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PloS One 2019The maximum entropy model, a commonly used species distribution model (SDM) normally combines observations of the species occurrence with environmental information to...
The maximum entropy model, a commonly used species distribution model (SDM) normally combines observations of the species occurrence with environmental information to predict the geographic distributions of animal or plant species. However, it only produces point estimates for the probability of species existence. To understand the uncertainty of the point estimates, we analytically derived the variance of the outputs of the maximum entropy model from the variance of the input. We applied the analytic method to obtain the standard deviation of dengue importation probability and Aedes aegypti suitability. Dengue occurrence data and Aedes aegypti mosquito abundance data, combined with demographic and environmental data, were applied to obtain point estimates and the corresponding variance. To address the issue of not having the true distributions for comparison, we compared and contrasted the performance of the analytical expression with the bootstrap method and Poisson point process model which proved of equivalence of maximum entropy model with the assumption of independent point locations. Both Dengue importation probability and Aedes aegypti mosquito suitability examples show that the methods generate comparatively the same results and the analytic method we introduced is dramatically faster than the bootstrap method and directly apply to maximum entropy model.
Topics: Aedes; Algorithms; Animals; Biodiversity; Dengue; Dengue Virus; Ecosystem; Entropy; Models, Theoretical; Mosquito Vectors; Uncertainty
PubMed: 31120909
DOI: 10.1371/journal.pone.0214190 -
Analytical Chemistry Jan 2023The study of non-polar compounds in aqueous environments has always been challenging due to their poor solubility in aqueous media. The low affinity of non-polar...
The study of non-polar compounds in aqueous environments has always been challenging due to their poor solubility in aqueous media. The low affinity of non-polar compounds toward polar solutions facilitates their attachment to glassware, which results in unstable sample concentrations. To address this challenge, and to enable the preparation of a stable mixture of hydrophobic compounds in an aquatic environment, we introduce an in-vial standard water generating system consisting of a vial containing appropriate aqueous solution and a polydimethylsiloxane thin film spiked with target compounds. In this system, a solution with a stable analyte concentration is attained once equilibrium between the thin-film and aqueous solution has been achieved. The developed standard water system was studied using endocannabinoids and phospholipids as model hydrophobic compounds of biological importance, with results indicating that the concentration of hydrophobic compounds in water can remain stable over multiple days. The results also showed that analytes released from the thin film can compensate for analyte loss due to extractions with solid-phase microextraction fibers, thereby re-establishing equilibrium. Thus, the vial is suitable for the repeatable generation of non-polar standards for routine analysis and quality control. The results of this work show that the developed system is stable and reproducible and therefore appropriate for studies requiring the measurement of free concentrations and accurate quantification.
Topics: Water; Solid Phase Microextraction; Hydrophobic and Hydrophilic Interactions; Reference Standards; Quality Control
PubMed: 36546835
DOI: 10.1021/acs.analchem.2c02993 -
The AAPS Journal Mar 2016The importance of appropriate sample management in regulated bioanalysis is undeniable for clinical and non-clinical study support due to the fact that if the samples... (Review)
Review
The importance of appropriate sample management in regulated bioanalysis is undeniable for clinical and non-clinical study support due to the fact that if the samples are compromised at any stage prior to analysis, the study results may be affected. Health authority regulations do not contain specific guidance on sample management; therefore, as part of the Global Bioanalysis Consortium (GBC), the A5 team was established to discuss sample management requirements and to put forward recommendations. The recommendations from the team concern the entire life span of the sample and include the following: 1. Sampling procedures should be described in the protocol or within the laboratory manual. This information should include the volume of the sample to be collected, the required anticoagulant, light sensitivity, collection and storage containers, and labeling with a unique identifier. 2. The correct procedures for processing and then storing the samples after collection at the clinical/non-clinical testing site and during shipment are also very important to ensure the analyte(s) stability and should be documented. 3. Chain of custody for the samples must be maintained throughout the complete life span of each sample. This is typically maintained via paper and electronic data systems, including Laboratory Information Management Systems (LIMS) where available. 4. Pre- and post-analysis storage location and conditions must also be clearly defined at the analytical laboratory. The storage temperature of the samples must be traceable and controlled by monitoring and warning alerts. The team suggests moving away from using temperatures and to adopt standard terminology of "room temperature," "refrigerator," "freezer," and "ultra-freezer" that have defined and industry-wide accepted temperature ranges. 5. At the end of the study, documentation of the samples' disposal is required.
Topics: Biological Specimen Banks; Congresses as Topic; Humans; Internationality; Medical Laboratory Science; Specimen Handling
PubMed: 26821803
DOI: 10.1208/s12248-016-9869-2 -
Analytical and Bioanalytical Chemistry Aug 2022A common method to quantify chronic stress is the analysis of stress markers in keratinized matrices such as hair or nail. In this study, we aimed to validate a...
A common method to quantify chronic stress is the analysis of stress markers in keratinized matrices such as hair or nail. In this study, we aimed to validate a sensitive liquid chromatography-tandem mass spectrometry (LC-MS/MS) method for the combined quantification of steroid hormones and endocannabinoids (eCBs) in the keratinized matrix nail. Furthermore, we aimed to investigate the suitability of the nail matrix for the detection of these stress markers in a pilot study. An LC-MS/MS method was used for the simultaneous identification and quantification of four eCBs (2-arachidonoylglycerol (2-AG), anandamide (AEA), oleoylethanolamide (OEA), palmitoylethanolamide (PEA)) and five steroid hormones (cortisol, cortisone, androstenedione, progesterone, testosterone) in human nails using a surrogate analyte method for each analyte. The method was validated in terms of selectivity, response factor, linearity, limit of quantification (LOQ), precision, accuracy, matrix effect, recovery, robustness, and autosampler stability. Nail samples were extracted for 1 h with methanol following a clean-up with a fully automated supported liquid extraction (SLE). The influence of nail weight on the quantification was investigated by using 0.5-20 mg of nail sample. As a proof of concept, nail samples (N = 57) were analyzed from a cohort representing newborns (1 month old), children (between 1 and 10 years), and adults (up to 43 years). It could be shown that the established workflow using a 1 hour extraction and clean-up by SLE was very robust and resulted in a short sample preparation time. The LC-MS/MS method was successfully validated. Matrix effects with ion enhancement occurred mainly for 2-AG. Sample weights below 5 mg showed variations in quantification for some analytes. Certain analytes such as PEA and progesterone could be accurately quantified at a sample weight lower than 5 mg. This is the first study where steroids and eCBs could be simultaneously detected and quantified in infant and adult nails. These results show that nails may serve as an alternative keratinized matrix (compared to hair) for the retrospective monitoring of cumulative eCB and steroid hormone levels. The combined assessment of eCBs and steroids from nails could provide a new approach to gain new insights into stress exposure in newborns and adults.
Topics: Adult; Child; Humans; Infant; Infant, Newborn; Chromatography, Liquid; Endocannabinoids; Hydrocortisone; Nails; Pilot Projects; Progesterone; Retrospective Studies; Steroids; Tandem Mass Spectrometry
PubMed: 35781588
DOI: 10.1007/s00216-022-04189-y -
Biochemia Medica 2014Improper design or use of blood collection devices can adversely affect the accuracy of laboratory test results. Vascular access devices, such as catheters and needles,... (Review)
Review
Improper design or use of blood collection devices can adversely affect the accuracy of laboratory test results. Vascular access devices, such as catheters and needles, exert shear forces during blood flow, which creates a predisposition to cell lysis. Components from blood collection tubes, such as stoppers, lubricants, surfactants, and separator gels, can leach into specimens and/or adsorb analytes from a specimen; special tube additives may also alter analyte stability. Because of these interactions with blood specimens, blood collection devices are a potential source of pre-analytical error in laboratory testing. Accurate laboratory testing requires an understanding of the complex interactions between collection devices and blood specimens. Manufacturers, vendors, and clinical laboratorians must consider the pre-analytical challenges in laboratory testing. Although other authors have described the effects of endogenous substances on clinical assay results, the effects/impact of blood collection tube additives and components have not been well systematically described or explained. This review aims to identify and describe blood collection tube additives and their components and the strategies used to minimize their effects on clinical chemistry assays.
Topics: Blood Specimen Collection; Clinical Laboratory Techniques; Humans; Specimen Handling; Surface-Active Agents
PubMed: 24627713
DOI: 10.11613/BM.2014.006 -
The Analyst May 2017The ability to separate analytes with increasingly similar properties drives the field of separation science. One way to achieve such separations is using trapping and...
The ability to separate analytes with increasingly similar properties drives the field of separation science. One way to achieve such separations is using trapping and streaming dielectrophoresis (DEP), which directly exploits the subtle differences in the electrophysical properties of analytes. The non-uniform fields necessary for DEP can be formed using various insulator shapes in microchannels. Current insulator shapes include triangles, diamonds, circles, and rectangles. However, all of these insulators pose problems for trapping, streaming, and sorting (deflection) as the induced fields/gradients are not behaviorally consistent across the lateral dimension. This leads to analytes experiencing different forces depending on their pathline in the microchannel and result in low resolution separations. Based on an iterative process that explored approximately 40 different insulator shapes, a design was chosen that indicated improved particle streamlines, better trapping efficiency, and consistent electrical environments across the lateral dimension. The design was assessed by simulations where the electric field, gradient of the electric field squared, and the ratio of the two were plotted. The improved design includes a unique new multi-length scale element. The multi-length scale structure streamlines the analyte(s) and improves homogeneity in the lateral dimension, while still achieving high gradients necessary for analyte separation using DEP. The design is calculated to keep analytes on the centerline which should improve resolution, and eliminate extraneous trapping zones. Behaviors consistent with the features of the simulations were observed in proof of principle experiments using representative test probes.
PubMed: 28394391
DOI: 10.1039/c6an02509a -
Chemosphere Apr 2022Plastic particle pollution has been shown to be almost completely ubiquitous within our surrounding environment. This ubiquity in combination with a variety of unique... (Review)
Review
Plastic particle pollution has been shown to be almost completely ubiquitous within our surrounding environment. This ubiquity in combination with a variety of unique properties (e.g. density, hydrophobicity, surface functionalization, particle shape and size, transition temperatures, and mechanical properties) and the ever-increasing levels of plastic production and use has begun to garner heightened levels of interest within the scientific community. However, as a result of these properties, plastic particles are often reported to be challenging to study in complex (i.e. real) environments. Therefore, this review aims to summarize research generated on multiple facets of the micro- and nanoplastics field; ranging from size and shape definitions to detection and characterization techniques to generating reference particles; in order to provide a more complete understanding of the current strategies for the analysis of plastic particles. This information is then used to provide generalized recommendations for researchers to consider as they attempt to study plastics in analytically complex environments; including method validation using reference particles obtained via the presented creation methods, encouraging efforts towards method standardization through the reporting of all technical details utilized in a study, and providing analytical pathway recommendations depending upon the exact knowledge desired and samples being studied.
Topics: Hydrophobic and Hydrophilic Interactions; Microplastics; Plastics; Water Pollutants, Chemical
PubMed: 35016963
DOI: 10.1016/j.chemosphere.2022.133514 -
EJIFCC Apr 2024A business intelligence (BI) tool in a laboratory workflow offers various benefits, including data consolidation, real-time monitoring, process optimization, cost... (Review)
Review
A business intelligence (BI) tool in a laboratory workflow offers various benefits, including data consolidation, real-time monitoring, process optimization, cost analysis, performance benchmarking (quality indicators), predictive analytics, compliance reporting, and decision support. These tools improve operational efficiency, quality control, inventory management, cost analysis, and clinical decision-making. This write up reveals the workflow process and implementation of BI in a private hospital laboratory. By identifying challenges and overcoming them, laboratories can utilize the power of BI and analytics solutions to accelerate healthcare performance, lower costs, and improve care quality. We used navify (Viewics) as a BI platform which relies on an infinity data warehouse for analytics and dashboards. We applied it for pre-analytic, analytic and post-analytic phases in laboratory. We conclude, digitalization is crucial for innovation and competitiveness, enhancing productivity, efficiency, and flexibility in future laboratories.
PubMed: 38706734
DOI: No ID Found -
ACS Omega Jul 2022The use of immunodetection assays including the widely used enzyme-linked immunosorbent assay (ELISA) in applications such as point-of-care detection is often limited by...
The use of immunodetection assays including the widely used enzyme-linked immunosorbent assay (ELISA) in applications such as point-of-care detection is often limited by the need for protein immobilization and multiple binding and washing steps. Here, we describe an experimental and analytical framework for the development of simple and modular "mix-and-read" enzymatic complementation assays based on split luciferase that enable sensitive detection and quantification of analytes in solution. In this assay, two engineered protein binders targeting nonoverlapping epitopes on the target analyte were each fused to nonactive fragments of luciferase to create biosensor probes. Binding proteins to two model targets, lysozyme and Sso6904, were isolated from a combinatorial library of Sso7d mutants using yeast surface display. In the presence of the analyte, probes were brought into close proximity, reconstituting enzymatic activity of luciferase and enabling detection of low picomolar concentrations of the analyte by chemiluminescence. Subsequently, we constructed an equilibrium binding model that relates binding affinities of the binding proteins for the target, assay parameters such as the concentrations of probes used, and assay performance (limit of detection and concentration range over which the target can be quantified). Overall, our experimental and analytical framework provides the foundation for the development of split luciferase assays for detection and quantification of various targets.
PubMed: 35874239
DOI: 10.1021/acsomega.2c02319 -
Turkish Journal of Pharmaceutical... Nov 2023Chemical neurotransmission, managed by neurotransmitters, has a crucial role in brain processes such as fear, memory, learning, and pain, or neuropathology such as...
OBJECTIVES
Chemical neurotransmission, managed by neurotransmitters, has a crucial role in brain processes such as fear, memory, learning, and pain, or neuropathology such as schizophrenia, epilepsy, anxiety/depression, and Parkinson's disease. The measurement of these compounds is used to elucidate the disease mechanisms and evaluate the outcomes of therapeutic interventions. However, this can be quite difficult because of various matrix effects and the problems of chromatographic separation of analysts. In the current study; for the first time, an optimized and fully validated high-performance liquid chromatography-electrochemical detection (HPLC-EC) method according to Food and Drug Administration and European Medicines Agency Bioanalytical Validation Guidance was developed for the simultaneous analysis of nine neurotransmitter compounds, namely dopamine, homovanilic acid, vanilmandelic acid, serotonin (SER), 5-hydroxyindole-3-acetic acid, 4-hydroxy-3-methoxyphenylglycol, norepinephrine, 3,4 dihydroxyphenylacetic acid, and 3-methoxytyramine and simultaneously determined in rat brain samples.
MATERIALS AND METHODS
Separation was achieved with 150 mm x 4.6 mm, 2.6 μm Kinetex F5 (Phenomenex, USA) column isocratically, and analysis was carried out by HPLC equipped with a DECADE II EC detector.
RESULTS
The method exhibited good selectivity, and the correlation coefficient values for each analyte's calibration curves were > 0.99. The detection and quantification limits ranged from 0.01 to 0.03 ng/mL and 3.04 to 9.13 ng/mL, respectively. The stability of the analyses and method robustness were also examined in detail in the study, and the obtained results are presented statistically.
CONCLUSION
The developed and fully validated method has been successfully applied to actual rat brain samples, and important results have been obtained. In the rat brain sample analysis, the lowest number of SER and the highest amount of noradrenaline were found.
PubMed: 37933822
DOI: 10.4274/tjps.galenos.2022.06606