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PubMed2004

High-salt stacking principles and sweeping: comments and contrasts on mechanisms for high-sensitivity analysis in capillary electrophoresis.

High-salt stacking in electrokinetic chromatography (EKC) is defined and contrasted to the sweeping method. A recent paper argued the two methods are identical, where high concentrations of micelle in the sample were intended to mimic the effect of high-salt stacking. However, high micelle concentration in the sample matrix in EKC is analogous to using a high-conductivity sample instead of a low-conductivity sample in field amplified stacking. High-salt stacking does not require a sample free of pseuostationary phase, only a sample with a high-mobility co-ion compared to the separation buffer electrokinetic vector. High-salt stacking uses a discontinuous buffer system and should not be confused with continuous buffer stacking systems such as sweeping.

Electrophoresis, Capillary↗
PubMed2003

Recurrence of low back pain: definition-sensitivity analysis using administrative data.

STUDY DESIGN: Retrospective analysis of administrative claims data in a single workers' compensation jurisdiction. OBJECTIVES: To evaluate the effects of alternative definitions and follow-up parameters on rates of low back pain recurrence based on detailed administrative data. SUMMARY OF BACKGROUND DATA: Previous studies reported low back pain recurrence rates ranging from 14% to 45%, without consistency in definitions of recurrence or specifications of follow-up. METHODS: Patients with new claims for low back pain reported in New Hampshire to a large workers' compensation provider in 1996 and 1997 were selected (N = 2944). Definitions of recurrence included: new workers' compensation claim, new episode of care, and new episode of lost work time (work disability). For the latter two definitions, various minimum between-episode gaps were applied and related to recurrence rates. Two follow-up structures (constant length of follow-up post end of the first episode and fixed-period length of follow-up since the onset of low back pain) were examined for sensitivity of recognizing low back pain recurrence, with a maximum of 3-year follow-up. RESULTS: Recurrence rate using a claims-based definition was 7.9% and 7.1% for the entire cohort and the subset with work disability days, respectively, for the 3 years of follow-up. Care-based recurrence rates ranged between 12% and 49%, whereas disability-based recurrence rates ranged between 6% and 17% over the 3 years, inversely related to the length of the minimum between-episode gap (R = -0.86 for disability and care, P < 0.001). Two-year follow-up was sufficient to identify 85% to 100% of recurrences regardless of the follow-up structure. CONCLUSIONS: Recurrence rates are highly sensitive to variations in definitions. Consistency of definitions and application across studies is required to enable valid comparisons.

Adolescent↗
PubMed2005

Differential chemical diagnosis of primary hyperoxaluria type II. Highly sensitive analysis of optical isomers of glyceric acid by GC/MS as diastereoisomeric derivatives.

We established a separation method for the optical isomers of glyceric acid in urine by modifying the derivatization steps of the procedure used for the screening and diagnosis. The trimethylsilyl derivatization step in the mass screening procedure was replaced by O-acetyl-(+)-2-butylation, and the samples were analyzed under equivalent GC/MS conditions by capillary gas chromatography on a DB-5MS column. This method can be applied to cases that show a high urinary concentration of glyceric acid to obtain a differential diagnosis of primary hyperoxaluria type II and d-glyceric aciduria easily. l-Glyceric acid was also isolated from the urine of healthy controls as one of the main peaks.

Diagnosis, Differential↗
PubMed2001

Highly sensitive analysis of the antifolate pemetrexed sodium, a new cancer agent, in human plasma and urine by high-performance liquid chromatography.

A reversed-phase high-performance liquid chromatography method was developed and validated for the quantitation of pemetrexed (LY231514, ALIMTA) in human urine and plasma. Plasma samples were spiked with the internal standard lometrexol and extracted using Certify II columns. Pemetrexed was assayed in diluted urine by an external calibration method. A C8 column was used for the separation of analytes with a mobile phase composed of sodium formate buffer and acetonitrile. Between- and within-day precision and accuracy were acceptable down to the limit of quantitation of 5 ng/ml in plasma. This method was used successfully for an investigation of the disposition of pemetrexed in patients receiving 500 mg/m2 as a 10-min infusion.

Antineoplastic Agents↗
PubMed2006

Sensitivity analysis of a biofilm model describing mixed growth of nitrite oxidisers in a CSTR.

A simple kinetic model has been developed for describing nitrite oxidation by autotrophic aerobic nitrifiers in a CSTR reactor, in which mixed (suspended and attached) growth conditions are prevailing. In this work, a critical dimensionless parameter is identified containing both biofilm characteristics and microbial kinetic parameters, as well as the specific (per volume) surface of the reactor configuration used. Evaluation of this dimensionless parameter can easily provide information on whether or not wall attachment is critical, and should be taken into account either in kinetic studies or in reactor design, when specific pollutants are to be removed from the waste influent stream. The effect of bulk dissolved oxygen (DO) concentration on the validity of this model is addressed and minimum non-limiting DO concentrations are proposed depending on the reactor configuration.

Aerobiosis↗
PubMed2006

Non-radioisotope detection of pol sequences of HTLV-1 proviral DNA: Standardisation and sensitivity analysis.

Proviral DNA amplification methods may be used for identification of HTLV-1 infection or in basic virology research. Published standardised methods in this regard usually depend on hybridisation of PCR products with radioisotope-labelled probes. However, this procedure has limited use in routine testing, due to environmental and health risks. The aim was to assess the feasibility of routine use and the accuracy of an alternative detection system that employs an HTLV-1-specific enzyme-labelled probe. For this purpose DNA was extracted from MT-2 cells, quantified and submitted to serial dilution (1:10), starting from 1.2 microg of genomic DNA. Primary and nested PCR amplifications of pol sequences of the HTLV-1 genome were carried out with standardised primers (SK110/111 and POL1.1/3.1). After Southern blotting, two different detection systems were compared, consisting of hybridisation with either 32P- or alkaline phosphatase-labelled SK112 probes. Both detection systems yielded similar results, detecting PCR products generated from 120 pg of DNA (genomic DNA amount equivalent to 20 diploid human cells) after primary and nested PCR. The alkaline phosphatase-labelled detection technique was feasible for the diagnosis of HTLV-1 with the advantage of precluding the handling of radioisotopes.

Alkaline Phosphatase↗
PubMed2003

A simple method to determine body segment masses in vivo: reliability, accuracy and sensitivity analysis.

OBJECTIVE: To show that force plates can be used to quickly acquire subject-specific segment mass data. DESIGN: In vivo measurements were performed on subjects belonging to three populations: female varsity swimmers, female varsity volleyball players, and male college students. Segmental masses were measured using a force plate technique, and were compared with published data. BACKGROUND: Patients from populations for which data from the literature are not applicable (e.g. pathological, aging females, obese, children, etc.) would benefit from a direct measure of inertial parameters for accurate joint moment calculations. METHODS: Eight female varsity volleyball players, 17 female varsity swimmers, and 10 male college students were measured anthropometrically. They then lay on a board placed on a force plate and the center of pressure was recorded while the subjects adopted various prescribed limb positions. Their limb masses were subsequently calculated from the center of pressure data given estimated center of mass locations. RESULTS: The method was highly reproducible with an average reliability coefficient of 0.83 and yielded results similar to those of published methods. Significantly different mass distributions were found between the two female populations tested (P<0.025). CONCLUSIONS: The method can quickly provide subject-specific limb segment mass information. RELEVANCE: Measuring subjects' segment masses individualizes clinical assessments and may be necessary for those from special populations to avoid erroneous biomechanical conclusions.

Adult↗
PubMed2002

Sweeping: concentration mechanism and applications to high-sensitivity analysis in capillary electrophoresis.

Sweeping in capillary electrophoresis (CE) involves the interaction of a pseudostationary phase (PS) in the separation solution and a sample in the matrix that is free of the PS used. The PS includes not only the PSs employed in electrokinetic chromatography, but also complexation reagents such as borate. The sample matrix could have a lower, similar, or higher conductance than the separation solution. Thus, the basic condition for sweeping is a sample matrix free of the additive. The accumulation of analyte molecules during the interaction makes this interesting phenomenon very useful as an on-line preconcentration method for CE. Preconcentration occurs due to chromatographic partitioning, complexation, or any interaction between analytes and PS. Contact between analyte and PS is facilitated by the action of electrophoresis and is independent of electroosmosis. The analyte, PS, or both should have electrophoretic velocities when an electric field is applied. The extent of preconcentration is dictated by the strength of the interaction involved. From tens to several thousand-fold improvements in detector response for many neutral and charged analytes have been achieved with this technique, suggesting sweeping as a general approach to on-line preconcentration in CE. The mechanism and applications of the sweeping phenomenon under different experimental conditions are discussed in this review, with particular emphasis on a better understanding of the sweeping mechanism under reduced electric field (high conductivity) in the sample zone.

Electrophoresis, Capillary↗
PubMed2005

CT-3D rotational angiography automatic registration: a sensitivity analysis.

Preprocessing, binning and dataset subsampling are investigated with regard to simultaneous maximisation of the speed, accuracy and robustness of CT-3D rotational angiography (3DRA) registration. Clinical diagnosis and treatment can both take advantage of this integration, because 3DRA allows the shape of vessel structures to be evaluated three-dimensionally with respect to standard 2D projective angiography. The method for optimising preprocessing, binning and subsampling consisted of independent variation of the corresponding parameters to maximise robustness and speed while maintaining subvoxel accuracy; the latter was computed as the sum of the mean squared errors initially present in the registrations with the errors relative to both binning and subsampling. The results suggest the choice of 256 bins, steps between 14 mm (coarse optimisation) and 2.5 mm (fine optimisation) and bone segmentation by threshold, for binning, subsampling and preprocessing, respectively. The application of this parameter set-up to 50 CT-3DRA registrations resulted in a saving, on average, of 40% of the time with respect to the method previously used, while registration error was maintained within 2 mm (1.97 mm, 90% confidence interval) and robustness was increased, so that no manual initial realignment was needed in 48 registrations. Validation by the registration of images acquired for a head phantom showed subvoxel residual errors. In conclusion, the proposed procedure can be considered a satisfactory strategy to optimise CT-3DRA registration.

Angiography↗
PubMed2005

Dynamic modeling of photothermal interactions for laser-induced interstitial thermotherapy: parameter sensitivity analysis.

A two-dimensional model was developed to model the effects of dynamic changes in the physical properties on tissue temperature and damage to simulate laser-induced interstitial thermotherapy (LITT) treatment procedures with temperature monitoring. A modified Monte Carlo method was used to simulate photon transport in the tissue in the non-uniform optical property field with the finite volume method used to solve the Pennes bioheat equation to calculate the temperature distribution and the Arrhenius equation used to predict the thermal damage extent. The laser light transport and the heat transfer as well as the damage accumulation were calculated iteratively at each time step. The influences of different laser sources, different applicator sizes, and different irradiation modes on the final damage volume were analyzed to optimize the LITT treatment. The numerical results showed that damage volume was the smallest for the 1,064-nm laser, with much larger, similar damage volumes for the 980- and 850-nm lasers at normal blood perfusion rates. The damage volume was the largest for the 1,064-nm laser with significantly smaller, similar damage volumes for the 980- and 850-nm lasers with temporally interrupted blood perfusion. The numerical results also showed that the variations in applicator sizes, laser powers, heating durations and temperature monitoring ranges significantly affected the shapes and sizes of the thermal damage zones. The shapes and sizes of the thermal damage zones can be optimized by selecting different applicator sizes, laser powers, heating duration times, temperature monitoring ranges, etc.

Algorithms↗
PubMed2003

Composition-sensitive analysis of the human genome for regulatory signals.

Known transcription regulatory signals which generally act as transcription factor binding sites (TFs) differ significantly in their base composition. Therefore, their occurrence in a genome largely depends on the local base composition. In an attempt to initiate an all human genome analysis for the occurrence of potential TFs, we systematically analyzed the GC-content of distinct functional regions (e. g., upstream and downstream gene regions, exons, long and short introns, repetitive elements) and correlated the frequencies of potential binding sites of a representative set of TFs in these regions. For these analyses, we used the pattern collection of the TRANSFAC database on transcriptional regulation, the information about functionally relevant combinations of them from the database TRANSCompel, and our new resource, TRANSGenomeTM, which provides an overall annotation of the human genome with emphasis on its regulatory characteristics. We show that the occurrence of sequence patterns with regulatory potential may be supported by, but cannot be fully explained by either the GC content of a whole chromosome or its putative promoter regions, nor by the information content of the patterns. Several patterns, HNF-3, NFAT, and GC box, show a clear overrepresentation in all promoter groups as well as in all chromosomes. Other patterns, like E2F and CRE-BP1, are underrepresented in all promoter groups as well as in all chromosomes in comparison with random sequences. Simultaneously, both patterns are over-represented in promoters in comparison with repetitive elements. We define several structural characteristics of the proximal promoters that differentiate them from other functional genomic regions. Two well-known promoter elements, GC- and TATA-boxes, are statistically enriched in promoters in comparison with random sequences, repetitive elements and exons. Altogether, our findings provide insights into the macroheterogeneity amongst the individual chromosomes, into the microheterogeneity among different functional regions of individual chromosomes, contribute to further understanding of structural organization of gene regulatory regions, and give first hints on the development of regulatory features during evolution.

Animals↗
PubMed2001

Sensitivity analysis of longitudinal binary quality of life data with drop-out: an example using the EORTC QLQ-C30.

Analysing quality of life data (QOL) may be complicated for several reasons. Quality of life data not only involves repeated measures but is also usually collected on ordered categorical responses. In addition, it is evident that not all patients provide the same number of assessments, due to attrition caused by death or other medical reasons. In the recent statistical literature, increasing attention is given to methods which can handle non-continuous outcomes in the presence of missing data. The aim of this paper is to investigate the effect on statistical conclusions of applying different modelling techniques to QOL data generated from an EORTC phase III trial. Treatment effects and treatment differences are of major concern. First, a random-effects model is fitted, relating a binary longitudinal response (derived from the physical functioning scale of the QLQ-C30) to several covariates. In a second approach, marginal models are fitted, retaining the response variable and the mean structure used before. The fitted marginal models only differ with respect to the considered estimation procedure: generalized estimating equations (GEE); weighted generalized estimating equations (WGEE), and maximum likelihood (ML).

Antibiotics, Antineoplastic↗
PubMed1988

An extended physiological pharmacokinetic model of methadone disposition in the rat: validation and sensitivity analysis.

An extended physiological model of methadone disposition in the rat was constructed and evaluated in various tests of model validity. A separate circulation model of the fetus was included due to the large tissue concentration differences obtained after a constant rate infusion but also to propose the use of this type of model for optimization of toxicological tests. Simulations were performed with the animal model and scaled-up models of humans to elucidate the determinants of methadone disposition. The rationale of the use of an extended model for methadone was also discussed.

Animals↗
PubMed1997

The actions of calmodulin antagonists W-7 and TFP and of calcium on the gating kinetics of the calcium-activated large conductance potassium channel of the chara protoplasmic drop: a substate-sensitive analysis.

The effects of the calmodulin antagonists W-7 and trifluoperazine have been measured on the Ca2+-activated potassium channel in the membrane surrounding protoplasmic drops expressed from internodal cells of charophyte plants. The large-conductance (170 pS), voltage- and Ca2+-dependent gating, and prominent conductance substrate of this channel shows a strong kinetic resemblance to those of the Maxi-K channel from animal cells. This is the first study of the action of calmodulin antagonists which measures their effects on the most populated substates as well as the closed and main open states of Maxi-K channels. The substate analysis provides new evidence for different modes of action of- and different bindings sites for these calmodulin antagonists. Neither antagonist produces the simple closure of the channel reported previously as its effect on the Maxi-K channel, though both do induce flicker-block, reducing the mean current to near zero at high concentrations following an inverted Michaelis-Menten curve. W-7 reduces residence time in the fully open state, thus raising, in the same proportions, the probabilities of finding the channel in the closed state or a pre-existing substate. Its binding to the channel is voltage- and calcium-dependent. In contrast, trifluoperazine reduces residence in the open state and promotes an apparently new substate which overlaps the closed state at -50 mV but is distinguishable from it at voltages more negative than -100 mV. This substate may represent times that trifluoperazine is bound to the channel. Both antagonists have effects clearly distinguishable from that of withdrawing calcium from the channel, which does not affect open state residence time but increases closed state residence time. Thus neither antagonist reverses the activating effect of Ca2-. This is good kinetic evidence against the view that the channel is activated by Ca2+-calmodulin and that the effect of a calmodulin antagonist is to reverse this process by making Ca2--calmodulin less available.

Calcium↗