Influence of preanalytical variables on the quality of cell-free DNA. Biobanking of cell-free DNA material

The search for early disease markers and the development of diagnostic systems has recently been expanding within genomics. Genomic deoxyribonucleic acid (DNA), cell-free DNA (cfDNA) and microbiome DNA obtained from different types of samples (tissues, blood and its derivatives, feces, etc.) are used as objects of genetic research. It has been shown that cfDNA that enters the bloodstream, in particular, as a result of apoptosis, necrosis, active tumor secretion and metastasis, is of great importance for studying molecular mechanisms of the pathological process and application in clinical practice. Circulating nucleic acid analysis can be used to monitor response to treatment, assess drug resistance, and quantify minimal residual disease. The review article reflects the following information about the biomaterial: source of cfDNA, methods of cfDNA isolation, storage and use for the diagnosis of certain diseases. Cell-free DNA can be present in biological fluids such as blood, urine, saliva, synovial and cerebrospinal fluid. In most cases, cfDNA is isolated from blood derivatives (serum and plasma), while it is most correct to use blood plasma for cfDNA isolation. Optimal and economically justifiable is the use of ethylenediaminetetra-acetic acid tubes for taking blood and obtaining plasma with subsequent cfDNA isolation. There is evidence that the optimal shelf life in an ethylenediaminetetra-acetic acid tube from the moment of blood sampling to subsequent isolation is a 2-hour interval. After centrifugation, cfDNA in plasma (or serum) can be stored for a long time at a temperature of -80O C. Storage at -20O C is undesirable, since DNA fragmentation increases.

High-Performance Image Acquisition and Processing for Stereoscopic Diagnostic Systems with the Application of Graphical Processing Units

In recent years, cinematography and other digital content creators have been eagerly turning to Three-Dimensional (3D) imaging technology. The creators of movies, games, and augmented reality applications are aware of this technology’s advantages, possibilities, and new means of expression. The development of electronic and IT technologies enables the achievement of a better and better quality of the recorded 3D image and many possibilities for its correction and modification in post-production. However, preparing a correct 3D image that does not cause perception problems for the viewer is still a complex and demanding task. Therefore, planning and then ensuring the correct parameters and quality of the recorded 3D video is essential. Despite better post-production techniques, fixing errors in a captured image can be difficult, time consuming, and sometimes impossible. The detection of errors typical for stereo vision related to the depth of the image (e.g., depth budget violation, stereoscopic window violation) during the recording allows for their correction already on the film set, e.g., by different scene layouts and/or different camera configurations. The paper presents a prototype of an independent, non-invasive diagnostic system that supports the film crew in the process of calibrating stereoscopic cameras, as well as analysing the 3D depth while working on a film set. The system acquires full HD video streams from professional cameras using Serial Digital Interface (SDI), synchronises them, and estimates and analyses the disparity map. Objective depth analysis using computer tools while recording scenes allows stereographers to immediately spot errors in the 3D image, primarily related to the violation of the viewing comfort zone. The paper also describes an efficient method of analysing a 3D video using Graphics Processing Unit (GPU). The main steps of the proposed solution are uncalibrated rectification and disparity map estimation. The algorithms selected and implemented for the needs of this system do not require knowledge of intrinsic and extrinsic camera parameters. Thus, they can be used in non-cooperative environments, such as a film set, where the camera configuration often changes. Both of them are implemented with the use of a GPU to improve the data processing efficiency. The paper presents the evaluation results of the algorithms’ accuracy, as well as the comparison of the performance of two implementations—with and without the GPU acceleration. The application of the described GPU-based method makes the system efficient and easy to use. The system can process a video stream with full HD resolution at a speed of several frames per second.

Review of the algorithms used in exhaled breath analysis for the detection of diabetes

Currently, intensive work is underway on the development of truly noninvasive medical diagnostic systems, including respiratory analysers based on the detection of biomarkers of several diseases including diabetes. In terms of diabetes, acetone is considered as a one of the potential biomarker, although is not the single one. Therefore, the selective detection is crucial. Most often, the analysers of exhaled breath are based on the utilization of several commercially available gas sensors or on specially designed and manufactured gas sensors to obtain the highest selectivity and sensitivity to diabetes biomarkers present in the exhaled air. An important part of each system are the algorithms that are trained to detect diabetes based on data obtained from sensor matrices. The prepared review of the literature showed that there are many limitations in the development of the versatile breath analyser, such as high metabolic variability between patients, but the results obtained by researchers using the algorithms described in this paper are very promising and most of them achieve over 90% accuracy in the detection of diabetes in exhaled air. This paper summarizes the results using various measurement systems, feature extraction and feature selection methods as well as algorithms such as Support Vector Machines, k-Nearest Neighbours and various variations of Neural Networks for the detection of diabetes in patient samples and simulated artificial breath samples.

Bovine mastitis caused by rapid-growth environmental mycobacteria

Rapid-growth mycobacteria were isolated from two cases of cow mastitis with similar clinical appearance and within a narrow time frame. Mycobacteria were isolated on blood esculine agar. The isolated mycobacteria were Gram stained, Ziehl-Nielsen stained and tested for growth at 25°C, 37°C and 42°C, iron uptake, growth on Löwenstein-Jensen (LJ) agar with and without 5% NaCl, arylsulphatase (3 days), tween 80 hydrolysis, tellurite reduction, nitrate reductase and niacin synthesis. Molecular identification was performed using the Mycobacteria GenoType CM and AS tests (Hain Diagnostika, Nehren, Germany). One isolate was additionally sequenced for the hsp65, rpoB, 16S rRNA gene sequence and transcribed spacer sequence (ITS) DNA. Susceptibility testing of isolates was performed on the Sensititre Rapmycol plate (TREK Diagnostic Systems Ltd.) for trimethoprim/sulfamethoxasole, linezolid, ciprofloxacin, imipenem, moxifloxacin, cefepime, cefoxitin, amoxicillin / clavulanic acid, amikacin, ceftriaxone, doxycycline, minocycline, tigecycline, tobramycine and clarythromycine. Gram-positive acid-resistant rods were observed in stained smears. Both strains grew at 25°C, 37°C and 42°C on LJ medium, and on LJ medium containing 5 % NaCl. The conventional biochemical tests for iron uptake, arylsulphatase (3 days), Tween 80 hydrolysis, tellurite reduction and nitrate reductase were positive, while the niacin test was negative. Both isolates were identified by the GenoType Mycobacterium CM as Mycobacterium fortuitum II/ Mycobacterium mageritense, while application of the GenoType Mycobacterium AS kit identified both isolates as belonging to the species Mycobacterium smegmatis. Analysis of the isolate sequences (strain DS) for 16S ribosomal RNA confirmed a 100% identical result with Mycobacterium smegmatis strain INHR2. According to the CLSI criteria, both strains were sensitive to sulfametoxazole/trimethoprim, linezolid, doxicycline, amikacin and tobramycin. The strains differed in their sensitivity to cefoxitim, and both strains were resistant to clarithromycin. There was a strong difference between the isolates in sensitivity toward cefoxitime and tigecycline.

Big Data in Railway O&M

Railway systems are complex with respect to technology and operations with the involvement of a wide range of human actors, organizations and technical solutions. For the operations and control of such complexity, a viable solution is to apply intelligent computerized systems, for instance, computerized traffic control systems for coordinating airline transportation, or advanced monitoring and diagnostic systems in vehicles. Moreover, transportation assets cannot compromise the safety of the passengers by only applying operation and maintenance activities. Indeed, safety is a more difficult goal to achieve using traditional maintenance strategies and computerized solutions come into the picture as the only option to deal with complex systems interacting among them and trying to balance the growth in technical complexity together with stable and acceptable dependability indexes. Big data analytics are expected to improve the overall performance of the railways supported by smart systems and Internet-based solutions. Operation and Maintenance will be application areas, where benefits will be visible as a consequence of big data policies due to diagnosis and prognosis capabilities provided to the whole network of processes. This chapter shows the possibilities of applying the big data concept in the railway transportation industry and the positive effects on technology and operations from a systems perspective.

The Quest for Psychiatric Advancement through Theory, Beyond Serendipity

Over the past century, advancements in psychiatric treatments have freed countless individuals from the burden of life-long, incapacitating mental illness. These treatments have largely been discovered by chance. Theory has driven advancement in the natural sciences and other branches of medicine, but psychiatry remains a field in its “infancy”. The targets for healing in psychiatry lie within the realm of the mind’s subjective experience and thought, which we cannot yet describe in terms of their biological underpinnings in the brain. Our technology is sufficiently advanced to study brain neurons and their interactions on an electrophysiological and molecular level, but we cannot say how these form a single feeling or thought. While psychiatry waits for its “Copernican Revolution”, we continue the work in developing theories and associated experiments based on our existing diagnostic systems, for example, the Diagnostic and Statistical Manual of Mental Disorders (DSM), International Classification of Diseases (ICD), or the more newly introduced Research Domain Criteria (RDoC) framework. Understanding the subjective reality of the mind in biological terms would doubtless lead to huge advances in psychiatry, as well as to ethical dilemmas, from which we are spared for the time being.

Continuous Flow Labeling and In-Line Magnetic Separation of Cells

There is an identified need for point-of-care diagnostic systems for detecting and counting specific rare types of circulating cells in blood. By adequately labeling such cells with immunomagnetic beads and quantum dots, they can be efficiently collected magnetically for quantification using fluorescence methods. Automation of this process requires adequate mixing of the labeling materials with blood samples. A static mixing device can be employed to improve cell labeling efficiency and eliminate error-prone laboratory operations. Computational fluid dynamics (CFD) were utilized to simulate the flow of a labeling-materials/blood mixture through a 20-stage in-line static mixer of the interfacial-surface-generator type. Optimal fluid mixing conditions were identified and tested in a magnetic bead/tumor cell model, and it was found that labeled cells could be produced at 1.0 mL/min flow rate and fed directly into an in-line magnetic trap. The trap design consists of a dual flow channel with three bends and a permanent magnet positioned at the outer curve of each bend. The capture of labeled cells in the device was simulated using CFD, finite-element analysis and magnetophoretic mobility distributions of labeled cells. Testing with cultured CRL14777 human melanoma cells labeled with anti-CD146 1.5 μm diameter beads indicated that 90 ± 10% are captured at the first stage, and these cells can be captured when present in whole blood. Both in-line devices were demonstrated to function separately and together as predicted.

DIFFERENTIAL-GAME MODEL OF INFORMATION PROTECTION FOR COMPUTER SYSTEMS OF TRANSPORT INFRASTRUCTURE

The article considers the reliability and protection of information of computer systems of transport infrastructure and describes the synthesis and analysis of differential game models and methods of modeling cyberattack processes on the server of computer information and diagnostic systems of the railway power supply distance. A unified differential-game model of the cyberattack process on the multi-task server of the information-diagnostic computer system of the lower level of the railway has been developed, which allows to obtain optimal strategies for information protection in cyberattacks. The results of modeling the cyberattack process are presented, to assess the integrated indicators of server security, using the optimal strategies for each of the functions. The appearance of the unified model of the computer information system is shown, and the graphs of the transient processes of the probability of the server being in a protected state and the probability of server failure for any of the functionalities are given.

Assessment of serological tests for antibodies to different antigens of the SARS-CoV-2 virus: comparison of six immunoassays

The new coronavirus SARS-CoV-2 has become a global challenge to medicine and, in particular, laboratory diagnostics. The study of the antibodies’ level to SARS-CoV-2 can be used as a confirmation test in the diagnosis of a disease, but it becomes of paramount importance in assessing population immunity resulting from a disease or vaccination, as well as in selection of convalescent plasma donors. The kits developed in our country and abroad for detecting antibodies to the SARS-CoV-2 virus differ both in the methods of testing and in the used coronavirus antigens to which the antibodies are directed. The aim of this study was to compare the diagnostic sensitivity and specificity of five kits for the detection of IgG antibodies to the SARS-CoV-2 virus, based on different diagnostic methods. Serum samples from 137 COVID-19 convalescents and 166 donors of blood and its components were examined. The control group consisted of 50 blood sera collected at the beginning of 2019 and 19 sera collected in 2018 (before the advent of the SARS-CoV-2 virus) and stored at -70 °C. Testing was carried out in analytical systems: rapid test “COVID-19 IgM/IgG Rapid Test (Colloidal Gold)” (China), on an automatic immunochemical analyzer Abbott Architect™ i2000 and kit “SARS-CoV2-IgG” (Abbot, Chicago , IL USA), by the chemiluminescence method using an automatic analyzer of the CL series and kits of the “Mindray” company (China) “SARS-CoV-2 IgM” and “SARS-CoV-2 IgG” and by the enzyme immunoassay method on the kits of the companies “Diagnostic Systems” Ltd (Russia, Nizhny Novgorod) “DS-IFA-ANTI-SARS-CoV-2-G”, “Xema” Ltd (Federal State Budgetary Institution “National Medical Research Center of Hematology” of the Ministry of Health of Russia) “SARS-CoV-2-IgG-IFA” and “Vector-Best” CJSC (Russia, Novosibirsk)” SARS-COV-2-IgM-IFA-BEST” and “SARS-COV-2-IgG-IFABEST”. When comparing the results of testing 137 plasma samples on the Vector-Best and Mindray kits for IgG antibodies, 127 samples were positive, 7 samples were negative on both kits, the discrepancy was 2.2%. In the study of IgM antibodies, 32.1% were positive, and 52.6% were negative in both kits. The discrepancy rate was 15.3%. Out of 166 samples, 1 serum (0.6%) was negative in 5 kits. On the Mindray kit, IgG antibodies to the antigens of the SARS-CoV-2 virus were detected in 165 samples (99.4%), on Vector-Best – in 164 sera (98.8%), on Diagnostic systems – in 151 (90.96%), on Xema – in 154 (92.8%), and on Abbott – in 155 samples (93.4%). At the same time, 135 (81.33%) samples were positive in all kits, while 30 samples had discordant results (18.07%), and in 9 sera, specific IgG was not detected in 2 or more kits. ROC analysis revealed a high diagnostic value of all tested kits (AUC from 0.908 to 0.998), which indicates a high quality of the separation model of positive and negative samples (p < 0.001). With the cut-off set by the manufacturers, the sensitivity and specificity ranged from 82.8% and 93.3% for the Diagnostic Systems kit to 99.4% and 95.8% for the VectorBest kit. The calculated correlation coefficients were higher between kits with a similar composition of the antigen used in the kits; therefore, it is better to monitor the dynamics of antibodies by diagnostic kits from the same manufacturer.