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Efficient sharing and integration of phenotypic data is crucial for advancing biomedical research and enhancing patient outcomes in precision medicine and public health. To achieve ...this, the health data community has developed standards to promote the harmonization of variable names and values. However, the use of diverse standards across different research centers can hinder progress. Here we present Convert-Pheno, an open-source software toolkit that enables the interconversion of common data models for phenotypic data such as Beacon v2 Models, CDISC-ODM, OMOP-CDM, Phenopackets v2, and REDCap. Along with the software, we have created a detailed documentation that includes information on deployment and installation.
Abstract
Advances in DNA sequencing and proteomics mean that researchers must now regularly interrogate thousands of positional gene/protein changes in order to find those relevant for potential ...clinical application or biological insights. The abundance of already known information on protein interactions, mechanism, and tertiary structure provides the possible means to understand these changes rapidly, though a careful and systematic integration of these diverse datasets is first needed. For this purpose, we developed Mechnetor, a tool that allows users to quickly explore and visualize integrated mechanistic data for proteins or interactions of interest. Central to the system is a careful cataloguing of diverse sources of protein interaction mechanism, and an efficient means to visualize interactions between relevant and/or known protein regions. The result is a finer resolution interaction network that provides more immediate clues as to points of intervention or mechanistic understanding. Users can import protein, interactions, genetic variants or post-translational modifications and see these data in the best known mechanistic context. We demonstrate the tool with topical examples in human genetic diseases and cancer genomics. The tool is freely available at: mechnetor.russelllab.org.
Graphical Abstract
Graphical Abstract
Overview of Mechnetor showing examples of interaction mechanisms overlayed with disease variants.
Abstract
Introduction/Objective
A 34-year-old Amish woman G11P8A2L8, with a known PP1Pk antibody, presented to her OB with vaginal hemorrhage secondary to an incomplete spontaneous abortion. Despite ...medical treatment, her hemoglobin decreased from 12 g/dL to 8.4 g/dL. She was air transferred to a tertiary care hospital for further management and antigen negative RBC transfusion.
Upon arrival, her hemoglobin had decreased to 7.1 g/dL and her BP decreased to 92/64 mm Hg. Additional blood draws were discontinued to save blood wastage. Her blood pressure continued to decrease over the next several hours to a low of 78/36. The patient was briefly stabilized, and a successful dilation and curettage was performed.
Methods/Case Report
A national search was conducted for PP1Pk antigen negative blood. Her RBC phenotype: C+, c-, E-, e+, K-k-, Fy(a + b-), Jk(a+ b+), MN+, p, Le(a-b-). There was no history of blood product transfusion and the prior miscarriages where thought to be the source of alloimmunization. There was no known family history of the p (P- P1- Pk-) phenotype.
Results (if a Case Study enter NA)
One unit of PP1Pk antigen negative PRBCs was located approximately 48 hours after the patient’s admission, however, the consulting hematology team suggested withholding transfusion due the possibility of alloimmunization from other blood groups complicating future transfusions. She was treated with IV iron and discharged four days later with a hemoglobin level of 6 g/dL. She was asymptomatic upon discharge.
Conclusion
Anti-PP1Pk is a rare antibody (5.8 per 1 million people). In the Amish population, the incidence is approximately 1 in 5000 individuals. Our patient is planning for future pregnancies. Upon our suggestion, the patient was encouraged to consider frozen autologous blood donation after recovery and before the next pregnancy as well as close monitoring in high-risk maternal fetal medicine settings.
In a patients and donors with anti PP1PK, we recommend advance planning including frozen autologous blood donation and family members RBC antigen studies. They should be encouraged to become regular blood donors for themselves and others.
Introduction: The presence of commercial messages in continuing medical education (CME) is an ongoing cause of concern. This study identifies actions perceived by CME participants to convey ...commercial bias from CME faculty.
Methods: A questionnaire listing actions associated with CME activities was distributed to 230 randomly selected participants from 7 CME activities designated for AMA PRA Category 1 Credit™. The activities were held over an 8‐month period. Participants were asked to complete the questionnaire before participating in the live activity.
Results: Nine actions identified by over 50% of all respondents were perceived to convey commercial bias. The most critical ones reflecting commercial bias were speaking about only one agent, not providing a balanced presentation of all agents, and faculty relationships with commercial supporters. Ten actions identified by over 50% of the respondents were perceived to convey personal opinion of the faculty. The most prevalent actions were the influence of mentors or teachers, relating general practice habits from the faculty member's own experience, and cultural differences among patient populations. More than half the respondents who indicated they perceived commercial bias in certified activities attributed this perception to an overall impression, instead of 1 or 2 specific actions.
Discussion: Actions were identified that conveyed differences between commercial messages and personal opinion. CME providers should define commercial bias for participants, faculty, and planners and provide education about that definition.
Problem-based learning of research skills Davis, Thomas H.; Wagner, Galen S.; Gleim, Gilbert ...
Journal of electrocardiology,
2006, 2006-Jan, 2006-1-00, 20060101, Letnik:
39, Številka:
1
Journal Article
Recenzirano
To determine whether a short-term, problem-based educational intervention leads to increased research activity among health care practitioners.
Participant's success was evaluated as a composite of 2 ...outcomes. These were (1) reporting results for the project designed during the practicum and (2) conducting subsequent research activities. The study population included 36 clinical research outcomes projects developed by clinical practitioners, postgraduate trainees, and medical students during 6 separate practicums. All project teams received the same educational intervention, an “outcomes research practicum” that was divided into 4 primary learning modules administered over a 1 to 4 month period. Each module included a preparatory videotape lecture, supplemental readings, and a 90-minute interactive laboratory session during which faculty members worked with participants to develop answers to a series of predefined questions relating to the design of clinical outcomes research projects. Follow-up continued for a minimum of 12 months and a maximum of 36 months.
Eighty-three percent of project teams completed all 4 practicum modules, and 69% completed one of the study outcomes (50% completed their research project and 47% completing a subsequent research activity). Practitioners were more likely to complete subsequent research activities, whereas trainees were more likely to complete their study project.
This short-term, problem-based educational intervention was successful in increasing the collective research activities of participants. Further, more rigorous structured research is needed to determine the ultimate impact on practice change and patient outcomes.
The direct protein profiling of mammalian cells and bacteria has a growing influence in biotechnology as a high information bearing method for characterization of cells and cell states. Monitoring of ...proteins excreted in culture media not only serves to produce data on product yield and quality but provides important information on cell viability and nutrient supply that forms the basis for future process and expression optimization. Fast and simple MALDI mass spectrometry approaches were developed to efficiently characterize such complex biological systems. Several mammalian cell lines including CHO DXB11, CHOSSF3, and hybridomas were investigated; the lysis process, the sample pretreatment, and the matrix preparation were optimized for MALDI conditions. Initial experiments to observe the success of protein translation in gene expression experiments were performed. Using MALDI-compatible detergents, it was possible to extend the mass range detectable by MALDI mass spectrometry from the current range of 16 000 to 75 000 Da. In this mass range, the data are complementary (offering a better mass accuracy) to those obtained by SDS−PAGE electrophoresis experiments. These new methods were used to monitor a large-scale cultivation of hybridoma cells expressing an antibody of the IgG type. The increase in whole antibody and antibody light-chain protein, 8650 Da, and the decrease of insulin were followed during the monitoring period. Quantitative measurements of the IgG level during the cultivation compared favorably with those obtained by affinity HPLC.
Demonstrating outcomes of continuing medical education (CME) efforts has become increasingly important to CME providers, accrediting organizations, and licensing bodies. Many CME providers have ...difficulty defining the nature of the outcomes, much less documenting the outcomes for which they are responsible. The vague nature of the terms "outcome," "impact," or "result" in the complexity of health care and medical education environments is a particular obstacle to many education providers. To overcome these barriers, the VA's Employee Education System (EES), a large CME provider, created a model identifying five major domains of possible outcomes for CME interventions; these are the domains of individual participants, employee teams, the larger organization, patients, and the community. These domains are useful in either assessing a single CME activity's outcomes or comprehensively assessing a CME provider's outcomes-assessment strategy. The use of such a domains-based outcomes-management strategy links organizational mission, needs assessment, specific activity assessment, and assessment of the overall education program. This approach may be useful to CME providers, accrediting and licensing bodies, or others interested in the relationship of CME outcomes to the activities of CME providers.
Accreditation is one way of assuring that continuing education providers are credible and competent. The Accreditation Council for Continuing Medical Education has recently modified its accreditation ...standards to meet the needs of the health care system and continuing medical education providers. The standards (Essential Areas and Elements) from the new accreditation system will be reviewed and discussed to illustrate one system of accreditation as a potential model for the continuing veterinary medical education professional.
Transfusion management of the patient who is undergoing a marrow or peripheral blood stem and progenitor cell transplantation is often challenging. The situation is further complicated when the ...patient is IgA deficient with circulating anti-IgA.
This report describes an approach to transfusion therapy primarily using red cells washed by automated techniques and cryopreserved autologous plateletpheresis components. Additional platelet support was provided with manually washed allogeneic plateletpheresis components. Autologous fresh-frozen plasma was collected concurrently, and IgA-deficient allogeneic units were ordered and kept in storage, but they were not needed during transplantation. The patient experienced no transfusion sequelae as a result of the IgA deficiency.
With this approach, the transfusion needs of an IgA-deficient patient were adequately met during bone marrow transplantation.
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