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At least 307 records · Page 17Linked to original sources
PubMedDate not supplied

Effects of feeding and body weight loss on the 1H-NMR-based urine metabolic profiles of male Wistar Han rats: implications for biomarker discovery.

For almost two decades, 1H-NMR spectroscopy has been used as an 'open' system to study the temporal changes in the biochemical composition of biofluids, including urine, in response to adverse toxic events. Many of these in vivo studies have reported changes in individual metabolites and patterns of metabolites that correlated with toxicological changes. However, many of the proposed novel biomarkers are common to a number of different types of toxicity. These may therefore reflect non-specific effects of toxicity, such as weight loss, rather than a specific pathology. A study was carried out to investigate the non-specific effects on urinary metabolite profiles by administering four hepatotoxic compounds, as a single dose, to rats at two dose levels: hydrazine hydrate (0.06 or 0.08 g kg (1)), 1,2-dimethylhydrazine (0.1 or 0.3 g kg (-1)), alpha-napthylisothiocyanate (0.1 or 0.15 g kg(-1)) and carbon tetrachloride (1.58 or 3.16 g kg(-1)). The study included weight-matched control animals along with those that were dosed, which were then 'pair-fed' with the treated animals so they achieved a similar weight loss. The urinary metabolite profiles were investigated over time using 1H-NMR spectroscopy and compared with the pathology from the same animals. The temporal changes were analysed statistically using multivariate statistical data analysis including principal component analysis, partial least squares, parallel factor analysis and Fisher's criteria. A number of metabolites associated with energy metabolism or which are partially dietary in origin, such as creatine, creatinine, tricarboxylic acid (TCA) cycle intermediates, phenylacetylglycine, fumarate, glucose, taurine, fatty acids and N-methylnicotinamide, showed altered levels in the urine of treated and pair-fed animals. Many of these changes correlated well with weight loss. Interestingly, there was no increase in ketone bodies (acetate and beta-hydroxybutyrate), which might be expected if energy metabolism was switched from glycolysis to fatty acid beta-oxidation. In some instances, the metabolites that changed were considered to be non-specific markers of toxicity, but were also identified as markers of a specific type of toxicity. For example, taurine was raised significantly in carbon tetrachloride-treated animals but reduced in the pair-fed group. However, raised urinary bile acid levels were only seen after alpha-napthylisothiocyanate treatment. The methodology, statistical analysis used and the data generated will help improve the identification of specific markers or patterns of urinary markers of specific toxic effects.

1,2-Dimethylhydrazine↗
PubMedDate not supplied

Application of proteomic strategies to the identification of urinary biomarkers for prostate cancer: a review.

In the post-genomic era, genes and proteins are now studied on a more comprehensive scale. Studying disease processes at only the genetic or transcriptomic level will give an incomplete amount of information. A proteomic approach potentially allows for a more global overview of how disease processes affect the proteins present in cells, tissues and organisms. The challenge arises in determining which proteins are affected in specific diseases and establishing which of these changes are unique to a particular disease. Existing and emerging proteomic technologies allow for high throughput analysis of proteins in a variety of sample types. Prostate cancer is a significant male health problem in the Western world. It is widely accepted that more specific prognostic and diagnostic markers of prostate cancer are urgently required. The present paper suggests that urine may be an attractive biofluid in which to pursue the identification of novel biomarkers of prostate cancer. This review introduces some proteomic techniques including mass spectrometry and the newer, quantitative proteomic strategies. It focuses on the potential application of these platforms to novel urinary biomarker identification in prostate malignancy. It also includes a synopsis of the current literature on urinary proteomics.

Biomarkers, Tumor↗
PubMed2026

The Human Breath Volatilome Responds to Exercise and Recovery: An Untargeted Profiling Study.

Exercise induces metabolic and physiological changes across multiple organs. These changes have been studied via several human biofluids, including urine and blood; however, they remain mainly underexplored in exhaled breath. In this exploratory pilot study, we performed untargeted profiling of breath volatile compounds (VCs) to investigate how exercise and recovery influence breath chemical composition. Breath samples were collected from 71 university athletes from three sporting disciplines. Across 143 breath samples, a total of 1,204 unique breath VCs were detected. There were distinct volatilomic responses to physical activity and recovery, regardless of the athlete's sport. Comparison of paired samples using volcano analysis collected before and during exercise identified 80 breath VCs that significantly increased and 182 that significantly decreased. Similarly, a comparison of samples collected before and after exercise identified 11 compounds that decreased significantly. These findings demonstrate that exercise induces measurable changes in the breath volatilome. However, due to the lack of standardized exercise intensity measures and physiological monitoring, the results should be considered exploratory and interpreted cautiously within the field of exercise science.

Exhaled breath analysis↗
PubMed2006

Unravelling the proteome of formalin-fixed paraffin-embedded tissue.

Biofluid detectable biomarkers that originate at the site of diseased tissues would be advantageous, in that, they may provide mechanistic information concerning the manifestation and progression of the disease. Unfortunately, tissue biopsies are precious samples that can generally be acquired in small amounts due to the invasive nature of the sample collection. One of the foundations of pathological diagnosis for decades has been from formalin-fixed paraffin-embedded (FFPE) tissues, of which a vast archive exists worldwide. These tissues have also been widely used for immunohistochemistry and in situ hybridization studies examining for expression of specific proteins or transcripts. Unfortunately, the ability to analyse FFPE tissues using mass spectrometry (MS) has been essentially non-existent until recently. In this review, methods that allow the extraction of peptides from FFPE tissues and their proteomic analysis using MS are described. The ability to identify the proteins extracted from FFPE tissues allows comparative analyses that enable the potential discovery of novel biomarkers at the site of the diseased tissue.

Animals↗
PubMed2026

Machine learning approaches for cancer prognosis and diagnosis via non-coding RNA: a comprehensive review.

Non-coding RNAs (ncRNAs), once considered genomic dark matter, are now established as key regulators of gene expression with widespread roles in cellular homeostasis and disease. In cancer, ncRNA expression is frequently and systematically dysregulated, and many of these molecules circulate in stable, protected form within biofluids, offering a compelling basis for non-invasive or minimally invasive diagnostic strategies. However, their clinical translation remains substantially hindered to date due to biological complexity, technical noise, and high dimensionality inherent to ncRNA expression datasets. In this context, machine learning (ML) has emerged as a powerful analytical tool to address these challenges, enabling the identification of subtle, reproducible ncRNA signatures predictive of diverse malignancies. This review critically evaluates ML-driven frameworks for cancer diagnosis and prognosis across four ncRNA subclasses, namely miRNAs, lncRNAs, circRNAs, and piRNAs, while also acknowledging the biophysical and thermodynamic models that reinforce ncRNA bioinformatics. Despite substantial methodological progress in ML-based cancer diagnosis and prognosis, key challenges persist, including tumor biological heterogeneity, limited multicenter validation, and the lack of widely adopted standardized protocols for preprocessing, normalization, and reporting workflows. Furthermore, many current ML models lack interpretability in biological or clinical context, constraining their translational utility. By synthesizing recent advances and identifying unresolved barriers, this review charts a roadmap for developing a robust, clinically actionable ncRNA biomarker platform for cancer detection. With global cancer incidence projected to exceed 35 million annual cases by 2050, validated ncRNA-ML-driven frameworks hold potential to revolutionize early-stage detection and personalized therapeutic strategies, thereby reducing the escalating socio-economic burden of cancer worldwide.

Humans↗
PubMedDate not supplied

Correlation of saliva cocaine levels with plasma levels and with pharmacologic effects after intravenous cocaine administration in human subjects.

The behavioral and physiologic effects of single, intravenous bolus doses of cocaine in 5 male human subjects were correlated with cocaine levels in saliva and blood. All measures were performed under double-blind conditions. Two test doses of cocaine (15 mg and 40 mg) and one placebo test dose were administered to each subject in a random, cross-over design. Each test day was separated by a minimum of 48 h. Cocaine levels in saliva and blood significantly (p less than or equal to 0.05) correlated with responses on self-rating scales for drug sensation (Feel Drug scale), psychotomimetic effects (LSD scale), and feelings of rush (Rush scale). Significant (p less than or equal to 0.01) correlations also were obtained with cocaine biofluid levels and pulse rate. The close relationship observed between cocaine saliva levels and cocaine-induced behavior and physiologic effects presents the opportunity for development of a new noninvasive method for detection of current cocaine use.

Adult↗
PubMedDate not supplied

Prolonged occurrence of cocaine in human saliva and urine after chronic use.

Cocaine was detected by immunoassay in saliva and urine of chronic cocaine addicts for 5-10 days during abstinence. Confirmation by a less sensitive but highly specific GC/MS assay of unmetabolized cocaine was successful in saliva through the first 24 h of collection and for the initial 4-5 days in urine. Cocaine saliva concentrations and subject scores for cocaine craving and depression declined during this time and correlated significantly. The presence of unmetabolized cocaine in these biofluids long after the last drug administration suggests that multiple dosing and high exposure to cocaine in man leads to accumulation in deep body compartments and subsequent slow release back into circulation and eventual excretion. The prolonged presence of cocaine in saliva and urine may have implications in testing for cocaine use and in treatment of cocaine withdrawal.

Adult↗
PubMedDate not supplied

Limits of linearity and detection for some drugs of abuse.

The limits of linearity (LOL) and detection (LOD) are important factors in establishing the reliability of an analytical procedure for accurately assaying drug concentrations in urine specimens. Multiple analyses of analyte over an extended range of concentrations provide a measure of the ability of the analytical procedure to correctly identify known quantities of drug in a biofluid matrix. Each of the seven drugs of abuse gives linear analytical responses from concentrations at or near their LOD to concentrations several-fold higher than those generally encountered in the drug screening laboratory. The upper LOL exceeds the Department of Navy (DON) cutoff values by factors of approximately 2 to 160. The LOD varies from 0.4 to 5.0% of the DON cutoff value for each drug. The limit of quantitation (LOQ) is calculated as the LOD + 7 SD. The range for LOL is greater for drugs analyzed with deuterated internal standards compared with those using conventional internal standards. For THC acid, cocaine, PCP, and morphine, LOLs are 8 to 160-fold greater than the defined cutoff concentrations. For the other drugs, the LOL's are only 2 to 4-fold greater than the defined cutoff concentrations.

Gas Chromatography-Mass Spectrometry↗
PubMed2000

Analysis of underivatized amphetamines and related phenethylamines with high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry.

Amphetamine, methamphetamine, illicit designer phenethylamines (MDA, MDEA, MDMA, MBDB, and BDMPEA), and other phenethylamines (benzyl-1-phenylethylamine, cathinone, ephedrine, fenfluramine, norfenfluramine, phentermine, 1-phenylethylamine, phenylpropanolamine, and propylhexedrine) were extracted from serum using a solid-phase extraction procedure. The extracts were examined with high-performance liquid chromatography-atmospheric pressure chemical ionization mass spectrometry (LC-APCI-MS). The drugs were separated on ODS column in acetonitrile/50 mM ammonium formate buffer (pH 3.0) (25:75) as a mobile phase. Full-scan mass spectra of drugs examined by means of APCI with collision-induced dissociation showed protonated molecular ions and fragments typical for particular drugs. LC-APCI-MS allowed an unequivocal differentiation of all drugs involved. The quantitation was performed using selected ion monitoring of protonated molecular ions and fragments of drugs involved and their deuterated analogues. The limits of detection ranged from 1 to 5 microg/L serum, and the recoveries ranged from 58 to 96%. A linear response was observed for all drugs in the range from 5 to 500 microg/L. The method was applied for routine determination of amphetamine, MDMA, MDA, and MDEA in one run. Solid-phase extraction used assured simultaneous isolation of various groups of basic drugs of forensic interest (opiates, cocaines, phenethylamines, and benzodiazepines) from biofluids.

Amphetamines↗
PubMed2004

Identification and quantitation of six non-depolarizing neuromuscular blocking agents by LC-MS in biological fluids.

A liquid chromatography-electrospray-mass spectrometry technique for the screening and determination of five non-depolarizing neuromuscular blocking agents (NDBAs), atracurium and its product of degradation/metabolite laudanosine, rocuronium, pancuronium, vecuronium, and mivacurium has been developed using ambenonium as the internal standard (I.S.). Samples were acidified upon reception by adding 20 micro L 0.5M H(2)SO(4) to 500 micro L of biofluid. Sample preparation consisted of simple blood purification and/or protein precipitation using 1 mL I.S. in acetonitrile. Chromatographic separation was carried out on an X-TERRA trade mark column along with a gradient of acetonitrile in 2mM ammonium formate (pH 3). Detection was carried out in the positive selected ion monitoring mode, targeting one quantitation ion and one confirmation ion per compound. The limit of quantitation was 2.5 micro g/L for mivacurium and laudanosine, 5 micro g/L for rocuronium and pancuronium and 10 micro g/L for atracurium and vecuronium in serum (i.e., in the range of, or less than, therapeutic levels). The technique was found to be linear between the respective LOQs and 2000 micro g/L, with correlation coefficients higher than 0.999 in all matrices. Intra- and interday precision and accuracy in serum fulfilled the international criteria. This method was employed for the investigation of a case of suicide by infusion of drugs. Laudanosine, the metabolite or degradation product of both atracurium and cisatracurium, and rocuronium were found in urine and whole blood, at supratherapeutic concentrations in the latter (rocuronium: 1.53 and 2.18 mg/L, laudanosine: 8.86 and 0.31 mg/L, respectively), and even therapeutic concentrations would have been lethal in the absence of respiratory assistance.

Chromatography, High Pressure Liquid↗
PubMed2007

HMDB: the Human Metabolome Database.

The Human Metabolome Database (HMDB) is currently the most complete and comprehensive curated collection of human metabolite and human metabolism data in the world. It contains records for more than 2180 endogenous metabolites with information gathered from thousands of books, journal articles and electronic databases. In addition to its comprehensive literature-derived data, the HMDB also contains an extensive collection of experimental metabolite concentration data compiled from hundreds of mass spectra (MS) and Nuclear Magnetic resonance (NMR) metabolomic analyses performed on urine, blood and cerebrospinal fluid samples. This is further supplemented with thousands of NMR and MS spectra collected on purified, reference metabolites. Each metabolite entry in the HMDB contains an average of 90 separate data fields including a comprehensive compound description, names and synonyms, structural information, physico-chemical data, reference NMR and MS spectra, biofluid concentrations, disease associations, pathway information, enzyme data, gene sequence data, SNP and mutation data as well as extensive links to images, references and other public databases. Extensive searching, relational querying and data browsing tools are also provided. The HMDB is designed to address the broad needs of biochemists, clinical chemists, physicians, medical geneticists, nutritionists and members of the metabolomics community. The HMDB is available at: www.hmdb.ca.

Databases, Factual↗
PubMed1995

Analytic requirements for immunosuppressive drugs in clinical trials.

Essential to the evaluation of (1) the pharmacokinetics, (2) concentration-effect relationships, and (3) the application of therapeutic drug monitoring, during new immunosuppressive drug clinical trials, is the development of validated analytical methodology for the measurement of pharmacologically active drug and metabolites in biofluids and tissues. The characteristics of analytical methodology developed for cyclosporines A and G, FK-506, mycophenolate mofetil, and rapamycin during clinical trials will be described. The advantages of establishing validated analytical methodology as early as possible during clinical trials include: (a) early identification of metabolites and their quantitative and pharmacological significance; (b) early development of interpretable PK and PK-PD data; (c) accrual of experience that will be directly useful in patient monitoring after drug approval; (d) optimization of analysis conditions; and (e) early development of reference methodology for therapeutic drug monitoring tests. A suggested set of performance criteria for drug analysis during clinical trials and thereafter will be presented.

Clinical Trials as Topic↗
PubMed1996

Nuclear magnetic resonance and high-performance liquid chromatography-nuclear magnetic resonance studies on the toxicity and metabolism of ifosfamide.

A combination of high-resolution nuclear magnetic resonance (NMR) and high-performance liquid chromatography (HPLC)-NMR spectroscopic methods has been used to analyse urine from humans and rats treated with the anticancer drug ifosfamide. It was possible to detect a range of abnormal endogenous metabolites in urine after ifosfamide administration to human subjects undergoing cancer therapy and to relate the metabolic perturbations to the nephrotoxic effects of the drug. Changes observed by 1H NMR included increases in levels of urinary glucose, glycine, alanine, histidine, lactate, acetate, succinate, and trimethylamine-N-oxide and decreases in the levels of hippurate and citrate. Additional evidence was gained that ifosfamide-induced nephrotoxicity might be related to the level of oxidation of the coadministered drug mesna. By using both directly coupled continuous-flow 31P HPLC-NMR spectroscopy to determine the retention times of the phosphorus-containing metabolites and, subsequently, stop-flow 1H HPLC-NMR of the urine, it was possible to isolate and identify on-line the metabolites ifosfamide mustard, 4-hydroxy-ifosfamide, 2-dechloroethylifosfamide, and the parent compound itself. These studies illustrate the potential of combining 1H NMR spectroscopy of biofluids and HPLC-NMR spectroscopy for the investigation of drug metabolism and toxicity in humans and animals.

Animals↗
PubMed1998

Advances in separation science relating to clinical nutrition.

Advances in separation science are leading to more sensitive and more specific analysis of the complex mixtures of metabolites, vitamins and nutrients found in biofluids. Recent developments include capillary electrokinetic separations such as capillary electrophoresis, and the linking of separation methods to new forms of mass spectrometry.

Body Fluids↗
PubMed2005

Biomarkers for neurodegenerative diseases.

PURPOSE OF REVIEW: A major goal of current clinical research in neurodegenerative diseases is to improve early detection of disease and presymptomatic detection of neuronal dysfunction. We also need better tools to assess disease progression in this group of disorders. Currently, many potential disease-modifying therapies are being developed and evaluated at the preclinical stage, and will lead to clinical trials in the near future for which biomarkers are urgently needed. This review summarizes the field of biomarker research in the major neurodegenerative diseases. RECENT FINDINGS: Many different approaches are being undertaken to identify biomarkers and include imaging, neurophysiological and cognitive testing in addition to newer technologies such as biochemical, proteomic, metabanomic and gene array profiling of tissue and biofluids from patients. Key recent findings in each of these areas are discussed. SUMMARY: The ideal biomarker needs to be easy to quantify and measure, reproducible, not subject to wide variation in the general population and unaffected by co-morbid factors. For evaluation of therapies the biomarker needs to change linearly with disease progression and closely correlate with established clinico-pathological parameters of the disease. It is unlikely that any one biomarker will fulfil all these characteristics, and it is likely that more than one biomarker will be needed for early diagnosis and similarly for evaluation of disease progression for therapeutic trials. For example, the combination of more detailed clinical assessments encompassing specific cognitive and neurophysiological testing, in addition to imaging, biochemical and genomic profiling, is likely to be needed.

Animals↗
PubMed2004

Metabolic profiles to define the genome: can we hear the phenotypes?

There is an increased reliance on genetically modified organisms as a functional genomic tool to elucidate the role of genes and their protein products. Despite this, many models do not express the expected phenotype thought to be associated with the gene or protein. There is thus an increased need to further define the phenotype resultant from a genetic modification to understand how the transcriptional or proteomic network may conspire to alter the expected phenotype. This is best typified by the description of the silent phenotype in genetic manipulations of yeast. High-resolution proton nuclear magnetic resonance ((1)H NMR) spectroscopy provides an ideal mechanism for the profiling of metabolites within biofluids, tissue extracts or, with recent advances, intact tissues. These metabolic datasets can be readily mined using a range of pattern recognition techniques, including hierarchical cluster analysis, principal components analysis, partial least squares and neural networks, with the combined approach being termed metabolomics. This review describes the application of NMR-based metabolomics or metabonomics to genetic and chemical interventions in a number of different species, demonstrating the versatility of such an approach, as well as suggesting how it may be integrated with other "omic" technologies.

Animals↗
PubMed2005

Measurements of the bulk and interfacial velocity profiles in oscillating Newtonian and Maxwellian fluids.

We present the dynamic velocity profiles of a Newtonian fluid (glycerol) and a viscoelastic Maxwell fluid (CPyCl-NaSal in water) driven by an oscillating pressure gradient in a vertical cylindrical pipe. The frequency range explored has been chosen to include the first three resonance peaks of the dynamic permeability of the viscoelastic-fluid--pipe system. Three different optical measurement techniques have been employed. Laser Doppler anemometry has been used to measure the magnitude of the velocity at the center of the liquid column. Particle image velocimetry and optical deflectometry are used to determine the velocity profiles at the bulk of the liquid column and at the liquid-air interface respectively. The velocity measurements in the bulk are in good agreement with the theoretical predictions of a linear theory. The results, however, show dramatic differences in the dynamic behavior of Newtonian and viscoelastic fluids, and demonstrate the importance of resonance phenomena in viscoelastic fluid flows, biofluids in particular, in confined geometries.

Journal Article↗
PubMed2006

Performance evaluation of a valveless micropump driven by a ring-type piezoelectric actuator.

Presented in this paper is the study of the performance evaluation of a valveless micropump driven by a ring-type piezoelectric actuator. The application of this micropump is to circulate fuel inside a miniaturized direct methanol fuel cell (DMFC) power system. A theoretical model based on the theory of plates and shells is established to estimate the deflection and the volume change of this micropump without liquid loading. Both finite-element method (FEM) and experimental method are applied to verify this model. Using this model, the optimal design parameters such as the dimensions and the mechanical properties of the micropump can be obtained. Furthermore, various system parameters that will affect the performance of the micropump system with liquid loading are identified and analyzed experimentally. It is expected that this study will provide some vital information for many micropump applications such as fuel delivery in fuel cells, ink jet printers, and biofluidics.

Computer-Aided Design↗