Tool design/development
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BACKGROUND: The advancement of sequencing technologies today has made a plethora of whole-genome re-sequenced (WGRS) data publicly available. However, research utilizing the WGRS data without further configuration is nearly impossible. To solve this problem, our research group has developed an interactive Allele Catalog Tool to enable researchers to explore the coding region allelic variation present in over 1,000 re-sequenced accessions each for soybean, Arabidopsis, and maize. RESULTS: The Allele Catalog Tool was designed originally with soybean genomic data and resources. The Allele Catalog datasets were generated using our variant calling pipeline (SnakyVC) and the Allele Catalog pipeline (AlleleCatalog). The variant calling pipeline is developed to parallelly process raw sequencing reads to generate the Variant Call Format (VCF) files, and the Allele Catalog pipeline takes VCF files to perform imputations, functional effect predictions, and assemble alleles for each gene to generate curated Allele Catalog datasets. Both pipelines were utilized to generate the data panels (VCF files and Allele Catalog files) in which the accessions of the WGRS datasets were collected from various sources, currently representing over 1,000 diverse accessions for soybean, Arabidopsis, and maize individually. The main features of the Allele Catalog Tool include data query, visualization of results, categorical filtering, and download functions. Queries are performed from user input, and results are a tabular format of summary results by categorical description and genotype results of the alleles for each gene. The categorical information is specific to each species; additionally, available detailed meta-information is provided in modal popups. The genotypic information contains the variant positions, reference or alternate genotypes, the functional effect classes, and the amino-acid changes of each accession. Besides that, the results can also be downloaded for other research purposes. CONCLUSIONS: The Allele Catalog Tool is a web-based tool that currently supports three species: soybean, Arabidopsis, and maize. The Soybean Allele Catalog Tool is hosted on the SoyKB website ( https://soykb.org/SoybeanAlleleCatalogTool/ ), while the Allele Catalog Tool for Arabidopsis and maize is hosted on the KBCommons website ( https://kbcommons.org/system/tools/AlleleCatalogTool/Zmays and https://kbcommons.org/system/tools/AlleleCatalogTool/Athaliana ). Researchers can use this tool to connect variant alleles of genes with meta-information of species.
- MeSH
- alely * MeSH
- Arabidopsis * genetika MeSH
- data mining * metody MeSH
- datové soubory jako téma * MeSH
- frekvence genu MeSH
- genotyp MeSH
- Glycine max * genetika MeSH
- internet * MeSH
- kukuřice setá * genetika MeSH
- metadata MeSH
- mutace MeSH
- pigmentace genetika MeSH
- rostlinné geny genetika MeSH
- software * MeSH
- substituce aminokyselin MeSH
- vegetační klid genetika MeSH
- vizualizace dat MeSH
- Publikační typ
- časopisecké články MeSH
Pojem placebo účinku zahrnuje nespecifické působení lékařského zákroku nebo nefarmakodynamicky zprostředkované terapeutické účinky léku, které jsou založené především na očekávání nemocného. Placebo účinek byl považován především za psychologický jev, pozorovatelný u subjektivně hodnocených výsledných stavů. V posledních letech přibývá důkazů, že nespecificky působící lék, placebo, má účinky na metabolizmus mozku, na jeho biochemickou i elektrofyziologickou aktivitu. Změny v metabolické aktivitě navozené placebem se odehrávají v mozkových strukturách, které jsou zodpovědné také za skutečný účinek farmaka. Placebo je nástroj výzkumu v klinické farmakologii, který je nepostradatelný, pokud není známa účinná léčba nějaké poruchy nebo nemoci. Je mnohdy také zapotřebí, potřebujeme-li odlišit skutečný účinek experimentálního léku při srovnání se standardním referenčním lékem, v projektech postavených na metodě „double dummy“ (dvojitého zástupu), nebo během počátečního placebo období při klinickém zkoušení farmak. S použitím placeba ve výzkumu stejně jako v klinické praxi jsou spojeny etické problémy. Také etika použití placeba ve výzkumu se liší od etiky klinické praxe, protože oba přístupy mají rozdílné cíle. Byla vypracována vodítka, která slouží ochraně subjektů a zároveň umožňují odůvodněné užití placeba v lékařském výzkumu. To slouží v delší perspektivě zájmům pacientů i vědy.
Placebo effect is a term that sums up the non-specific effects of a medical intervention or non-pharmacodynamic effects of a drug. The effect is based on patient´s expectancy. It has been thought of as a pleasing psychological effect, that is best observed in subjective outcomes. However, there is an accumulating evidence, that placebo, in spite of being a non-specific drug, has an effect on metabolic, biochemical and electrophysiological activity of the brain. Changes in metabolic activity after placebo take place in those brain structures responsible also for a true drug effect. Placebo is an instrument of clinical drug research, that is indispensable in cases of the absence of an effective treatment for a disorder. It is also needed to confirm true effect of an experimental drug in comparisons with a reference drug, in double dummy designs and as a placebo lead-in period. There are ethical problems associated with the use of placebo in research as well as in clinical practice. However, some risks associated with placebo may be misjudged. The ethics of clinical practice and treatment may be different from ethics of research, because both serve different purpose. Effective guidelines have been developed to protect experimental subjects and also to define conditions for justified use of placebo in clinical research. In the long run, the guidelines serve the interests of science as well as patients.
BACKGROUND: Population-level physical activity increases are improbable without intersectoral collaboration across government levels and sectors to develop and implement physical activity promotion policies. This study aims to provide information about the development of the Interaction between National and Local Government Levels in Development and Implementation of Physical Activity Policies Tool (INTEGRATE PA-Pol). A framework was created to examine the development and implementation of national and subnational physical activity policies and the (mis)alignment between government levels. METHODS: The work was conducted in 3 phases: (1) a scoping review was carried out to identify local government physical activity promotion policies and instruments for assessing them, (2) an expert group designed 6 questionnaires, and (3) cognitive response testing was employed for validity testing and item modification with a panel of research and policy experts. RESULTS: The INTEGRATE PA-Pol Tool consists of 6 questionnaires assessing how national and subnational governments collaborate to develop and implement physical activity promotion policies. CONCLUSION: This tool can assist in better understanding the development and implementation of a public policy monitoring system that will allow for benchmarking and priority setting to comprehend how physical activity promotion policies are designed and executed.
- MeSH
- cvičení * MeSH
- lidé MeSH
- místní státní správa MeSH
- podpora zdraví * metody organizace a řízení MeSH
- průzkumy a dotazníky MeSH
- velkoměsta MeSH
- vytváření politiky * MeSH
- zdravotní politika * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
- Geografické názvy
- velkoměsta MeSH
OBJECTIVES: Our main objective is to design a method of, and supporting software for, interactive correction and semantic annotation of narrative clinical reports, which would allow for their easier and less erroneous processing outside their original context: first, by physicians unfamiliar with the original language (and possibly also the source specialty), and second, by tools requiring structured information, such as decision-support systems. Our additional goal is to gain insights into the process of narrative report creation, including the errors and ambiguities arising therein, and also into the process of report annotation by clinical terms. Finally, we also aim to provide a dataset of ground-truth transformations (specific for Czech as the source language), set up by expert physicians, which can be reused in the future for subsequent analytical studies and for training automated transformation procedures. METHODS: A three-phase preprocessing method has been developed to support secondary use of narrative clinical reports in electronic health record. Narrative clinical reports are narrative texts of healthcare documentation often stored in electronic health records. In the first phase a narrative clinical report is tokenized. In the second phase the tokenized clinical report is normalized. The normalized clinical report is easily readable for health professionals with the knowledge of the language used in the narrative clinical report. In the third phase the normalized clinical report is enriched with extracted structured information. The final result of the third phase is a semi-structured normalized clinical report where the extracted clinical terms are matched to codebook terms. Software tools for interactive correction, expansion and semantic annotation of narrative clinical reports has been developed and the three-phase preprocessing method validated in the cardiology area. RESULTS: The three-phase preprocessing method was validated on 49 anonymous Czech narrative clinical reports in the field of cardiology. Descriptive statistics from the database of accomplished transformations has been calculated. Two cardiologists participated in the annotation phase. The first cardiologist annotated 1500 clinical terms found in 49 narrative clinical reports to codebook terms using the classification systems ICD 10, SNOMED CT, LOINC and LEKY. The second cardiologist validated annotations of the first cardiologist. The correct clinical terms and the codebook terms have been stored in a database. CONCLUSIONS: We extracted structured information from Czech narrative clinical reports by the proposed three-phase preprocessing method and linked it to electronic health records. The software tool, although generic, is tailored for Czech as the specific language of electronic health record pool under study. This will provide a potential etalon for porting this approach to dozens of other less-spoken languages. Structured information can support medical decision making, quality assurance tasks and further medical research.
- MeSH
- elektronické zdravotní záznamy normy MeSH
- mezinárodní klasifikace nemocí MeSH
- psaní normy MeSH
- řízený slovník * MeSH
- sémantika * MeSH
- směrnice jako téma MeSH
- smysluplné využití normy MeSH
- software MeSH
- správnost dat MeSH
- strojové učení * MeSH
- uživatelské rozhraní počítače MeSH
- zpracování přirozeného jazyka * MeSH
- zpracování textu normy MeSH
- Publikační typ
- časopisecké články MeSH
Organoids are complex multicellular three-dimensional (3D) in vitro models that are designed to allow accurate studies of the molecular processes and pathologies of human organs. Organoids can be derived from a variety of cell types, such as human primary progenitor cells, pluripotent stem cells, or tumor-derived cells and can be co-cultured with immune or microbial cells to further mimic the tissue niche. Here, we focus on the development of 3D lung organoids and their use as disease models and drug screening tools. We introduce the various experimental approaches used to model complex human diseases and analyze their advantages and disadvantages. We also discuss validation of the organoids and their physiological relevance to the study of lung diseases. Furthermore, we summarize the current use of lung organoids as models of host-pathogen interactions and human lung diseases such as cystic fibrosis, chronic obstructive pulmonary disease, or SARS-CoV-2 infection. Moreover, we discuss the use of lung organoids derived from tumor cells as lung cancer models and their application in personalized cancer medicine research. Finally, we outline the future of research in the field of human induced pluripotent stem cell-derived organoids.
- Publikační typ
- časopisecké články MeSH
- přehledy MeSH
The continuous expansion of research in the field of stable carboranes and their wide potential in the drug design require carrying out fundamental studies regarding their chiral separations. Although supercritical fluid chromatography (SFC) is a viable technique for fast enantioseparations, no investigation concerning boron cluster compounds has been done yet. We aimed at the development of a straightforward method enabling chiral separations of racemic mixtures of anionic cluster carboranes and metallacarboranes that represent an analytical challenge. The fast gradient screening testing nine polysaccharide-based columns was used. The key parameters affecting the selectivity were the type of chiral selector, the type of alcohol, and the base in cosolvent. Moreover, the addition of acetonitrile or water to the cosolvent was identified as an effective tool for decreasing the analysis time while preserving the resolution. After the optimization, the chiral separations of 19 out of 20 selected compounds were achieved in less than 10 min. These results demonstrate the clear advantage of SFC over chiral separations using HPLC in terms of both analysis time and structural variety of successfully separated compounds.
This paper presents a newly-designed and realized Invasive Blood Pressure (IBP) device for the simulation on patient's monitors. This device shows improvements and presents extended features with respect to a first prototype presented by the authors and similar systems available in the state-of-the-art. A peculiarity of the presented device is that all implemented features can be customized from the developer and from the point of view of the end user. The realized device has been tested, and its performances in terms of accuracy and of the back-loop measurement of the output for the blood pressure regulation utilization have been described. In particular, an accuracy of ±1 mmHg at 25 °C, on a range from -30 to 300 mmHg, was evaluated under different test conditions. The designed device is an ideal tool for testing IBP modules, for zero setting, and for calibrations. The implemented extended features, like the generation of custom waveforms and the Universal Serial Bus (USB) connectivity, allow use of this device in a wide range of applications, from research to equipment maintenance in clinical environments to educational purposes. Moreover, the presented device represents an innovation, both in terms of technology and methodologies: It allows quick and efficient tests to verify the proper functioning of IBP module of patients' monitors. With this innovative device, tests can be performed directly in the field and faster procedures can be implemented by the clinical maintenance personnel. This device is an open source project and all materials, hardware, and software are fully available for interested developers or researchers.
- MeSH
- design vybavení MeSH
- kalibrace MeSH
- krevní tlak fyziologie MeSH
- lidé MeSH
- měření krevního tlaku přístrojové vybavení metody MeSH
- monitorování fyziologických funkcí přístrojové vybavení metody MeSH
- monitory krevního tlaku * MeSH
- software MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
BACKGROUND: Plant-based diets are not inherently healthy. Similar to omnivorous diets, they may contain excessive amounts of sugar, sodium, and saturated fats, or lack diversity. Moreover, vegans might be at risk of inadequate intake of certain vitamins and minerals commonly found in foods that they avoid. We developed the VEGANScreener, a tool designed to assess the diet quality of vegans in Europe. METHODS: Our approach combined best practices in developing diet quality metrics with scale development approaches and involved the following: (a) narrative literature synthesis, (b) evidence evaluation by an international panel of experts, and (c) translation of evidence into a diet screener. We employed a modified Delphi technique to gather opinions from an international expert panel. RESULTS: Twenty-five experts in the fields of nutrition, epidemiology, preventive medicine, and diet assessment participated in the first round, and nineteen participated in the subsequent round. Initially, these experts provided feedback on a pool of 38 proposed items from the literature review. Consequently, 35 revised items, with 17 having multiple versions, were suggested for further consideration. In the second round, 29 items were retained, and any residual issues were addressed in the final consensus meeting. The ultimate screener draft encompassed 29 questions, with 17 focusing on foods and nutrients to promote, and 12 addressing foods and nutrients to limit. The screener contained 24 food-based and 5 nutrient-based questions. CONCLUSIONS: We elucidated the development process of the VEGANScreener, a novel diet quality screener for vegans. Future endeavors involve contrasting the VEGANScreener against benchmark diet assessment methodologies and nutritional biomarkers and testing its acceptance. Once validated, this instrument holds potential for deployment as a self-assessment application for vegans and as a preliminary dietary screening and counseling tool in healthcare settings.
- MeSH
- delfská metoda MeSH
- dieta veganská * MeSH
- hodnocení stavu výživy MeSH
- lidé MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
AIMS: To describe a three-phase co-designed project to develop a culturally appropriate and relevant education assessment tool, and report on pilot and field-testing phases. BACKGROUND: High-quality midwifery education is essential for high-quality maternity care (WHO 2019); however midwifery education and maternity care vary in quality throughout Europe. To support countries in strengthening their midwifery education, World Health Organization (WHO) European Region commissioned development of the Midwifery Assessment Tool for Education (MATE). The tool was developed over three years, using an iterative, collaborative process with regional experts. Published by WHO in May 2020, MATE provides focused questions and evidence-informed resources to stimulate and inform discussions within country. DESIGN: Three-phase co-design approach to develop, pilot and field-test an education assessment tool. METHODS: Phase 1: initial development of MATE with expert midwifery support; Phase 2: MATE piloting workshops in Czech Republic and Lithuania focusing on clarity, usability and relevance; Phase 3: MATE field-testing workshop in Bulgaria exploring the process of using MATE and its effectiveness for generating discussion. Purposive selection of workshop participants ensured a broad range of perspectives: clinicians, educators, students, policy makers and service users. All participants were invited to give narrative feedback during workshops and via completion of a post-workshop online survey. The XX University Research Ethics Committee advised that formal ethical review was unnecessary. RESULTS: Feedback from collaborators in all phases indicated that engaging with MATE co-design and testing was a positive experience. A 'bottoms up' approach ensured that MATE content was relevant to regional needs, culturally acceptable and appropriate. Seventy-nine individuals participated in Phases 2 and 3 and all were sent a post-workshop online survey, with 31 responses (39 %). Qualitative and quantitative data indicated that the aim of MATE was well understood, and its usability and relevance were evaluated positively. In Phase 2, improvements to wording and format were suggested. MATE was subsequently amended prior to field testing. Phase 3 feedback indicated that MATE was highly effective for generating in-country dialogue and frank discussions about the future of midwifery education and practice. CONCLUSIONS: Using a co-design approach has ensured that MATE is culturally relevant, accessible and appropriate. This initial evaluation indicates that MATE can facilitate in-country dialogue and support the strengthening of midwifery education in accordance with WHO aims. Next steps are a fully evaluated trial of MATE in a selected partner country, where we will continue to work collaboratively to optimise engagement and ensure cultural appropriateness.
- MeSH
- babictví * výchova MeSH
- kvalita zdravotní péče MeSH
- lidé MeSH
- služby zdravotní péče o matku * MeSH
- Světová zdravotnická organizace MeSH
- těhotenství MeSH
- Check Tag
- lidé MeSH
- těhotenství MeSH
- ženské pohlaví MeSH
- Publikační typ
- časopisecké články MeSH
- Geografické názvy
- Evropa MeSH
