Daily Laboratory Work Research Articles

Core Analysis Using Nuclear Magnetic Resonance

Core analysis is critical for oil and gas exploration and recovery. Nuclear magnetic resonance (NMR) has been widely applied to the petroleum industry for many years, and NMR core analysis plays an important role in supporting borehole NMR formation evaluation and understanding the mechanisms of petrophysics and petrochemistry. It’s unfortunate, however, that there has been a lack of commented descriptions of the basic procedures for NMR rock core analysis in the literature, which has led to issues of comparability and repeatability of NMR measurements between different laboratories. In this paper, we present a brief guideline for NMR rock core analysis of conventional T2, T1, T1-T2, and D-T2 measurements. As an established procedure in daily laboratory work, NMR core analysis includes three sophisticated steps: rock sample preparation, an NMR experiment, and data analysis. The acquisition and saturation of rock samples are described, and corresponding solutions are also considered. Detailed NMR experimental measurements, data setting, and calibration are addressed. Laplace inversion for different NMR experiments and models for estimation of porosity, irreducible water, permeability, pore structure, and oil saturation are included. The aim of this paper is to try to standardize general NMR experiments for rock core analysis.

Large fragment Sanger sequencing identifies the newly encountered variant that caused null alleles in parentage testing.

Short tandem repeat (STR) is regarded as a crucial tool for personal identification as well as parentage testing. Thus, genotyping errors of STRs could have negative effects on the reliability of forensic identification. A null allele at the combined DNA index system (CODIS) core loci D2S1338 was found in a father-daughter pair with the AGCU Expressmarker 22 kit which was a commonly used commercial kit during our daily laboratory work. This null allele caused the father and daughter to not conform to the laws of inheritance, thus potentially generating erroneous conclusions that excluded parentage. To figure out the reason for this phenomenon, re-amplification with new primers and then large fragment Sanger sequencing was conducted. We found a G to G/T variation at the position which is fifty-nine bases away from the 3' end of the core repeat in both samples. This probably could be considered a novel variant at the primer binding region which had not been reported that resulted in the emergence of the null allele. We also found that there was more than one single-nucleotide polymorphism (SNP) with minor allele frequency (MAF) greater than 0.1 in the upstream and downstream sequences of D2S1338. When designing primers for amplification of D2S1338, the possible adverse results of these SNPs should be taken into account and avoided.

SARS-CoV-2 antibody progression and neutralizing potential in mild symptomatic COVID-19 patients - a comparative long term post-infection study.

BackgroundSince December 2019, SARS-CoV-2 has been keeping the world in suspense. Rapid tests, molecular diagnosis of acute infections, and vaccination campaigns with vaccines are building blocks of strategic pandemic control worldwide. For laboratory diagnostics, the quantification of the antibody titer of convalescents and vaccinated patients is thus increasingly coming to the fore.MethodsHere we present an evaluation on the comparability of five serological tests on a cohort of 13 patients with mild COVID-19 disease. Also participants who were vaccinated after recovery were included in this study. All common immune methods (ELISA, CLIA, PETIA) and SARS-CoV-2 specific antigens (N-, S1- and RBD-) were specifically tracked and directly compared for up to 455 days. The titer of recovered participants was also set to the degree of symptoms during infection and the occurrence of Long-COVID. In addition, relative comparability of different serological tests, all standardized to WHO, was set in reference to the neutralizing potential of the corresponding participants.FindingsThe individual immune responses over 455 days after a mild SARS-CoV-2 infection remain stable, in contrast to vaccinated participants. All sero-tests reveal comparable performance and dynamics during the study and compared well to a surrogate neutralization test.ConclusionThe information presented here will help clinicians in the daily laboratory work in the selection and evaluation of different serological tests offered. The data also will support in respect of a sero-test-based neutralization cutoff.

Ionotropic gelation method in the synthesis of nanoparticles/microparticles for biomedical purposes

AbstractThe encapsulation of drugs inside polymeric nanoparticles/microparticles is a strategy currently employed in the search for new and more effective therapies. The use of biocompatible and biodegradable polymers gives several advantages to these formulations. Protection of the active principals against the action of environmental and physiological agents, the reduced number of doses and a subsequent decrease in drug‐related adverse effects, and increased bioavailability are some of these advantages. Several methods and materials are now used to synthesize nanoparticles/microparticles for biomedical applications, from carbon‐derived structures to metallic and lipid particles. However, among the methods using polymers, ionotropic gelation is one of the more affordable and easier procedures to perform in daily laboratory work. In this mini‐review, we address relevant characteristics of ionotropic gelation, beginning with basic aspects of the technique, which reagents and conditions are commonly used, the factors affecting the stability of the formulation, the advantages and disadvantages of the method and some principal characterization techniques for the nanoparticulate/microparticulate formulation. Finally, we conclude with a few important considerations. © 2020 Society of Chemical Industry

Proof of Concept Evaluation of a New Diagnostic POCT Device for Culture- Independent Microbiological Diagnosis of Infective Endocarditis

Introduction: Accurate and fast microbiological diagnosis of infective endocarditis (IE) is of vital importance for patient outcome. Material & Methods: Forty culture-negative heart valves were evaluated with a new POCT multiplex-PCR cartridge (Unyvero™, Curetis AG, Holzgerlingen, Germany), advertised to detect several Gram positive/­negative bacteria and fungi, together with several antibiotic resistance genes. Those POCT results were compared to conventional 16S rDNA PCR/sequencing results. Results: POCT multiplex-PCR was positive in 13 cases [Staphylococcus aureus (n=5), Enterococcus spp. / E. faecalis (n=5), ConS (n=1), Granulicatella adjacens (n=1), Abiotrophia adjacens (n=1)]. Antibiotic resistances were found in 44 specimens, from which 2 specimens were without any pathogen identification. 16S rDNA PCR was positive in 20 cases. Consecutive sequencing identified those as Staphylococcus spp. (n=6), Enterococcus faecalis (n=4), Streptococcus spp. (n=4), Leifsonia shinshuensis (n=1), Granulicatella elegans / G. adjacens (n=2), Abiotrophia adjacens (n=1). One case was positive in 16S PCR without any reliable signal in sequencing. When comparing both methods, identification was consistent in 9 cases and divergent in other 9 cases. Discussion: This POCT cartridge is easy to integrate into the daily microbiology laboratory work flow, and is less laborious than 16S sequencing PCR. For the application in routine IE diagnosis, the system needs to be optimized to include targets for viridans streptococci and HACEK group. In addition, problems with invalid resistance and pathogen target detection need to be fixed by the producer. Conclusion: The analyzed POCT system might be a future diagnostic tool for IE detection following assay optimization.

Identification of a discordant genotype at the D2S1338 locus between Identifiler Plus®16 kit and Power Plex®21 system kit

Genotyping errors can perturb estimates of genetic diversity and adversely affects the reliability of forensic identification, which has become increasingly recognized. During our daily laboratory work, we hit upon a discordant short tandem repeat (STR) genotype at the D2S1338 locus between Identifiler Plus®16 system kit and Power Plex®21 system kit. To figure out the reason of the discordance, nested PCR was performed to amplify the D2S1338 locus and then the final amplicons were sequenced. We found a G to G/A transition at the position on which caused an allele dropout of Identifiler Plus®16 kit.

Oocytes with a Dark Zona Pellucida Demonstrate Lower Fertilization, Implantation and Clinical Pregnancy Rates in IVF/ICSI Cycles

The morphological assessment of oocytes is important for embryologists to identify and select MII oocytes in IVF/ICSI cycles. Dysmorphism of oocytes decreases viability and the developmental potential of oocytes as well as the clinical pregnancy rate. Several reports have suggested that oocytes with a dark zona pellucida (DZP) correlate with the outcome of IVF treatment. However, the effect of DZP on oocyte quality, fertilization, implantation, and pregnancy outcome were not investigated in detail. In this study, a retrospective analysis was performed in 268 infertile patients with fallopian tube obstruction and/or male factor infertility. In 204 of these patients, all oocytes were surrounded by a normal zona pellucida (NZP, control group), whereas 46 patients were found to have part of their retrieved oocytes enclosed by NZP and the other by DZP (Group A). In addition, all oocytes enclosed by DZP were retrieved from 18 patients (Group B). No differences were detected between the control and group A. Compared to the control group, the rates of fertilization, good quality embryos, implantation and clinical pregnancy were significantly decreased in group B. Furthermore, mitochondria in oocytes with a DZP in both of the two study groups (A and B) were severely damaged with several ultrastructural alterations, which were associated with an increased density of the zona pellucida and vacuolization. Briefly, oocytes with a DZP affected the clinical outcome in IVF/ICSI cycles and appeared to contain more ultrastructural alterations. Thus, DZP could be used as a potential selective marker for embryologists during daily laboratory work.

Sustainable production of chemicals – an educational perspective

Sustainability is a very general term and the question arises how to specify it within daily laboratory work. In this regard, appropriate metrics could support a socially acceptable, ecological and economic product development. The application of metrics for sustainability should be strengthened in education, because they do not belong to standard considerations in synthesis design so far. This article describes educational material (online resource) designated to students and chemists who are willing to quantify the benefits of green chemistry in the lab and to search for an optimization potential. As an example, bromination reactions are compared by considering mass balance, raw material costs and qualitative aspects such as, e.g., toxicology and combustibility. While keeping in mind the three dimensions of sustainability – economy, environment and social affairs – the idea of the concept of sustainable chemistry, i.e., green chemistry, takes shape in daily laboratory work.

Intercomparison of thermal conductivity measurements on a calcium silicate insulation material

The determination of reliable thermal conductivity values of insulation materials at high temperatures is important for target-oriented material research, further improvement of products and quality management. However, there is a lack of reference materials for high temperature thermal conductivity measurements which are needed to ensure and improve good measurement practise. In order to investigate porous calcium silicate as reference material for temperatures up to 1100 K, the German Thermophysics Working Group within GEFTA initiated an intercomparison of thermal conductivity measurements on a commercially available calcium silicate insulation material with seven participating laboratories. Stationary and instationary measurement methods were used to determine the effective total thermal conductivity of the calcium silicate material in the temperature range from 300 K to 1100 K. The derived weighted mean value of the thermal conductivity increases from 0.0846 W m −1 K −1 at 300 K to 0.173 W m −1 K −1 at 1100 K. Within the same temperature interval the relative uncertainty increases from 3.5% to 7%. The investigated product is commercially available and it could be therefore used in the daily laboratory work as reference material for thermal conductivity measurements at high temperatures.

The importance of preanalytics for the coagulation laboratory

Due to their complex preanalytics coagulation tests show a higher rate of rejected samples due to insufficient quality and a higher intra- and inter-individual test variability. In the last years several guidelines addressed this issue in an effort to standardize preanalytic procedures. However, in daily laboratory work, these guidelines frequently cannot be fully executed, due to technical limitations or sample transport logistics. In this manuscript several important issues in sample collection, handling and transportation will be discussed. Since the stability and variability of routine coagulation tests such as prothrombin time and partial prothrombin time are significantly influenced by a number of variables such as tube type, manufacturer, reagents used and analyzer systems, it is recommended that each laboratory develops its own manuals for sample collection, based on published data and internal evaluations.

6th HUPO Annual World Congress – Proteomics Standards Initiative Workshop 6–10 October 2007, Seoul, Korea

The plenary session of the Proteomics Standards Initiative of the Human Proteome Organisation at the 6th annual HUPO world congress updated the delegates on the current status of the ongoing work of this group. The new MS interchange format, mzML, had been entered into the HUPO document process immediately prior to the meeting and was already under active discussion by prospective users. It is anticipated this will become the de facto standard in this area in 2008. Minimal requirements documents are in the process of being published and proteomics journals are beginning to request data deposition as part of the manuscript submission process. The session ended with a lively debate on the practical implications these advances will have on daily laboratory work, on submission procedures and the tools which are being developed to assist in these activities.

Preparation of an estuarine sediment quality control material for the determination of trace metals

Quality Control Materials (QCM) have being used routinely in daily laboratory work as a tool to fill the gap between need and availability of Certified Reference Materials (CRM). The QCM are a low-cost alternative to CRMs, and they are in high demand, especially, for the implementation of quality control systems in laboratories of several areas. This paper describes the preparation of a QCM for the determination of trace metals in estuarine sediments and the results of an interlaboratory exercise. Homogeneity and stability studies were performed and analysis of variance was carried out with the results. No statistical significant differences were observed in the concentrations of Co, Cr, Cu, Mn, Pb and Zn between- or within bottle results. Neither the storage nor temperature affected the results. Therefore, the QCM produced is considered homogeneous and stable and can be used for statistical control charts, evaluation of reproducibility and interlaboratory exercises.

Tissue Engineering—Essentials for Daily Laboratory Work

Tissue Engineering—Essentials for Daily Laboratory Work

Analytical goals for coagulation tests based on biological variation.

Allowable imprecision and bias reference limits for laboratory data can be calculated based on measurements of biological variation. Although biological variation of clinical chemical data has been reported from many laboratories, there have been few reports of biological variation in coagulation tests. In this study, we calculated the biological variation of 13 coagulation tests in the clinical laboratory of Kyushu University Hospital and determined allowable imprecision and bias limits of variation. The participating subjects were 17 healthy individuals: three males and two females in their 20s, two males and two females in their 30s, one male and four females in their 40s, and two males and one female in their 50s. Monthly measurements were performed before breakfast 12 times from June 2001 to May 2002 and allowable imprecision and bias limits were calculated. Taken together with coefficient of variation of control plasma used in daily laboratory work at the hospital, the allowable imprecision limits of intra-laboratory variation determined in this study appear to be in attainable ranges.

Changes in portal vein flow after adult living-donor liver transplantation: Does it influence postoperative liver function?

In adult living donor liver transplantation, using small grafts in cirrhotic patients with severe portal hypertension may have unpredictable consequences. The so-called small-for-size syndrome is present in most series worldwide. The goal of this study was to prospectively evaluate the influence of hemodynamic changes on postoperative liver function and on the percentage of liver volume increase, in the setting of living donor liver transplantation. Twenty-two consecutive adult living donor liver transplantations were performed at our institution in a 2-year period. We measured right portal flow and right hepatic arterial flow with an ultrasonic flow meter in the donor, and then in the recipient 1 hour after reperfusion. Postoperative liver function was measured by daily laboratory work. We also performed duplex ultrasounds on postoperative days 1, 2, and 7. Liver volume increase was estimated by magnetic resonance imaging graft volumetry at 2 months posttransplantation. We compared the blood flow results with the immediate liver function and its liver volume increase rate at 2 months. There was a significant increase in portal flow in the recipients compared with the donors (up to fourfold in some cases). Higher portal flow increase rates significantly correlated with faster prothrombin time normalization and faster liver volume increases. Median graft volume increase at 2 months was 44.9%. The increase in blood flow to the graft is well tolerated by the liver mass not affecting hepatocellular function as long as the graft-to body weight ratio is maintained (>0.8) and adequate outflow is provided. (Liver Transpl 2003;9:564-569.)

Preparation of a soil reference material for the determination of radionuclides

Method performance in analytical chemistry is checked using certified reference material (CRM). Due to their high production cost, CRMs cannot be used routinely in daily laboratory work, therefore, laboratory reference materials (LRMs) is preferred. This paper describes the preparation of an LRM for the determination of radionuclides in soil. The LRM was prepared by mixing three soils — two from areas affected by the Chernobyl NPP accident, which present condensed radioactivity contamination, and one non-contaminated soil from inland Catalonia. The resulting solid dilution contained condensed radioactive contamination at environmental levels and natural radionuclides ( 137 Cs , 90 Sr , 40 K , 212 Pb , 214 Pb , 208 Tl , 214 Bi and 228 Ac ). Bulk homogeneity was checked before soil was bottled and, once bottled, final homogeneity and stability studies were performed. Analysis of variance was carried out with the results. No statistically significant differences were observed for within- or between-bottle results. Neither the storage temperature nor the time of the determination after bottling affected the results. Therefore, the material prepared is considered homogeneous and stable and will be used in a future intercomparison exercise for radiochemical laboratories in Spain.

Multiple ligand-ion solutions: a guide for solution preparation and computer program understanding.

This paper first gives an overview of the multitude of chemical reactions taking place in aqueous solutions with multiple ligands and ions. Then, recommendations to avoid pitfalls in preparing such solutions in daily laboratory work are summarized. Thereafter, the theoretical aspects for calculating multiple ligand-ion solutions are described in detail. Information necessary to perform corrections of the absolute stability constants for the influences of pH, ionic strength, and temperature are given. The calculation of apparent reaction constants for ligand-ion interactions by using the corrected absolute stability constants and considering all possible reactions between a ligand and an ion in an aqueous solution will be introduced. Thereafter, by employing the apparent reaction constants and an iterative method, the determination of multiple ligand-ion equilibria to find the desired ligand or ion concentrations are presented. Thus, this paper can be used as a guide to the principles of programs calculating multiple ligand-ion solutions, to choosing the appropriate program for one's special requirements, and to preparing multiple ligand-ion solutions properly.

Isoelectric focusing in non-amphoteric buffers : Catastrophe and non-catastrophe theories

Four potential modes of isoelectric focusing in non-amphoteric buffers are evaluated:(a)“stack” or “train” of free bases or acids “arrested by a deprotonation or protonation mechanism”, respectively (Chrambach); (b) “chemically bonded” (immobilized) pH gradients (Righetti et al.); (c) “physically bonded” or “quasi-immobilized” pH gradients (Bier et al.); (d) steady-state rheoelectrolysis (Rilbe). The first is based on a “catastrophe” theory, i.e., it confines the buffers in a pH region where they can create a pH gradient by an isotachophoretic mechanism, but where they do not have sufficient buffering capacity to stabilize it; no true isoelectric focusing can ever be achieved with this system. The last three are based on sound and well defined theories; however, at present, only system (b) (immobilized pH gradients) has proved to be a simple and reliable technique, easily transplantable in any laboratory. Bier et al.'s and Rilbe's approaches require complex and elaborate experimental set-ups and strict adherence of laboratory practice to a set of physical laws governing the system. In practice, owing to the divergence of experimental approaches from idealized physical equilibria, the last two approaches appear still to be far away from daily laboratory work.

A new production of mini-tomographic apparatus and their testing.

This paper describes two types of mini - tomographic apparatus recently manufactured by the authors for the purpose of introducing them in the laboratories of anatomy, pathology, etc. Hithertofore, the tomographic apparatus had not been in use by these laboratories of basic medical sciences because of its physical size and expensive cost of maintenance. Therefore, our mini - tomographic apparatus, made of wood or other material which is easily penetrable by X-ray, is small and light enough, so that anyone can operate them on his laboratory desk to aid him in his research routine. These tomographic apparatus are of two types : parallel incline type and revolving type. After our pilot manufacture of these devices, they were put to tests in the following manner in order to evaluate their practicability.1. Parallel incline movement type.When a material is put to test in the passage of X-ray with a film directly beneath the material, both the material and film perform an incline movement within a range of 30 to 50° to the front and back on the axis.2. Revolving type.On one side of this apparatus there are set up two sticks (one is 3cm in diameter the other being 10cm) and on the other side, the third stick is installed 10cm long with the handle to rotate itself. Between the first two sticks and the third there is a distance of 40cm and these sticks are so connected with a belt that they can move at the same speed simultaneously. A film is placed on a lower stick and a material on the taller one or the process can be reversed. In any case, the three sticks revolve at the same speed in one direction while being exposed to X-ray radiation (Fig. 1). Our initial purpose of a set of experiments was to extract a layer of tissues on a film from among many structure layers and we were successful in it. Further, we also succeeded in the traverse and transverse tomographic section of the head of a rabbit. Our attempt to take a tomographic section of the tooth, however, failed, for we used an ordinary dental film. But it is hoped that, with the future refinement of these apparatus and attendant techniques, better results will be obtained to aid us in our daily laboratory work more accurately and cheaply.

O líqüido cefalorraqueano no diagnóstico da criptococose do sistema nervoso

Baseados na observação de oito casos, os autores chamam a atenção sobre a importância do líquido cefalorraqueano no diagnóstico da criptococose do sistema nervoso. Atribuem a mair freqüência atual do diagnóstico desta moléstia à maior vigilância por parte do médico. Enumeram as etapas das pesquisas sôbre o líquor nas quais é possível descobrir o fundo. Julgam necessário incluir, na rotina dos exames de todos os casos suspeitos, uma série de pesquisas com as quais é possível descobrir o parasito. Em primeiro lugar, há a possibilidade da suspeita do parasito já na câmara de contagem das células, onde êles podem ser grosseiramente confundidos com hemátias; a observação microscópica com pouca luz, a formação do brôto e a prova do ácido acético permitem caraterizar êste cogumelo. Em segundo lugar, por ocasião da confecção do esfregaço para a contagem específica das células observa-se uma aparência gordurosa do material distendido. O estudo da lâmina corada mostra os parasitos dentro de sua cápsula gelatinosa, freqüentemente aglomerados; outras vêzes constatam-se formações semelhantes a ninho de abelha originadas dos espaços vasios deixados pelo fungo que foi arrancado de sua loja por ocasião da confecção do esfregaço; também podem ser observadas células gigantes fagocitando o fungo. Em terceiro lugar, pode-se perfeitamente identificar os parasitos no material corado pelos métodos de Gram e Ziehl onde êles aparecem, aglomerados ou isolados, intensamente corados e bem característicos. O diagnóstico de certeza é feito pelo exame a fresco com auxílio da tinta da China, na qual o fungo com sua cápsula e a formação do brôto são perfeitamente evidentes, e pela cultura em meio de Sabouraud. Os autores analisam, depois, as alterações observadas no líquor inicial nos 8 casos. Constataram grande hipertensão. O número de células variou de 9 a 411 por mm3, sendo em dois casos 9 e 18 respectivamente, apesar do aspecto do líquor ser turvo, o que era devido à presença de grande número de criptococos. Havia predomínio de linfócitos na maioria dos casos. A taxa das proteínas sempre se apresentou aumentada, variando de 32 a 140 mg% A taxa de açúcar sempre diminuida. O criptococo esteve presente em abundância, sendo o maior número observado de 1800 elementos por mm3. Em um caso de decurso sub-agudo foi possível acompanhar a evolução das alterações do líquor durante 40 dias, e sendo verificada a proporcionalidade entre a intensidade dessas alterações e o agravamento do quadro clínico. Em duas outras observações, em que a moléstia teve decurso crônico, com mais de um ano e quatro anos de seqüência respectivamente, os pacientes foram inicialmente tratados com o diagnóstico de presunção de meningite tuberculosa. Ulteriormente êste diagnóstico foi corrigido por um novo exame de liquor em que foi demonstrada a presença do fungo. Os autores concluem: 1 - Deve-se incluir na rotina do exame do líquido céfalorraqueano, em casos suspeitos, meios de identificação para o criptococo; 2 - O criptococo pode ser suspeitado na câmara de contagem das células por quem estiver alerta e fôr conhecedor do parasito; 3 - O criptococo é mais fàcilmente identificável nos esfregaços corados pelo método hematológico, pelos de Gram e Ziehl, pelo exame a fresco com auxílio da tinta da China e pela prova cultural; 4 - As alterações do líquor assemelham-se àquelas encontradas nos casos de meningite tuberculosa salvo em relação ao exame bacteriológico.