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PubMed1985

Retrieval of analytical data and substance identification in systematic toxicological analysis by the mean list length approach.

Chromatographic techniques are basic tools in systematic toxicological analysis. Extensive data bases with retention parameters of known drugs to aid in the identification of substances found are available or in preparation. For a search in such a data base the computer is indispenable. The commonly used window search has some disadvantages which can be overcome by a search based on the statistical concept, the mean list length. The latter retrieval system gives for each candidate in the identification process a probability value. It is shown that these probability values are highly influenced by the reproducibility of the retention parameters of the analytical systems used. Explanations for these phenomena are given.

Chromatography, Gas↗
PubMed2005

Use of a systematic risk analysis method to improve safety in the production of paediatric parenteral nutrition solutions.

BACKGROUND: Until recently, the preparation of paediatric parenteral nutrition formulations in our institution included re-transcription and manual compounding of the mixture. Although no significant clinical problems have occurred, re-engineering of this high risk activity was undertaken to improve its safety. Several changes have been implemented including new prescription software, direct recording on a server, automatic printing of the labels, and creation of a file used to pilot a BAXA MM 12 automatic compounder. The objectives of this study were to compare the risks associated with the old and new processes, to quantify the improved safety with the new process, and to identify the major residual risks. METHODS: A failure modes, effects, and criticality analysis (FMECA) was performed by a multidisciplinary team. A cause-effect diagram was built, the failure modes were defined, and the criticality index (CI) was determined for each of them on the basis of the likelihood of occurrence, the severity of the potential effect, and the detection probability. The CIs for each failure mode were compared for the old and new processes and the risk reduction was quantified. RESULTS: The sum of the CIs of all 18 identified failure modes was 3415 for the old process and 1397 for the new (reduction of 59%). The new process reduced the CIs of the different failure modes by a mean factor of 7. The CI was smaller with the new process for 15 failure modes, unchanged for two, and slightly increased for one. The greatest reduction (by a factor of 36) concerned re-transcription errors, followed by readability problems (by a factor of 30) and chemical cross contamination (by a factor of 10). The most critical steps in the new process were labelling mistakes (CI 315, maximum 810), failure to detect a dosage or product mistake (CI 288), failure to detect a typing error during the prescription (CI 175), and microbial contamination (CI 126). CONCLUSIONS: Modification of the process resulted in a significant risk reduction as shown by risk analysis. Residual failure opportunities were also quantified, allowing additional actions to be taken to reduce the risk of labelling mistakes. This study illustrates the usefulness of prospective risk analysis methods in healthcare processes. More systematic use of risk analysis is needed to guide continuous safety improvement of high risk activities.

Child↗
PubMed2003

Is capillary electrophoresis a method of choice for systematic toxicological analysis?

This review presents an overview of current research on the use of capillary electrophoretic techniques for the analysis of drugs in biological matrices. The discussion focuses on the applicability of the methods for the identification of unknown toxic compounds, which is defined as systematic toxicological analysis (STA). The aim is to establish whether or not capillary electrophoresis (CE), in one or more of its separation modes, is a method of choice in systematic toxicological analysis. To answer this question, various aspects are discussed, including sample work-up, separation modes, detection techniques, electrophoretic concentration, and identification by database retrieval. Several ways to improve the poor reproducibility and sensitivity are discussed. This leads to the conclusion that CE can be comparable to HPLC in those respects, while it is more favorable in speed, efficiency, and cost. Thus, we conclude that CE is a method of choice for STA, keeping in mind that every method has its limitations and that a combination of several non-correlated methods is always required for the identification of unknown compounds.

Chromatography, High Pressure Liquid↗
PubMed2002

A DNA repair system specific for thermophilic Archaea and bacteria predicted by genomic context analysis.

During a systematic analysis of conserved gene context in prokaryotic genomes, a previously undetected, complex, partially conserved neighborhood consisting of more than 20 genes was discovered in most Archaea (with the exception of Thermoplasma acidophilum and Halobacterium NRC-1) and some bacteria, including the hyperthermophiles Thermotoga maritima and Aquifex aeolicus. The gene composition and gene order in this neighborhood vary greatly between species, but all versions have a stable, conserved core that consists of five genes. One of the core genes encodes a predicted DNA helicase, often fused to a predicted HD-superfamily hydrolase, and another encodes a RecB family exonuclease; three core genes remain uncharacterized, but one of these might encode a nuclease of a new family. Two more genes that belong to this neighborhood and are present in most of the genomes in which the neighborhood was detected encode, respectively, a predicted HD-superfamily hydrolase (possibly a nuclease) of a distinct family and a predicted, novel DNA polymerase. Another characteristic feature of this neighborhood is the expansion of a superfamily of paralogous, uncharacterized proteins, which are encoded by at least 20-30% of the genes in the neighborhood. The functional features of the proteins encoded in this neighborhood suggest that they comprise a previously undetected DNA repair system, which, to our knowledge, is the first repair system largely specific for thermophiles to be identified. This hypothetical repair system might be functionally analogous to the bacterial-eukaryotic system of translesion, mutagenic repair whose central components are DNA polymerases of the UmuC-DinB-Rad30-Rev1 superfamily, which typically are missing in thermophiles.

Amino Acid Sequence↗
PubMed2005

Discordant 16S and 23S rRNA gene phylogenies for the genus Helicobacter: implications for phylogenetic inference and systematics.

Analysis of 16S rRNA gene sequences has become the primary method for determining prokaryotic phylogeny. Phylogeny is currently the basis for prokaryotic systematics. Therefore, the validity of 16S rRNA gene-based phylogenetic analyses is of fundamental importance for prokaryotic systematics. Discrepancies between 16S rRNA gene analyses and DNA-DNA hybridization and phenotypic analyses have been noted in the genus Helicobacter. To clarify these discrepancies, we sequenced the 23S rRNA genes for 55 helicobacter strains representing 41 taxa (>2,700 bases per sequence). Phylogenetic-tree construction using neighbor-joining, parsimony, and maximum likelihood methods for 23S rRNA gene sequence data yielded stable trees which were consistent with other phenotypic and genotypic methods. The 16S rRNA gene sequence-derived trees were discordant with the 23S rRNA gene trees and other data. Discrepant 16S rRNA gene sequence data for the helicobacters are consistent with the horizontal transfer of 16S rRNA gene fragments and the creation of mosaic molecules with loss of phylogenetic information. These results suggest that taxonomic decisions must be supported by other phylogenetically informative macromolecules, such as the 23S rRNA gene, when 16S rRNA gene-derived phylogeny is discordant with other credible phenotypic and genotypic methods. This study found Wolinella succinogenes to branch with the unsheathed-flagellum cluster of helicobacters by 23S rRNA gene analyses and whole-genome comparisons. This study also found intervening sequences (IVSs) in the 23S rRNA genes of strains of 12 Helicobacter species. IVSs were found in helices 10, 25, and 45, as well as between helices 31' and 27'. Simultaneous insertion of IVSs at three sites was found in H. mesocricetorum.

Base Sequence↗
PubMed2003

Standardization of protocols in cDNA microarray analysis.

Systematic variations can occur at various steps of a cDNA microarray experiment and affect the measurement of gene expression levels. Accepted standards integrated into every cDNA microarray analysis can assess these variabilities and aid the interpretation of cDNA microarray experiments from different sources. A universally applicable approach to evaluate parameters such as input and output ratios, signal linearity, hybridization specificity and consistency across an array, as well as normalization strategies, is the utilization of exogenous control genes as spike-in and negative controls. We suggest that the use of such control sets, together with a sufficient number of experimental repeats, in-depth statistical analysis and thorough data validation should be made mandatory for the publication of cDNA microarray data.

DNA, Complementary↗
PubMed2000

Intra- and interinstrument reproducibility of migration parameters in capillary electrophoresis for substance identification in systematic toxicological analysis.

The intra- and interinstrument reproducibilities of four capillary electrophoresis instruments were studied for identification purposes in systematic toxicological analysis (STA). A test set of 20 acidic test compounds and 5 reference compounds were analyzed for five days on each instrument using capillary zone electrophoresis (CZE) and micellar electrokinetic chromatography (MEKC). The buffers consisted of 90 mM borate set at pH 8.4 (CZE) and 20 mM phosphate and 50 mM sodium dodecyl sulfate set at pH 7.5 (MEKC). All analyses were carried out using fused silica capillaries at an electric field strength of 52.6 kV/m. The use of a reproducible identification parameter is very important in STA. To deal with the poor reproducibility of the migration time, we recently introduced the corrected effective mobility. In this study, we investigated the intra- and interinstrument reproducibility of the migration time, the effective mobility, and the corrected effective mobility. Large differences in intra-instrument reproducibility were found when the migration time was used. The calculation of the effective mobility and the corrected effective mobility diminished these differences and enhanced the interinstrument reproducibility roughly by a factor 3. For (corrected) effective mobilities, intrainstrument reproducibilities were between 0.8-2.6% and interinstrument reproducibilities were between 3.2-3.9%.

Chromatography, Micellar Electrokinetic Capillary↗
PubMed1995

Systematic toxicological analysis using HPLC/DAD.

A high-performance liquid chromatographic method with diode-array detection (HPLC/DAD) for systematic toxicological analysis of human blood or plasma samples is presented. After single-step liquid/liquid extraction at pH 9.5 using chloroform/2-propanol/n-heptane (60:14:26, v/v/v), the drugs elute isocratically from a NovaPak C18 (Waters) 4-micrometers column (300 mm x 3.9 mm, i.d.) at 30 degrees C, with methanol/tetrahydrofuran/pH 2.6 phosphate buffer (65:5:30, v/v/v) as the mobile phase (flow rate 0.8 mL/min). Full UV spectra from 200 to 400 nm (resolution 1.3 nm) are recorded on-line during the 20 min chromatographic run. Solute identification may be automatically performed by comparison of analytical data (retention times and UV spectra) with references of 311 pharmaceuticals, toxicants and drugs of abuse stored in a computerized library. The method is simple, rapid, relatively inexpensive and highly specific. The previously reported applications of HPLC/DAD technology to drug screening are reviewed, and the interests and limitations of the method are discussed in the light of this literature.

Chromatography, High Pressure Liquid↗
PubMed1997

Gas chromatography-mass spectrometry (GC-MS) and liquid chromatography-mass spectrometry (LC-MS) in toxicological analysis. Studies on the detection of clobenzorex and its metabolites within a systematic toxicological analysis procedure by GC-MS and by immunoassay and studies on the detection of alpha- and beta-amanitin in urine by atmospheric pressure ionization electrospray LC-MS.

GC-MS is the method of choice for toxicological analysis of toxicants volatile in GC while non-volatile and/or thermally labile toxicants need LC-MS for their determination. Studies are presented on the toxicological detection of the amphetamine-like anorectic clobenzorex in urine by GC-MS after acid hydrolysis, extraction and acetylation and by fluorescence polarization immunoassay (FPIA, TDx (meth)amphetamine II). After ingestion of 60 mg of clobenzorex, the parent compound and/or its metabolites could be detected by GC-MS for up to 84 h or by FPIA for up to 60 h. Since clobenzorex shows no cross-reactivity with the used immunoassay, the N-dealkylated metabolite amphetamine is responsible for the positive TDx results. The intake of clobenzorex instead of amphetamine can be differentiated by GC-MS detection of hydroxyclobenzorex which is detectable for at least as long as amphetamine. In addition, the described GC-MS procedure allows the simultaneous detection of most of the toxicologically relevant drugs. Furthermore, studies are described on the atmospheric pressure ionization electrospray LC-MS detection of alpha- and beta-amanitin, toxic peptides of amanita mushrooms, in urine after solid-phase extraction on RP-18 columns. Using the single ion monitoring mode with the ions m/z 919 and 920 the amanitins could be detected down to 10 ng/ml of urine which allows us to diagnose intoxications with amanita mushrooms.

Amanitins↗
PubMed1988

[Morphometric analysis of systematic colonic biopsies].

Using an automatic image analysis processor we measured the cellular density of the lamina propria and the mean glandular area on biopsies issued from 10 normal patients. The microscopic image was automatically digitalized and filtered. The operator manually traced the perimeter of the mucosal glands. The mean nucleus number for a 32,000 microns2 chorionic area is 177 +/- 24. The mean glandular area is 51.2 +/- 2.9%. This method is fast (2 min by field) and reproducible. It can be proposed for the study of inflammatory conditions on systematic colonic biopsy material.

Biopsy↗
PubMed1999

Systematic toxicological analysis procedures for acidic drugs and/or metabolites relevant to clinical and forensic toxicology and/or doping control.

This paper reviews systematic toxicological analysis (STA) procedures for acidic drugs and/or metabolites relevant to clinical and forensic toxicology or doping control using gas chromatography, gas chromatography-mass spectrometry, liquid chromatography, thin-layer chromatography and capillary electrophoresis. Papers from 1992 to 1998 have been taken into consideration. Screening procedures in biosamples (whole blood, plasma, serum, urine, vitreous humor, brain, liver or hair) of humans or animals (horse, or rat) are included for the following drug classes: angiotensin-converting enzyme (ACE) inhibitors and angiotensin II (AT-II) blockers, anticoagulants of the 4-hydroxy coumarin type, barbiturates, dihydropyridine calcium channel blockers (calcium antagonists), diuretics, hypoglycemic sulfonylureas and non-steroidal anti-inflammatory drugs (NSAIDs). Methods for confirmation of preliminary results obtained by screening procedures using immunoassay or chromatographic techniques are also included. Furthermore, procedures for the simultaneous detection of several drug classes are reviewed. The toxicological question to be answered and the consequences for the choice of an adequate method, the sample preparation and the chromatography itself are discussed. The basic information about the biosample assayed, work-up, separation column, mobile phase or separation buffer, detection mode and validation data of each procedure is summarized in 16 tables. They are arranged according to the drug class and the analytical method. Examples of typical applications are presented. Finally, STA procedures are reviewed and described allowing simultaneous screening for different (acidic) drug classes.

Chromatography↗
PubMed1996

X-linked Alport syndrome: an SSCP-based mutation survey over all 51 exons of the COL4A5 gene.

The COL4A5 gene encodes the alpha5 (type IV) collagen chain and is defective in X-linked Alport syndrome (AS). Here, we report the first systematic analysis of all 51 exons of COL4A5 gene in a series of 201 Italian AS patients. We have previously reported nine major rearrangements, as well as 18 small mutations identified in the same patient series by SSCP analysis of several exons. After systematic analysis of all 51 exons of COL4A5, we have now identified 30 different mutations: 10 glycine substitutions in the triple helical domain of the protein, 9 frameshift mutations, 4 in-frame deletions, 1 start codon, 1 nonsense, and 5 splice-site mutations. These mutations were either unique or found in two unrelated families, thus excluding the presence of a common mutation in the coding part of the gene. Overall, mutations were detected in only 45% of individuals with a certain or likely diagnosis of X-linked AS. This finding suggests that mutations in noncoding segments of COL4A5 account for a high number of X-linked AS cases. An alternative hypothesis is the presence of locus heterogeneity, even within the X-linked form of the disease. A genotype/phenotype comparison enabled us to better substantiate a significant correlation between the degree of predicted disruption of the alpha5 chain and the severity of phenotype in affected male individuals. Our study has significant implications in the diagnosis and follow-up of AS patients.

Adult↗
PubMed2026

Test-retest reliability of spatiotemporal, kinematic, and kinetic measures in marker-based 3D gait analysis: A systematic review.

BACKGROUND: Marker-based 3D gait analysis (3DGA) is widely used to quantify impairments and evaluate treatment effects. For longitudinal clinical interpretation, clinicians and researchers need reference values for inter-session measurement error. For this purpose, this systematic review synthesized Standard Error of Measurement (SEM) values for spatiotemporal, kinematic, and kinetic (moments) outcomes obtained from marker-based 3DGA studies. METHODS: PubMed and Scopus were searched (final search: 11 December 2025). Studies reporting inter-session test-retest SEM and/or MDC for steady-state overground or treadmill walking using marker-based motion capture were included. Two authors screened records and appraised methodological/reporting quality using a custom tool informed by COSMIN, GRRAS, and biomechanics-specific items. Due to heterogeneity, results were synthesized descriptively using study-level median SEM values, stratified by joint, plane, population (healthy, pathological, single subgroups), and walking condition. Minimal Detectable Change (MDC) values were computed for all available data. RESULTS: Thirty-four studies (762 participants, 44.2% females) were included, with substantially more evidence for overground than treadmill walking. Overground spatiotemporal outcomes showed low errors (walking speed SEM of 0.06 m/s; timing typically ≤0.03 s; spatial parameters generally ≤0.03 m). For joint kinematics during overground walking, median SEMs were 2.4° (sagittal), 1.9° (frontal), and 3.3° (transverse). The corresponding joint-kinetic SEMs were approximately 0.06, 0.04, and 0.03 Nm/kg, respectively. Treadmill data followed similar patterns. SIGNIFICANCE: Marker-based 3DGA allows for accurate assessment of spatiotemporal, kinematic, and kinetic gait features. We provided detailed SEM/MDC lookup tables to support clinical decision-making. Results further offer a benchmark for validating emerging gait assessment technologies (e.g., markerless systems) against realistic limits of marker-based 3DGA.

Humans↗
PubMed1992

Systematic toxicological analysis of drugs and their metabolites by gas chromatography-mass spectrometry.

Gas chromatographic-mass spectrometric (GC-MS) procedures for the systematic toxicological analysis of several categories of drugs relevant to clinical toxicology, forensic toxicology and doping control are reviewed. Papers from 1981 to 1991 are taken into consideration. They describe the detection of acute or chronic intoxication and the detection of drug abuse. Screening procedures are included for the following categories: barbiturates and other sedative-hypnotics, anticonvulsants, benzodiazepines, antidepressants, phenothiazine and butyrophenone neuroleptics, central stimulants (amphetamines, cocaine), hallucinogens (LSD, phencyclidine, tetrahydrocannabinol), opioid (narcotic) and other potent analgesics, non-opioid analgesics, antihistamines (histamine H1-receptor blockers), antiparkinsonian drugs, beta-blockers (beta-adrenoceptor blockers), antiarrhythmics (class I and IV), diuretics, laxatives and their metabolites. Methods for confirmation of results obtained by screening procedures using immunoassay or chromatographic techniques are also included. GC-MS procedures for the simultaneous detection of several categories of drugs, the so-called "general unknown analysis", are reviewed. The toxicological question to be answered and the consequence for the choice of an adequate method, the sample preparation and the chromatography itself are discussed. The basic information about the biosample assayed, work-up, GC column, mass spectral detection mode, reference data and sensitivity of each procedure are summarized in tables, arranged according to the category of drug. Examples of typical GC-MS applications are presented. Fragment ions that are suitable for mass spectral screening for particular categories of drugs and for general unknown are tabulated.

Gas Chromatography-Mass Spectrometry↗
PubMed2006

Subtractive SELEX against two heterogeneous target samples: numerical simulations and analysis.

Systematic evolution of ligands by exponential (SELEX) is a revolutionary technology that integrates combinatorial chemistry with high throughput screening to generate from synthesized nucleic acid ligand libraries the high affinity nucleic acid ligands (aptamers) for interesting targets. Recently, the SELEX experiments have advanced from targeting the ligand libraries by a single purified target to multiple heterogeneous target samples. Having the potential of bringing enormous technical and economical advantages to drug discovery, the new application suffers from unpredictable performances. To gain an insight of the new method, we develop a computer model to numerically analyze the subtractive SELEX alternatively against two distinct heterogeneous samples of unknown targets. The model features the discretization of ligand library, the ligand-target binding equilibrium equations, and the separation efficiency of bound and unbound ligands in experiments. By computer simulations, we investigate how aptamers for desired targets embedded in undefined target mixtures are generated under different experimental conditions. We find the iterative screening scheme is fundamentally capable of developing desired aptamers. On the other hand, target sample configuration and separation efficiency may all together significantly diversify the screening dynamics and results.

Aptamers, Nucleotide↗
PubMedDate not supplied

System evaluation and substance identification in systematic toxicological analysis by the mean list length approach.

In systematic toxicological analyses (STA), analytical methods are needed with a high Identification Power. The mean list length (MLL) approach, which is an improved and extended version of the Identification Power concept, provides an objective tool for the evaluation and optimum choice of analytical methods for STA. The MLL approach is elucidated and applied to the screening for basic drugs by thin layer chromatography (TLC) and gas-liquid chromatography (GLC). Its usefulness for TLC and GLC systems for the identification of these basic drugs has been evaluated for both single systems and combinations of systems. The MLL approach is also substance directed and can be applied to computerized data searches and substance identification. The method is applicable for single analytical systems and combinations of systems. Mixtures of substances can also be handled.

Chromatography, Gas↗
PubMed1999

Systematic toxicological analysis of drugs and poisons in biosamples by hyphenated chromatographic and spectroscopic techniques.

The introduction of hyphenated chromatographic-spectroscopic techniques represented a substantial step-forward for Systematic Toxicological Analysis (STA), increasing the amount and quality of information obtainable from the analysis of a biological sample, and enhancing the possibilities of identifying unknown drugs and poisons. STA methods based either on GC-MS or on HPLC-UV published in the last decade are reviewed in this paper. The different analytical phases, i.e. sample preparation (pretreatment, extraction, derivatisation), chromatographic separation and detection/identification are examined in detail in order to emphasise the complementarity of the two approaches. In addition, the first STA method based on HPLC-MS is illustrated and some applications of TLC-UV to drug screening are also described. Finally, an overview of semi- and fully-automated STA methods is given.

Chromatography↗
PubMed1998

Fully-automated systematic toxicological analysis of drugs, poisons, and metabolites in whole blood, urine, and plasma by gas chromatography-full scan mass spectrometry.

The availability of automated, rapid and reliable methods for the systematic toxicological analysis (STA) of drugs and poisons in biosamples is of great importance in clinical and forensic toxicology laboratories. Gas chromatography-continuous scan mass spectrometry (GC-MS) possesses a high potential in STA because of its selectivity and identification power. However, in order to develop a fully automated STA method based on GC-MS two main obstacles have to be overcome: (a) sample preparation is rather sophisticated owing to the need to isolate analytes from the aqueous matrix and to allow a correct GC repartition of polar analytes; (b) the large amount of information collected within a single analysis makes it difficult to isolate relevant analytical information (mass spectra of analytes) from the chemical noise. Using a bench-top GC-MS system equipped with a laboratory robot for sample preparation (the Hewlett-Packard 7686 PrepStation) and an original method for mass spectral purification, a fully automated STA procedure was developed involving isolation of drugs from the sample (whole blood with minimal pretreatment, plasma, urine) by means of solid-phase extraction, derivatization (trimethylsilylation) of the acidic-neutral and of the basic extracts, GC-MS analysis, processing of data, and reporting of results. Each step of the procedure, and the method for data analysis in particular, can be easily integrated with other existing STA methods based on GC-MS.

Autoanalysis↗