Implementing Epic Beaker Laboratory Information System for Diagnostics in Anatomic Pathology

Sergi, Consolato

doi:10.2147/rmhp.s332109

Cited by 9 publications

(9 citation statements)

References 8 publications

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“…Translating a newly developed methodology from the research laboratory to the clinical laboratory must consider analytical validity, clinical advantageousness, and financial responsibility. Therefore, using this approach in the routine clinical context and the implementation in laboratory information systems are not yet recommended ( Sergi, 2022b ). However, we need to stay tuned because it could be beneficial for identifying genera and species in the nearest future after validation and certification according to regulatory agencies, such as the College of American Pathologists.…”

Section: Discussionmentioning

confidence: 99%

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease

et al. 2022

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Microbiotas are the range of microorganisms (mainly bacteria and fungi) colonizing multicellular, macroscopic organisms. They are crucial for several metabolic functions affecting the health of the host. However, difficulties hamper the investigation of microbiota composition in cultivating microorganisms in standard growth media. For this reason, our knowledge of microbiota can benefit from the analysis of microbial macromolecules (DNA, transcripts, proteins, or by-products) present in various samples collected from the host. Various omics technologies are used to obtain different data. Metagenomics provides a taxonomical profile of the sample. It can also be used to obtain potential functional information. At the same time, metatranscriptomics can characterize members of a microbiome responsible for specific functions and elucidate genes that drive the microbiotas relationship with its host. Thus, while microbiota refers to microorganisms living in a determined environment (taxonomy of microorganisms identified), microbiome refers to the microorganisms and their genes living in a determined environment and, of course, metagenomics focuses on the genes and collective functions of identified microorganisms. Metabolomics completes this framework by determining the metabolite fluxes and the products released into the environment. The gallbladder is a sac localized under the liver in the human body and is difficult to access for bile and tissue sampling. It concentrates the bile produced in the hepatocytes, which drains into bile canaliculi. Bile promotes fat digestion and is released from the gallbladder into the upper small intestine in response to food. Considered sterile originally, recent data indicate that bile microbiota is associated with the biliary tract’s inflammation and carcinogenesis. The sample size is relevant for omic studies of rare diseases, such as gallbladder carcinoma. Although in its infancy, the study of the biliary microbiota has begun taking advantage of several omics strategies, mainly based on metagenomics, metabolomics, and mouse models. Here, we show that omics analyses from the literature may provide a more comprehensive image of the biliary microbiota. We review studies performed in this environmental niche and focus on network-based approaches for integrative studies.

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Section: Discussionmentioning

confidence: 99%

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease

et al. 2022

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“…The institutions of worldwide accessible biorepositories are vital due to the rarity ad variability of CRMO. Randomized controlled trials have been difficult to execute in places where a laboratory information system is not fully operative ( 68 ). The CNO/CRMO subgroup of the Childhood Arthritis and Rheumatology Research Alliance recently produced a consensus treatment plan with three treatment arms ( 29 ).…”

Section: Treatmentmentioning

confidence: 99%

Chronic recurrent multifocal osteomyelitis. A narrative and pictorial review

et al. 2022

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Chronic recurrent and multifocal osteomyelitis (CRMO) is a nonsporadic autoinflammatory disorder. Currently, it is diagnosed based on clinical, radiologic, pathological, and longitudinal data. Numerous aspects should be highlighted due to increased knowledge in imaging and immunology. We emphasize the use of whole-body MRI, which is a non-invasive diagnostic strategy. A literature review was carried out on longitudinal studies. Commonly, the mean age at diagnosis is 11 years, ranging between 3 and 17. The most common sites are the long bone metaphysis, particularly femoral and tibial metaphysis. In addition, the pelvis, spine, clavicle, and mandible may be involved. In long bones, the radiologic appearance can show typical structure, mixed lytic and sclerotic, sclerotic or lytic. It is frequently metaphyseal or juxta-physeal, with hyperostosis or periosteal thickening. The involvement of the vertebral skeleton is often multifocal. Therefore, whole-body MRI is essential in identifying subclinical lesions. CRMO is a polymorphic disorder in which whole-body MRI is beneficial to demonstrate subclinical edema. Vertebral collapse requires long-term monitoring.

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“…Наличие доступа у врача-патологоанатома к истории болезни пациента может быть необходимо для решения о проведении дополнительных исследований тканей, использования специальных методов окраски [18]. В настоящее время разрабатываются и внедряются в медицинских учреждениях программные обеспечения, обеспечивающие патологоанатомам прямой доступ к клинической и радиологической информации [19].…”

Section: выставление показаний для патоморфологического исследованияunclassified

Digital transformation of the pathological service as a way to improve the quality of medical care.

Lebedev¹,

Shaderkin²,

Tertychny³

et al. 2022

RJTEH

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Introduction. Pathology plays an essential and important role in diagnostic and choosing patients’ management strategies. The aim of our analytical article is to review opportunities of digital technologies applying to pathology with a focus on converges with clinical disciplines. Materials and methods. The search was conducted on Medline and Pubmed database and websites of laboratory equipment developers. Results. The emergence of a new direction – ‘digital pathology’, underlines a high interest of professional society in this theme. Nowadays there are enough solutions for each part of pathological workflow which provides development of fully digitalized pathological laboratories. In this article we present opportunities and perspectives of business-process organization from statements of objectives for pathologist, tissue collection, laboratory study to multidisciplinary analysis for further patients’ management based on opportunities of information technologies. Conclusion. Digital pathology is a transfer of all pathological routine workflow on digital platform which allows to unite efforts of clinicians, pathologists, public health organizers and patients. Separated blocks, which should constitute a united digital pathological platform, already exist and effort and time are required for full consolidation of all stages of pathological research.

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Implementing Epic Beaker Laboratory Information System for Diagnostics in Anatomic Pathology

Cited by 9 publications

References 8 publications

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease

A systematic review on omics data (metagenomics, metatranscriptomics, and metabolomics) in the role of microbiome in gallbladder disease

Chronic recurrent multifocal osteomyelitis. A narrative and pictorial review

Digital transformation of the pathological service as a way to improve the quality of medical care.

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