 790–815. http://dx.doi.org/10.1145/3656409.

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This article presents GenSQL, a probabilistic programming system for querying probabilistic generative models of database tables. By augmenting SQL with only a few key primitives for querying probabilistic models, GenSQL enables complex Bayesian inference workflows to be concisely implemented. GenSQL’s query planner rests on a unified programmatic interface for interacting with probabilistic models of tabular data, which makes it possible to use models written in a variety of probabilistic programming languages that are tailored to specific workflows. Probabilistic models may be automatically

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Kang, Mengjia, Jose A. Alvarado-Guzman, Luke V. Rasmussen, and Justin B. Starren. "Evolution of a Graph Model for the OMOP Common Data Model." Applied Clinical Informatics 15, no. 05 (2024): 1056–65. https://doi.org/10.1055/s-0044-1791487.

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Abstract Objective Graph databases for electronic health record (EHR) data have become a useful tool for clinical research in recent years, but there is a lack of published methods to transform relational databases to a graph database schema. We developed a graph model for the Observational Medical Outcomes Partnership (OMOP) common data model (CDM) that can be reused across research institutions. Methods We created and evaluated four models, representing two different strategies, for converting the standardized clinical and vocabulary tables of OMOP into a property graph model within the Neo4

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Schwabe-Fry, Kristen, Mark Bollenbeck, Merilee Teylan, et al. "THE NATIONAL ALZHEIMER'S COORDINATING CENTER: QUERYING THE DATABASE AND REQUESTING DATA." Alzheimer's & Dementia 13, no. 7 (2017): P158. http://dx.doi.org/10.1016/j.jalz.2017.06.2599.

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Priyatna, Freddy, Raul Alonso-Calvo, Sergio Paraiso-Medina, and Oscar Corcho. "Querying clinical data in HL7 RIM based relational model with morph-RDB." Journal of Biomedical Semantics 8, no. 1 (2017): 49. https://doi.org/10.1186/s13326-017-0155-8.

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<strong>Background: </strong>Semantic interoperability is essential when carrying out post-genomic clinical trials where several institutions collaborate, since researchers and developers need to have an integrated view and access to heterogeneous data sources. One possible approach to accommodate this need is to use RDB2RDF systems that provide RDF datasets as the unified view. These RDF datasets may be materialized and stored in a triple store, or transformed into RDF in real time, as virtual RDF data sources. Our previous efforts involved materialized RDF datasets, hence losing data freshne

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Bollenbeck, Mark, Kristen Schwabe-Fry, Merilee Teylan, et al. "[P1-555]: THE NATIONAL ALZHEIMER'S COORDINATING CENTER: QUERYING THE DATABASE AND REQUESTING DATA." Alzheimer's & Dementia 13, no. 7S_Part_10 (2017): P507. http://dx.doi.org/10.1016/j.jalz.2017.06.571.

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Nagarakshitha, B. R., K. S. Lohith, K. P. Aarthy, Arjun Gopkumar, and Uma Satya Ranjan. "Application of NoSQL Technology to Facilitate Storing and Retrieval of Clinical Data Using IndexedDb in Offline Conditions." Journal of Computational and Theoretical Nanoscience 17, no. 9 (2020): 4012–15. http://dx.doi.org/10.1166/jctn.2020.9010.

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Data collection is a very important aspect of any research, especially while dealing with the collection of clinical data. This paper presents a way to collect and manage clinical data using a web application with offline functionality. The whole application is an end-to-end PWA providing an interface to collect the data, store, and query. The available data is very huge and it is unstructured. To store it, a NoSQL database such as Cassandra is most suitable. The data will mostly be used for an OLAP system for querying the data, cleaning and performing analysis on it. In the process of collect

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Dong, Qun, Feng Li, Yanjun Xu, et al. "RNAactDrug: a comprehensive database of RNAs associated with drug sensitivity from multi-omics data." Briefings in Bioinformatics 21, no. 6 (2019): 2167–74. http://dx.doi.org/10.1093/bib/bbz142.

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Abstract Drug sensitivity has always been at the core of individualized cancer chemotherapy. However, we have been overwhelmed by large-scale pharmacogenomic data in the era of next-generation sequencing technology, which makes it increasingly challenging for researchers, especially those without bioinformatic experience, to perform data integration, exploration and analysis. To bridge this gap, we developed RNAactDrug, a comprehensive database of RNAs associated with drug sensitivity from multi-omics data, which allows users to explore drug sensitivity and RNA molecule associations directly.

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Rosano-Gonzalez, María L., Vipin T. Sreedharan, Antoine Hanns, Daniel J. Stekhoven, and Franziska Singer. "CIViCutils: Matching and downstream processing of clinical annotations from CIViC." F1000Research 12 (October 11, 2023): 1304. http://dx.doi.org/10.12688/f1000research.136986.1.

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Background: With the advent of next-generation sequencing, profiling the genetic landscape of tumors entered clinical diagnostics, bringing the resolution of precision oncology to unprecedented levels. However, the wealth of information generated in a sequencing experiment can be difficult to manage, especially if hundreds of mutations need to be interpreted in a clinical context. Dedicated methods and databases are required that assist in interpreting the importance of a mutation for disease progression, prognosis, and with respect to therapy. Here, the CIViC knowledgebase is a valuable curat

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Rolston, John D., Seunggu J. Han, Catherine Y. Lau, Mitchel S. Berger, and Andrew T. Parsa. "Frequency and predictors of complications in neurological surgery: national trends from 2006 to 2011." Journal of Neurosurgery 120, no. 3 (2014): 736–45. http://dx.doi.org/10.3171/2013.10.jns122419.

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Object Surgical complications increase the cost of health care worldwide and directly contribute to patient morbidity and mortality. In an effort to mitigate morbidity and incentivize best practices, stakeholders such as health insurers and the US government are linking reimbursement to patient outcomes. In this study the authors analyzed a national database to determine basic metrics of how comorbidities specifically affect the subspecialty of neurosurgery. Methods Data on 1,777,035 patients for the years 2006–2011 were acquired from the American College of Surgeons (ACS) National Surgical Qu

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Chrimes, Dillon, and Hamid Zamani. "Using Distributed Data over HBase in Big Data Analytics Platform for Clinical Services." Computational and Mathematical Methods in Medicine 2017 (2017): 1–16. http://dx.doi.org/10.1155/2017/6120820.

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Big data analytics (BDA) is important to reduce healthcare costs. However, there are many challenges of data aggregation, maintenance, integration, translation, analysis, and security/privacy. The study objective to establish an interactive BDA platform with simulated patient data using open-source software technologies was achieved by construction of a platform framework with Hadoop Distributed File System (HDFS) using HBase (key-value NoSQL database). Distributed data structures were generated from benchmarked hospital-specific metadata of nine billion patient records. At optimized iteration

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Kopanitsa, Georgy. "Integration of Hospital Information and Clinical Decision Support Systems to Enable the Reuse of Electronic Health Record Data." Methods of Information in Medicine 56, no. 03 (2017): 238–47. http://dx.doi.org/10.3414/me16-01-0057.

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SummaryBackground: The efficiency and acceptance of clinical decision support systems (CDSS) can increase if they reuse medical data captured during health care delivery. High heterogeneity of the existing legacy data formats has become the main barrier for the reuse of data. Thus, we need to apply data modeling mechanisms that provide standardization, transformation, accumulation and querying medical data to allow its reuse.Objectives: In this paper, we focus on the interoperability issues of the hospital information systems (HIS) and CDSS data integration.Materials and Methods: Our study is

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Lopez, Gianluca, Giulia Lazzeri, Alessandra Rappa, et al. "Comprehensive Genomic Analysis Reveals the Prognostic Role of LRRK2 Copy-Number Variations in Human Malignancies." Genes 11, no. 8 (2020): 846. http://dx.doi.org/10.3390/genes11080846.

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Genetic alterations of leucine-rich repeat kinase 2 (LRRK2), one of the most important contributors to familial Parkinson’s disease (PD), have been hypothesized to play a role in cancer development due to demographical and preclinical data. Here, we sought to define the prevalence and prognostic significance of LRRK2 somatic mutations across all types of human malignancies by querying the publicly available online genomic database cBioPortal. Ninety-six different studies with 14,041 cases were included in the analysis, and 761/14,041 (5.4%) showed genetic alterations in LRRK2. Among these, 585

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Katz, Joseph, and Ilan Rotstein. "Asthma and acute periapical abscesses." Journal of Oral Medicine and Oral Surgery 31, no. 3 (2025): 20. https://doi.org/10.1051/mbcb/2025015.

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Aim: To assess the prevalence of acute periapical abscesses (PAs) in patients with asthma treated in a large medical facility. Materials and Methods: Integrated data of hospital patients were used. History of asthma diagnosis was retrieved by querying the institutional database in the database. All cases were diagnosed for acute PAs by calibrated dentists in a hospital setting for patients admitted to urgent care. Diagnosis was made based on clinical examination and imaging data confirming the diagnosis of acute PAs without sinus tract. The odds ratio (OR) for the prevalence of acute PAs and i

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Hong, Zongchao, Xueyun Duan, Songtao Wu, Yang Yanfang, and Hezhen Wu. "Network Pharmacology Integrated Molecular Docking Reveals the Anti-COVID-19 Mechanism of Qing-Fei-Da-Yuan Granules." Natural Product Communications 15, no. 6 (2020): 1934578X2093421. http://dx.doi.org/10.1177/1934578x20934219.

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Coronavirus disease (COVID-19), caused by the novel severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2), is a highly infectious viral disease. Clinical observations have shown that Qing-Fei-Da-Yuan (QFDY) granules have good anti-COVID-19 effects, but the underlying molecular mechanisms are unclear. In this study, we explored the potential mechanism of QFDY with regard to its anti-COVID-19 effect. We first screened the active chemical constituents of QFDY based on the pharmacodynamic activity parameters, followed by screening with the Traditional Chinese Medicine Systems Pharmacology D

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Noorbakhsh, Cameron, Yang Liu, Frederick Lang, et al. "EPCO-19. SYSTEMS BIOLOGY APPROACH ON MGMT-METHYLATED, IDH WILD-TYPE SHORT-TERM SURVIVORS REVEALS MUTATIONS IN THE BRCA1-MEDIATED DNA REPAIR SIGNALING PATHWAY." Neuro-Oncology 23, Supplement_6 (2021): vi5—vi6. http://dx.doi.org/10.1093/neuonc/noab196.018.

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Abstract Numerous multi-omic studies have revealed the vast molecular complexity of glioblastoma; however, these studies have failed to identify actionable drivers for definitive therapy. Unlike conventional relational data analysis methods used to examine such data, systems biology approaches using graph databases have emerged as powerful tools with flexibility and scalability needed to reveal specific vulnerabilities. Here we demonstrate the utility of a patient-centric graph database in identifying novel factors associated with poor outcome (survival &lt; 8 months) in patients with MGMT

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Jamjoom, Aimun A. B., Angus B. Gane, and Andreas K. Demetriades. "Randomized controlled trials in neurosurgery: an observational analysis of trial discontinuation and publication outcome." Journal of Neurosurgery 127, no. 4 (2017): 857–66. http://dx.doi.org/10.3171/2016.8.jns16765.

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OBJECTIVEThis study aimed to determine the trial discontinuation and publication rate of randomized controlled trials (RCTs) in neurosurgery.METHODSTrials registered from 2000 to 2012 were identified on the website clinicaltrials.gov using a range of key words related to neurosurgery. Any trials that were actively recruiting or had unknown status were excluded. Included trials were assessed for whether they were discontinued early on the clinicaltrials.gov database; this included trials identified as withdrawn, suspended, or terminated in the database. For included trials, a range of parameter

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Kalanithi, Paul, Ryan D. Schubert, Shivanand P. Lad, Odette A. Harris, and Maxwell Boakye. "Hospital costs, incidence, and inhospital mortality rates of traumatic subdural hematoma in the United States." Journal of Neurosurgery 115, no. 5 (2011): 1013–18. http://dx.doi.org/10.3171/2011.6.jns101989.

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Object This study provides the first US national data regarding frequency, cost, and mortality rate of traumatic subdural hematoma (SDH), and identifies demographic factors affecting morbidity and death in patients with traumatic SDH undergoing surgical drainage. Methods A retrospective analysis was conducted by querying the Nationwide Inpatient Sample, the largest all-payer database of nonfederal community hospitals. All cases of traumatic SDH were identified using ICD-9 codes. The study consisted of 2 parts: 1) trends data, which were abstracted from the years 1993–2006, and 2) univariate an

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Gutman, I. M., and S. R. Gilbert. "Trends in slipped capital femoral epiphysis: is the rate declining?" Journal of Children's Orthopaedics 12, no. 5 (2018): 428–33. http://dx.doi.org/10.1302/1863-2548.12.180081.

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Purpose Slipped capital femoral epiphysis (SCFE) is an adolescent hip condition with a high risk of complication. The purpose of this study was to evaluate trends in treatment using a prospectively collected paediatric nationally representative database. Methods A total of 9034 patients undergoing treatment for idiopathic SCFE were selected by querying the Healthcare Cost and Utilization Project’s Kids’ Inpatient Database for the years 1997, 2000, 2003, 2006, 2009 and 2012. The selected patients were separated based on operative approach and these cohorts were analyzed based on temporal and ca

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Du, Jingcheng, Qing Wang, Jingqi Wang, et al. "COVID-19 trial graph: a linked graph for COVID-19 clinical trials." Journal of the American Medical Informatics Association 28, no. 9 (2021): 1964–69. http://dx.doi.org/10.1093/jamia/ocab078.

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Abstract Objective Clinical trials are an essential part of the effort to find safe and effective prevention and treatment for COVID-19. Given the rapid growth of COVID-19 clinical trials, there is an urgent need for a better clinical trial information retrieval tool that supports searching by specifying criteria, including both eligibility criteria and structured trial information. Materials and Methods We built a linked graph for registered COVID-19 clinical trials: the COVID-19 Trial Graph, to facilitate retrieval of clinical trials. Natural language processing tools were leveraged to extra

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Basharat, Amna, and Muddassar Farooq. "A smart clinical cohort selection system for clinical oncology research." Journal of Clinical Oncology 41, no. 16_suppl (2023): e13613-e13613. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.e13613.

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e13613 Background: Cohort selection for specialized clinical trials is a cardinal pillar of the evidence-based medicine; however, it is the most difficult, complex, time consuming, and expensive step. Determining the efficacy of a new treatment (or intervention) requires finding eligible patients meeting the inclusion and exclusion criteria. In specialized scenarios, the complex criteria may even require researchers to do time consuming manual reviews and analyses of electronic health records (EHRs) to shortlist qualified patients. The major contribution of this research is a set of novel sema

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Klann, Jeffrey G., Aaron Abend, Vijay A. Raghavan, Kenneth D. Mandl, and Shawn N. Murphy. "Data interchange using i2b2." Journal of the American Medical Informatics Association 23, no. 5 (2016): 909–15. http://dx.doi.org/10.1093/jamia/ocv188.

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Abstract Objective Reinventing data extraction from electronic health records (EHRs) to meet new analytical needs is slow and expensive. However, each new data research network that wishes to support its own analytics tends to develop its own data model. Joining these different networks without new data extraction, transform, and load (ETL) processes can reduce the time and expense needed to participate. The Informatics for Integrating Biology and the Bedside (i2b2) project supports data network interoperability through an ontology-driven approach. We use i2b2 as a hub, to rapidly reconfigure

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Yiu, Allen J., Graham Stephenson, Emilie Chow, and Ryan O'Connell. "Discrepancies in Aggregate Patient Data between Two Sources with Data Originating from the Same Electronic Health Record: A Case Study." Applied Clinical Informatics 16, no. 01 (2025): 137–44. https://doi.org/10.1055/a-2441-3677.

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Abstract Background Data exploration in modern electronic health records (EHRs) is often aided by user-friendly graphical interfaces providing “self-service” tools for end users to extract data for quality improvement, patient safety, and research without prerequisite training in database querying. Other resources within the same institution, such as Honest Brokers, may extract data sourced from the same EHR but obtain different results leading to questions of data completeness and correctness. Objectives Our objectives were to (1) examine the differences in aggregate output generated by a “se

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Srinivasan, Visish M., Gouthami Chintalapani, Edward A. M. Duckworth, and Peter Kan. "Advanced cone-beam CT venous angiographic imaging." Journal of Neurosurgery 129, no. 1 (2018): 114–20. http://dx.doi.org/10.3171/2017.2.jns162997.

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OBJECTIVEThe evaluation of the venous neurovasculature, especially the dural venous sinuses, is most often performed using MR or CT venography. For further assessment, diagnostic cerebral angiography may be performed. Three-dimensional rotational angiography (3D-RA) can be applied to the venous system, producing 3D rotational venography (3D-RV) and cross-sectional reconstructions, which function as an adjunct to traditional 2D digital subtraction angiography.METHODSAfter querying the database of Baylor St. Luke’s Medical Center in Houston, Texas, the authors reviewed the radiological and clini

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Loen, Harry Van, Mary Thiongo, and Yven Van Herrewege. "PO 8495 DATA SHARING IS PART OF DATA MANAGEMENT: THE NEED FOR A HOLISTIC AND COHERENT VIEW ON RESEARCH DATA MANAGEMENT." BMJ Global Health 4, Suppl 3 (2019): A46.1—A46. http://dx.doi.org/10.1136/bmjgh-2019-edc.120.

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BackgroundAwareness of data management (DM) is often restricted to ‘the cost of computers’ or ‘the need for a database’. Recently, ‘data sharing’ can be added to this shortlist. Indeed, in recent years data sharing became often required or so strongly promoted that the importance of all other aspects related to DM or data handling in clinical tended still to be overlooked. However, the development of data sharing guidelines and associated privacy regulations (e.g. the EU General Data Protection Regulation) created a new momentum for highlighting the importance of qualitative data management.Me

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Dookeran, Keith A., James M. Groh, David G. Ritacco, Lydia R. Marcus, Yang Wang, and Janine Y. Khan. "An assessment of prevalence and expenditure associated with discharge brain MRI in preterm infants." PLOS ONE 16, no. 3 (2021): e0247857. http://dx.doi.org/10.1371/journal.pone.0247857.

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To assess national expenditure associated with preterm-infant brain MRI and potential impact of reduction per Choosing Wisely campaign 2015 recommendation to “avoid routine screening term-equivalent or discharge brain MRIs in preterm-infants”. Cross-sectional U.S. trend data from the Agency for Healthcare Research and Quality (AHRQ), Healthcare Cost and Utilization Project (HCUP) Kids’ Inpatient Database (KID) database (2006, 2009, 2012, 2016) was used to estimate overall national expenditure associated with brain MRI among infants with gestational age (GA) ≤36 weeks, and also when classified

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Rolston, John D., Seunggu J. Han, Orin Bloch, and Andrew T. Parsa. "What clinical factors predict the incidence of deep venous thrombosis and pulmonary embolism in neurosurgical patients?" Journal of Neurosurgery 121, no. 4 (2014): 908–18. http://dx.doi.org/10.3171/2014.6.jns131419.

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Object Venous thromboembolisms (VTEs) occur frequently in surgical patients and can manifest as pulmonary emboli (PEs) or deep venous thromboses (DVTs). While many medical therapies have been shown to prevent VTEs, neurosurgeons are concerned about the use of anticoagulants in the postoperative setting. To better understand the prevalence of and the patient-level risk factors for VTE, the authors analyzed data from the National Surgical Quality Improvement Program (NSQIP). Methods Retrospective data on 1,777,035 patients for the years from 2006 to 2011 were acquired from the American College o

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Gabetta, M., G. Milani, M. Bucalo, et al. "Supporting Translational Research on Inherited Cardiomyopathies through Information Technology." Methods of Information in Medicine 52, no. 02 (2013): 137–47. http://dx.doi.org/10.3414/me12-01-0046.

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SummaryObjectives: The INHERITANCE project, funded by the European Commission, is aimed at studying genetic or inherited Dilated cardiomyopathies (DCM) and at understanding the impact and management of the disease within families that suffer from heart conditions that are caused by DCMs. The biomedical informatics research activity of the project aims at implementing information technology solutions to support the project team in the different phases of their research, in particular in genes screening prioritization and new gene-disease association discovery.Methods: In order to manage the hug

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Nadir, Umer, Areeba Ahmed, Michael D. Yi, et al. "Protocol of a scoping review of outcome domains in dermatology." BMJ Open 14, no. 2 (2024): e079632. http://dx.doi.org/10.1136/bmjopen-2023-079632.

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IntroductionCore outcome sets (COSs) are agreed outcomes (domains (subdomains) and instruments) that should be measured as a minimum in clinical trials or practice in certain diseases or clinical fields. Worldwide, the number of COSs is increasing and there might be conceptual overlaps of domains (subdomains) and instruments within disciplines. The aim of this scoping review is to map and to classify all outcomes identified with COS projects relating to skin diseases.Methods and analysisWe will conduct a scoping review of outcomes of skin disease-related COS initiatives to identify all concept

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Combi, Carlo, Giuseppe Pozzi, and Rosalba Rossato. "Querying temporal clinical databases on granular trends." Journal of Biomedical Informatics 45, no. 2 (2012): 273–91. http://dx.doi.org/10.1016/j.jbi.2011.11.005.

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Ragg, Susanne, Marc B. Rosenman, Eve M. Doucette, et al. "Data Visualization of Multiparameter Information in Acute Lymphoblastic Leukemia Expands the Ability To Explore Prognostic Factors." Blood 106, no. 11 (2005): 862. http://dx.doi.org/10.1182/blood.v106.11.862.862.

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Abstract In clinical studies and for patient care, data collections have become more and more complex. Clinical studies often include millions of data points, and even data collections about individual patients can include several thousand data points. To enable searches for meaningful relationships and patterns, and to gain understanding and knowledge of the data, state-of-the-art visualization approaches have to be adapted to the needs of clinicians and clinical researchers, in order to best reveal relevant patterns in the data. However, despite the progress that has been made in the field o

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Scherschinski, Lea, Joshua S. Catapano, Katherine Karahalios, et al. "Electroencephalography for detection of vasospasm and delayed cerebral ischemia in aneurysmal subarachnoid hemorrhage: a retrospective analysis and systematic review." Neurosurgical Focus 52, no. 3 (2022): E3. http://dx.doi.org/10.3171/2021.12.focus21656.

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OBJECTIVE Good functional outcomes after aneurysmal subarachnoid hemorrhage (aSAH) are often dependent on early detection and treatment of cerebral vasospasm (CVS) and delayed cerebral ischemia (DCI). There is growing evidence that continuous monitoring with cranial electroencephalography (cEEG) can predict CVS and DCI. Therefore, the authors sought to assess the value of continuous cEEG monitoring for the detection of CVS and DCI in aSAH. METHODS The cerebrovascular database of a quaternary center was reviewed for patients with aSAH and cEEG monitoring between January 1, 2017, and July 31, 20

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Kirby, Chaim, Peter F. Ambros, David Billiter, et al. "Development of an open-source, flexible framework for interinstitutional data sharing and collaboration." Journal of Clinical Oncology 30, no. 15_suppl (2012): 9583. http://dx.doi.org/10.1200/jco.2012.30.15_suppl.9583.

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9583 Background: Clinical information, “-omic” datasets, and tissue samples are becoming more difficult to harmonize and manage for advanced data mining. We believe that clinical research data can be centralized and provide direct access to sample availability and associated data from a variety of information stores. Methods: We obtained a standardized set of anonymized patient data from the International Neuroblastoma Risk Group. The cohort consists of more than 11,000 children diagnosed worldwide between 1974 and 2002. The data consist of 34 metrics, such as age at diagnosis, stage of tumor,

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Safari, Leila, and Jon D. Patrick. "Restricted natural language based querying of clinical databases." Journal of Biomedical Informatics 52 (December 2014): 338–53. http://dx.doi.org/10.1016/j.jbi.2014.07.012.

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Pressl, Christina, Caroline Jiang, Joel Correa da Rosa, Maximilian Friedrich, Winrich Freiwald, and Jonathan Tobin. "2093." Journal of Clinical and Translational Science 1, S1 (2017): 23. http://dx.doi.org/10.1017/cts.2017.93.

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OBJECTIVES/SPECIFIC AIMS: We aim to examine the epidemiological characteristics of prosopagnosia by querying and analyzing a large deidentified clinical data set from 12 New York City-based hospitals and Federally Qualified Health Centers (FQHCs). The PCORI-funded New York City Clinical Data Research Network (NYC-CDRN) contains ~4.5 million deidentified ICD-coded electronic health records (EHRs) with comprehensive longitudinal information on demographics, patient visits, clinical conditions/diagnoses, laboratory and radiology results, medications, and clinical procedures. The NYC-CDRN will be

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Berg, Kaja C. G., Paula Bousquet, Milena Blaga, et al. "Abstract A003: High-throughput TCR sequencing demonstrates induction of long-lasting HPV16-specific T cell responses in VB10.16 vaccinated advanced cervical cancer patients." Cancer Immunology Research 11, no. 12_Supplement (2023): A003. http://dx.doi.org/10.1158/2326-6074.tumimm23-a003.

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Abstract Background: Assessment of vaccine-induced T cell responses is a primary pharmacodynamic readout in cancer vaccine clinical trials. High-throughput sequencing of T cell receptors (TCRs) is emerging as a rapid and scalable method, suitable for late-stage clinical trials, and offers sensitive and accurate quantification of the full T cell repertoire. Here we performed ELISpot and TCR sequencing on serial peripheral blood mononuclear cell (PBMC) samples from a clinical phase 2 trial investigating the therapeutic HPV16 cancer vaccine VB10.16 in combination with atezolizumab in advanced cer

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Soualmia, L. F., and T. Lecroq. "From Genome Sequencing to Bedside." Yearbook of Medical Informatics 22, no. 01 (2013): 175–77. http://dx.doi.org/10.1055/s-0038-1638852.

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Summary Objectives: To summarize excellent current research in the field of Bioinformatics and Translational Informatics with application in the health domain and evidence-based medicine. Method: We provide a synopsis of the articles selected for the IMIA Yearbook 2013, from which we attempt to derive a synthetic overview of current and future activities in the field. Three steps of selection were performed by querying PubMed and Web of Science. A first set of 5,549 articles was refined into a second set of 1,272 articles from which 15 articles were retained for peer-review. Results: The selec

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Lubarsky, David A., Peter S. A. Glass, Brian Ginsberg, et al. "The Successful Implementation of Pharmaceutical Practice Guidelines." Anesthesiology 86, no. 5 (1997): 1145–60. http://dx.doi.org/10.1097/00000542-199705000-00019.

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Background Although approximately 2,000 medical practice guidelines have been proposed, few have been successfully implemented and sustained. We hypothesized that we could develop and institute practice guidelines to promote more appropriate use of costly anesthetics, to generate and sustain widespread compliance from a large physician group, and to decrease costs without adversely affecting clinical outcomes. Methods A prospective before and after comparison study was performed at a tertiary care medical center. Clinical outcomes data and times indicative of perioperative patient flow were co

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Haston, Julia C., Christina A. Rostad, Robert C. Jerris, et al. "Prospective Cohort Study of Next-Generation Sequencing as a Diagnostic Modality for Unexplained Encephalitis in Children." Journal of the Pediatric Infectious Diseases Society 9, no. 3 (2019): 326–33. http://dx.doi.org/10.1093/jpids/piz032.

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Abstract Background Encephalitis is an inflammatory condition of the brain associated with long-term neurologic sequelae and even death in children. Although viruses are often implicated, an etiology is not identified in the majority of cases. Metagenomics-based next-generation sequencing (mNGS) is a high-throughput sequencing technique that can enhance the detection of novel or low-frequency pathogens. Methods Hospitalized immunocompetent children aged 6 months to 18 years with encephalitis of unidentified etiology were eligible for enrollment. Demographic, historical, and clinical informatio

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Tayari, Oumaima, Wissal Slimene, and Jamila Jaouadi. "Risk factors for implant-supported overdenture failures: A systematic review." Journal of Indian Prosthodontic Society 24, no. 2 (2024): 109–21. http://dx.doi.org/10.4103/jips.jips_18_24.

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Aim: Implant-supported overdenture presents failures. To minimize and avoid the occurrence of implant and prosthetic complications, a number of considerations must be taken into account. This systematic review aimed to point out variables associated with failure rates of implant-supported overdenture. Settings and Design: The Preferred Reporting Items for Systematic Reviews and Meta-Analyses (PRISMA) guidelines were implemented during carrying out this systematic review. Materials and Method: An automatic electronic literature search of peer-review articles was conducted on the MEDLINE databas

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Uttiramerur, Arvind. "Best Practices for Data Management in Clinical Trials." Journal of Mathematical & Computer Applications, March 31, 2023, 1–3. http://dx.doi.org/10.47363/jmca/2023(2)169.

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This study explores the potential of LangChain, a framework for constructing applications with advanced language models, to translate natural language queries into executable SQL code. Study propose an innovative LangChain-based architecture that receives a natural language query, analyzes it with a language model, and generates the corresponding SQL statement for database querying. This approach aims to empower non-technical users, facilitate inter-team collaboration, and enable data-informed decision-making. However, challenges persist, including managing complex queries and grasping domain-

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Tradigo, G., P. Veltri, and S. Greco. "Geomedica: managing and querying clinical data distributions on geographical database systems." June 2, 2010. https://doi.org/10.1016/j.procs.2010.04.108.

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Lee, Chien-Yueh, Amrita Chattopadhyay, Li-Mei Chiang, et al. "VariED: the first integrated database of gene annotation and expression profiles for variants related to human diseases." Database 2019 (January 1, 2019). http://dx.doi.org/10.1093/database/baz075.

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Abstract Integrated analysis of DNA variants and gene expression profiles may facilitate precise identification of gene regulatory networks involved in disease mechanisms. Despite the widespread availability of public resources, we lack databases that are capable of simultaneously providing gene expression profiles, variant annotations, functional prediction scores and pathogenic analyses. VariED is the first web-based querying system that integrates an annotation database and expression profiles for genetic variants. The database offers a user-friendly platform and locates gene/variant names

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Seemab, Umair, Anna Kalatanova, Saad Hassan, Ziaurrehman Tanoli, and Henri Leinonen. "ODDB: An interactive database for clinical and translational research in ocular diseases." Acta Ophthalmologica 103, S284 (2025). https://doi.org/10.1111/aos.17041.

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Aims/Purpose: To develop and validate a comprehensive web‐based interactive database of ocular diseases, including information of, for instance, associated genes, biomarkers, and medications.Methods: Initially, a thorough literature review was conducted to identify key ocular diseases and their associated genes and biomarkers. Data was then curated from multiple reputable sources, including peer‐reviewed journals, clinical trial repositories and drug regulatory agency databases. Advanced data integration techniques were employed to link various data types. The database interface was designed t

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Seemab, Umair, Anna Kalatanova, Saad Hassan, Ziaurrehman Tanoli, and Henri Leinonen. "ODDB: An interactive database for clinical and translational research in ocular diseases." Acta Ophthalmologica 103, S284 (2025). https://doi.org/10.1111/aos.17313.

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Aims/Purpose: To develop and validate a comprehensive web‐based interactive database of ocular diseases, including information of, for instance, associated genes, biomarkers, and medications.Methods: Initially, a thorough literature review was conducted to identify key ocular diseases and their associated genes and biomarkers. Data was then curated from multiple reputable sources, including peer‐reviewed journals, clinical trial repositories and drug regulatory agency databases. Advanced data integration techniques were employed to link various data types. The database interface was designed t

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