Background
Qualitative research approaches are increasingly integrated into medical education research to answer relevant questions that quantitative methodologies cannot accommodate. However, ...researchers have found that traditional qualitative methodological approaches reflect the foundations and objectives of disciplines whose aims are recognizably different from the medical education domain of inquiry (Thorne, 2016, Interpretive description. New York, NY: Routledge). Interpretive description (ID), a widely used qualitative research method within nursing, offers an accessible and theoretically flexible approach to analysing qualitative data within medical education research. ID is an appropriate methodological alternative for medical education research, as it can address complex experiential questions while producing practical outcomes. It allows for the advancement of knowledge surrounding educational experience without sacrificing methodological integrity that long‐established qualitative approaches provide.
Purpose
In this paper, we present interpretive description as a useful research methodology for qualitative approaches within medical education. We then provide a toolkit for medical education researchers interested in incorporating interpretive description into their study design. We propose a coherent set of strategies for identifying analytical frameworks, sampling, data collection, analysis, rigour and the limitations of ID for medical education research. We conclude by advocating for the interpretive description approach as a viable and flexible methodology for medical education research.
In the latest "Research Approaches" article, Thompson‐Burdine et al. introduce us to Interpretive Description as a means for addressing complex experiential questions while producing practical outcomes.
Multiple sequence alignments are fundamental to many sequence analysis methods. Most alignments are computed using the progressive alignment heuristic. These methods are starting to become a ...bottleneck in some analysis pipelines when faced with data sets of the size of many thousands of sequences. Some methods allow computation of larger data sets while sacrificing quality, and others produce high‐quality alignments, but scale badly with the number of sequences. In this paper, we describe a new program called Clustal Omega, which can align virtually any number of protein sequences quickly and that delivers accurate alignments. The accuracy of the package on smaller test cases is similar to that of the high‐quality aligners. On larger data sets, Clustal Omega outperforms other packages in terms of execution time and quality. Clustal Omega also has powerful features for adding sequences to and exploiting information in existing alignments, making use of the vast amount of precomputed information in public databases like Pfam.
Multiple sequence alignments are fundamental to many sequence analysis methods. The new program Clustal Omega can align virtually any number of protein sequences quickly and has powerful features for adding sequences to existing precomputed alignments.
The Covid19 infection is caused by the SARS-CoV-2 virus, a novel member of the coronavirus (CoV) family. CoV genomes code for a ORF1a / ORF1ab polyprotein and four structural proteins widely studied ...as major drug targets. The genomes also contain a variable number of open reading frames (ORFs) coding for accessory proteins that are not essential for virus replication, but appear to have a role in pathogenesis. The accessory proteins have been less well characterized and are difficult to predict by classical bioinformatics methods.
We propose a computational tool GOFIX to characterize potential ORFs in virus genomes. In particular, ORF coding potential is estimated by searching for enrichment in motifs of the X circular code, that is known to be over-represented in the reading frames of viral genes.
We applied GOFIX to study the SARS-CoV-2 and related genomes including SARS-CoV and SARS-like viruses from bat, civet and pangolin hosts, focusing on the accessory proteins. Our analysis provides evidence supporting the presence of overlapping ORFs 7b, 9b and 9c in all the genomes and thus helps to resolve some differences in current genome annotations. In contrast, we predict that ORF3b is not functional in all genomes. Novel putative ORFs were also predicted, including a truncated form of the ORF10 previously identified in SARS-CoV-2 and a little known ORF overlapping the Spike protein in Civet-CoV and SARS-CoV.
Our findings contribute to characterizing sequence properties of accessory genes of SARS coronaviruses, and especially the newly acquired genes making use of overlapping reading frames.
Multiple comparison or alignmentof protein sequences has become a fundamental tool in many different domains in modern molecular biology, from evolutionary studies to prediction of 2D/3D structure, ...molecular function and inter-molecular interactions etc. By placing the sequence in the framework of the overall family, multiple alignments can be used to identify conserved features and to highlight differences or specificities. In this paper, we describe a comprehensive evaluation of many of the most popular methods for multiple sequence alignment (MSA), based on a new benchmark test set. The benchmark is designed to represent typical problems encountered when aligning the large protein sequence sets that result from today's high throughput biotechnologies. We show that alignmentmethods have significantly progressed and can now identify most of the shared sequence features that determine the broad molecular function(s) of a protein family, even for divergent sequences. However,we have identified a number of important challenges. First, the locally conserved regions, that reflect functional specificities or that modulate a protein's function in a given cellular context,are less well aligned. Second, motifs in natively disordered regions are often misaligned. Third, the badly predicted or fragmentary protein sequences, which make up a large proportion of today's databases, lead to a significant number of alignment errors. Based on this study, we demonstrate that the existing MSA methods can be exploited in combination to improve alignment accuracy, although novel approaches will still be needed to fully explore the most difficult regions. We then propose knowledge-enabled, dynamic solutions that will hopefully pave the way to enhanced alignment construction and exploitation in future evolutionary systems biology studies.
The title of this article signals increasing collaboration across boundaries aimed at understanding and solving complex scientific and societal problems. The article is a reflective analysis of five ...intersecting keywords in discussions of sustainability and boundary crossing. This genre of discourse studies interprets language use, drawing in this case on a representative sample of authoritative definitions, case studies, and state-of-the-art accounts. The Introduction situates the discussion around the increasing number and size of teams as well as research across both academic disciplines and other sectors, followed by the five keywords that structure the overall argument. Section 2 examines the first of the five keywords, defining interdisciplinarity by marking its alignment with integration, confluence, interdependence, interaction, and balance. Section 3 considers the second keyword—transdisciplinarity—by tracing evolution of a problem-focused connotation, links to sustainability, inclusion of stakeholders, the imperative of critique, and transdisciplinary action research. Section 4 brings together insights on inter- and trans-disciplinarity in a composite “crossdisciplinary” alignment with collaboration, factoring in the nature of teamwork, public engagement, and translation. Section 5 then turns to learning, noting the difference between education and training then emphasizing transformative capacity, double- and triple-loop learning, reflexivity, and a transdisciplinary orientation. Section 6 takes up the final keyword—knowledge—by calling attention to inclusion, indigenous and local perspectives, nomothetic versus idiographic perspectives, the question of fit, and the nature of crossdisciplinary knowledge. The article concludes by identifying future research needs.
The draft genome assemblies produced by new sequencing technologies present important challenges for automatic gene prediction pipelines, leading to less accurate gene models. New benchmark methods ...are needed to evaluate the accuracy of gene prediction methods in the face of incomplete genome assemblies, low genome coverage and quality, complex gene structures, or a lack of suitable sequences for evidence-based annotations.
We describe the construction of a new benchmark, called G3PO (benchmark for Gene and Protein Prediction PrOgrams), designed to represent many of the typical challenges faced by current genome annotation projects. The benchmark is based on a carefully validated and curated set of real eukaryotic genes from 147 phylogenetically disperse organisms, and a number of test sets are defined to evaluate the effects of different features, including genome sequence quality, gene structure complexity, protein length, etc. We used the benchmark to perform an independent comparative analysis of the most widely used ab initio gene prediction programs and identified the main strengths and weaknesses of the programs. More importantly, we highlight a number of features that could be exploited in order to improve the accuracy of current prediction tools.
The experiments showed that ab initio gene structure prediction is a very challenging task, which should be further investigated. We believe that the baseline results associated with the complex gene test sets in G3PO provide useful guidelines for future studies.
Aim(s)
To assess the effectiveness of sub‐epidermal moisture (SEM) assessment technology in the detection of early‐stage pressure damage in a critical care unit (CCU) and dark skin tone patients and ...its impact on hospital‐acquired pressure injury (HAPI) incidence.
Design
Quality improvement study employing Kurt Lewin's change model emphasizing planning, implementation, evaluation and sustainable change.
Methods
The study evaluated 140 adult patients admitted to the CCU over a 24‐week period, from July to December 2022. Retrospective analysis of standard PI care pathways was performed in 90 patients admitted during a 12‐week pre‐implementation period. Fifty patients were admitted through the subsequent 12‐week implementation period. SEM assessments were performed daily at the sacrum and heels and interventions were applied based on SEM assessments; SEM delta ≥0.6 indicating localized oedema or persistent focal oedema. Statistical analyses were performed on anonymized data.
Results
Pre‐implementation HAPI incidence was 8.9% (N = 8/90). All eight patients were African American with varying skin tones. A 100% reduction in HAPI incidence was achieved in the implementation period which included 35 African American patients. The relative risk of HAPI incidence was 1.6 times higher in the pre‐implementation group.
Conclusion
Implementing SEM assessment technology enabled equitable PI care for all population types and resulted in a 100% reduction of PIs in our CCU. Objective SEM assessments detected early‐stage PIs, regardless of skin tone and enabled providing interventions to specific anatomies developing tissue damage as opposed to universal preventive interventions.
Implications
PI care pathways relying on visual and tactile skin assessments are inherently biased in providing equitable care for dark skin tone patients. Implementing SEM assessments empowers healthcare practitioners in driving objective clinical interventions, eliminates bias and enables positive PI health outcomes.
Impact
Implementing SEM assessment technology had three main effects: it detected early tissue damage regardless of skin tone (detection effect), enabled anatomy‐specific interventions (treatment effect) and prevented PIs across all population types (prevention effect).
The authors have adhered to the Standards for Quality Improvement Reporting Excellence (SQUIRE) 2.0 guidelines.
Patient or Public Contribution
No patient or public contribution.
What does this paper contribute to the wider global clinical community? Addressing health inequities in pressure injury prevention; Demonstrated effectiveness across patient populations; Resource optimization and enhanced patient safety.
Rising mortality in the United States due to alcoholic liver disease (ALD) and the dearth of effective treatments for ALD have led to increased research in this area, particularly in alcoholic ...hepatitis. To understand the burden of illness and potential economic value of effective treatments, we conducted a health care claims analysis of over 15,000 commercially insured adults who were hospitalized with alcoholic hepatitis (AH) between 2006 and 2013 and followed for up to 5 years. Their average age was 54 years and 68% were male. Over 5 years, about two-thirds of these adults died (44% in the first year), and fewer than 500 received liver transplants. There were nearly 40,000 re-hospitalizations, with over 50% of the survivors re-hospitalized within a year and nearly 75% through the second year. The total costs were nearly $145,000 per patient, with costs decreasing over time from over $50,000 in the first year (including the index hospitalization) to about $10,000 per year in the later years. Total costs for the cohort over 5 years were $2.2 billion. Patients who received a liver transplant averaged about $300,000 in transplant-related costs and over $1,000,000 in total health care costs over 5 years. Average costs in years following the index hospitalization were similar to diabetes. AH has a high mortality and is a high-cost condition.
•There is an increasing rate of hospitalizations due to alcohol-related conditions.•Medical treatment for AH has limited efficacy. Only transplantation is life-saving, but it is not widely accepted.•The total average annual per-patient costs for AH are higher than for heart failure or diabetes.•Patients with the condition tend to be people of middle age in their prime working years.
Three-base periodicity (TBP), where nucleotides and higher order n-tuples are preferentially spaced by 3, 6, 9, etc. bases, is a well-known intrinsic property of protein-coding DNA sequences. ...However, its origins are still not fully understood. One hypothesis is that the periodicity reflects a primordial coding system that was used before the emergence of the modern standard genetic code (SGC). Recent evidence suggests that the X circular code, a set of 20 trinucleotides allowing the reading frames in genes to be retrieved locally, represents a possible ancestor of the SGC. Motifs from the X circular code have been found in the reading frame of protein-coding regions in extant organisms from bacteria to eukaryotes, in many transfer RNA (tRNA) genes and in important functional regions of the ribosomal RNA (rRNA), notably in the peptidyl transferase centre and the decoding centre. Here, we have used a powerful correlation function to search for periodicity patterns involving the 20 trinucleotides of the X circular code in a large set of bacterial protein-coding genes, as well as in the translation machinery, including rRNA and tRNA sequences. As might be expected, we found a strong circular code periodicity 0 modulo 3 in the protein-coding genes. More surprisingly, we also identified a similar circular code periodicity in a large region of the 16S rRNA. This region includes the 3ʹ major domain corresponding to the primordial proto-ribosome decoding centre and containing numerous sites that interact with the tRNA and messenger RNA (mRNA) during translation. Furthermore, 3D structural analysis shows that the periodicity region surrounds the mRNA channel that lies between the head and the body of the SSU. Our results support the hypothesis that the X circular code may constitute an ancestral translation code involved in reading frame retrieval and maintenance, traces of which persist in modern mRNA, tRNA and rRNA despite their long evolution and adaptation to the SGC.
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