Mass Spectrometry-Based System for Identifying and Typing Norovirus Major Capsid Protein VP1

Norovirus-associated diseases are the most common foodborne illnesses worldwide. Polymerase chain reaction-based methods are the primary diagnostics for clinical samples; however, the high mutation rate of norovirus makes viral amplification and genotyping challenging. Technological advances in mass spectrometry (MS) make it a promising tool for identifying disease markers. Besides, the superior sensitivity of MS and proteomic approaches may enable the detection of all variants. Thus, this study aimed to establish an MS-based system for identifying and typing norovirus. We constructed three plasmids containing the major capsid protein VP1 of the norovirus GII.4 2006b, 2006a, and 2009a strains to produce virus-like particles for use as standards. Digested peptide signals were collected using a nano-flow ultra-performance liquid chromatography mass spectrometry (nano-UPLC/MSE) system, and analyzed by ProteinLynx Global SERVER and TREE-PUZZLE software. Results revealed that the LC/MSE system had an excellent coverage rate: the system detected more than 94% of amino acids of 3.61 femtomole norovirus VP1 structural protein. In the likelihood-mapping analysis, the proportions of unresolved quartets were 2.9% and 4.9% in the VP1 and S domains, respectively, which is superior to the 15.1% unresolved quartets in current PCR-based methodology. In summary, the use of LC/MSE may efficiently monitor genotypes, and sensitively detect structural and functional mutations of noroviruses.

Machine learning-based tissue of origin classification for cancer of unknown primary diagnostics using genome-wide mutation features

Tumor tissue of origin (TOO) is an important factor for guiding treatment decisions. However, TOO cannot be determined for ~3% of metastatic cancer patients and are categorized as cancers of unknown primary (CUP). As whole genome sequencing (WGS) of tumors is now transitioning from the research domain to diagnostic practice in order to address the increasing demand for biomarker detection, its use for detection of TOO in routine diagnostics also starts becoming within reach. While proof of concept for the use of genome-wide features has been demonstrated before, more complex WGS mutation features, including structural variant (SV) driver and passenger events, have never been integrated into TOO-classifiers even though they bear highly characteristic links with tumor TOO. Using a uniformly processed dataset containing 6820 whole-genome sequenced primary and metastatic tumors, we have developed Cancer of Unknown Primary Location Resolver (CUPLR), a random forest based TOO classifier that employs 502 features based on simple and complex somatic driver and passenger mutations. Our model is able to distinguish 33 cancer (sub)types with an overall accuracy of 91% and 89% based on cross-validation (n=6139) and hold out set (n=681) predictions respectively. We found that SV derived features increase the accuracy and utility of TOO classification for specific cancer types. To ensure that predictions are human-interpretable and suited for use in routine diagnostics, CUPLR reports the top contributing features and their values compared to cohort averages. The comprehensive output of CUPLR is complementary to existing histopathological procedures and may thus improve diagnostics for patients with CUP.

Perimetry as a technique from the standpoint of practicing ophthalmologists

PURPOSE. To study the needs of practical ophthalmologists concerning the functionality and performance of automatic perimeters, and offer a possible solution to meet these needs.METHODS. An online survey of Russian ophthalmologists was organized and conducted. The survey was attended by specialists representing various medical institutions and medical research centers. As a result of the survey, 132 filled questionnaire forms were received and analyzed using the Kano and 4C models.RESULTS. According to experts, it is necessary for ophthalmologists to have an accessible automatic perimeter equipped with the screening (for the initial examination of patients) and threshold (to clarify the depth of photosensitivity disturbance of detected visual field defects) strategies. The general requirements for the functional characteristics of the screening and threshold tests of the automatic perimeter have been determined: small variability of repeated results, the speed and simplicity of the study — particularly, by employing the Frequency Doubling Technology (FDT), a non-standard perimetry technique. The requirements of users for the operational method of the automatic perimeter have been determined: absence of the need for a specially prepared room and place, mobility, portability, maximum ease of use to ensure the possibility of performing screening and primary diagnostics outside medical institutions, including by mobile medical teams, and also to allows examinations of individuals with disabilities, including bedridden patients, both in the hospital and at home.CONCLUSION. Based on the study data, the needs of ophthalmologists in the functional and operational characteristics of modern automatic perimeters were identified showing that the automatic perimeters presently used by modern medical institutions are far from optimal in terms of their properties/characteristics. These devices do not allow perimetry to be performed on patients with disabilities, including bedridden patients, neither at home nor in the hospitals. In addition, these devices require a darkened room, they are difficult to use, while their licensing documentation states that only ophthalmologists can conduct the examinations. Manufacturers do not offer solutions tailored to the individual needs of specific user groups — outpatient ophthalmologists who in particular work with disabled patients.

Update on the current opinion, status and future development of digital pathology in Switzerland in light of COVID-19

AimsThe transition from analogue to digital pathology (DP) in Switzerland has coincided with the COVID-19 crisis. The Swiss Digital Pathology Consortium conducted a national survey to assess the experience of pathologists in dealing with the challenges of the pandemic and how this has influenced the outlook and adoption of DP.MethodsA survey containing 20 questions relating to DP, personal experiences and challenges during the pandemic was addressed to Swiss pathologists at different experience stages in private practice, community and university hospitals.ResultsAll 74 respondents were pathologists, with 81.1% reporting more than 5 years of diagnostic service experience. 32.5% reported having read 100 digital slides or more in a diagnostic context. 39.2% reported using whole slide imaging systems at their primary workplace. Key DP use cases before the COVID-19 lockdown were tumour boards (39.2%), education (60.8%) and research (44.6%), with DP used for primary diagnosis in 13.5%. During the COVID-19 crisis, the use of DP for primary diagnostics more than doubled (30% vs 13.5%), with internal consults as important drivers (22.5% vs 16.5%), while research use (25% vs 44.6%) and external consults (17.5% vs 41.9%) strongly decreased. Key challenges identified included a lack of established standard operating procedures and availability of specialised hardware and software.ConclusionsThis survey indicates that the crisis acted as a catalyst in promoting DP adoption in centres where basic workflows were already established while posing major technical and organisational challenges in institutions that were at an early stage of DP implementation.

Application of the international classification of functioning, disability and health in the system of comprehensive study of young children with down syndrome

Introduction. The article is devoted to the problem of complex study of early development of children with down syndrome based on the principles of ICF. The analysis of the comparability of parameters describing the current level of development of a child with normal and impaired ontogenesis in popular methods of early development diagnostics with the description parameters adopted in the new classification system of the ICF Presents the experience of processing and interpreting the results of psychological and pedagogical study of the cognitive, speech and motor spheres of young children in the context of the severity of restrictions on their daily life and health. The article describes the method of establishing a functional and rehabilitation diagnosis, as well as the procedure for documenting the results of the psychological and pedagogical study, taking into account the classification categories adopted in the ICF. The significance of the results obtained for the interaction of an interdisciplinary team of specialists within the framework of the early aid Service is determined.Materials and Methods. When writing the article, we used methods of studying domestic and foreign literature sources; generalization and systematization of the results of studying the cognitive, speech and motor spheres of young children with down syndrome; experimental methods and scales for assessing the timeliness of early childhood development.Results. The variety of approaches to studying the development of children with normal and impaired development in early ontogenesis is considered. Based on the study of domestic and foreign literature sources, the most common methods of comprehensive assessment of the cognitive, speech and motor spheres of young children with developmental disabilities were selected and their comparability with the description parameters adopted in the ICF domain classification system was evaluated. Data analysis has shown that in the process of studying individual or systemic indicators of early development of young children with down syndrome, any diagnostic tools familiar to the specialist that have passed the procedure of experimental testing and validation can be used. At the same time, only the process of processing, interpreting and finalizing the test results in the Protocol needs modification, while the stimulus material and the research procedure do not need any modification.Discussion and Conclusions. The study concluded that the ICF can be effectively applied at all stages of the study of young children with not only down syndrome, but also any variants of impaired development. The introduction of ICF profiles in the process of documenting the results of primary diagnostics and dynamic monitoring ensures consistency of interaction between specialists of the early care Service both within the organization and at the interdepartmental level

Abstract P-32: Lung Structural Changes in Covid-19 Patients

Background: The main causes of death from Covid-19 are lung lesions with the development of respiratory failure. However, structural changes in the lung tissue in this pathology are poorly studied. We examined autopsy material from patients with Covid-19. The severe condition of patients, the manifestation of pulmonary symptoms of damage (cough, dyspnea) and the high probability of viral pneumonia at COVID-19 led to the widespread use of CT diagnostics in this group of patients, which allowed to identify of the primary signs of the disease, their subsequent transformation as well as the most adverse radiation symptoms corresponding to the severe course of the process (Speranskaya, 2020; Pan et al., 2019). In the cases studied by us, the detection of typical symptoms revealed by radiation diagnostics of COVID-19 was subsequently confirmed by PCR data, which may indicate a high information content and specificity of detecting CT symptoms of a lesion as a method of primary diagnostics. The aim of our study is to confirm at the microscopic level the correspondence of MSCT changes. Methods: The material was taken at autopsy of deceased patients, fixed in 10% formalin solution in phosphate buffer, paraffin sections were stained with hematoxylin and eosin. The autopsy material was examined using a Carl Zeiss light microscope, Axioskop 40. Results: Studies have shown that most of the alveoli of the lung tissue kept their airiness. However, their lumens were significantly reduced due to a significant thickening of the interalveolar septa caused by pronounced inflammatory infiltration mainly by lymphocytes. The most significant changes were revealed from the side of the microvasculature. There are numerous blood clots of various sizes in the lumen of most micro-vessels. The walls of microvessels have been significantly thickened with pronounced inflammatory infiltration and significant edema. The lumens of microvessels have been characterized by significant polymorphism. Intraluminal clots have been also characterized by pronounced polymorphism. The parietal pleura has been thickened. This has been reflected in the MSCT images and corresponds to the processes of perivascular infiltration. Conclusion: The primary CT pattern of COVID-19 is a picture of infiltration of individual secondary pulmonary lobules of the "ground glass" type, followed by a decrease in the lesion volume at a favorable course of the disease, or their increase, the addition of a CT picture of a "cobblestone pavement" and the appearance of alveolar infiltration in the area of "ground glass" at the unfavorable course of the disease.

Multiparametric magnetic resonance imaging and combined prostate biopsy: opportunities, advantages and pitfalls

Multiparametric MRI (mpMRI) has superb sensitivity in prostate cancer detection. mpMRI is increasingly used not only for primary diagnostics, but for location of suspicious lesion before biopsy in case of targeted biopsy (TB). In many recent studies have been shown higher level of TB accuracy in prostate cancer detection in comparison with traditional systemic biopsy. In recent EAU, NICE, ACR recommendations mpMRI is indicated for men with high level of prostate cancer suspicion with previous negative results of systemic biopsy. However, it is not absolutely clear, whether mpMRI is indicated for biopsy-naïve men. This study is dedicated for prostate biopsy planning in the groups of biopsy-naïve men and with the history of previous biopsy.

A Whole-slide Imaging Based Workflow Reduces the Reading Time of Pathologists

Aims: Even though entirely digitized microscopic tissue sections (whole slide images) are increasingly being used in histopathology diagnostics, little data is still available on the effect of this technique on pathologists’ reading time. This study aimed to compare the time required to perform microscopic assessment by pathologists between a conventional workflow (using an optical microscope and glass slides) and digitized whole slide images (WSI).Methods: The study was performed in the Laboratory for Pathology Eastern Netherlands (LabPON, Hengelo, The Netherlands), which has been using WSI in primary diagnostics for several years. Cases were either read in a conventional workflow, while the pathologist recorded the time required for diagnostics and reporting or were read using a fully digitized workflow. The digitized workflow was fully integrated with the laboratory information system, and reading times were extracted from the log files of the image management system. Results: Analysis of over 3800 cases showed a time gain in favour of the digital workflow for most case categories, with the highest gain (68% time gain) for prostate biopsies (prostate care program). On average, a gain of 12.3% was found for the digital workflow, taking the case distribution into account. Conclusions: It was concluded that transitioning from conventional microscopy to use of WSI significantly reduces the pathologists’ reading times. A fully integrated pathologist working environment is required to fully benefit from the benefits of a digital workflow.

PRIMARY DIAGNOSTICS OF TEACHERS OF SPECIAL DISCIPLINES OF TECHNICAL COLLEGE

The article raises the issue of readiness for teaching in the Ukrainian Technical College of specialists who do not have pedagogical education. It is determined that the motivating factor is an important factor influencing the work of a young teacher, the formation and development of future professionals, and the problem of determining the readiness of a specialist with engineering education to teach, his motivation for a new activity, ability to acquire knowledge and skills is extremely relevant and needs attention from the head of scientific and methodological work. It is proposed to introduce the primary scientific and diagnostic development of the mechanism of differentiated psychological and pedagogical influence on teachers of special disciplines of the technical college, which will determine the types of teachers, taking into account the level of their motivation for teaching. The algorithm of application of methods, including author’s, is considered, methodical recommendations concerning their application, calculation, use of results of research are given. It is concluded that the application of primary scientific and diagnostic development of the mechanism of differentiated psychological and pedagogical influence in the technical college will help to adjust group and individual scientific and methodical work with beginning teachers and teaching staff as a whole, to plan further stages of development of psychological and pedagogical competence.