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Seminars in Oncology Nursing Apr 2023This article provides practical guidance on developing a comprehensible abstract, including those required for funding applications, conferences, and publication. In... (Review)
Review
OBJECTIVES
This article provides practical guidance on developing a comprehensible abstract, including those required for funding applications, conferences, and publication. In addition, we discuss and demonstrate the practicalities of editing and revising an abstract for conference or peer review and identify emerging formats that may be more relevant to nurses and researchers.
DATA SOURCES
This article has been informed by literature and the coauthors' respective experiences of preparing and reviewing abstracts for publication and conference presentation.
CONCLUSION
Abstracts are a valuable tool to communicate the most important elements of the methods and results of a research project for a conference, manuscript, or even a research funding application. However, abstracts may often be an overlooked part of the dissemination process. An abstract determines whether or not a piece of research is relevant for presentation at a conference or valuable enough to be considered for peer review and subsequent publication. A strong and clearly written abstract positively predisposes reviewers of grant applications.
IMPLICATIONS FOR NURSING PRACTICE
Writing an abstract is arguably the most challenging component of academic writing, summarizing the results of a substantive research project in three to five sentences and positioning them concisely within the background and implications for future practice, policy, and research. A well-written abstract is clear, concise, and critical and requires time and revision to ensure success.
Topics: Humans; Abstracting and Indexing; Writing; Peer Review; Language
PubMed: 36841679
DOI: 10.1016/j.soncn.2023.151395 -
JCO Clinical Cancer Informatics Feb 2021Lack of interoperability is one of the greatest challenges facing healthcare informatics. Recent interoperability efforts have focused primarily on data transmission and...
Lack of interoperability is one of the greatest challenges facing healthcare informatics. Recent interoperability efforts have focused primarily on data transmission and generally ignore data capture standardization. Structured Data Capture (SDC) is an open-source technical framework that enables the capture and exchange of standardized and structured data in interoperable data entry forms (DEFs) at the point of care. Some of SDC's primary use cases concern complex oncology data such as anatomic pathology, biomarkers, and clinical oncology data collection and reporting. Its interoperability goals are the preservation of semantic, contextual, and structural integrity of the captured data throughout the data's lifespan. SDC documents are written in eXtensible Markup Language (XML) and are therefore computer readable, yet technology agnostic-SDC can be implemented by any EHR vendor or registry. Any SDC-capable system can render an SDC XML file into a DEF, receive and parse an SDC transmission, and regenerate the original SDC form as a DEF or synoptic report with the response data intact. SDC is therefore able to facilitate interoperable data capture and exchange for patient care, clinical trials, cancer surveillance and public health needs, clinical research, and computable care guidelines. The usability of SDC-captured oncology data is enhanced when the SDC data elements are mapped to standard terminologies. For example, an SDC map to Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) enables aggregation of SDC data with other related data sets and permits advanced queries and groupings on the basis of SNOMED CT concept attributes and description logic. SDC supports terminology maps using separate map files or as terminology codes embedded in an SDC document.
Topics: Delivery of Health Care; Humans; Medical Oncology; Semantics; Systematized Nomenclature of Medicine
PubMed: 33591796
DOI: 10.1200/CCI.20.00103 -
Bioinformatics (Oxford, England) Oct 2022Transcriptome-based gene co-expression analysis has become a standard procedure for structured and contextualized understanding and comparison of different conditions...
MOTIVATION
Transcriptome-based gene co-expression analysis has become a standard procedure for structured and contextualized understanding and comparison of different conditions and phenotypes. Since large study designs with a broad variety of conditions are costly and laborious, extensive comparisons are hindered when utilizing only a single dataset. Thus, there is an increased need for tools that allow the integration of multiple transcriptomic datasets with subsequent joint analysis, which can provide a more systematic understanding of gene co-expression and co-functionality within and across conditions. To make such an integrative analysis accessible to a wide spectrum of users with differing levels of programming expertise it is essential to provide user-friendliness and customizability as well as thorough documentation.
RESULTS
This article introduces horizontal CoCena (hCoCena: horizontal construction of co-expression networks and analysis), an R-package for network-based co-expression analysis that allows the analysis of a single transcriptomic dataset as well as the joint analysis of multiple datasets. With hCoCena, we provide a freely available, user-friendly and adaptable tool for integrative multi-study or single-study transcriptomics analyses alongside extensive comparisons to other existing tools.
AVAILABILITY AND IMPLEMENTATION
The hCoCena R-package is provided together with R Markdowns that implement an exemplary analysis workflow including extensive documentation and detailed descriptions of data structures and objects. Such efforts not only make the tool easy to use but also enable the seamless integration of user-written scripts and functions into the workflow, creating a tool that provides a clear design while remaining flexible and highly customizable. The package and additional information including an extensive Wiki are freely available on GitHub: https://github.com/MarieOestreich/hCoCena. The version at the time of writing has been added to Zenodo under the following link: https://doi.org/10.5281/zenodo.6911782.
SUPPLEMENTARY INFORMATION
Supplementary data are available at Bioinformatics online.
Topics: Gene Expression Profiling; Phenotype; Software; Transcriptome; Workflow
PubMed: 36018233
DOI: 10.1093/bioinformatics/btac589 -
Advances in Health Sciences Education :... Oct 2023Therapeutic reasoning is when the purpose, task, or goal for engaging in reasoning is to determine the patient's management plan. As the field's understanding of the... (Review)
Review
Therapeutic reasoning is when the purpose, task, or goal for engaging in reasoning is to determine the patient's management plan. As the field's understanding of the process of therapeutic reasoning is less well understood, we focused on studies that collected data on the process of therapeutic reasoning. To synthesize previous studies of therapeutic reasoning characteristics, methodological approaches, theoretical underpinnings, and results. We conducted a scoping review with systematic searching for English language articles with no date limits. Databases included MEDLINE, CINAHL Plus, Scopus, Embase, Proquest Dissertations and Theses Global, and ERIC. Search terms captured therapeutic reasoning in health professions education research. Initial search yielded 5450 articles. The title and abstract screening yielded 180 articles. After full-text review, 87 studies were included in this review. Articles were excluded if they were outside health professions education, did not collect data on the process of therapeutic reasoning, were not empirical studies, or not focused on therapeutic reasoning. We analyzed the included articles according to scoping questions using qualitative content analysis. 87 articles dated from 1987 to 2019 were included. Several study designs were employed including think-aloud protocol, interview and written documentation. More than half of the articles analyzed the data using qualitative coding. Authors often utilized several middle-range theories to explain therapeutic reasoning processes. The hypothetico-deductive model was most frequently mentioned. The included articles rarely built off the results from previous studies. Six key result categories were found: identifying themes, characterizing and testing previous local theory, exploring factors, developing new local theory, testing tools, and testing hypothesis. Despite the cast body of therapeutic reasoning research, individual study results remain isolated from previous studies. Our future recommendations include synthesizing pre-existing models, developing novel methodologies, and investigating other aspects of therapeutic reasoning.
Topics: Humans; Empirical Research; Health Personnel; Motivation
PubMed: 37043070
DOI: 10.1007/s10459-022-10187-7 -
Journal of Immigrant and Minority Health Feb 2021The medical-legal partnership addresses social and political determinants of health. Yet, relatively little is known about best practices for these two service providers... (Review)
Review
The medical-legal partnership addresses social and political determinants of health. Yet, relatively little is known about best practices for these two service providers collaborating to deliver integrated services, particularly to im/migrant communities. To investigate evaluations of existing medical-legal partnerships in order to understand how they function together, what they provide, and how they define and deliver equitable, integrated care. We searched five databases (PubMed, Medline, Web of Science, HeinOnline, and Nexus Uni) using search terms related to "medical-legal partnerships", "migrants", and "United States". We systematically evaluated ten themes related to how medical and legal teams interacted, were situated, organized, and who they served. Articles were published in English between 2010 and 2019; required discussion about a direct partnership between medical and legal professionals; and focused on providing clinical care and legal services to im/migrant populations. Eighteen articles met our inclusion criteria. The most common form of partnership was a model in which legal clinics make regular referrals to medical clinics, although the reverse was also common. Most services were not co-located. Partnerships often engaged in advocacy work, provided translation services, and referred clients to non-medical providers and legal services. This review demonstrates the benefits of a legal-medical partnership, such as enhancing documentation and care for im/migrants and facilitating a greater attention to political determinants of health. Yet, this review demonstrates that, despite the increasing salience of such partnership, few have written up their lessons learned and best practices.
Topics: Delivery of Health Care; Emigrants and Immigrants; Humans; Legal Services; Transients and Migrants; United States
PubMed: 32978741
DOI: 10.1007/s10903-020-01088-1 -
HCA Healthcare Journal of Medicine 2023Quality improvement (QI) is a major focus of all departments and fields of health care, including emergency medical services. The chaotic and rapidly evolving atmosphere...
INTRODUCTION
Quality improvement (QI) is a major focus of all departments and fields of health care, including emergency medical services. The chaotic and rapidly evolving atmosphere in which paramedics must practice can lead to inconsistency between what is documented and the actual events. This leads to difficulty when trying to evaluate the practitioners and when implementing a QI program. In this study, we evaluated the prevalence of discrepancy between the video and written record for Rapid Sequence Intubation (RSI) performed in the field as a demonstration of the utility of video documentation in QI.
METHODS
We used a systematic retrospective chart review to compare written with video documentation in 100 consecutive prehospital RSI encounters in a single EMS agency.
RESULTS
Of the patient care records (PCRs), only 6% matched the video record for all quality measures tracked. The largest reason for the discrepancy was in the time required to intubate (58%) whether LEMON was evaluated (42%), total number of intubation attempts (36%), first attempt success (24%), BVM used (18%), and whether an airway introducer device was used (12%).
CONCLUSION
Written documentation is inaccurate compared to video documentation when used as a quality improvement process for EMS prehospital RSI encounters.
PubMed: 37753416
DOI: 10.36518/2689-0216.1183 -
Viruses Dec 2023Despite the outstanding progress that has been made in the prevention, detection, and management of hepatitis B during the past decades, hepatitis B remains a problem... (Review)
Review
Despite the outstanding progress that has been made in the prevention, detection, and management of hepatitis B during the past decades, hepatitis B remains a problem among healthcare personnel (HCP) in many countries. We reviewed studies on all aspects of hepatitis B in HCP published from 2017 through April 2023. They revealed wide variations on the prevalence of infection among HCP, ranging from 0.6% in Europe to >8.7% in Africa, almost always in association with very low vaccination rates. Many studies found a significant association between HCP's knowledge about hepatitis B and hepatitis B vaccines, their vaccination status, and practices. This research also discloses global inequities regarding vaccination policies against hepatitis B, free-of-charge vaccinations, and access to post-exposure prophylaxis (PEP). Strategies to prevent and manage accidental exposures are needed in order to reduce the burden of hepatitis B on HCP, while written policies for all aspects of infection prevention, protective equipment, and PEP should be available. Lastly, HCP should be accordingly educated. These are all imperative given the decline of routine vaccinations in the COVID-19 era, particularly in countries with fragile vaccination programs, and the disruptions of interventions for hepatitis B that are expected to provide a pool of virus transmission to future generations.
Topics: Humans; Health Personnel; Hepatitis B; Vaccination; Hepatitis B Vaccines; Delivery of Health Care
PubMed: 38140695
DOI: 10.3390/v15122454 -
Lakartidningen Oct 2023The scientific documentation of prehospital emergency care in Sweden is slowly expanding. The first thesis on the value of a mobile coronary care unit was defended in...
The scientific documentation of prehospital emergency care in Sweden is slowly expanding. The first thesis on the value of a mobile coronary care unit was defended in 1982. Since then, at least 106 theses have been defended at 15 educational institutes in Sweden. The theses can be divided into nine different themes, of which acute disease and prognostic factors (n = 30) is the most common, followed in order of frequency by caring, assessment and decision (n = 18), patient and next of kin perspective (n = 14), trauma (n = 1 1), competence, learning, and education (n = 10), care needs, cooperation, and prioritization (n = 10), disaster (n = 7), workers' health and environment (n = 3), and ethics and values (n = 3). The University of Gothenburg had the highest number of theses defended (n = 28), followed by the Karolinska Institute (n = 24) and the University of Umeå (n = 10). The theses were written by 64 nurses, 36 physicians, two public health specialists, one physiotherapist, one priest, one social worker, and one statistician.
Topics: Humans; Emergency Medical Services; Documentation; Sweden
PubMed: 37860864
DOI: No ID Found -
PeerJ 2022Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the...
BACKGROUND
Protein function prediction is an important part of bioinformatics and genomics studies. There are many different predictors available, however most of these are in the form of web-servers instead of open-source locally installable versions. Such local versions are necessary to perform large scale genomics studies due to the presence of limitations imposed by web servers such as queues, prediction speed, and updatability of databases.
METHODS
This paper describes Wei2GO: a weighted sequence similarity and python-based open-source protein function prediction software. It uses DIAMOND and HMMScan sequence alignment searches against the UniProtKB and Pfam databases respectively, transfers Gene Ontology terms from the reference protein to the query protein, and uses a weighing algorithm to calculate a score for the Gene Ontology annotations.
RESULTS
Wei2GO is compared against the Argot2 and Argot2.5 web servers, which use a similar concept, and DeepGOPlus which acts as a reference. Wei2GO shows an increase in performance according to precision and recall curves, F scores, and S scores for biological process and molecular function ontologies. Computational time compared to Argot2 and Argot2.5 is decreased from several hours to several minutes.
AVAILABILITY
Wei2GO is written in Python 3, and can be found at https://gitlab.com/mreijnders/Wei2GO.
Topics: Software; Algorithms; Molecular Sequence Annotation; Proteins; Databases, Protein
PubMed: 35186498
DOI: 10.7717/peerj.12931 -
JAMA Network Open Sep 2022Duplicated text is a well-documented hazard in electronic medical records (EMRs), leading to wasted clinician time, medical error, and burnout. This study hypothesizes...
IMPORTANCE
Duplicated text is a well-documented hazard in electronic medical records (EMRs), leading to wasted clinician time, medical error, and burnout. This study hypothesizes that text duplication is prevalent and increases with time and EMR size and that duplicate information is shared across authors.
OBJECTIVE
To examine the prevalence and scope of duplication behavior in clinical notes from a large academic health system and the factors associated with duplication.
DESIGN, SETTING, AND PARTICIPANTS
This retrospective, cross-sectional analysis of note length and content duplication rates used a set of 10 adjacent word tokens (ie, a 10-gram) sliding-window approach to identify spans of text duplicated exactly from earlier notes in a patient's record for all inpatient and outpatient notes written within the University of Pennsylvania Health System from January 1, 2015, through December 31, 2020. Text duplicated from a different author vs text duplicated from the same author was quantified. Furthermore, novel text and duplicated text per author for various note types and author types, as well as per patient record by number of notes in the record, were quantified. Information scatter, another documentation hazard, was defined as the inverse of novel text per note, and the association between information duplication and information scatter was graphed. Data analysis was performed from January to March 2022.
MAIN OUTCOMES AND MEASURES
Total, novel, and duplicate text by note type and note author were determined, as were the mean intra-author and inter-author duplication per note by type and author.
RESULTS
There were a total of 104 456 653 notes for 1 960 689 unique patients consisting of 32 991 489 889 words; 50.1% of the total text in the record (16 523 851 210 words) was duplicated from prior text written about the same patient. The duplication fraction increased year-over-year, from 33.0% for notes written in 2015 to 54.2% for notes written in 2020. Of the text duplicated, 54.1% came from text written by the same author, whereas 45.9% was duplicated from a different author. Records with more notes had more total duplicate text, approaching 60%. Note types with high information scatter tended to have low information overload, and vice versa, suggesting a trade-off between these 2 hazards under the current documentation paradigm.
CONCLUSIONS AND RELEVANCE
Duplicate text casts doubt on the veracity of all information in the medical record, making it difficult to find and verify information in day-to-day clinical work. The findings of this cross-sectional study suggest that text duplication is a systemic hazard, requiring systemic interventions to fix, and simple solutions such as banning copy-paste may have unintended consequences, such as worsening information scatter. The note paradigm should be further examined as a major cause of duplication and scatter, and alternative paradigms should be evaluated.
Topics: Cross-Sectional Studies; Documentation; Electronic Health Records; Humans; Prevalence; Retrospective Studies
PubMed: 36156143
DOI: 10.1001/jamanetworkopen.2022.33348