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Advanced Biology Apr 2024The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering...
The continuous evolution of molecular biology and gene synthesis methods paired with an ever-increasing potential of synthetic biology approaches and genome engineering toolkits enables the rapid design of genetic bioparts and genetically modified organisms. Although various software solutions assist with specific design tasks and challenges, lab internal documentation and ensuring compliance with governmental regulations on biosafety assessment of the generated organisms remain the responsibility of individual academic researchers. This results in inconsistent and redundant documentation regimes and a significant time and labor burden. GMOCU (GMO documentation) is a standardized semi-automatic user-oriented software approach -written in Python and freely available- that unifies lab internal data documentation on genetic parts and genetically modified organisms (GMOs). It automatizes biological risk evaluations and maintains a shared up-to-date inventory of bioparts for team-wide data navigation and sharing. GMOCU further enables data export into customizable formats suitable for scientific publications, official biosafety documents, and the research community.
Topics: Software; Risk Assessment; Documentation; Government Regulation
PubMed: 38263723
DOI: 10.1002/adbi.202300529 -
Bioinformatics Advances 2024DIAgui is an R package to simplify the processing of the report file from the DIA-NN software thanks to a Shiny application. It returns the quantification of either the...
SUMMARY
DIAgui is an R package to simplify the processing of the report file from the DIA-NN software thanks to a Shiny application. It returns the quantification of either the precursors, the peptides, the proteins, or the genes thanks to the MaxLFQ algorithm. In addition, the latest version provides the Top3 and iBAQ quantification and the number of peptides used for the quantification. In the end, DIAgui produces ready-to-interpret files from the results of DIA mass spectrometry analysis and provides visualization and statistical tools that can be used in a user-friendly way.
AVAILABILITY AND IMPLEMENTATION
Code and documentation are available on GitHub at https://github.com/marseille-proteomique/DIAgui. The package is written in R and also uses C++ code. A vignette shows its use in an R command line workflow.
PubMed: 38249340
DOI: 10.1093/bioadv/vbae001 -
International Journal of Environmental... Dec 2023This systematic review identifies and describes the use of the Expert Recommendation for Implementing Change (ERIC) concepts and strategies using public health... (Review)
Review
This systematic review identifies and describes the use of the Expert Recommendation for Implementing Change (ERIC) concepts and strategies using public health approaches to drowning prevention interventions as a case study. International calls for action have identified the need to better understand the implementation of drowning prevention interventions so that intervention design and implementation is improved. In high-income countries (HICs), interventions are sophisticated but still little is known or written about their implementation. The review was registered on PROSPERO (number CRD42022347789) and followed the PRISMA guidelines. Eight databases were searched. Articles were assessed using the Public Health Ontario Meta-tool for quality appraisal of public health evidence. Forty-nine articles were included. Where ERIC strategies were reported, the focus was on evaluative and iterative strategies, developing partnerships and engaging the target group. The review identified few articles that discussed intervention development and implementation sufficiently for strategies to be replicated. Findings will inform further research into the use and measurement of implementation strategies by practitioners and researchers undertaking work in drowning prevention in HICs and supports a call to action for better documentation of implementation in public health interventions.
Topics: Humans; Implementation Science; Developed Countries; Drowning; Databases, Factual; Documentation
PubMed: 38248510
DOI: 10.3390/ijerph21010045 -
International Journal of Gynaecology... Jun 2024To use machine learning to optimize the detection of obstetrics and gynecology (OBGYN) Chat Generative Pre-trained Transformer (ChatGPT) -written abstracts of all OBGYN...
OBJECTIVES
To use machine learning to optimize the detection of obstetrics and gynecology (OBGYN) Chat Generative Pre-trained Transformer (ChatGPT) -written abstracts of all OBGYN journals.
METHODS
We used Web of Science to identify all original articles published in all OBGYN journals in 2022. Seventy-five original articles were randomly selected. For each, we prompted ChatGPT to write an abstract based on the title and results of the original abstracts. Each abstract was tested by Grammarly software and reports were inserted into a database. Machine-learning modes were trained and examined on the database created.
RESULTS
Overall, 75 abstracts from 12 different OBGYN journals were randomly selected. There were seven (58%) Q1 journals, one (8%) Q2 journal, two (17%) Q3 journals, and two (17%) Q4 journals. Use of mixed dialects of English, absence of comma-misuse, absence of incorrect verb forms, and improper formatting were important prediction variables of ChatGPT-written abstracts. The deep-learning model had the highest predictive performance of all examined models. This model achieved the following performance: accuracy 0.90, precision 0.92, recall 0.85, area under the curve 0.95.
CONCLUSIONS
Machine-learning-based tools reach high accuracy in identifying ChatGPT-written OBGYN abstracts.
Topics: Obstetrics; Gynecology; Machine Learning; Humans; Abstracting and Indexing; Periodicals as Topic
PubMed: 38234125
DOI: 10.1002/ijgo.15365 -
AMIA ... Annual Symposium Proceedings.... 2023With the recent advances in natural language processing and deep learning, the development of tools that can assist medical coders in ICD-10 diagnosis coding and...
With the recent advances in natural language processing and deep learning, the development of tools that can assist medical coders in ICD-10 diagnosis coding and increase their efficiency in coding discharge summaries is significantly more viable than before. To that end, one important component in the development of these models is the datasets used to train them. In this study, such datasets are presented, and it is shown that one of them can be used to develop a BERT-based language model that can consistently perform well in assigning ICD-10 codes to discharge summaries written in Swedish. Most importantly, it can be used in a coding support setup where a tool can recommend potential codes to the coders. This reduces the range of potential codes to consider and, in turn, reduces the workload of the coder. Moreover, the de-identified and pseudonymised dataset is open to use for academic users.
Topics: Humans; International Classification of Diseases; Patient Discharge; Natural Language Processing; Clinical Coding
PubMed: 38222373
DOI: No ID Found -
Journal of Alzheimer's Disease : JAD 2024The evidence underpinning palliative care in dementia is mostly based on research in older populations. Little is known about the palliative care needs of people with... (Observational Study)
Observational Study
BACKGROUND
The evidence underpinning palliative care in dementia is mostly based on research in older populations. Little is known about the palliative care needs of people with young-onset dementia (YOD).
OBJECTIVE
To describe palliative care practices including advance care planning (ACP) in people with YOD residing in Dutch nursing homes.
METHODS
The study presents baseline questionnaire data from an observational cohort study. Physicians, family caregivers, and nursing staff completed questionnaires about 185 residents with YOD. The questionnaires included items on sociodemographics, quality of life measured with the quality of life in late-stage dementia (QUALID) scale, dementia-related somatic health problems, symptoms, pain medication, psychotropic drugs, and ACP.
RESULTS
The mean age was 63.9 (SD 5.8) years. Half (50.3%) of them were female. Alzheimer's disease dementia (42.2%) was the most prevalent subtype. The mean QUALID score was 24.0 (SD 7.9) as assessed by family caregivers, and 25.3 (SD 8.6) as assessed by the nursing staff. Swallowing problems were the most prevalent dementia-related health problem (11.4%). Agitation was often reported by physicians (42.0%) and nursing staff (40.5%). Psychotropics were prescribed frequently (72.3%). A minority had written advance directives (5.4%) or documentation on treatment preferences by the former general practitioner (27.2%). Global care goals most often focused on comfort (73.9%). Proportions of do-not-treat orders were higher than do-treat orders for all interventions except for hospitalization and antibiotics.
CONCLUSIONS
ACP must be initiated earlier, before nursing home admission. A palliative approach seems appropriate even though residents are relatively young and experience few dementia-related health problems.
Topics: Humans; Female; Aged; Male; Palliative Care; Caregivers; Quality of Life; Dementia; Nursing Homes; Alzheimer Disease
PubMed: 38217594
DOI: 10.3233/JAD-230486 -
BMJ Open Jan 2024Rapid population ageing is a demographic trend being experienced and documented worldwide. While increased health screening and assessment may help mitigate the burden...
INTRODUCTION
Rapid population ageing is a demographic trend being experienced and documented worldwide. While increased health screening and assessment may help mitigate the burden of illness in older people, issues such as misdiagnosis may affect access to interventions. This study aims to elicit the values and preferences of evidence-informed older people living in the community on early screening for common health conditions (cardiovascular disease, diabetes, dementia and frailty). The study will proceed in three Phases: (1) generating recommendations of older people through a series of Citizens' Juries; (2) obtaining feedback from a diverse range of stakeholder groups on the jury findings; and (3) co-designing a set of Knowledge Translation resources to facilitate implementation into research, policy and practice. Conditions were chosen to reflect common health conditions characterised by increasing prevalence with age, but which have been underexamined through a Citizens' Jury methodology.
METHODS AND ANALYSIS
This study will be conducted in three Phases-(1) Citizens' Juries, (2) Policy Roundtables and (3) Production of Knowledge Translation resources. First, older people aged 50+ (n=80), including those from traditionally hard-to-reach and diverse groups, will be purposively recruited to four Citizen Juries. Second, representatives from a range of key stakeholder groups, including consumers and carers, health and aged care policymakers, general practitioners, practice nurses, geriatricians, allied health practitioners, pharmaceutical companies, private health insurers and community and aged care providers (n=40) will be purposively recruited for two Policy Roundtables. Finally, two researchers and six purposively recruited consumers will co-design Knowledge Translation resources. Thematic analysis will be performed on documentation and transcripts.
ETHICS AND DISSEMINATION
Ethical approval has been obtained through the Torrens University Human Research Ethics Committee. Participants will give written informed consent. Findings will be disseminated through development of a policy brief and lay summary, peer-reviewed publications, conference presentations and seminars.
Topics: Humans; Aged; Community Participation; Decision Making; Policy Making; Policy
PubMed: 38216190
DOI: 10.1136/bmjopen-2023-075501 -
Qualitative Research in Medicine &... Dec 2023Written communication is essential to staff and patient experience in healthcare. The Royal Literary Fund has hosted a writing fellow in an NHS Trust since 2018...
Written communication is essential to staff and patient experience in healthcare. The Royal Literary Fund has hosted a writing fellow in an NHS Trust since 2018 providing professional writing training. The aim of this evaluation was to explore the experiences of staff using the service. Semi-structured interviews were conducted with 21 staff members from a range of professions who had accessed the service. Data were analysed using thematic analysis. Findings: The writing service was highly valued. Three themes emerged: feelings about writing at work, reported benefits of attending sessions, and perceived barriers to accessing them. Staff felt underskilled in professional writing and described the wish to write more succinctly and reflectively. Self-reported confidence increased after sessions. Stigma around writing skills prevented some staff from recommending the service. Wider adoption of professional writing skills training through the NHS could have benefits in terms of increasing self-perceived skills and confidence.
PubMed: 38213668
DOI: 10.4081/qrmh.2023.11601 -
GigaScience Jan 2024Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to...
BACKGROUND
Jupyter notebooks facilitate the bundling of executable code with its documentation and output in one interactive environment, and they represent a popular mechanism to document and share computational workflows, including for research publications. The reproducibility of computational aspects of research is a key component of scientific reproducibility but has not yet been assessed at scale for Jupyter notebooks associated with biomedical publications.
APPROACH
We address computational reproducibility at 2 levels: (i) using fully automated workflows, we analyzed the computational reproducibility of Jupyter notebooks associated with publications indexed in the biomedical literature repository PubMed Central. We identified such notebooks by mining the article's full text, trying to locate them on GitHub, and attempting to rerun them in an environment as close to the original as possible. We documented reproduction success and exceptions and explored relationships between notebook reproducibility and variables related to the notebooks or publications. (ii) This study represents a reproducibility attempt in and of itself, using essentially the same methodology twice on PubMed Central over the course of 2 years, during which the corpus of Jupyter notebooks from articles indexed in PubMed Central has grown in a highly dynamic fashion.
RESULTS
Out of 27,271 Jupyter notebooks from 2,660 GitHub repositories associated with 3,467 publications, 22,578 notebooks were written in Python, including 15,817 that had their dependencies declared in standard requirement files and that we attempted to rerun automatically. For 10,388 of these, all declared dependencies could be installed successfully, and we reran them to assess reproducibility. Of these, 1,203 notebooks ran through without any errors, including 879 that produced results identical to those reported in the original notebook and 324 for which our results differed from the originally reported ones. Running the other notebooks resulted in exceptions.
CONCLUSIONS
We zoom in on common problems and practices, highlight trends, and discuss potential improvements to Jupyter-related workflows associated with biomedical publications.
Topics: Reproducibility of Results; Documentation; Records; Reproduction; Workflow
PubMed: 38206590
DOI: 10.1093/gigascience/giad113 -
Evidence-based Dentistry Mar 2024Seven databases (MEDLINE, CINAHL, Embase, Scopus, ProQuest, Cochrane and Google Scholar) were searched up to the third week in June 2022. Keyword search terms were based... (Review)
Review
DATA SOURCES AND SEARCH STRATEGY
Seven databases (MEDLINE, CINAHL, Embase, Scopus, ProQuest, Cochrane and Google Scholar) were searched up to the third week in June 2022. Keyword search terms were based on four key concepts: oral health, primary health, strategies, and integration.
STUDY SELECTION
Peer-reviewed studies that evaluated any strategies to integrate oral health into primary care (e.g., guidelines, policies, workforce programmes) were included in the review. Eligibility was restricted to papers written in English language. Papers in non-primary care settings or which did not describe an evaluation were excluded. Two reviewers independently screened titles and abstracts and thereafter full texts. Disagreements were resolved by consulting a third reviewer.
DATA EXTRACTION AND SYNTHESIS
Data were extracted by one reviewer; a second person verified accuracy. Covidence was used for data extraction. Two independent reviewers critically appraised the papers using the relevant tools (e.g. Critical Appraisal Skills Programme, Cochrane Collaboration, and STrengthening the Reporting of Observational studies in Epidemiology). PRISMA flow diagram was used to present the study selection process. Review findings were reported using a narrative synthesis approach. The Health System Building Blocks (HSBB) was used as a basis for structuring the results/discussion. Heterogeneity among the included studies was high and therefore no meta-analysis was conducted.
RESULTS
Forty-nine studies were included, of which two were RCTs. Most studies described oral healthcare delivered by non-dental primary care professionals within primary care services. Other settings included community, schools, and care homes. Outcomes of interest included: access to oral healthcare, knowledge/attitudes/perceptions, change in dental caries estimates. Almost all studies, except two studies which found no difference in the outcomes measured, favoured an integration strategy. Integration was achieved by enhancing competency (e.g. oral health promotion-trained educators), re-orientating responsibilities of health professionals at an organisation level and/or policy changes (e.g. expanded health insurance policy coverage to include oral health). Integration strategies enhanced access through improved referral pathways, documentation processes, operating efficiency, the number of health staff on hand, increased visits for oral health issues, higher fluoride varnish application rates for children, and more visits to dental health professionals.
CONCLUSIONS
In this review, promoting an integrated approach for oral health was associated with improvements across a range of outcomes. Integrating oral health into primary care is complex but holds promise for reducing the burden of dental diseases. Identifying the best practice models of service integration requires further research and evaluation.
Topics: Child; Humans; Oral Health; Dental Caries; Health Promotion; Health Personnel; Primary Health Care
PubMed: 38195743
DOI: 10.1038/s41432-023-00962-9