Clinical laboratory medicine measurements correlation analysis under uncertainty.

BACKGROUND: The Spearman rank correlation test under classical statistics cannot be applied when the paired data is in interval or indeterminacy is presented in the paired data. METHODS: In this paper, the Spearman rank correlation test under neutrosophic statistics will be introduced. The proposed Spearman rank correlation test will be a generalization of the existing Spearman rank correlation test. RESULTS: The proposed test is supposed to be more informative, flexible, and adequate to apply for the analysis of the measurement data. The application of the proposed test is given using the measurement of luteotropichormone data obtained from the clinical laboratory. Based on the information, the probability of accepting the null hypothesis H0N is 0.95, the chance of committing a type-I error is 0.05 and the chance of indeterminacy about the acceptance of H0N is 69%. CONCLUSIONS: From the analysis, it is noted that the proposed test is more efficient in terms of the measure of indeterminacy as compared with the existing test. From the study, it is concluded that the proposed test is more informative, applicable and useable under an indeterminate environment as compared with the existing test under classical statistics. Therefore, it is recommended to apply the proposed test in clinical laboratories for testing the correlation between instruments.

Best practice in statistics: Use the Welch t-test when testing the difference between two groups.

Clinical biochemists often wish to compare two groups of measurements. In order to do so, they must be familiar with Student's t-test. This article provides guidance for the use of the Welch t-test, with subtle but important differences and validity in a broader range of settings: advises the use of the Welch t-test rather than Student's t-test.

[Recommendations for urinary organic acids analysis]. / Recommandations concernant l'analyse des acides organiques urinaires.

Biochemical diagnosis of hereditary metabolic diseases requires the detection and simultaneous identification of a large number of compounds, hence the interest in metabolic profiles. Organic acid chromatography allows the identification of several hundred compounds and the quantification of the main molecules of interest. As part of the accreditation process for medical biology examinations according to standard NF EN ISO 15189, the group from the French society for inborn errors of metabolism (SFEIM) recommends an approach to accredit organic acid chromatography. Validation parameters and recommendations are discussed in this specific framework.

[SFBC working group "Biochemical markers of COVID-19"]. / Groupe de travail SFBC « Marqueurs biochimiques de COVID-19 ¼.

The SARS-CoV-2 virus is responsible for an epidemic disease called COVID-19, which was initially evidenced in Wuhan, China, and spread very rapidly in China and around the world. In France, the first isolated case seems now to be reported in December 2019, stage 3 of the COVID-19 epidemic was triggered on March 14th, the start of the planned containment exit from May 11th. Healthcare services have faced a large influx of patients who may be beyond their capacity to receive and care, particularly in the Large-East and Ile-de-France regions. Some patients show an evolution of the disease never observed before with other coronaviruses and develop in a few days a very important inflammatory reaction, which can lead to death of patients. A working group of the French Society of Clinical Biology (SFBC) was set up with the objective of providing updated information on the current status of the biological prescriptions (focusing on biochemistry ones) and their evolution during the epidemic, and of analyzing the biological parameters associated with comorbidities and patient evolution in order to link biological results with medical events. The expanded working group covers all sectors of medical biology in France and extends to the French-speaking world: hospital sectors (CHU and CH, Army Training Hospitals) and the private sector opening a field of view on the biological situation in establishments for dependent elderly, social establishments and clinical medical institutions. The purpose of this article is the presentation of this working group and its immediate and future actions.

Choosing the adequate thermodynamic reference state: The evolution of pyrophosphate bioenergetics as an example.

The use of the thermodynamic formalism in the investigation of biochemical reactions constitutes one of the key analysis in bioenergetics, and the first step in such analysis is the selection of the adequate reference state. For biochemistry majors, thermodynamic analysis based on the chemical reference state is used in Physical Chemistry courses, while the biological and biochemical reference states are used in Biochemistry courses. As these definitions are introduced in different courses, it is difficult that students can understand the need to select a reference state as a first step in the energy analysis of a system. The lack of suitable examples in textbooks to illustrate the importance of the adequate selection of the reference state in a thermodynamic analysis, promoted the present analysis of the energetic role of pyrophosphate (PPi) in comparison with adenosine-triphosphate in different ambient conditions, namely, the early PPi world (better described by the chemical reference state), the enclosed systems like the cells (better described by the biological reference state), and the actual thioester world (better described by the biochemical reference state). This example not only provides a new interesting point of view on the evolution of two biochemical fuels but also represents a biochemical example in which the use of different reference states can illustrate a single process from different points of views.

Practical application of Six Sigma management in analytical biochemistry processes in clinical settings.

BACKGROUND: Six Sigma methodology with a zero-defect goal has long been applied in commercial settings and was utilized in this study to assure/improve the quality of various analytes. METHODS: Daily internal quality control (QC) and external quality assessment data were collected and analyzed by calculating the sigma (σ) values for 19 analytes based on the coefficient of variation, bias, and total error allowable. Standardized QC sigma charts were established with these parameters. Quality goal index (QGI) analysis and root cause analysis (RCA) were used to discover potential problems for the analytes. RESULTS: Five analytes with σ ≥ 6 achieved world-class performance, and only the Westgard rule (13s ) with one control measurement at two QC material levels (N2) per QC event and a run size of 1000 patient samples between QC events (R1000) was needed for QC. In contrast, more control rules (22s /R4s /41s ) along with high N values and low R values were needed for quality assurance for five analytes with 4 ≤ σ < 6. However, the sigma levels of nine analytes were σ < 4 at one or more QC levels, and a more rigorous QC procedure (13s /22s /R4s /41s /8x with N4 and R45) was implemented. The combination of QGI analysis and RCA further revealed inaccuracy or imprecision problems for these analytes with σ < 4 and discovered five aspects of potential causes considered for quality improvement. CONCLUSIONS: Six Sigma methodology is an effective tool for evaluating the performance of biochemical analytes and is conducive to quality assurance and improvement.

Establishing and validating of an laboratory information system-based auto-verification system for biochemical test results in cancer patients.

BACKGROUND: To establish and validate an laboratory information system (LIS)-based auto-verification (AV) system by using large amounts of biochemical test results in cancer patients. METHODS: An algorithm of the AV process was designed for pre-analysis, analysis, and post-analysis. The limit range check was adjusted three times, while the delta check criteria were first replaced by the same patients' historical extremum results. AV rules of 51 biochemical test items were tested by using data of 121 123 samples (6 177 273 tests) in 2016 that were manually reviewed through the simulative i-Vertification software of Roche. The improved and optimal AV rules were programed into our LIS and validated by using 140 113 clinical specimens in 2018. RESULTS: The AV passing rate for samples tested in our laboratory increased from 15.57% to the current overall passing rate of 49.70%. The passing rate of each item for rule 3 was between 71.16% and 99.91%. Different cancer groups had different passing rate, while the disease group of liver, gallbladder, and pancreas always had the lowest passing rate. A total of 9420 reports (6.72%) were not verified by AV but could be verified by MV in 2018, while there were no reports that were verified by AV but not by MV. The TAT of March 2018 decreased with increase in sample size compared with the same time in 2017. CONCLUSION: We have firstly established an LIS-based AV system and implemented it in actual clinical care for cancer patients.

Individual identification and correction of mistakes in statements of biochemical significance: An effective learning process for graduate medical students.

Focused self-directed learning process needs to be promoted at present among graduate medical students in view of the information load and limited time available with them. In this study, comparison of the effect of identifying and correcting the mistakes in a given set of wrong statements with the effect of studying correct statements individually by graduate medical students on their understanding of the topic "Cancer Biology" was carried out. At the end of regular teaching module, students were asked to identify the mistakes in a set of seven incorrect statements and correct them individually without peer consultation. Another set of seven correct statements were also provided to them and were asked to study their significance. The effects on low, medium, and high achievers were evaluated by pre- and post-tests with the same set of Multiple Choice Questions (MCQs). Mean post-test marks were significantly higher among all the three groups compared to pretest marks for the wrong statements given. For the correct statements, the post-test marks were significantly higher than the pretest marks only for the low and medium achievers. The gain from identifying the mistakes was higher than studying the correct statements for all the three groups of students. Individual correction of errors in statements is a superior active learning process in comparison to the study of correct statements. © 2019 International Union of Biochemistry and Molecular Biology, 47(4):476-480, 2019.

Inconsistencies in some common terms and notations in enzymology: Textbook examples and suggestions.

A number of terms have been defined and inconsistently used across various texts in enzymology which may attract the attention of undergraduate students and instructors. At some places, inconsistent use results in confusions as well as leads to the misuse of these terms. Although it is difficult to resolve such inconsistencies, attempts have constantly been made by international regulatory forums such as International Union of Biochemistry and Molecular Biology (IUBMB) and other similar organizations to abolish the inconsistencies. This article highlights some of the most commonly occurring confusing and inconsistent terms in enzymology. We have gathered shreds of evidences and provide here possible suggestions and caution for readers and instructors, so that mistakes can be minimized and possible guidelines can be prepared for their usage. A few inconsistencies observed and discussed here include different notations of activation energy, differences in terms uncompetitive and noncompetitive in enzyme inhibition, classification of cofactors and definitions of their sub-types, and confusing usage of the enzyme-inhibitor dissociation constant. Besides this, we have also highlighted the inconsistencies in the enzyme nomenclature. © 2018 International Union of Biochemistry and Molecular Biology, 47(2): 140-144, 2019.

Human Milk Lipidomics: Current Techniques and Methodologies.

Human milk contains a complex combination of lipids, proteins, carbohydrates, and minerals, which are essential for infant growth and development. While the lipid portion constitutes only 5% of the total human milk composition, it accounts for over 50% of the infant's daily energy intake. Human milk lipids vary throughout a feed, day, and through different stages of lactation, resulting in difficulties in sampling standardization and, like blood, human milk is bioactive containing endogenous lipases, therefore appropriate storage is critical in order to prevent lipolysis. Suitable sample preparation, often not described in studies, must also be chosen to achieve the aims of the study. Gas chromatography methods have classically been carried out to investigate the fatty acid composition of human milk lipids, but with the advancement of other chromatographic techniques, such as liquid and supercritical fluid chromatography, as well as mass spectrometry, intact lipids can also be characterized. Despite the known importance, concise and comprehensive analysis of the human milk lipidome is limited, with gaps existing in all areas of human milk lipidomics, discussed in this review. With appropriate methodology and instrumentation, further understanding of the human milk lipidome and the influence it has on infant outcomes can be achieved.

Standardized assays for determining the catalytic activity and kinetics of peroxidase-like nanozymes.

Nanozymes are nanomaterials exhibiting intrinsic enzyme-like characteristics that have increasingly attracted attention, owing to their high catalytic activity, low cost and high stability. This combination of properties has enabled a broad spectrum of applications, ranging from biological detection assays to disease diagnosis and biomedicine development. Since the intrinsic peroxidase activity of Fe3O4 nanoparticles (NPs) was first reported in 2007, >40 types of nanozymes have been reported that possess peroxidase-, oxidase-, haloperoxidase- or superoxide dismutase-like catalytic activities. Given the complex interdependence of the physicochemical properties and catalytic characteristics of nanozymes, it is important to establish a standard by which the catalytic activities and kinetics of various nanozymes can be quantitatively compared and that will benefit the development of nanozyme-based detection and diagnostic technologies. Here, we first present a protocol for measuring and defining the catalytic activity units and kinetics for peroxidase nanozymes, the most widely used type of nanozyme. In addition, we describe the detailed experimental procedures for a typical nanozyme strip-based biological detection test and demonstrate that nanozyme-based detection is repeatable and reliable when guided by the presented nanozyme catalytic standard. The catalytic activity and kinetics assays for a nanozyme can be performed within 4 h.

[Thanatobiochemistry: post mortem study of the vitreous humor for the diagnosis of diabetic ketoacidosis death]. / Biochimie thanatologique : intérêt de l'étude post mortem de l'humeur vitrée pour le diagnostic de décès par acidocétose diabétique.

Thanatobiochemistry refers to a post mortem study of biochemical parameters enabling to shed light on a cause of death. This discipline shines when suspected lethal pathology doesn't have any noticeable macroscopic or microscopic features such as diabetic ketoacidosis. We relate the case of fourty-five years old patient followed-up for type I diabetes mellitus, discovered dead at home, for which only post mortem biochemical exploration of vitreous humor allowed to determine the cause of death by diabetic ketoacidosis.

Preanalytical external quality assessment of the Croatian Society of Medical Biochemistry and Laboratory Medicine and CROQALM: finding undetected weak spots.

INTRODUCTION: The aim of this paper is to present results of first two years of preanalytical external quality assessment (EQA) in Croatia. MATERIALS AND METHODS: This paper summarizes results from 6 rounds of preanalytical EQA during 2014-2016 in 161-175 Croatian laboratories (number ranged between cycles). EQA was designed as an online survey of the compliance with National recommendations for phlebotomy (NRP). Forty-seven questions in 5 categories are analyzed (materials and equipment, patient identification, patient preparation, sampling and storage). Additionally, preanalytical cases are presented. Overall performance scores (Question score (Qscore) for compliance with NRP and Case score (Cscore) for preanalytical cases) are calculated for each question/case as a proportion of laboratories with satisfactory procedure (x 100). Qscores and Cscores ≥ 70 were classified as acceptable (maximal score = 100). RESULTS: In investigation of compliance with NRP, acceptable Qscores were obtained for 34/47 questions. The lowest scores were observed for the availability of sterile disposable tourniquets (Qscore = 15) and safe-sharp needles (Qscore = 34), obtaining patients address as an identifier (Qscore = 21), using glycolysis inhibitor tubes for glucose concentration measurement (Qscore = 21) and verification of manufacturers declarations on temperature and time of storage (Qscore = 31). There was no statistically significant difference in overall Qscore according to different categories of phlebotomy procedures (P = 0.284). The results of preanalytical cases showed acceptable Cscore values for all cases (89-96). CONCLUSION: First two years of preanalytical EQA showed good compliance with the NRP and excellent expertise in resolving complex preanalytical issues. Major critical spots are lack of availability of safe-sharp needles, disposable tourniquets and glucose inhibitor tubes.

Policies and practices in haemostasis testing among laboratories in Croatia: a survey on behalf of a Working Group for Laboratory Coagulation of the Croatian Society of Medical Biochemistry and Laboratory Medicine.

INTRODUCTION: The objective of this survey was to assess current policies and practice in haemostasis testing among both hospital and outpatient laboratories in Republic of Croatia. MATERIALS AND METHODS: A questionnaire with seventy questions divided into nine sections was created in May 2015. Participants were asked about their practice related to test request form, sample collection, prothrombin time (PT) and activated partial thromboplastin time assays, other individual haemostasis assays, point-of-care testing (POCT), reporting of coagulation tests results and quality assurance of procedures, the personnel and other laboratory resources, as well as on issues related to education and implementation of additional coagulation assays in their laboratory. The survey was administered and data were collected between June and September 2015. RESULTS: A total survey response rate was 104/170 (61.2%). Most respondents were faced with incomplete information on prescribed therapy and diagnosis on the test request or inappropriate samples withdrawn on distant locations, but also do not have protocols for handling samples with high haematocrit values. Reporting of PT-INR and D-dimer results was different between laboratories. Although almost all laboratories developed a critical value reporting system, reporting a value to general practitioners is still a problem. Result on coagulation POCT testing showed that not all devices were supervised by laboratories, which is not in compliance with Croatian Chamber of Medical Biochemistry acts. CONCLUSION: Obtained results highlighted areas that need improvement and different practice patterns in particular field of haemostasis testing among laboratories. A harmonization of the overall process of haemostasis testing at national level should be considered and undertaken.

Biochemistry and neuroscience: the twain need to meet.

Neuroscience has come to mean the study of electrophysiology of neurons and synapses, micro and macro-scale neuroanatomy, and the functional organization of brain areas. The molecular axis of the field, as reflected in textbooks, often includes only descriptions of the structure and function of individual channels and receptor proteins, and the extracellular signals that guide development and repair. Studies of cytosolic 'molecular machines', large assemblies of proteins that orchestrate regulation of neuronal functions, have been neglected. However, a complete understanding of brain function that will enable new strategies for treatment of the most intractable neural disorders will require that in vitro biochemical studies of molecular machines be reintegrated into the field of neuroscience.

[External quality assessment in clinical biochemistry laboratories: pilot study in 11 laboratories of Lomé (Togo)]. / Évaluation externe de la qualité des examens de biochimie clinique : étude pilote dans 11 laboratoires de Lomé (Togo).

This study aims to evaluate the performance of a few biochemistry analysis and make recommendations to the place of the stakeholders. It is a cross-sectional study conducted between the October 1(st), 2012 and the July 31, 2013 bearing on the results of 5 common examinations of clinical biochemistry, provided by 11 laboratories volunteers opening in the public and private sectors. These laboratories have analysed during the 3 cycles, 2 levels (medium and high) of serum concentration of urea, glucose, creatinine and serum aminotransferases. The performance of laboratories have been determined from the acceptable limits corresponding to the limits of total errors, defined by the French Society of Clinical Biology (SFBC). A system of internal quality control is implemented by all laboratories and 45% of them participated in international programs of external quality assessment (EQA). The rate of acceptable results for the entire study was of 69%. There was a significant difference (p<0.002) between the performance of the group of laboratories engaged in a quality approach and the group with default implementation of the quality approach. Also a significant difference was observed between the laboratories of the central level and those of the peripheral level of our health system (p<0.047). The performance of the results provided by the laboratories remains relatively unsatisfactory. It is important that the Ministry of Health put in place a national program of EQA with mandatory participation.

Integrative, dynamic structural biology at atomic resolution--it's about time.

Biomolecules adopt a dynamic ensemble of conformations, each with the potential to interact with binding partners or perform the chemical reactions required for a multitude of cellular functions. Recent advances in X-ray crystallography, nuclear magnetic resonance (NMR) spectroscopy and other techniques are helping us realize the dream of seeing--in atomic detail--how different parts of biomolecules shift between functional substates using concerted motions. Integrative structural biology has advanced our understanding of the formation of large macromolecular complexes and how their components interact in assemblies by leveraging data from many low-resolution methods. Here, we review the growing opportunities for integrative, dynamic structural biology at the atomic scale, contending there is increasing synergistic potential between X-ray crystallography, NMR and computer simulations to reveal a structural basis for protein conformational dynamics at high resolution.