-
Metabolomics : Official Journal of the... Feb 2023Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a popular approach for metabolomics data acquisition and requires many data processing software... (Review)
Review
BACKGROUND
Liquid chromatography-high resolution mass spectrometry (LC-HRMS) is a popular approach for metabolomics data acquisition and requires many data processing software tools. The FAIR Principles - Findability, Accessibility, Interoperability, and Reusability - were proposed to promote open science and reusable data management, and to maximize the benefit obtained from contemporary and formal scholarly digital publishing. More recently, the FAIR principles were extended to include Research Software (FAIR4RS).
AIM OF REVIEW
This study facilitates open science in metabolomics by providing an implementation solution for adopting FAIR4RS in the LC-HRMS metabolomics data processing software. We believe our evaluation guidelines and results can help improve the FAIRness of research software.
KEY SCIENTIFIC CONCEPTS OF REVIEW
We evaluated 124 LC-HRMS metabolomics data processing software obtained from a systematic review and selected 61 software for detailed evaluation using FAIR4RS-related criteria, which were extracted from the literature along with internal discussions. We assigned each criterion one or more FAIR4RS categories through discussion. The minimum, median, and maximum percentages of criteria fulfillment of software were 21.6%, 47.7%, and 71.8%. Statistical analysis revealed no significant improvement in FAIRness over time. We identified four criteria covering multiple FAIR4RS categories but had a low %fulfillment: (1) No software had semantic annotation of key information; (2) only 6.3% of evaluated software were registered to Zenodo and received DOIs; (3) only 14.5% of selected software had official software containerization or virtual machine; (4) only 16.7% of evaluated software had a fully documented functions in code. According to the results, we discussed improvement strategies and future directions.
Topics: Metabolomics; Chromatography, Liquid; Mass Spectrometry; Software; Data Management
PubMed: 36745241
DOI: 10.1007/s11306-023-01974-3 -
Journal of Alternative and... Sep 2014To present the results of a systematic review of studies on acupuncture patients' health beliefs and treatment experiences. (Review)
Review
OBJECTIVES
To present the results of a systematic review of studies on acupuncture patients' health beliefs and treatment experiences.
SEARCH STRATEGY
The search was conducted using CINAHL, PubMed, Ovid MEDLINE, ISI Web of Science, and PsychINFO for qualitative and mixed-methods studies expressing the voice of acupuncture patients. Reference lists of relevant articles were also searched. The review was restricted to studies published in English.
DATA COLLECTION AND ANALYSIS
Study selection, quality appraisal, and data extraction were performed sequentially. Quality was appraised using the Joanna Briggs Institute Qualitative Assessment and Review Instrument, and the Dedoose mixed methods tool was used in data management and analysis.
RESULTS
Four overarching themes were identified: reasons for using acupuncture, treatment experiences, treatment outcomes, and therapeutic model.
CONCLUSIONS
Patients' reasons for using acupuncture are diverse and include dissatisfaction with conventional medicine and attraction to holistic and empowering models of healthcare. Treatment is thought to relieve symptoms of the presenting concern and a range of other effects that improve well-being. This review highlights the need to improve understanding of patients' health-seeking behaviors and how individually meaningful treatment outcomes may be understood and assessed, particularly within complementary and alternative medicine.
Topics: Acupuncture Therapy; Humans; Patient Acceptance of Health Care; Treatment Outcome
PubMed: 25072404
DOI: 10.1089/acm.2013.0446 -
Oral Health & Preventive Dentistry Jul 2020Halitosis is an unpleasant breath odor which can be bothersome to individuals. Extra-oral halitosis is a type of halitosis caused by systemic conditions, bloodborne...
PURPOSE
Halitosis is an unpleasant breath odor which can be bothersome to individuals. Extra-oral halitosis is a type of halitosis caused by systemic conditions, bloodborne diseases, or pharmaceutical therapy. It is not related to local factors in the oral cavity. This systematic review aimed to identify the medications that can cause extra-oral halitosis.
MATERIALS AND METHODS
This study was conducted in accordance with the preferred reporting items for systematic reviews and meta-analyses (PRISMA). We searched online databases and also included hand searching to find relevant articles. Two authors independently performed the screening, data extraction and quality assessment of the included articles using the Cochrane Collaboration assessment tool.
RESULTS
Thirty-four studies met the eligibility criteria. The medications which can cause extra-oral halitosis were categorised into 10 groups: acid reducers, aminothiols, anticholinergics, antidepressants, antifungals, antihistamines and steroids, antispasmodics, chemotherapeutic agents, dietary supplements, and organosulfur substances.
CONCLUSION
Pharmaceutical therapy is a potential source of extra-oral halitosis. This finding can help clinicians detect the probable causes of halitosis. Further studies are needed to definitely determine the role of various medications in causing extra-oral halitosis.
Topics: Data Management; Drug-Related Side Effects and Adverse Reactions; Halitosis; Humans; Mouth; Pharmaceutical Preparations
PubMed: 32515409
DOI: 10.3290/j.ohpd.a44679 -
Anaesthesia, Critical Care & Pain... Aug 2020Hyperthermic intraperitoneal chemotherapy (HIPEC) is a surgical technique for peritoneal carcinomatosis combining cytoreduction surgery and peritoneal irrigation of... (Review)
Review
CONTEXT
Hyperthermic intraperitoneal chemotherapy (HIPEC) is a surgical technique for peritoneal carcinomatosis combining cytoreduction surgery and peritoneal irrigation of cytotoxic agents responsible for haemodynamics and fluid homeostasis alterations. To this day, no guidelines exist concerning intraoperative management.
OBJECTIVES
To review data on haemodynamic monitoring and management of patients undergoing HIPEC and to help design a standardised anaesthetic protocol.
DATA SOURCES
MEDLINE, EMBASE and Cochrane library were searched using the following.
STUDY SELECTION
Original articles and case-reports. Letters to editors and reviews were excluded.
DATA EXTRACTION
Data on haemodynamic management, morbidity and mortality.
DATA SYNTHESIS
Haemodynamic management during HIPEC is highly variable and depends on local protocols. Only one randomised controlled trial evaluated the benefit of goal-directed fluid administration (GDFA). GDFA guided by advanced haemodynamic monitoring resulted in significantly less complication, shorter length of stay and less mortality compared to standard fluid administration. Renal protection protocol did not decrease the risk of acute kidney injury (AKI).
CONCLUSION
Our review reveals that fluid administration guided by advanced monitoring seems to be associated with less postoperative morbidity and mortality after HIPEC. Nevertheless, the literature review shows that intraoperative haemodynamic management is highly variable for this surgery. The use of renal protection strategy does not decrease the prevalence of AKI. Further prospective trials comparing different fluid management and haemodynamic monitoring strategies are urgently needed (PROSPERO registration CRD42018115720).
Topics: Combined Modality Therapy; Cytoreduction Surgical Procedures; Fluid Therapy; Hemodynamics; Humans; Hyperthermia, Induced; Peritoneal Neoplasms
PubMed: 32320757
DOI: 10.1016/j.accpm.2020.03.019 -
Iranian Journal of Pharmaceutical... 2021Poisoning, as a well-known medical condition, puts everyone at risk. As a data management tool, a registry plays an important role in monitoring the poisoned patients.... (Review)
Review
Poisoning, as a well-known medical condition, puts everyone at risk. As a data management tool, a registry plays an important role in monitoring the poisoned patients. Having a poisoning minimum data set is a major requirement for creating a poisoning registry. Therefore, the present systematic review was conducted in 2019 to identify the minimum data set for a poisoning registry. Searches were performed in four scientific databases, ., PubMed, Scopus, Web of Science, and Embase. The keywords used in the searches included minimum data set, "poison", and "registry". Two researchers independently evaluated the titles, abstracts, and texts of the papers. The data were collected from the related papers. Ultimately, the minimum data set was identified for the poisoning registry. Data elements extracted from the sources were classified into two general categories: administrative data and clinical data. Ninety-eight data elements in the administrative data category were subdivided into three sections: general data, admission data, and discharge data. One-hundred and thirty-one data elements in the clinical data category were subdivided into five sections: clinical observation data, clinical assessment data, past medical history data, diagnosis data, and treatment plan data. The minimum data set is a prerequisite for creating and using a poisoning registry and data system. It is suggested to evaluate and use the poisoning minimum data set in accordance with the national laws, needs, and standards based on the opinion of the local experts.
PubMed: 34567176
DOI: 10.22037/ijpr.2020.113869.14538 -
BMC Public Health May 2023Human Papilloma Virus (HPV) is the most common sexually transmitted infection worldwide. Globally, both men and women have a 50% risk of being infected at least once in...
BACKGROUND
Human Papilloma Virus (HPV) is the most common sexually transmitted infection worldwide. Globally, both men and women have a 50% risk of being infected at least once in their life. HPV prevalence is among the highest in sub-Saharan Africa (SSA), at an average of 24%. HPV causes different types of cancers, including cervical cancer (CC), which is the leading cause of cancer deaths among women in SSA. HPV-vaccination has been proven to be effective in reducing HPV induced cancers. SSA countries are delayed in reaching the WHO's target of fully vaccinating 90% of girls within the age of 15 by 2030. Our systematic review aims to identify barriers and facilitators of HPV-vaccination in SSA to inform national implementation strategies in the region.
METHODS
This is a mixed method systematic review based on the PRISMA statement and The Joanna Briggs Institute Reviewers' Manual. Search strategies were adapted to each selected database: PubMed/MEDLINE, Livivo, Google Scholar, Science Direct, and African Journals Online for papers published in English, Italian, German, French and Spanish between 1 December 2011 and 31 December 2021. Zotero and Rayyan were the software used for data management. The appraisal was conducted by three independent reviewers.
RESULTS
A total of 20 articles were selected for appraisal from an initial 536 articles. Barriers included: limited health system capacities, socio-economic status, stigma, fear and costs of vaccines, negative experience with vaccinations, COVID-19 pandemic, lack of correct information, health education (HE) and consent. Additionally, we found that boys are scarcely considered for HPV-vaccination by parents and stakeholders. Facilitators included: information and knowledge, policy implementation, positive experience with vaccinations, HE, stakeholders' engagement, women's empowerment, community engagement, seasonality, and target-oriented vaccination campaigns.
CONCLUSIONS
This review synthesizes barriers and facilitators of HPV-vaccinations in SSA. Addressing these can contribute to the implementation of more effective HPV immunization programs targeted at eliminating CC in line with the WHO 90/70/90 strategy.
REGISTRATION AND FUNDING
Protocol ID: CRD42022338609 registered in the International Prospective Register of Systematic Reviews (PROSPERO). Partial funds: German Centre for Infection research (DZIF) project NAMASTE: 8,008,803,819.
Topics: Male; Humans; Female; Papillomavirus Infections; Pandemics; COVID-19; Africa South of the Sahara; Vaccination; Uterine Cervical Neoplasms; Papillomavirus Vaccines
PubMed: 37237329
DOI: 10.1186/s12889-023-15842-1 -
International Journal of Medical... Sep 2020Building on initial work carried out by the Faculty of Clinical Informatics (FCI) in the UK, the creation of a national competency framework for Clinical Informatics is... (Meta-Analysis)
Meta-Analysis Review
BACKGROUND
Building on initial work carried out by the Faculty of Clinical Informatics (FCI) in the UK, the creation of a national competency framework for Clinical Informatics is required for the definition of clinical informaticians' professional attributes and skills. We aimed to systematically review the academic literature relating to competencies, skills and existing course curricula in the clinical and health related informatics domains.
METHODS
Two independent reviewers searched Web of Science, EMBASE, ERIC, PubMed and CINAHL. Publications were included if they reported details of relevant competencies, skills and existing course curricula. We report findings using the Preferred Reporting Items for Systematic Reviews and Meta-Analysis (PRISMA) statement.
RESULTS
A total of 82 publications were included. The most frequently used method was surveys (30 %) followed by narrative descriptions (28 %). Most of the publications describe curriculum design (23 %) followed by competency definition (18 %) and skills, qualifications & training (18 %). Core skills surrounding data, information systems and information management appear to be cross-cutting across the various informatics disciplines with Bioinformatics and Pharmacy Informatics expressing the most unique competency requirements.
CONCLUSION
We identified eight key domains that cut across the different sub-disciplines of health informatics, including data, information management, human factors, project management, research skills/knowledge, leadership and management, systems development and evaluation, and health/healthcare. Some informatics disciplines such as Nursing Informatics appear to be further ahead at achieving widespread competency standardisation. Attempts at standardisation for competencies should be tempered with flexibility to allow for local variation and requirements.
Topics: Curriculum; Humans; Information Management; Leadership; Medical Informatics; Nursing Informatics; Professional Competence
PubMed: 32771960
DOI: 10.1016/j.ijmedinf.2020.104237 -
Psychiatric Rehabilitation Journal Sep 2017Internet (eHealth) and smartphone-based (mHealth) approaches to self-management for bipolar disorder are increasingly common. Evidence-based self-management strategies... (Review)
Review
OBJECTIVE
Internet (eHealth) and smartphone-based (mHealth) approaches to self-management for bipolar disorder are increasingly common. Evidence-based self-management strategies are available for bipolar disorder and provide a useful framework for reviewing existing eHealth/mHealth programs to determine whether these strategies are supported by current technologies. This review assesses which self-management strategies are most supported by technology.
METHOD
Based on 3 previous studies, 7 categories of self-management strategies related to bipolar disorder were identified, followed by a systematic literature review to identify existing eHealth and mHealth programs for this disorder. Searches were conducted by using PubMed, CINAHL, PsycINFO, EMBASE, and the Cochrane Database of Systematic Reviews for relevant peer-reviewed articles published January 2005 to May 2015. eHealth and mHealth programs were summarized and reviewed to identify which of the 7 self-management strategy categories were supported by eHealth or mHealth programs.
RESULTS
From 1,654 publications, 15 papers were identified for inclusion. From these, 9 eHealth programs and 2 mHealth programs were identified. The most commonly supported self-management strategy categories were "ongoing monitoring," "maintaining hope," "education," and "planning for and taking action"; the least commonly supported categories were "relaxation" and "maintaining a healthy lifestyle." eHealth programs appear to provide more comprehensive coverage of self-management strategies compared with mHealth programs.
CONCLUSIONS AND IMPLICATIONS FOR PRACTICE
Both eHealth and mHealth programs present a wide range of self-management strategies for bipolar disorder, although individuals seeking comprehensive interventions might be best served by eHealth programs, while those seeking more condensed and direct interventions might prefer mHealth programs. (PsycINFO Database Record
Topics: Bipolar Disorder; Humans; Internet; Medical Informatics Applications; Mobile Applications; Self-Management; Telemedicine
PubMed: 28594196
DOI: 10.1037/prj0000270 -
Journal of Vascular Surgery Jul 2020Abdominal aortic aneurysm (AAA) is a life-threatening disease, and the only curative treatment relies on open or endovascular repair. The decision to treat relies on the...
OBJECTIVE
Abdominal aortic aneurysm (AAA) is a life-threatening disease, and the only curative treatment relies on open or endovascular repair. The decision to treat relies on the evaluation of the risk of AAA growth and rupture, which can be difficult to assess in practice. Artificial intelligence (AI) has revealed new insights into the management of cardiovascular diseases, but its application in AAA has so far been poorly described. The aim of this review was to summarize the current knowledge on the potential applications of AI in patients with AAA.
METHODS
A comprehensive literature review was performed. The MEDLINE database was searched according to the Preferred Reporting Items for Systematic Reviews and Meta-Analyses guidelines. The search strategy used a combination of keywords and included studies using AI in patients with AAA published between May 2019 and January 2000. Two authors independently screened titles and abstracts and performed data extraction. The search of published literature identified 34 studies with distinct methodologies, aims, and study designs.
RESULTS
AI was used in patients with AAA to improve image segmentation and for quantitative analysis and characterization of AAA morphology, geometry, and fluid dynamics. AI allowed computation of large data sets to identify patterns that may be predictive of AAA growth and rupture. Several predictive and prognostic programs were also developed to assess patients' postoperative outcomes, including mortality and complications after endovascular aneurysm repair.
CONCLUSIONS
AI represents a useful tool in the interpretation and analysis of AAA imaging by enabling automatic quantitative measurements and morphologic characterization. It could be used to help surgeons in preoperative planning. AI-driven data management may lead to the development of computational programs for the prediction of AAA evolution and risk of rupture as well as postoperative outcomes. AI could also be used to better evaluate the indications and types of surgical treatment and to plan the postoperative follow-up. AI represents an attractive tool for decision-making and may facilitate development of personalized therapeutic approaches for patients with AAA.
Topics: Aortic Aneurysm, Abdominal; Artificial Intelligence; Clinical Decision-Making; Decision Support Systems, Clinical; Decision Support Techniques; Diagnosis, Computer-Assisted; Humans; Image Interpretation, Computer-Assisted; Patient Selection; Predictive Value of Tests; Risk Assessment; Risk Factors; Treatment Outcome
PubMed: 32093909
DOI: 10.1016/j.jvs.2019.12.026