Pub Date : 2024-06-10DOI: 10.12688/wellcomeopenres.21725.1
Faith Campbell, Scott McGregor, Louise Marryat, Ryan Stewart, Jan Clarkson, Heather Cassie
Objective The objective of this scoping review is to map the extent and type of evidence in relation to the association between maternal health conditions, including multimorbidity and child oral health. Introduction Child oral health research has historically focussed on toothbrushing, diet and neglect of care, including not taking children to dental appointments. Newer theories are emerging that detail the many factors that can influence child oral health at child, family and community levels 1 . More recently, the association between maternal general health and child oral health has been explored, with preliminary evidence suggesting a link between shared environmental factors and direct maternal-to-child transfer of bacteria and diet/substance use during pregnancy causing childhood caries 2,3 . Inclusion criteria This review will include all published studies that describe the relationship between maternal health (including multimorbidity) and child oral health. There will be no limitation on the date of publication due to the limited number of studies available from the initial search of PubMed. The review will exclude case studies, abstracts, and grey literature. Literature must be in English language. Methods The following databases will be searched; CINAHL, Cochrane Library, Maternity and Infant Care, Medline via PubMed, Scopus, Web of Science. The search will include sources in English only and will be undertaken between April and July 2024. Studies to be included will be of any type of study design that describe a relationship between maternal health factors, including maternal oral health, and child oral health. Data extraction will be undertaken using tabulation of results by at least two independent reviewers. Narrative analysis of the evidence will be undertaken, and results will be presented in a narrative and tabular manner due to the heterogenous and limited evidence base found in the test search. This review has been registered prospectively on Open Science Framework, (https://doi.org/10.17605/OSF.IO/ECSWJ). The review will also inform an Evidence Gap Map (EGM) to illustrate the current evidence base regarding maternal health factors that influence child oral health.
目标 本范围界定综述旨在了解与产妇健康状况（包括多病症）和儿童口腔健康之间的关联有关的证据的范围和类型。引言 儿童口腔健康研究历来侧重于刷牙、饮食和忽视护理，包括不带儿童去看牙医。新出现的理论详细说明了在儿童、家庭和社区层面影响儿童口腔健康的诸多因素1。最近，人们开始探讨孕产妇总体健康与儿童口腔健康之间的联系，初步证据表明，共同的环境因素与孕期细菌和饮食/使用药物直接从孕产妇传给儿童导致儿童龋齿之间存在联系2,3。纳入标准 本综述将包括所有描述孕产妇健康（包括多病）与儿童口腔健康之间关系的已发表研究。由于最初在 PubMed 上搜索到的研究数量有限，因此对发表日期没有限制。综述将排除个案研究、摘要和灰色文献。文献必须使用英语。方法 将检索以下数据库：CINAHL、Cochrane Library、Maternity and Infant Care、Medline via PubMed、Scopus、Web of Science。搜索范围仅限于英语资料，搜索时间为 2024 年 4 月至 7 月。纳入的研究将采用任何类型的研究设计，描述产妇健康因素（包括产妇口腔健康）与儿童口腔健康之间的关系。数据提取工作将由至少两名独立评审员通过制表的方式进行。将对证据进行叙述性分析，由于试验性检索中发现的证据基础不尽相同且数量有限，因此将以叙述性和表格的方式呈现结果。本综述已在开放科学框架（https://doi.org/10.17605/OSF.IO/ECSWJ）上进行了前瞻性注册。本综述还将提供证据差距图（EGM），以说明影响儿童口腔健康的孕产妇健康因素的现有证据基础。
{"title":"The influence of maternal health factors including multimorbidity on child oral health: A scoping review and evidence gap map protocol","authors":"Faith Campbell, Scott McGregor, Louise Marryat, Ryan Stewart, Jan Clarkson, Heather Cassie","doi":"10.12688/wellcomeopenres.21725.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21725.1","url":null,"abstract":"Objective The objective of this scoping review is to map the extent and type of evidence in relation to the association between maternal health conditions, including multimorbidity and child oral health. Introduction Child oral health research has historically focussed on toothbrushing, diet and neglect of care, including not taking children to dental appointments. Newer theories are emerging that detail the many factors that can influence child oral health at child, family and community levels 1 . More recently, the association between maternal general health and child oral health has been explored, with preliminary evidence suggesting a link between shared environmental factors and direct maternal-to-child transfer of bacteria and diet/substance use during pregnancy causing childhood caries 2,3 . Inclusion criteria This review will include all published studies that describe the relationship between maternal health (including multimorbidity) and child oral health. There will be no limitation on the date of publication due to the limited number of studies available from the initial search of PubMed. The review will exclude case studies, abstracts, and grey literature. Literature must be in English language. Methods The following databases will be searched; CINAHL, Cochrane Library, Maternity and Infant Care, Medline via PubMed, Scopus, Web of Science. The search will include sources in English only and will be undertaken between April and July 2024. Studies to be included will be of any type of study design that describe a relationship between maternal health factors, including maternal oral health, and child oral health. Data extraction will be undertaken using tabulation of results by at least two independent reviewers. Narrative analysis of the evidence will be undertaken, and results will be presented in a narrative and tabular manner due to the heterogenous and limited evidence base found in the test search. This review has been registered prospectively on Open Science Framework, (https://doi.org/10.17605/OSF.IO/ECSWJ). The review will also inform an Evidence Gap Map (EGM) to illustrate the current evidence base regarding maternal health factors that influence child oral health.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141365424","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-10DOI: 10.12688/wellcomeopenres.21388.1
Oscar Castro, Gabriela Fajardo, Marie Johnston, Denise Laroze, Eduardo Leiva-Pinto, O. Figueroa, Elizabeth Corker, Jeanette A. Chacón-Candia, Giuliano Duarte
Background Precise and unequivocal specification of intervention content is key to facilitating the accumulation and implementation of knowledge. The Behaviour Change Technique Taxonomy v1 (BCTTv1) is the most widely used classification of behaviour change techniques (BCTs), providing a shared, standardized vocabulary to identify the active ingredients of behavioural interventions. However, the BCTTv1 is only available in English and this hampers its broad use and adoption. The aim of the present article is to report the process of translation of the BCTTv1 into Spanish. Methods A bilingual team led the translation of the BCTTv1, involving seven iterative steps: (i) establish a Committee, (ii) forward translation from English to Spanish, (iii) back translation from Spanish to English, (iv) comparison of original BCTTv1 and back translation, (v) opportunistic comparison against an independent BCTTv1 translation, (vi) empirical testing, and (vii) final Committee review. Results Changes as a result of the translation process included relabelling BCTs, amending definitions, and fixing conceptual and grammatical inconsistencies, yielding the final version. Very satisfactory inter-coder reliability in BCT identification was observed as part of the empirical testing (i.e., prevalence and bias-adjusted kappa scores > 0.8). Conclusions This work provides the Spanish-speaking population with a rigorous and validated BCTTv1 translation which can be used in both research and practice to provide a greater level of intervention detail for evidence synthesis, comparison, and replication of behaviour change interventions. The translation process described here may prove helpful to guide future translation efforts in behavioural science and beyond.
{"title":"Translating the behaviour change technique taxonomy version 1 into Spanish: Methodology and validation","authors":"Oscar Castro, Gabriela Fajardo, Marie Johnston, Denise Laroze, Eduardo Leiva-Pinto, O. Figueroa, Elizabeth Corker, Jeanette A. Chacón-Candia, Giuliano Duarte","doi":"10.12688/wellcomeopenres.21388.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21388.1","url":null,"abstract":"Background Precise and unequivocal specification of intervention content is key to facilitating the accumulation and implementation of knowledge. The Behaviour Change Technique Taxonomy v1 (BCTTv1) is the most widely used classification of behaviour change techniques (BCTs), providing a shared, standardized vocabulary to identify the active ingredients of behavioural interventions. However, the BCTTv1 is only available in English and this hampers its broad use and adoption. The aim of the present article is to report the process of translation of the BCTTv1 into Spanish. Methods A bilingual team led the translation of the BCTTv1, involving seven iterative steps: (i) establish a Committee, (ii) forward translation from English to Spanish, (iii) back translation from Spanish to English, (iv) comparison of original BCTTv1 and back translation, (v) opportunistic comparison against an independent BCTTv1 translation, (vi) empirical testing, and (vii) final Committee review. Results Changes as a result of the translation process included relabelling BCTs, amending definitions, and fixing conceptual and grammatical inconsistencies, yielding the final version. Very satisfactory inter-coder reliability in BCT identification was observed as part of the empirical testing (i.e., prevalence and bias-adjusted kappa scores > 0.8). Conclusions This work provides the Spanish-speaking population with a rigorous and validated BCTTv1 translation which can be used in both research and practice to provide a greater level of intervention detail for evidence synthesis, comparison, and replication of behaviour change interventions. The translation process described here may prove helpful to guide future translation efforts in behavioural science and beyond.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":" 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141364930","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-05DOI: 10.12688/wellcomeopenres.18972.3
H. Doan
Background It appears that underneath many propositions or actions, there might have been certain expectations. The reality of the complexity of human beings and interactions within a society yields expectations which, in turn, further interact with each other. Methods This paper offers the first in-depth study on ‘expectations’ in bioethical and health law studies, taking Vietnam’s responses to coronavirus disease (COVID-19) as an illustration. Results It defines ‘expectations’ as normative imaginaries that can induce or guide actions and inactions at individual and collective levels. Conclusions It argues that violations of human rights and certain related propositions within the Vietnamese context can be understood in terms of expectations. Within such contexts as Vietnam, expectations account for behaviours, including human rights violations. It suggests that ‘expectations’ is a fruitful concept for bioethical and health law studies. Studying expectations thus has implications for governance and future research agendas.
{"title":"Expectations and Vietnam’s responses during COVID-19: potential human rights violations and related propositions","authors":"H. Doan","doi":"10.12688/wellcomeopenres.18972.3","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.18972.3","url":null,"abstract":"Background It appears that underneath many propositions or actions, there might have been certain expectations. The reality of the complexity of human beings and interactions within a society yields expectations which, in turn, further interact with each other. Methods This paper offers the first in-depth study on ‘expectations’ in bioethical and health law studies, taking Vietnam’s responses to coronavirus disease (COVID-19) as an illustration. Results It defines ‘expectations’ as normative imaginaries that can induce or guide actions and inactions at individual and collective levels. Conclusions It argues that violations of human rights and certain related propositions within the Vietnamese context can be understood in terms of expectations. Within such contexts as Vietnam, expectations account for behaviours, including human rights violations. It suggests that ‘expectations’ is a fruitful concept for bioethical and health law studies. Studying expectations thus has implications for governance and future research agendas.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"344 9","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141385726","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-06-03DOI: 10.12688/wellcomeopenres.21505.1
Luís M. A. Perdigão, Casper Berger, Neville B.-y. Yee, Michele Darrow, Mark Basham
The experimental limitations with optics observed in many microscopy and astronomy instruments result in detrimental effects for the imaging of objects. This can be generally described mathematically as a convolution of the real object image with the point spread function that characterizes the optical system. The popular Richardson-Lucy (RL) deconvolution algorithm is widely used for the inverse process of restoring the data without these optical aberrations, often a critical step in data processing of experimental data. Here we present the versatile RedLionfish python package, that was written to make the RL deconvolution of volumetric (3D) data easier to run, very fast (by exploiting GPU computing capabilities) and with automatic handling of hardware limitations for large datasets. It can be used programmatically in Python/numpy using conda or PyPi package managers, or with a graphical user interface as a napari plugin.
{"title":"RedLionfish – fast Richardson-Lucy Deconvolution package for efficient point spread function suppression in volumetric data","authors":"Luís M. A. Perdigão, Casper Berger, Neville B.-y. Yee, Michele Darrow, Mark Basham","doi":"10.12688/wellcomeopenres.21505.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21505.1","url":null,"abstract":"The experimental limitations with optics observed in many microscopy and astronomy instruments result in detrimental effects for the imaging of objects. This can be generally described mathematically as a convolution of the real object image with the point spread function that characterizes the optical system. The popular Richardson-Lucy (RL) deconvolution algorithm is widely used for the inverse process of restoring the data without these optical aberrations, often a critical step in data processing of experimental data. Here we present the versatile RedLionfish python package, that was written to make the RL deconvolution of volumetric (3D) data easier to run, very fast (by exploiting GPU computing capabilities) and with automatic handling of hardware limitations for large datasets. It can be used programmatically in Python/numpy using conda or PyPi package managers, or with a graphical user interface as a napari plugin.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"13 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141388459","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-16DOI: 10.12688/wellcomeopenres.21281.1
Fredrick Mutisya, Rachael Kanguha
Background To train and develop machine learning models on the Pfizer antibacterial and antifungal datasets with subsequent deployment to an interactive Web Application. Methods We utilized R version 4.3.1 to perform descriptive analysis to obtain features/predictors. Python 3.10 libraries NumPy, Pandas, Scikit learn, Pycaret were used to train machine learning models. All these models were scored using area under the curve, recall, precision, F1, Kappa and the Mathews correlation coefficient. The best performing model was then deployed into a web application built on Streamlit after which deployment was done using GitHub and Streamlit cloud. A prototype android app was also developed using GoNative. Results The exploratory data analysis, S Aureus (17.2%) was the most common species however in the sub group analysis of the isolates with genotypic values, K Pneumoniae(48.2%) and E Coli (36.9%) were dominant. Amongst the fungi, Candida albicans (38.3%) and Candida glabrata (15.5%) were dominant. Feature selection was done using Shapley additive explanation plots. Using Extreme Gradient Boosting (XGBoost), we were able to achieve 99% and 97.8% AUC in the prediction of antibacterial and antifungal susceptibility respectively with minimal overfitting. Conclusions Decision tree based methods are a viable options of predicting antibacterial and antifungal drug resistance. When presented in visually appealing modes like web applications and android apps, it can be a useful guide to clinicians on initial treatment while awaiting definitive phenotypic testing. It can also be a surveillance tool that can craft antimicrobial resistance strategies.
{"title":"AntiMicro.ai: An Artificial Intelligence powered web application for predicting antibacterial/antifungal susceptibility and constructing personalized machine learning models","authors":"Fredrick Mutisya, Rachael Kanguha","doi":"10.12688/wellcomeopenres.21281.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21281.1","url":null,"abstract":"Background To train and develop machine learning models on the Pfizer antibacterial and antifungal datasets with subsequent deployment to an interactive Web Application. Methods We utilized R version 4.3.1 to perform descriptive analysis to obtain features/predictors. Python 3.10 libraries NumPy, Pandas, Scikit learn, Pycaret were used to train machine learning models. All these models were scored using area under the curve, recall, precision, F1, Kappa and the Mathews correlation coefficient. The best performing model was then deployed into a web application built on Streamlit after which deployment was done using GitHub and Streamlit cloud. A prototype android app was also developed using GoNative. Results The exploratory data analysis, S Aureus (17.2%) was the most common species however in the sub group analysis of the isolates with genotypic values, K Pneumoniae(48.2%) and E Coli (36.9%) were dominant. Amongst the fungi, Candida albicans (38.3%) and Candida glabrata (15.5%) were dominant. Feature selection was done using Shapley additive explanation plots. Using Extreme Gradient Boosting (XGBoost), we were able to achieve 99% and 97.8% AUC in the prediction of antibacterial and antifungal susceptibility respectively with minimal overfitting. Conclusions Decision tree based methods are a viable options of predicting antibacterial and antifungal drug resistance. When presented in visually appealing modes like web applications and android apps, it can be a useful guide to clinicians on initial treatment while awaiting definitive phenotypic testing. It can also be a surveillance tool that can craft antimicrobial resistance strategies.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"108 5","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140968209","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-16DOI: 10.12688/wellcomeopenres.21289.1
Tochukwu Agboeze, Oluwasegun I. Daramola, Ayobami Akomolafe, Roqeeb Adedeji, Julius Markwei
Background Translating available AMR surveillance data to observe evolving patterns of microbial resistance to antimicrobial agents while identifying regions at high risk of resistant cases and serving as a decision-support tool is an aspect of AMR surveillance that is rarely explored nationwide and uncommon globally. Therefore, we developed a two-tier dashboard algorithm (PATHFINDER) that can analyse antimicrobial surveillance datasets, observe evolving global spatiotemporal patterns of AMR, and integrate local AMR gene resources to identify functional AMR determinant genes and antibiotic classes from the query organism genome. Methods The Python-based plotly library was used to develop the interactive variables of the Antimicrobial Testing Leadership Surveillance (ATLAS) dataset in an adjustable spatiotemporal environment. A lightweight database containing multiple known resistant genes from the ResFinder database was used as a prototype to identify unique AMR determinant genes from query nucleotide sequences. In R, a function was created to accept query genome sequences and generate Kmers of length 250 using the blaster package. The GPT-4 API plug-in was embedded with adequate prompt parsing for it as an interpretation LLM function. Results AMR trendline plots were designed for invasive infections and customised based on the class of antibiotics and infection types on the surveillance dashboard. The decision-support tool correctly predicted resistant genes with a sensitivity of 75% on pre-confirmed organisms. The observed specificity score (51.5%) was due to the need for more filtering and optimisation and not to PATHFINDER performance. When run against the reference gene dataset containing pre-identified AMR genes, the support tool generated a BLAST table with identified AMR gene determinants in a nucleotide sequence. Conclusions The PATHFINDER algorithm has the potential to revolutionise healthcare decision-making. It can inform targeted interventions, guide antimicrobial stewardship efforts at a national level, promote appropriate antibiotic use, and significantly reduce the risk of resistance development.
背景 将现有的 AMR 监测数据转化为观察微生物对抗菌药物耐药性演变模式的数据，同时确定耐药病例高风险地区，并将其作为决策支持工具，这是 AMR 监测的一个方面，但在全国范围内鲜有探索，在全球范围内也不常见。因此，我们开发了一种双层仪表板算法（PATHFINDER），它可以分析抗微生物监测数据集，观察不断演变的全球 AMR 时空模式，并整合本地 AMR 基因资源，从查询生物基因组中识别功能性 AMR 决定基因和抗生素类别。方法 使用基于 Python 的 plotly 库，在可调整的时空环境中开发抗菌药物检测领导力监测（ATLAS）数据集的交互式变量。以 ResFinder 数据库中包含多个已知耐药基因的轻量级数据库为原型，从查询核苷酸序列中识别出独特的 AMR 决定基因。在 R 中创建了一个函数，用于接受查询的基因组序列，并使用 blaster 软件包生成长度为 250 的 Kmers。嵌入了 GPT-4 API 插件，并对其进行了充分的提示解析，将其作为一个解释 LLM 的函数。结果 针对入侵性感染设计了 AMR 趋势线图，并根据监测仪表板上的抗生素类别和感染类型进行了定制。决策支持工具能正确预测耐药基因，对预先确认的生物体的灵敏度为 75%。观察到的特异性得分（51.5%）是由于需要进行更多过滤和优化，而非 PATHFINDER 的性能所致。当与包含预先确定的 AMR 基因的参考基因数据集运行时，支持工具生成了一个 BLAST 表，其中包含核苷酸序列中已确定的 AMR 基因决定因子。结论 PATHFINDER 算法有可能彻底改变医疗决策。它可以为有针对性的干预措施提供信息，指导国家层面的抗菌药物管理工作，促进抗生素的合理使用，并显著降低耐药性产生的风险。
{"title":"A predictive algorithm for the analysis of AMR trends and healthcare decision support","authors":"Tochukwu Agboeze, Oluwasegun I. Daramola, Ayobami Akomolafe, Roqeeb Adedeji, Julius Markwei","doi":"10.12688/wellcomeopenres.21289.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21289.1","url":null,"abstract":"Background Translating available AMR surveillance data to observe evolving patterns of microbial resistance to antimicrobial agents while identifying regions at high risk of resistant cases and serving as a decision-support tool is an aspect of AMR surveillance that is rarely explored nationwide and uncommon globally. Therefore, we developed a two-tier dashboard algorithm (PATHFINDER) that can analyse antimicrobial surveillance datasets, observe evolving global spatiotemporal patterns of AMR, and integrate local AMR gene resources to identify functional AMR determinant genes and antibiotic classes from the query organism genome. Methods The Python-based plotly library was used to develop the interactive variables of the Antimicrobial Testing Leadership Surveillance (ATLAS) dataset in an adjustable spatiotemporal environment. A lightweight database containing multiple known resistant genes from the ResFinder database was used as a prototype to identify unique AMR determinant genes from query nucleotide sequences. In R, a function was created to accept query genome sequences and generate Kmers of length 250 using the blaster package. The GPT-4 API plug-in was embedded with adequate prompt parsing for it as an interpretation LLM function. Results AMR trendline plots were designed for invasive infections and customised based on the class of antibiotics and infection types on the surveillance dashboard. The decision-support tool correctly predicted resistant genes with a sensitivity of 75% on pre-confirmed organisms. The observed specificity score (51.5%) was due to the need for more filtering and optimisation and not to PATHFINDER performance. When run against the reference gene dataset containing pre-identified AMR genes, the support tool generated a BLAST table with identified AMR gene determinants in a nucleotide sequence. Conclusions The PATHFINDER algorithm has the potential to revolutionise healthcare decision-making. It can inform targeted interventions, guide antimicrobial stewardship efforts at a national level, promote appropriate antibiotic use, and significantly reduce the risk of resistance development.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"118 4","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140967638","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-16DOI: 10.12688/wellcomeopenres.21678.1
G. Broad, D. Boyes, Riccardo Poloni
We present a genome assembly from an individual female Cydalima perspectalis (the Box-tree Moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 483.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.
我们展示了一个雌性盒树蛾（Cydalima perspectalis；节肢动物门；昆虫纲；鳞翅目；克氏蛾科）个体的基因组序列。基因组序列跨度为 483.7 兆字节。大部分基因组组装成 32 个染色体假分子支架，包括 Z 和 W 性染色体。线粒体基因组也已组装完成，长度为 15.25 千碱基。
{"title":"The genome sequence of the Box-tree Moth, Cydalima perspectalis (Walker, 1859)","authors":"G. Broad, D. Boyes, Riccardo Poloni","doi":"10.12688/wellcomeopenres.21678.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21678.1","url":null,"abstract":"We present a genome assembly from an individual female Cydalima perspectalis (the Box-tree Moth; Arthropoda; Insecta; Lepidoptera; Crambidae). The genome sequence is 483.7 megabases in span. Most of the assembly is scaffolded into 32 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 15.25 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"7 3","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140969457","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-16DOI: 10.12688/wellcomeopenres.21665.1
D. Boyes, David C. Lees, Denise C. Wawman
We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.
我们展示了一个雌性 Plemyria rubiginata（蓝边地毯蛾；节肢动物门；昆虫纲；鳞翅目；尺蠖蛾科）个体的基因组序列。基因组序列跨度为 356.2 兆字节。大部分基因组组装成 30 个染色体假分子支架，包括 Z 和 W 性染色体。线粒体基因组也已组装完成，长度为 17.64 千碱基。
{"title":"The genome sequence of the Blue-bordered Carpet moth Plemyria rubiginata (Denis & Schiffermüller) 1775","authors":"D. Boyes, David C. Lees, Denise C. Wawman","doi":"10.12688/wellcomeopenres.21665.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21665.1","url":null,"abstract":"We present a genome assembly from an individual female Plemyria rubiginata (the Blue-bordered Carpet moth; Arthropoda; Insecta; Lepidoptera; Geometridae). The genome sequence is 356.2 megabases in span. Most of the assembly is scaffolded into 30 chromosomal pseudomolecules, including the Z and W sex chromosomes. The mitochondrial genome has also been assembled and is 17.64 kilobases in length.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"3 6","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140967489","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21450.1
J. Ndyetukira, Richard Kwizera, C. Ahimbisibwe, C. Namujju, D. Meya
Background In Uganda where the burden of HIV-associated cryptococcal meningitis is high, conventional amphotericin B deoxycholate has been standard to manage patients with cryptococcal meningitis in research settings. However, liposomal amphotericin B (AmBisome) is now available via the efforts of UNITAID. We sought to describe our nursing experience using AmBisome within a clinical trial for cryptococcal meningitis. Methods We describe the experience of using single-dose 10mg/kg liposomal amphotericin B from the perspective of a research nurse in Uganda. Second, we described the process of preparing and administering amphotericin. Third, we assessed the nursing time required for the administration of daily amphotericin B versus single-dose liposomal amphotericin. Fourth, we discuss the major challenges faced while using liposomal amphotericin B. Results We provide estimates for the nursing time required for reconstituting, filtering, diluting and administering liposomal amphotericin B and a visual aid for nursing tasks. Based on five trained nurses, the process of reconstitution and filtration lasts an average of 52 minutes (Range: 40 to 60 minutes), to reconstitute a mean of 11 (range: 8 to 15) 50mg vials (median weight 55kg). Overall, less nursing time was required for single-dose administration than for daily amphotericin B dosing. From a nursing perspective, liposomal amphotericin B was preferable to amphotericin B deoxycholate due to its reduced infusion reactions and other toxicities. Conclusions Single-dose liposomal amphotericin B is a better alternative to daily amphotericin B. In addition to less toxicity, nosocomial infections, reduced hospital stay, and the potential for lower hospitalisation costs, the nursing implications should not be discounted. Quality nursing care is a finite resource in low- and middle-income countries, and single-dose amphotericin B reduced the nursing time required for the care of patients with cryptococcal meningitis.
背景在乌干达，艾滋病毒相关隐球菌脑膜炎的发病率很高，在研究环境中，传统的两性霉素 B 去氧胆酸盐一直是治疗隐球菌脑膜炎患者的标准药物。然而，在国际药品采购机制的努力下，脂质体两性霉素 B（AmBisome）现已上市。我们试图描述在隐球菌性脑膜炎临床试验中使用 AmBisome 的护理经验。方法 我们从乌干达一名研究护士的角度描述了使用单剂量 10 毫克/千克脂质体两性霉素 B 的经验。其次，我们描述了准备和使用两性霉素的过程。第三，我们评估了每日使用两性霉素 B 和单剂量脂质体两性霉素所需的护理时间。第四，我们讨论了在使用脂质体两性霉素 B 时所面临的主要挑战。 结果 我们提供了重构、过滤、稀释和给药脂质体两性霉素 B 所需的护理时间估算以及护理任务的视觉辅助工具。以五名受过培训的护士为基础，重组和过滤过程平均持续 52 分钟（范围：40 至 60 分钟），平均重组 11 个（范围：8 至 15 个）50 毫克小瓶（中位数重量为 55 千克）。总体而言，单剂量给药所需的护理时间少于每日两性霉素 B 给药。从护理角度来看，脂质体两性霉素 B 比脱氧胆酸两性霉素 B 更为可取，因为脂质体两性霉素 B 可减少输液反应和其他毒性反应。结论 单剂量脂质体两性霉素 B 是替代每日两性霉素 B 的更好选择。除了毒性更低、非医院感染更少、住院时间更短、住院费用更低之外，护理方面的影响也不容忽视。在中低收入国家，优质护理是有限的资源，而单剂两性霉素 B 减少了护理隐球菌脑膜炎患者所需的护理时间。
{"title":"Using single-dose liposomal amphotericin B for cryptococcal meningitis induction therapy: nurse pearls and practical perspectives","authors":"J. Ndyetukira, Richard Kwizera, C. Ahimbisibwe, C. Namujju, D. Meya","doi":"10.12688/wellcomeopenres.21450.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21450.1","url":null,"abstract":"Background In Uganda where the burden of HIV-associated cryptococcal meningitis is high, conventional amphotericin B deoxycholate has been standard to manage patients with cryptococcal meningitis in research settings. However, liposomal amphotericin B (AmBisome) is now available via the efforts of UNITAID. We sought to describe our nursing experience using AmBisome within a clinical trial for cryptococcal meningitis. Methods We describe the experience of using single-dose 10mg/kg liposomal amphotericin B from the perspective of a research nurse in Uganda. Second, we described the process of preparing and administering amphotericin. Third, we assessed the nursing time required for the administration of daily amphotericin B versus single-dose liposomal amphotericin. Fourth, we discuss the major challenges faced while using liposomal amphotericin B. Results We provide estimates for the nursing time required for reconstituting, filtering, diluting and administering liposomal amphotericin B and a visual aid for nursing tasks. Based on five trained nurses, the process of reconstitution and filtration lasts an average of 52 minutes (Range: 40 to 60 minutes), to reconstitute a mean of 11 (range: 8 to 15) 50mg vials (median weight 55kg). Overall, less nursing time was required for single-dose administration than for daily amphotericin B dosing. From a nursing perspective, liposomal amphotericin B was preferable to amphotericin B deoxycholate due to its reduced infusion reactions and other toxicities. Conclusions Single-dose liposomal amphotericin B is a better alternative to daily amphotericin B. In addition to less toxicity, nosocomial infections, reduced hospital stay, and the potential for lower hospitalisation costs, the nursing implications should not be discounted. Quality nursing care is a finite resource in low- and middle-income countries, and single-dose amphotericin B reduced the nursing time required for the care of patients with cryptococcal meningitis.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"66 12","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140972268","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Pub Date : 2024-05-15DOI: 10.12688/wellcomeopenres.21627.1
K. Lohse, R. Vila, Alex Hayward
We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.
{"title":"The genome sequence of the Lulworth Skipper, Thymelicus acteon (Rottemburg, 1775)","authors":"K. Lohse, R. Vila, Alex Hayward","doi":"10.12688/wellcomeopenres.21627.1","DOIUrl":"https://doi.org/10.12688/wellcomeopenres.21627.1","url":null,"abstract":"We present a genome assembly from an individual male Thymelicus acteon (the Lulworth Skipper; Arthropoda; Insecta; Lepidoptera; Hesperiidae). The genome sequence is 537.0 megabases in span. Most of the assembly is scaffolded into 28 chromosomal pseudomolecules, including the Z sex chromosome. The mitochondrial genome has also been assembled and is 17.08 kilobases in length. Gene annotation of this assembly on Ensembl identified 12,813 protein-coding genes.","PeriodicalId":508490,"journal":{"name":"Wellcome Open Research","volume":"9 1","pages":""},"PeriodicalIF":0.0,"publicationDate":"2024-05-15","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140971901","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：