Improving Blood Product Transfusion Premedication Plan Documentation: A Single-institution Quality Improvement Effort.

Introduction: Premedication with acetaminophen and/or diphenhydramine to prevent febrile nonhemolytic transfusion reactions and minor allergic transfusion reactions is a common practice based on historical recommendations. However, recent small randomized-controlled trials showed no benefit of premedication. This inconsistency leads to practice variability, which results in the inefficiency of our institution's blood product ordering process. This project aimed to improve the number of transfusion encounters with premedication plan documentation from a baseline of 19% to 80% in 12 months. Methods: A multidisciplinary quality improvement (QI) team used QI tools to design interventions to improve the efficiency of the ordering process for blood products. Measures were tracked monthly and analyzed using statistical process control. Results: From September 2018 to January 2021, 5,351 blood product transfusion visits were scheduled. At baseline, 34% of patients received premedication, and 19% had premedication plans documented. Interventions included a passive computerized provider order entry alert, clinical care pathway development, and clinician education. Postimplementation, the average number of encounters with a premedication plan increased from 19% to 87%, whereas encounters receiving premedication decreased from 34% to 25%. There was no change in the average number of transfusion reactions (1.8 per 100 transfusions). Conclusions: Using QI methods, our team successfully standardized the blood product premedication plan documentation despite unclear best practices regarding blood product transfusion premedication. The team added premedication plan documentation training to new employee orientation for sustainability.

Data and its (dis)contents: A survey of dataset development and use in machine learning research.

In this work, we survey a breadth of literature that has revealed the limitations of predominant practices for dataset collection and use in the field of machine learning. We cover studies that critically review the design and development of datasets with a focus on negative societal impacts and poor outcomes for system performance. We also cover approaches to filtering and augmenting data and modeling techniques aimed at mitigating the impact of bias in datasets. Finally, we discuss works that have studied data practices, cultures, and disciplinary norms and discuss implications for the legal, ethical, and functional challenges the field continues to face. Based on these findings, we advocate for the use of both qualitative and quantitative approaches to more carefully document and analyze datasets during the creation and usage phases.

A global assessment of cancer genomic alterations in epigenetic mechanisms.

BACKGROUND: The notion that epigenetic mechanisms may be central to cancer initiation and progression is supported by recent next-generation sequencing efforts revealing that genes involved in chromatin-mediated signaling are recurrently mutated in cancer patients. RESULTS: Here, we analyze mutational and transcriptional profiles from TCGA and the ICGC across a collection 441 chromatin factors and histones. Chromatin factors essential for rapid replication are frequently overexpressed, and those that maintain genome stability frequently mutated. We identify novel mutation hotspots such as K36M in histone H3.1, and uncover a general trend in which transcriptional profiles and somatic mutations in tumor samples favor increased transcriptionally repressive histone methylation, and defective chromatin remodeling. CONCLUSIONS: This unbiased approach confirms previously published data, uncovers novel cancer-associated aberrations targeting epigenetic mechanisms, and justifies continued monitoring of chromatin-related alterations as a class, as more cancer types and distinct cancer stages are represented in cancer genomics data repositories.

ChromoHub V2: cancer genomics.

SUMMARY: Cancer genomics data produced by next-generation sequencing support the notion that epigenetic mechanisms play a central role in cancer. We have previously developed Chromohub, an open access online interface where users can map chemical, structural and biological data from public repositories on phylogenetic trees of protein families involved in chromatin mediated-signaling. Here, we describe a cancer genomics interface that was recently added to Chromohub; the frequency of mutation, amplification and change in expression of chromatin factors across large cohorts of cancer patients is regularly extracted from The Cancer Genome Atlas and the International Cancer Genome Consortium and can now be mapped on phylogenetic trees of epigenetic protein families. Explorators of chromatin signaling can now easily navigate the cancer genomics landscape of writers, readers and erasers of histone marks, chromatin remodeling complexes, histones and their chaperones. AVAILABILITY AND IMPLEMENTATION: http://www.thesgc.org/chromohub/.

Development of a rapid phage-based method for the detection of viable Mycobacterium avium subsp. paratuberculosis in blood within 48 h.

The aim of this study was to develop a methodology to rapidly detect viable Mycobacterium avium subsp. paratuberculosis (MAP) in clinical blood samples. MAP cells spiked into commercially available blood were recovered using optimised peptide-mediated magnetic separation (PMMS) and detected using a phage-based method, and the identity of the cells detected confirmed using nested-PCR amplification of MAP signature sequences (IS900). The limit of detection was determined to be 10 MAP cells per ml of blood and was used to detect MAP present in clinical bovine blood samples. Using the PMMS-phage method there was no difference when detecting MAP from whole blood or from isolated buffy coat. MAP was detected in animals that were milk-ELISA positive (15 animals) by PMMS-phage and no MAP was detected in blood samples from an accredited Johne's disease free herd (5 animals). In a set of samples from one herd (10 animals) that came from animals with variable milk ELISA status, the PMMS-phage results agreed with the positive milk-ELISA results in all but one case. These results show that the PMMS-phage method can detect MAP present in naturally infected blood. Total assay time is 48 h and, unlike PCR-based detection tests, only viable cells are detected. A rapid method for detecting MAP in blood could further the understanding of disseminated infection in animals with Johne's disease.

ChromoHub: a data hub for navigators of chromatin-mediated signalling.

UNLABELLED: The rapidly increasing research activity focused on chromatin-mediated regulation of epigenetic mechanisms is generating waves of data on writers, readers and erasers of the histone code, such as protein methyltransferases, bromodomains or histone deacetylases. To make these data easily accessible to communities of research scientists coming from diverse horizons, we have created ChromoHub, an online resource where users can map on phylogenetic trees disease associations, protein structures, chemical inhibitors, histone substrates, chromosomal aberrations and other types of data extracted from public repositories and the published literature. The interface can be used to define the structural or chemical coverage of a protein family, highlight domain architectures, interrogate disease relevance or zoom in on specific genes for more detailed information. This open-access resource should serve as a hub for cell biologists, medicinal chemists, structural biologists and other navigators that explore the biology of chromatin signalling. AVAILABILITY: http://www.thesgc.org/chromohub/.