This \"Best Practices in User Consultation\" article is the result of a 2022 International Society for the Advancement of Cytometry (ISAC) membership survey that collected valuable insights from the shared research laboratory (SRL) community and of a group discussion at the CYTO 2022 workshop of the same name. One key takeaway is the importance of initiating a consultation at the outset of a flow cytometry project, particularly for trainees. This approach enables the improvement and standardization of every step, from planning experiments to interpreting data. This proactive approach effectively mitigates experimental bias and avoids superfluous trial and error, thereby conserving valuable time and resources. In addition to guidelines, the optimal approaches for user consultation specify communication channels, methods, and critical information, thereby establishing a structure for productive correspondence between SRL and users. This framework functions as an exemplar for establishing robust and autonomous collaborative relationships. User consultation adds value by providing researchers with the necessary information to conduct reproducible flow cytometry experiments that adhere to scientific rigor. By following the steps, instructions, and strategies outlined in these best practices, an SRL can readily tailor them to its own setting, establishing a personalized workflow and formalizing user consultation services. This article provides a pragmatic guide for improving the caliber and efficacy of flow cytometry research and aggregates the flow cytometry SRL community\'s collective knowledge regarding user consultation.

BACKGROUND: A major obstacle faced by families with rare diseases is obtaining a genetic diagnosis. The average \"diagnostic odyssey\" lasts over five years and causal variants are identified in under 50%, even when capturing variants genome-wide. To aid in the interpretation and prioritization of the vast number of variants detected, computational methods are proliferating. Knowing which tools are most effective remains unclear. To evaluate the performance of computational methods, and to encourage innovation in method development, we designed a Critical Assessment of Genome Interpretation (CAGI) community challenge to place variant prioritization models head-to-head in a real-life clinical diagnostic setting.
METHODS: We utilized genome sequencing (GS) data from families sequenced in the Rare Genomes Project (RGP), a direct-to-participant research study on the utility of GS for rare disease diagnosis and gene discovery. Challenge predictors were provided with a dataset of variant calls and phenotype terms from 175 RGP individuals (65 families), including 35 solved training set families with causal variants specified, and 30 unlabeled test set families (14 solved, 16 unsolved). We tasked teams to identify causal variants in as many families as possible. Predictors submitted variant predictions with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on the rank position of causal variants, and the maximum F-measure, based on precision and recall of causal variants across all EPCR values.
RESULTS: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performers recalled causal variants in up to 13 of 14 solved families within the top 5 ranked variants. Newly discovered diagnostic variants were returned to two previously unsolved families following confirmatory RNA sequencing, and two novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant in an unsolved proband with phenotypes consistent with asparagine synthetase deficiency.
CONCLUSIONS: Model methodology and performance was highly variable. Models weighing call quality, allele frequency, predicted deleteriousness, segregation, and phenotype were effective in identifying causal variants, and models open to phenotype expansion and non-coding variants were able to capture more difficult diagnoses and discover new diagnoses. Overall, computational models can significantly aid variant prioritization. For use in diagnostics, detailed review and conservative assessment of prioritized variants against established criteria is needed.

BACKGROUND: Asthma is a chronic respiratory disorder requiring long-term pharmacotherapy and judicious patient self-management. Few studies have systematically evaluated asthma mobile health (mHealth) apps for quality and functionality; however, none have systematically assessed these apps for their content alignment with international best practice guidelines.
OBJECTIVE: This review aims to conduct a systematic search and evaluation of current mHealth apps in the Australian marketplace for their functionality, quality, and consistency with best practice guidelines.
METHODS: The most recent Global Initiative for Asthma (GINA) guidelines were reviewed to identify key recommendations that could be feasibly incorporated into an mHealth app. We developed a checklist based on these recommendations and a modified version of a previously developed framework. App stores were reviewed to identify potential mHealth apps based on predefined criteria. Evaluation of suitable apps included the assessment of technical information, an app quality assessment using the validated Mobile App Rating Scale (MARS) framework, and an app functionality assessment using the Intercontinental Medical Statistics Institute for Health Informatics (IMS) Functionality Scoring System. Finally, the mHealth apps were assessed for their content alignment with the GINA guidelines using the checklist we developed.
RESULTS: Of the 422 apps initially identified, 53 were suitable for further analysis based on inclusion and exclusion criteria. The mean number of behavioral change techniques for a single app was 3.26 (SD 2.27). The mean MARS score for all the reviewed apps was 3.05 (SD 0.54). Of 53 apps, 27 (51%) achieved a total MARS score of ≥3. On average, the reviewed apps achieved 5.1 (SD 2.79) functionalities on the 11-point IMS functionality scale. The median number of functionalities identified was 5 (IQR 2-7). Overall, 10 (22%) of the 45 apps with reviewer consensus in this domain provided general knowledge regarding asthma. Of 53 apps, skill training in peak flow meters, inhaler devices, recognizing or responding to exacerbations, and nonpharmacological asthma management were identified in 8 (17%), 12 (25%), 11 (28%), and 14 (31%) apps, respectively; 19 (37%) apps could track or record \"asthma symptoms,\" which was the most commonly recorded metric. The most frequently identified prompt was for taking preventive medications, available in 9 (20%) apps. Five (10%) apps provided an area for patients to store or enter their asthma action plan.
CONCLUSIONS: This study used a unique checklist developed based on the GINA guidelines to evaluate the content alignment of asthma apps. Good-quality asthma apps aligned with international best practice asthma guidelines are lacking. Future app development should target the currently lacking key features identified in this study, including the use of asthma action plans and the deployment of behavioral change techniques to engage and re-engage with users. This study has implications for clinicians navigating the ever-expanding mHealth app market for chronic diseases.
BACKGROUND: PROSPERO CRD42021269894; https://www.crd.york.ac.uk/prospero/display_record.php?RecordID=269894.
UNASSIGNED: RR2-10.2196/33103.

UNASSIGNED: A major obstacle faced by rare disease families is obtaining a genetic diagnosis. The average \"diagnostic odyssey\" lasts over five years, and causal variants are identified in under 50%. The Rare Genomes Project (RGP) is a direct-to-participant research study on the utility of genome sequencing (GS) for diagnosis and gene discovery. Families are consented for sharing of sequence and phenotype data with researchers, allowing development of a Critical Assessment of Genome Interpretation (CAGI) community challenge, placing variant prioritization models head-to-head in a real-life clinical diagnostic setting.
UNASSIGNED: Predictors were provided a dataset of phenotype terms and variant calls from GS of 175 RGP individuals (65 families), including 35 solved training set families, with causal variants specified, and 30 test set families (14 solved, 16 unsolved). The challenge tasked teams with identifying the causal variants in as many test set families as possible. Ranked variant predictions were submitted with estimated probability of causal relationship (EPCR) values. Model performance was determined by two metrics, a weighted score based on rank position of true positive causal variants and maximum F-measure, based on precision and recall of causal variants across EPCR thresholds.
UNASSIGNED: Sixteen teams submitted predictions from 52 models, some with manual review incorporated. Top performing teams recalled the causal variants in up to 13 of 14 solved families by prioritizing high quality variant calls that were rare, predicted deleterious, segregating correctly, and consistent with reported phenotype. In unsolved families, newly discovered diagnostic variants were returned to two families following confirmatory RNA sequencing, and two prioritized novel disease gene candidates were entered into Matchmaker Exchange. In one example, RNA sequencing demonstrated aberrant splicing due to a deep intronic indel in ASNS, identified in trans with a frameshift variant, in an unsolved proband with phenotype overlap with asparagine synthetase deficiency.
UNASSIGNED: By objective assessment of variant predictions, we provide insights into current state-of-the-art algorithms and platforms for genome sequencing analysis for rare disease diagnosis and explore areas for future optimization. Identification of diagnostic variants in unsolved families promotes synergy between researchers with clinical and computational expertise as a means of advancing the field of clinical genome interpretation.

ChatGPT is receiving increasing attention and has a variety of application scenarios in clinical practice. In clinical decision support, ChatGPT has been used to generate accurate differential diagnosis lists, support clinical decision-making, optimize clinical decision support, and provide insights for cancer screening decisions. In addition, ChatGPT has been used for intelligent question-answering to provide reliable information about diseases and medical queries. In terms of medical documentation, ChatGPT has proven effective in generating patient clinical letters, radiology reports, medical notes, and discharge summaries, improving efficiency and accuracy for health care providers. Future research directions include real-time monitoring and predictive analytics, precision medicine and personalized treatment, the role of ChatGPT in telemedicine and remote health care, and integration with existing health care systems. Overall, ChatGPT is a valuable tool that complements the expertise of health care providers and improves clinical decision-making and patient care. However, ChatGPT is a double-edged sword. We need to carefully consider and study the benefits and potential dangers of ChatGPT. In this viewpoint, we discuss recent advances in ChatGPT research in clinical practice and suggest possible risks and challenges of using ChatGPT in clinical practice. It will help guide and support future artificial intelligence research similar to ChatGPT in health.

Flow cytometry has emerged as a uniquely flexible, accurate, and widely applicable technology for the analysis of plant cells. One of its most important applications centers on the measurement of nuclear DNA contents. This chapter describes the essential features of this measurement, outlining the overall methods and strategies, but going on to provide a wealth of technical details to ensure the most accurate and reproducible results. The chapter is aimed to be equally accessible to experienced plant cytometrists as well as those newly entering the field. Besides providing a step-by-step guide for estimating genome sizes and DNA-ploidy levels from fresh tissues, special attention is paid to the use of seeds and desiccated tissues for such purposes. Methodological aspects regarding field sampling, transport, and storage of plant material are also given in detail. Finally, troubleshooting information for the most common problems that may arise during the application of these methods is provided.

The Western Pacific Region has one of the fastest-growing populations of older adults (≥ 65 years) globally, among whom tuberculosis (TB) poses a particular concern. This study reports country case studies from China, Japan, the Republic of Korea, and Singapore reflecting on their experiences in managing TB among older adults.
Across all four countries, TB case notification and incidence rates were highest among older adults, but clinical and public health guidance focused on this population was limited. Individual country reports illustrated a range of practices and challenges. Passive case finding remains the norm, with limited active case finding (ACF) programs implemented in China, Japan, and the Republic of Korea. Different approaches have been trialled to assist older adults in securing an early diagnosis, as well as adhering to their TB treatment. All countries emphasised the need for person-centred approaches that include the creative application of new technology and tailored incentive programs, as well as reconceptualisation of how we provide treatment support. The use of traditional medicines was found to be culturally entrenched among older adults, with a need for careful consideration of their complementary use. TB infection testing and the provision of TB preventive treatment (TPT) were underutilised with highly variable practice.
Older adults require specific consideration in TB response policies, given the burgeoning aging population and their high TB risk. Policymakers, TB programs and funders must invest in and develop locally contextualised practice guidelines to inform evidence-based TB prevention and care practices for older adults.

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The rapid increase in both the quantity and complexity of data that are being generated daily in the field of environmental science and engineering (ESE) demands accompanied advancement in data analytics. Advanced data analysis approaches, such as machine learning (ML), have become indispensable tools for revealing hidden patterns or deducing correlations for which conventional analytical methods face limitations or challenges. However, ML concepts and practices have not been widely utilized by researchers in ESE. This feature explores the potential of ML to revolutionize data analysis and modeling in the ESE field, and covers the essential knowledge needed for such applications. First, we use five examples to illustrate how ML addresses complex ESE problems. We then summarize four major types of applications of ML in ESE: making predictions; extracting feature importance; detecting anomalies; and discovering new materials or chemicals. Next, we introduce the essential knowledge required and current shortcomings in ML applications in ESE, with a focus on three important but often overlooked components when applying ML: correct model development, proper model interpretation, and sound applicability analysis. Finally, we discuss challenges and future opportunities in the application of ML tools in ESE to highlight the potential of ML in this field.

Instrumentation for flow cytometry and sorting is designed around the assumption that samples are single-cell suspensions. However, with few exceptions, higher plants comprise complex multicellular tissues and organs, in which the individual cells are held together by shared cell walls. Single-cell suspensions can be obtained through digestion of the cells walls and release of the so-called protoplasts (plants without their cell wall). Here we describe best practices for protoplast preparation, and for analysis through flow cytometry and cell sorting. Finally, the numerous downstream applications involving sorted protoplasts are discussed.