Following publication of the original article [1], the authors flagged that the name of 'Asal Hojjat' was misspelled; the name had been spelled as 'Asal Hojat'.BACKGROUND In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering methods have been developed in the past decade. When a single source of data is at play, hierarchical clustering (HC) is extremely popular, as a tree structure is highly interpretable and arguably more informative than just a partition of the data. However, applying blindly HC to multiple sources of data raises computational and interpretation issues. RESULTS We propose mergeTrees, a method that aggregates a set of trees with the same leaves to create a consensus tree. In our consensus tree, a cluster at height h contains the individuals that are in the same cluster for all the trees at height h. The method is exact and proven to be [Formula see text], n being the individuals and q being the number of trees to aggregate. Our implementation is extremely effective on simulations, allowing us to process many large trees at a time. We also rely on mergeTrees to perform the cluster analysis of two real -omics data sets, introducing a spectral variant as an efficient and robust by-product. CONCLUSIONS Our tree aggregation method can be used in conjunction with hierarchical clustering to perform efficient cluster analysis. This approach was found to be robust to the absence of clustering information in some of the data sets as well as an increased variability within true clusters. The method is implemented in R/C++ and available as an R package named mergeTrees, which makes it easy to integrate in existing or new pipelines in several research areas.IntroductionThe Eph-ephrin is a cell-cell communication system generating a forward signal in cell expressing Eph receptors and a reverse signal in ephrin-ligand expressing cells. https://www.selleckchem.com/products/Idarubicin.html While clearly involved in the insurgence and progression of cancer, the understanding of the molecular mechanisms regulated by this system needs development; this is a hurdle to the development of therapeutic strategies that can target the Eph receptors and/or their ephrin ligandsAreas covered We have taken the opportunity to share some key questions on the most effective strategies to target the Eph-ephrin system. This article is based on our experience of the field and therefore is a Perspective and not comprehensive examination of the literature.Expert opinionTargeting of the Eph-ephrin system has emerged as a potential valuable approach for cancer therapy. Pharmacological tools have been reported in the last 15 years and these include forward signaling blockers such as kinases inhibitors and antagonists of forward and reverse signaling. Also, biologics including antibodies and recombinant proteins have been developed and some have reached early clinical stages. Data deem the Eph-ephrin system as a signaling axis that is an elusive target. A better understanding of the basic pharmacology behind the activity of available agents and a comprehensive knowledge of the ephrin biology is necessary. We are looking forward to knowing the opinion of the readers.This study investigated the impact of empathy training on medical students using a project-based learning approach on the development of their empathic abilities. Study participants were Year 2 students in the six-year medical program, to whom a one credit-hour course on empathic communication was offered over a semester. In this course, students worked on collaborative team projects in which they were asked to interview a person and to report the empathy that they shared with the interviewee. Development in student empathy was measured using the Interpersonal Reactivity Index inventory in a pre- and post-test format over the semester and their reflective reports were qualitatively analyzed to identify emerging themes on the lessons they learned from the project experience. A total of 45 students completed the questionnaires (a 97.8% response rate). Students' overall empathy scores did not change over time (t = 1.943, p = .06). Still, students with lower empathy in the pre-test improved significantly in their empathy scores (t = 3.44, p less then .01). Students reported that the empathy project was beneficial in improving their understanding of empathy and enhancing their empathic communication skills. This study shows the project-based learning approach was effective in developing medical student empathy especially for those with lower empathy.Objectives The study aims to investigate occupational exposure to carbon fibers impregnated with epoxy resins (carbon fiber reinforced [CFR]) in workers at an airplane fuselage section construction plant, by environmental and biological monitoring.Materials and methods Determination of airborne CFR was done by environmental sampling with active samplers, 11 of which were stationary and 19 personal samplings. The subsequent analyses were performed in the scanning electron microscope fitted with an X-ray microanalysis system (SEM-EDXA). Biological monitoring was carried out by determining CFR in exhaled breath condensate (EBC) collected from 19 male workers who wore personal environmental samplers (exposed workers) and from 10 male workers at the same factory who had no occupational exposure to CFR (internal controls). CFR analysis was done by SEM, applying the method used for determining asbestos fibers in aqueous samples.Results The airborne CFR concentrations were found to be significantly higher (p = 0.03) at personal samplings (median value 7.01 ff/L, range 1.24-11.16 ff/L) than stationary samplings (median value 1.93 ff/L, range 0.55-10.09 ff/L). The aerodynamic diameters calculated starting from the length and geometric diameter of the sampled CFRs were always higher than 20 µm. CFR was not found in any of the EBC samples collected from the exposed workers and controls.Conclusions Despite the evidence of occupational exposure to low concentrations of CFR, the absence of such fibers in the EBC in the exposed workers confirms their non-respirability, as expected based on their aerodynamic diameter.
Following publication of the original article [1], the authors flagged that the name of 'Asal Hojjat' was misspelled; the name had been spelled as 'Asal Hojat'.BACKGROUND In unsupervised learning and clustering, data integration from different sources and types is a difficult question discussed in several research areas. For instance in omics analysis, dozen of clustering methods have been developed in the past decade. When a single source of data is at play, hierarchical clustering (HC) is extremely popular, as a tree structure is highly interpretable and arguably more informative than just a partition of the data. However, applying blindly HC to multiple sources of data raises computational and interpretation issues. RESULTS We propose mergeTrees, a method that aggregates a set of trees with the same leaves to create a consensus tree. In our consensus tree, a cluster at height h contains the individuals that are in the same cluster for all the trees at height h. The method is exact and proven to be [Formula see text], n being the individuals and q being the number of trees to aggregate. Our implementation is extremely effective on simulations, allowing us to process many large trees at a time. We also rely on mergeTrees to perform the cluster analysis of two real -omics data sets, introducing a spectral variant as an efficient and robust by-product. CONCLUSIONS Our tree aggregation method can be used in conjunction with hierarchical clustering to perform efficient cluster analysis. This approach was found to be robust to the absence of clustering information in some of the data sets as well as an increased variability within true clusters. The method is implemented in R/C++ and available as an R package named mergeTrees, which makes it easy to integrate in existing or new pipelines in several research areas.IntroductionThe Eph-ephrin is a cell-cell communication system generating a forward signal in cell expressing Eph receptors and a reverse signal in ephrin-ligand expressing cells. https://www.selleckchem.com/products/Idarubicin.html While clearly involved in the insurgence and progression of cancer, the understanding of the molecular mechanisms regulated by this system needs development; this is a hurdle to the development of therapeutic strategies that can target the Eph receptors and/or their ephrin ligandsAreas covered We have taken the opportunity to share some key questions on the most effective strategies to target the Eph-ephrin system. This article is based on our experience of the field and therefore is a Perspective and not comprehensive examination of the literature.Expert opinionTargeting of the Eph-ephrin system has emerged as a potential valuable approach for cancer therapy. Pharmacological tools have been reported in the last 15 years and these include forward signaling blockers such as kinases inhibitors and antagonists of forward and reverse signaling. Also, biologics including antibodies and recombinant proteins have been developed and some have reached early clinical stages. Data deem the Eph-ephrin system as a signaling axis that is an elusive target. A better understanding of the basic pharmacology behind the activity of available agents and a comprehensive knowledge of the ephrin biology is necessary. We are looking forward to knowing the opinion of the readers.This study investigated the impact of empathy training on medical students using a project-based learning approach on the development of their empathic abilities. Study participants were Year 2 students in the six-year medical program, to whom a one credit-hour course on empathic communication was offered over a semester. In this course, students worked on collaborative team projects in which they were asked to interview a person and to report the empathy that they shared with the interviewee. Development in student empathy was measured using the Interpersonal Reactivity Index inventory in a pre- and post-test format over the semester and their reflective reports were qualitatively analyzed to identify emerging themes on the lessons they learned from the project experience. A total of 45 students completed the questionnaires (a 97.8% response rate). Students' overall empathy scores did not change over time (t = 1.943, p = .06). Still, students with lower empathy in the pre-test improved significantly in their empathy scores (t = 3.44, p less then .01). Students reported that the empathy project was beneficial in improving their understanding of empathy and enhancing their empathic communication skills. This study shows the project-based learning approach was effective in developing medical student empathy especially for those with lower empathy.Objectives The study aims to investigate occupational exposure to carbon fibers impregnated with epoxy resins (carbon fiber reinforced [CFR]) in workers at an airplane fuselage section construction plant, by environmental and biological monitoring.Materials and methods Determination of airborne CFR was done by environmental sampling with active samplers, 11 of which were stationary and 19 personal samplings. The subsequent analyses were performed in the scanning electron microscope fitted with an X-ray microanalysis system (SEM-EDXA). Biological monitoring was carried out by determining CFR in exhaled breath condensate (EBC) collected from 19 male workers who wore personal environmental samplers (exposed workers) and from 10 male workers at the same factory who had no occupational exposure to CFR (internal controls). CFR analysis was done by SEM, applying the method used for determining asbestos fibers in aqueous samples.Results The airborne CFR concentrations were found to be significantly higher (p = 0.03) at personal samplings (median value 7.01 ff/L, range 1.24-11.16 ff/L) than stationary samplings (median value 1.93 ff/L, range 0.55-10.09 ff/L). The aerodynamic diameters calculated starting from the length and geometric diameter of the sampled CFRs were always higher than 20 µm. CFR was not found in any of the EBC samples collected from the exposed workers and controls.Conclusions Despite the evidence of occupational exposure to low concentrations of CFR, the absence of such fibers in the EBC in the exposed workers confirms their non-respirability, as expected based on their aerodynamic diameter.
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