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Acta Informatica Medica : AIM : Journal... Jun 2023Transfusion treatment during life, as well as pregnancy in women, can stimulate the sensitization of the person who received blood, which after the transfusion of blood...
BACKGROUND
Transfusion treatment during life, as well as pregnancy in women, can stimulate the sensitization of the person who received blood, which after the transfusion of blood products can result in the occurrence of moderate to very severe posttransfusion reactions.
OBJECTIVE
The aim of this study was to examine the specificity and frequency of antierythrocyte antibodies during the pretransfusion treatment of patients depending on the gender, to determine the origin of antibodies in patients serum, as well as to examine their clinical significance.
METHODS
Retrospective analysis of documentation was performed in the Department for Pretransfusion Testing, therapy and distribution of blood products, Polyclinic for Transfusion, UKC Tuzla. Data was analyzed by reviewing the written and electronic documentation from the period of 5 years (2018-2022).
RESULTS
A retrospective analysis of 378 procedures for the identification of antierythrocyte antibodies was performed. It was evident that 140 of all detected antibodies belonged to the Rh-system (66.7%), of which 32.4% were anti RhD-antibodies, 20% anti Rh-E, anti Rh-c 7.1%, and in a low percent of anti-C, anti-e and anti-Cw antibodies. Combinations of anti-D and anti-C antibodies showed the highest frequency (34.2%), followed by a combination of anti-E and anti-c antibodies (21%).
CONCLUSION
Pretransfusion testing represents a very important link in the safety of the use of blood. The identification of antierythrocyte antibodies and the use of phenotyped blood products significantly reduces the risk of posttransfusion reactions and facilitates the implementation of the safe blood policy.
PubMed: 37711496
DOI: 10.5455/aim.2023.31.121-125 -
PloS One 2021While potentially timesaving, there is no program to automatically transform diagnosis codes of the ICD-10 German modification (ICD-10-GM) into the injury severity score...
BACKGROUND
While potentially timesaving, there is no program to automatically transform diagnosis codes of the ICD-10 German modification (ICD-10-GM) into the injury severity score (ISS).
OBJECTIVE
To develop a mapping method from ICD-10-GM into ICD-10 clinical modification (ICD-10-CM) to calculate the abbreviated injury scale (AIS) and ISS of each patient using the ICDPIC-R and to compare the manually and automatically calculated scores.
METHODS
Between January 2019 and June 2021, the most severe AIS of each body region and the ISS were manually calculated using medical documentation and radiology reports of all major trauma patients of a German level I trauma centre. The ICD-10-GM codes of these patients were exported from the electronic medical data system SAP, and a Java program was written to transform these into ICD-10-CM codes. Afterwards, the ICDPIC-R was used to automatically generate the most severe AIS of each body region and the ISS. The automatically and manually determined ISS and AIS scores were then tested for equivalence.
RESULTS
Statistical analysis revealed that the manually and automatically calculated ISS were significantly equivalent over the entire patient cohort. Further sub-group analysis, however, showed that equivalence could only be demonstrated for patients with an ISS between 16 and 24. Likewise, the highest AIS scores of each body region were not equal in the manually and automatically calculated group.
CONCLUSION
Though achieving mapping results highly comparable to previous mapping methods of ICD-10-CM diagnosis codes, it is not unrestrictedly possible to automatically calculate the AIS and ISS using ICD-10-GM codes.
Topics: Adolescent; Adult; Aged; Aged, 80 and over; Automation; Child; Child, Preschool; Emergency Service, Hospital; Hip Fractures; Humans; Injury Severity Score; International Classification of Diseases; Middle Aged; Observer Variation; Young Adult
PubMed: 34506562
DOI: 10.1371/journal.pone.0257183 -
Saudi Pharmaceutical Journal : SPJ :... Nov 2023High-quality documentation is critical in medical settings for providing safe patient care. This study was done with the objective of assessing the standard of medical...
BACKGROUND AND OBJECTIVES
High-quality documentation is critical in medical settings for providing safe patient care. This study was done with the objective of assessing the standard of medical records in anticoagulation clinics and investigating the distinctions between notes written by pharmacists and physicians.
METHODS
A retrospective cross-sectional analysis of data from electronic health records (EHRs) was performed on patients who received anticoagulation and were observed at anticoagulation clinics from October to December 2020. Patients were monitored in two anticoagulation clinics, one administered by pharmacists and the other by physicians. The quality of the documentation was assessed using a score, and the note was assigned one of five categories according to its score: very good, good, average, poor, and very poor. The data was analyzed using Stata/SE 13.1. P value<0.05 was considered significant in all analytical tests.
RESULTS
A total of 331 patients were included. While 160 patients (48.3%) were followed by the physician-led clinic, 171 (51.6%) were by the pharmacist-led clinic. The average age of the patients was 54 ± 15. 60.73% of them were female, and 90.3% of them were Saudi nationals. Warfarin was the most widely used anticoagulant (70%), followed by rivaroxaban (15.7%). Compared to physicians, pharmacists demonstrated very strong documentation (54% vs. 18%). The examination of the variables considered in the study revealed that physicians had significantly less drug-drug interaction documentation (17 vs. 71 times) or drug-food interaction documentation (23 vs. 71 times) than pharmacists. In terms of follow-up frequency, pharmacists were found to adhere to the clinic protocol (150 times) more frequently than physicians (104 times). However, there was no significant difference in therapeutic plan documentation between the two groups. ( = 0.416).
CONCLUSION
Pharmacists were more comprehensive in their documentation than physicians in anticoagulation clinics. Unified clinic documentation can ensure consistent documentation within EHRs across all disciplines.
PubMed: 37822696
DOI: 10.1016/j.jsps.2023.101795 -
BMJ Open Quality Nov 2022The purpose of this quality improvement project was to improve the rate of pregnancy counselling and documentation regarding the risk of being on teratogenic...
The purpose of this quality improvement project was to improve the rate of pregnancy counselling and documentation regarding the risk of being on teratogenic medications, including leflunomide, mycophenolate, methotrexate or cyclophosphamide in women of childbearing age (17-50 years). Our goal was to increase documentation rates by 25% in 6 months. We first performed an EMR chart review of 103 women who were seen in the 6 months prior to intervention by faculty at a single rheumatology academic centre. We then determined how many of those women had documented contraception or pregnancy counselling, which included written documentation anywhere in the note or ICD codes which were specific to pregnancy counselling or contraception counselling. Interventions were then implemented. The percentage of women who had documented pregnancy counselling did not change preintervention and postintervention; preintervention 37% of women received documented pregnancy counselling and postintervention 35% of women received documented pregnancy counselling. The percentage of women who had documented contraception counselling did however change preintervention and postintervention; preintervention 37% of women received documented contraception counselling and postintervention 51% of women received documented contraception counselling, which is a 14% improvement.
Topics: Pregnancy; Female; Humans; Adolescent; Young Adult; Adult; Middle Aged; Quality Improvement; Rheumatology; Contraception; Counseling; Documentation
PubMed: 36332937
DOI: 10.1136/bmjoq-2022-001871 -
Biological Imaging 2022In this paper, we summarize a global survey of 484 participants of the imaging community, conducted in 2020 through the NIH Center for Open BioImage Analysis (COBA)....
In this paper, we summarize a global survey of 484 participants of the imaging community, conducted in 2020 through the NIH Center for Open BioImage Analysis (COBA). This 23-question survey covered experience with image analysis, scientific background and demographics, and views and requests from different members of the imaging community. Through open-ended questions we asked the community to provide feedback for the open-source tool developers and tool user groups. The community's requests for tool developers include general improvement of tool documentation and easy-to-follow tutorials. Respondents encourage tool users to follow the best practices guidelines for imaging and ask their image analysis questions on the Scientific Community Image forum (forum.image.sc). We analyzed the community's preferred method of learning, based on level of computational proficiency and work description. In general, written step-by-step and video tutorials are preferred methods of learning by the community, followed by interactive webinars and office hours with an expert. There is also enthusiasm for a centralized location online for existing educational resources. The survey results will help the community, especially developers, trainers, and organizations like COBA, decide how to structure and prioritize their efforts.
PubMed: 35387317
DOI: 10.1017/S2633903X21000039 -
BMC Medical Informatics and Decision... Jan 2023The lack of interoperability between health information systems reduces the quality of care provided to patients and wastes resources. Accordingly, there is an urgent...
BACKGROUND
The lack of interoperability between health information systems reduces the quality of care provided to patients and wastes resources. Accordingly, there is an urgent need to develop integration mechanisms among the various health information systems. The aim of this review was to investigate the interoperability requirements for heterogeneous health information systems and to summarize and present them.
METHODS
In accordance with the PRISMA guideline, a broad electronic search of all literature was conducted on the topic through six databases, including PubMed, Web of science, Scopus, MEDLINE, Cochrane Library and Embase to 25 July 2022. The inclusion criteria were to select English-written articles available in full text with the closest objectives. 36 articles were selected for further analysis.
RESULTS
Interoperability has been raised in the field of health information systems from 2003 and now it is one of the topics of interest to researchers. The projects done in this field are mostly in the national scope and to achieve the electronic health record. HL7 FHIR, CDA, HIPAA and SNOMED-CT, SOA, RIM, XML, API, JAVA and SQL are among the most important requirements for implementing interoperability. In order to guarantee the concept of data exchange, semantic interaction is the best choice because the systems can recognize and process semantically similar information homogeneously.
CONCLUSIONS
The health industry has become more complex and has new needs. Interoperability meets this needs by communicating between the output and input of processor systems and making easier to access the data in the required formats.
Topics: Humans; Health Information Systems; Electronic Health Records; Systematized Nomenclature of Medicine
PubMed: 36694161
DOI: 10.1186/s12911-023-02115-5 -
BMC Bioinformatics Jun 2022The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is...
BACKGROUND
The three-dimensional nuclear arrangement of chromatin impacts many cellular processes operating at the DNA level in animal and plant systems. Chromatin organization is a dynamic process that can be affected by biotic and abiotic stresses. Three-dimensional imaging technology allows to follow these dynamic changes, but only a few semi-automated processing methods currently exist for quantitative analysis of the 3D chromatin organization.
RESULTS
We present an automated method, Nuclear Object DetectionJ (NODeJ), developed as an imageJ plugin. This program segments and analyzes high intensity domains in nuclei from 3D images. NODeJ performs a Laplacian convolution on the mask of a nucleus to enhance the contrast of intra-nuclear objects and allow their detection. We reanalyzed public datasets and determined that NODeJ is able to accurately identify heterochromatin domains from a diverse set of Arabidopsis thaliana nuclei stained with DAPI or Hoechst. NODeJ is also able to detect signals in nuclei from DNA FISH experiments, allowing for the analysis of specific targets of interest.
CONCLUSION AND AVAILABILITY
NODeJ allows for efficient automated analysis of subnuclear structures by avoiding the semi-automated steps, resulting in reduced processing time and analytical bias. NODeJ is written in Java and provided as an ImageJ plugin with a command line option to perform more high-throughput analyses. NODeJ can be downloaded from https://gitlab.com/axpoulet/image2danalysis/-/releases with source code, documentation and further information avaliable at https://gitlab.com/axpoulet/image2danalysis . The images used in this study are publicly available at https://www.brookes.ac.uk/indepth/images/ and https://doi.org/10.15454/1HSOIE .
Topics: Animals; Arabidopsis; Cell Nucleus; Chromatin; Image Processing, Computer-Assisted; Imaging, Three-Dimensional; Software
PubMed: 35668354
DOI: 10.1186/s12859-022-04743-6 -
Archives of Disease in Childhood. Fetal... Mar 2020To assess the accuracy of real-time delivery room resuscitation documentation. (Observational Study)
Observational Study
OBJECTIVE
To assess the accuracy of real-time delivery room resuscitation documentation.
DESIGN
Retrospective observational study.
SETTING
Level 3 academic neonatal intensive care unit.
PARTICIPANTS
Fifty infants with video recording of neonatal resuscitation.
MAIN OUTCOME MEASURES
Vital sign assessments and interventions performed during resuscitation. The accuracy of written documentation was compared with video gold standard.
RESULTS
Timing of initial heart rate assessment agreed with video in 44/50 (88%) records; the documented heart rate was correct in 34/44 (77%) of these. Heart rate and oxygen saturation were documented at 5 min of life in 90% of resuscitations. Of these, 100% of heart rate and 93% of oxygen saturation values were correctly recorded. Written records accurately reflected the mode(s) of respiratory support for 89%-100%, procedures for 91%-100% and medications for 100% of events.
CONCLUSION
Real-time documentation correctly reflects interventions performed during delivery room resuscitation but is less accurate for early vital sign assessments.
Topics: Academic Medical Centers; Delivery Rooms; Documentation; Heart Rate; Humans; Infant, Newborn; Intensive Care Units, Neonatal; Oxygen; Resuscitation; Retrospective Studies; Time Factors; Video Recording
PubMed: 30472661
DOI: 10.1136/archdischild-2018-315723 -
CHAPERON: A tool for automated GROMACS-based molecular dynamics simulations and trajectory analyses.Computational and Structural... 2023Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide...
Molecular dynamics (MD) simulation is a powerful computational tool used in biomolecular studies to investigate the dynamics, energetics, and interactions of a wide range of biological systems at the atomic level. GROMACS is a widely used free and open-source biomolecular MD simulation software recognized for its efficiency, accuracy, and extensive range of simulation options. However, the complexity of setting up, running, and analyzing MD simulations for diverse systems often poses a significant challenge, requiring considerable time, effort, and expertise. Here, we introduce CHAPERON, a tool that automates the GROMACS MD simulation pipelines for protein and protein-ligand systems. CHAPERON also integrates seamlessly with GROMACS modules and third-party tools to provide comprehensive analyses of MD simulation trajectories, offering up to 20 post-simulation processing and trajectory analyses. It also streamlines and automates established pipelines for conducting and analyzing biased MD simulations via the steered MD-umbrella sampling workflow. Thus, CHAPERON makes MD simulations more accessible to beginner GROMACS users whilst empowering experts to focus on data interpretation and other less programmable aspects of MD simulation workflows. CHAPERON is written in Bash and Python, and the source code is freely available at https://github.com/abeebyekeen/CHAPERONg. Detailed documentation and tutorials are available online at dedicated web pages accessible via https://abeebyekeen.com/chaperong-online.
PubMed: 37854635
DOI: 10.1016/j.csbj.2023.09.024 -
Database : the Journal of Biological... Oct 2022The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and...
The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such as preprint publications, i.e. articles not yet validated by peer review, have become crucial hubs for the dissemination of scientific results. Natural language processing (NLP) systems have been recently developed to extract and organize COVID-19 data in reasoning systems. Given this scenario, the BioCreative COVID-19 text mining tool interactive demonstration track was created to assess the landscape of the available tools and to gauge user interest, thereby providing a two-way communication channel between NLP system developers and potential end users. The goal was to inform system designers about the performance and usability of their products and to suggest new additional features. Considering the exploratory nature of this track, the call for participation solicited teams to apply for the track, based on their system's ability to perform COVID-19-related tasks and interest in receiving user feedback. We also recruited volunteer users to test systems. Seven teams registered systems for the track, and >30 individuals volunteered as test users; these volunteer users covered a broad range of specialties, including bench scientists, bioinformaticians and biocurators. The users, who had the option to participate anonymously, were provided with written and video documentation to familiarize themselves with the NLP tools and completed a survey to record their evaluation. Additional feedback was also provided by NLP system developers. The track was well received as shown by the overall positive feedback from the participating teams and the users. Database URL: https://biocreative.bioinformatics.udel.edu/tasks/biocreative-vii/track-4/.
Topics: COVID-19; Data Mining; Databases, Factual; Documentation; Humans; Natural Language Processing
PubMed: 36197453
DOI: 10.1093/database/baac084