Epithelial-mesenchymal plasticity contributes to many biological processes, including tumor progression. Various epithelial-mesenchymal transition (EMT) responses have been reported and no common, ...EMT-defining gene expression program has been identified. Here, we have performed a comparative analysis of the EMT response, leveraging highly multiplexed single-cell RNA sequencing (scRNA-seq) to measure expression profiles of 103,999 cells from 960 samples, comprising 12 EMT time course experiments and independent kinase inhibitor screens for each. We demonstrate that the EMT is vastly context specific, with an average of only 22% of response genes being shared between any two conditions, and over half of all response genes were restricted to 1-2 time course experiments. Further, kinase inhibitor screens revealed signaling dependencies and modularity of these responses. These findings suggest that the EMT is not simply a single, linear process, but is highly variable and modular, warranting quantitative frameworks for understanding nuances of the transition.
Transcriptional dynamic in response to environmental and developmental cues are fundamental to biology, yet many mechanistic aspects are poorly understood. One such example is fungal plant pathogens, ...which use secreted proteins and small molecules, termed effectors, to suppress host immunity and promote colonization. Effectors are highly expressed in planta but remain transcriptionally repressed ex planta, but our mechanistic understanding of these transcriptional dynamics remains limited. We tested the hypothesis that repressive histone modification at H3-Lys27 underlies transcriptional silencing ex planta, and that exchange for an active chemical modification contributes to transcription of in planta induced genes. Using genetics, chromatin immunoprecipitation and sequencing and RNA-sequencing, we determined that H3K27me3 provides significant local transcriptional repression. We detail how regions that lose H3K27me3 gain H3K27ac, and these changes are associated with increased transcription. Importantly, we observed that many in planta induced genes were marked by H3K27me3 during axenic growth, and detail how altered H3K27 modification influences transcription. ChIP-qPCR during in planta growth suggests that H3K27 modifications are generally stable, but can undergo dynamics at specific genomic locations. Our results support the hypothesis that dynamic histone modifications at H3K27 contributes to fungal genome regulation and specifically contributes to regulation of genes important during host infection.
Objective
To succinctly summarise five contemporary theories about motivation to learn, articulate key intersections and distinctions among these theories, and identify important considerations for ...future research.
Results
Motivation has been defined as the process whereby goal‐directed activities are initiated and sustained. In expectancy‐value theory, motivation is a function of the expectation of success and perceived value. Attribution theory focuses on the causal attributions learners create to explain the results of an activity, and classifies these in terms of their locus, stability and controllability. Social‐ cognitive theory emphasises self‐efficacy as the primary driver of motivated action, and also identifies cues that influence future self‐efficacy and support self‐regulated learning. Goal orientation theory suggests that learners tend to engage in tasks with concerns about mastering the content (mastery goal, arising from a ‘growth’ mindset regarding intelligence and learning) or about doing better than others or avoiding failure (performance goals, arising from a ‘fixed’ mindset). Finally, self‐determination theory proposes that optimal performance results from actions motivated by intrinsic interests or by extrinsic values that have become integrated and internalised. Satisfying basic psychosocial needs of autonomy, competence and relatedness promotes such motivation. Looking across all five theories, we note recurrent themes of competence, value, attributions, and interactions between individuals and the learning context.
Conclusions
To avoid conceptual confusion, and perhaps more importantly to maximise the theory‐building potential of their work, researchers must be careful (and precise) in how they define, operationalise and measure different motivational constructs. We suggest that motivation research continue to build theory and extend it to health professions domains, identify key outcomes and outcome measures, and test practical educational applications of the principles thus derived.
Discuss ideas arising from the article at www.mededuc.com discuss.
The stable fly,
(L.) (Diptera: Muscidae), remains a significant economic pest globally in situations where intensive animal production or horticultural production provide a suitable developmental ...medium. Stable flies have been recorded as pests of livestock and humans since the late 1800s to early 1900s. Over 100 years of research has seen numerous methodologies used to control this fly, in particular to protect cattle from flies to minimise production losses. Reduced milk production in dairy cows and decreased weight gain in beef cattle account for losses in the US alone of > $2000 million annually. Rural lifestyles and recreation are also seriously affected. Progress has been made on many control strategies against stable fly over a range of chemical, biological, physical and cultural options. This paper reviews management options from both a historical and a technical perspective for controlling this pest. These include the use of different classes of insecticides applied to affected animals as toxicants or repellents (livestock and humans), as well as to substrates where stable fly larvae develop. Arthropod predators of stable flies are listed, from which potential biological control agents (e.g., wasps, mites, and beetles) are identified. Biopesticides (e.g., fungi, bacteria and plant-derived products) are also discussed along with Integrated Pest Management (IPM) against stable flies for several animal industries. A review of cultural and physical management options including trapping, trap types and methodologies, farm hygiene, scheduled sanitation, physical barriers to fly emergence, livestock protection and amendments added to animal manures and bedding are covered. This paper presents a comprehensive review of all management options used against stable flies from both a historical and a technical perspective for use by any entomologist, livestock producer or horticulturalist with an interest in reducing the negative impact of this pest fly.
Context
Studies that investigate research questions that have already been resolved represent a waste of resources. However, the failure to collect sufficient evidence to resolve a given question ...results in ambiguity.
Objectives
The present study was conducted to reanalyse the results of a meta‐analysis of simulation‐based education (SBE) to determine: (i) whether researchers continue to replicate research studies after the answer to a research question has become known, and (ii) whether researchers perform enough replications to definitively answer important questions.
Methods
A systematic search of multiple databases to May 2011 was conducted to identify original research evaluating SBE for health professionals in comparison with no intervention or any active intervention, using skill outcomes. Data were extracted by reviewers working in duplicate. Data synthesis involved a cumulative meta‐analysis to illuminate patterns of evidence by sequentially adding studies according to a variable of interest (e.g. publication year) and re‐calculating the pooled effect size with each addition. Cumulative meta‐analysis by publication year was applied to 592 comparative studies using several thresholds of ‘sufficiency’, including: statistical significance; stable effect size classification and magnitude (Hedges’ g ± 0.1), and precise estimates (confidence intervals of less than ± 0.2).
Results
Among studies that compared the outcomes of SBE with those of no intervention, evidence supporting a favourable effect of SBE on skills existed as early as 1973 (one publication) and further evidence confirmed a quantitatively large effect of SBE by 1997 (28 studies). Since then, a further 404 studies were published. Among studies comparing SBE with non‐simulation instruction, the effect initially favoured non‐simulation training, but the addition of a third study in 1997 brought the pooled effect to slightly favour simulation, and by 2004 (14 studies) this effect was statistically significant (p < 0.05) and the magnitude had stabilised (small effect). A further 37 studies were published after 2004. By contrast, evidence from studies evaluating repetition continued to show borderline statistical significance and wide confidence intervals in 2011.
Conclusions
Some replication is necessary to obtain stable estimates of effect and to explore different contexts, but the number of studies of SBE often exceeds the minimum number of replications required.
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The Medical Education Research Study Quality Instrument (MERSQI) and the Newcastle-Ottawa Scale-Education (NOS-E) were developed to appraise methodological quality in medical education research. The ...study objective was to evaluate the interrater reliability, normative scores, and between-instrument correlation for these two instruments.
In 2014, the authors searched PubMed and Google for articles using the MERSQI or NOS-E. They obtained or extracted data for interrater reliability-using the intraclass correlation coefficient (ICC)-and normative scores. They calculated between-scale correlation using Spearman rho.
Each instrument contains items concerning sampling, controlling for confounders, and integrity of outcomes. Interrater reliability for overall scores ranged from 0.68 to 0.95. Interrater reliability was "substantial" or better (ICC > 0.60) for nearly all domain-specific items on both instruments. Most instances of low interrater reliability were associated with restriction of range, and raw agreement was usually good. Across 26 studies evaluating published research, the median overall MERSQI score was 11.3 (range 8.9-15.1, of possible 18). Across six studies, the median overall NOS-E score was 3.22 (range 2.08-3.82, of possible 6). Overall MERSQI and NOS-E scores correlated reasonably well (rho 0.49-0.72).
The MERSQI and NOS-E are useful, reliable, complementary tools for appraising methodological quality of medical education research. Interpretation and use of their scores should focus on item-specific codes rather than overall scores. Normative scores should be used for relative rather than absolute judgments because different research questions require different study designs.
Abstract
DNA double-strand breaks require repair or risk corrupting the language of life. To ensure genome integrity and viability, multiple DNA double-strand break repair pathways function in ...eukaryotes. Two such repair pathways, canonical non-homologous end joining and homologous recombination, have been extensively studied, while other pathways such as microhomology-mediated end joint and single-strand annealing, once thought to serve as back-ups, now appear to play a fundamental role in DNA repair. Here, we review the molecular details and hierarchy of these four DNA repair pathways, and where possible, a comparison for what is known between animal and fungal models. We address the factors contributing to break repair pathway choice, and aim to explore our understanding and knowledge gaps regarding mechanisms and regulation in filamentous pathogens. We additionally discuss how DNA double-strand break repair pathways influence genome engineering results, including unexpected mutation outcomes. Finally, we review the concept of biased genome evolution in filamentous pathogens, and provide a model, termed Biased Variation, that links DNA double-strand break repair pathways with properties of genome evolution. Despite our extensive knowledge for this universal process, there remain many unanswered questions, for which the answers may improve genome engineering and our understanding of genome evolution.
This review summarizes and compares the molecular mechanism, hierarchy, and regulation of four DNA double-strand break repair pathways in animal and fungal models, with the aim to connect these DNA repair pathways to genome engineering outcomes and biased genome evolution in filamentous pathogens.
Context
Assessment is central to medical education and the validation of assessments is vital to their use. Earlier validity frameworks suffer from a multiplicity of types of validity or failure to ...prioritise among sources of validity evidence. Kane's framework addresses both concerns by emphasising key inferences as the assessment progresses from a single observation to a final decision. Evidence evaluating these inferences is planned and presented as a validity argument.
Objectives
We aim to offer a practical introduction to the key concepts of Kane's framework that educators will find accessible and applicable to a wide range of assessment tools and activities.
Results
All assessments are ultimately intended to facilitate a defensible decision about the person being assessed. Validation is the process of collecting and interpreting evidence to support that decision. Rigorous validation involves articulating the claims and assumptions associated with the proposed decision (the interpretation/use argument), empirically testing these assumptions, and organising evidence into a coherent validity argument. Kane identifies four inferences in the validity argument: Scoring (translating an observation into one or more scores); Generalisation (using the scores as a reflection of performance in a test setting); Extrapolation (using the scores as a reflection of real‐world performance), and Implications (applying the scores to inform a decision or action). Evidence should be collected to support each of these inferences and should focus on the most questionable assumptions in the chain of inference. Key assumptions (and needed evidence) vary depending on the assessment's intended use or associated decision. Kane's framework applies to quantitative and qualitative assessments, and to individual tests and programmes of assessment.
Conclusions
Validation focuses on evaluating the key claims, assumptions and inferences that link assessment scores with their intended interpretations and uses. The Implications and associated decisions are the most important inferences in the validity argument.
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Virtual patients (VPs) have long been used to teach and assess clinical reasoning. VPs can be programmed to simulate authentic patient-clinician interactions and to reflect a variety of contextual ...permutations. However, their use has historically been limited by the high cost and logistical challenges of large-scale implementation. We describe a novel globally-accessible approach to develop low-cost VPs at scale using artificial intelligence (AI) large language models (LLMs). We leveraged OpenAI Generative Pretrained Transformer (GPT) to create and implement two interactive VPs, and created permutations that differed in contextual features. We used systematic prompt engineering to refine a prompt instructing ChatGPT to emulate the patient for a given case scenario, and then provide feedback on clinician performance. We implemented the prompts using GPT-3.5-turbo and GPT-4.0, and created a simple text-only interface using the OpenAI API. GPT-4.0 was far superior. We also conducted limited testing using another LLM (Anthropic Claude), with promising results. We provide the final prompt, case scenarios, and Python code. LLM-VPs represent a 'disruptive innovation' - an innovation that is unmistakably inferior to existing products but substantially more accessible (due to low cost, global reach, or ease of implementation) and thereby able to reach a previously underserved market. LLM-VPs will lay the foundation for global democratization via low-cost-low-risk scalable development of educational and clinical simulations. These powerful tools could revolutionize the teaching, assessment, and research of management reasoning, shared decision-making, and AI evaluation (e.g. 'software as a medical device' evaluations).Virtual patients (VPs) have long been used to teach and assess clinical reasoning. VPs can be programmed to simulate authentic patient-clinician interactions and to reflect a variety of contextual permutations. However, their use has historically been limited by the high cost and logistical challenges of large-scale implementation. We describe a novel globally-accessible approach to develop low-cost VPs at scale using artificial intelligence (AI) large language models (LLMs). We leveraged OpenAI Generative Pretrained Transformer (GPT) to create and implement two interactive VPs, and created permutations that differed in contextual features. We used systematic prompt engineering to refine a prompt instructing ChatGPT to emulate the patient for a given case scenario, and then provide feedback on clinician performance. We implemented the prompts using GPT-3.5-turbo and GPT-4.0, and created a simple text-only interface using the OpenAI API. GPT-4.0 was far superior. We also conducted limited testing using another LLM (Anthropic Claude), with promising results. We provide the final prompt, case scenarios, and Python code. LLM-VPs represent a 'disruptive innovation' - an innovation that is unmistakably inferior to existing products but substantially more accessible (due to low cost, global reach, or ease of implementation) and thereby able to reach a previously underserved market. LLM-VPs will lay the foundation for global democratization via low-cost-low-risk scalable development of educational and clinical simulations. These powerful tools could revolutionize the teaching, assessment, and research of management reasoning, shared decision-making, and AI evaluation (e.g. 'software as a medical device' evaluations).
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