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PubMed1989

Sources of improvement in between laboratory variation in estrogen and progestin receptor measurement using tissue samples during the Australian Quality Assurance Programme.

Tissue and cytosol samples were compared as quality control material for assessment of between and within laboratory error in measurement of estrogen and progestin receptors (ER and PR) in a series of four trials for a total of 17 participating laboratories during the Australasian Quality Assurance Programme. For tissue samples, a substantial reduction in between laboratory CVs for both ER and PR from about 90 to 50% was achieved during the programme. In contrast, for cytosol samples a substantially lower between laboratory CV of about 30% was obtained. Tissue sample heterogeneity could be excluded as a major source of variation between laboratories. The likely source of the observed improvement in CV for tissue samples during the trials was due to a reduction of the initial under-estimation of receptor concentration in tissue samples by some of the participants. Although cytosol preparation from tissue samples was shown to be one major source of error, other sources of error such as the receptor assay itself and the associated protein measurements were identified. It is concluded that fragmented tissue samples are essential for a realistic assessment of between laboratory error in receptor measurements in biopsy material such as obtained from clinical breast cancer samples.

Animals↗

PubMed1989

Spatial resolution of transcranial pulsed Doppler technique in vitro evaluation of the sensitivity distribution of the sample volume.

The spatial resolution of pulsed Doppler sonography is determined by the size of the sample volume. It is known that the axial length is dependent upon the duration of the range gate interval and the lateral extension upon the beam width. In addition, the working size is also a function of the sensitivity distribution within the sample volume. All of these parameters determine the working size of the sample volume. Especially for the transcranial Doppler evaluation of the basal cerebral arteries, the site and the working size of the sample volume are essential diagnostic criteria. To measure the working size of the sample volume a flow rig with a thin tube target has been developed and used. The highest sensitivity (100% level) was registered only in a relatively small area and only if the center of the sample volume hit the target. At the 10% level the size of the sample volume increased 5 to 10 times in the lateral and axial dimension in comparison with the 90% level. Therefore, the Doppler signal from a strong reflector distant from the center of the sample volume may mask the signal of a weak reflector located within the center. This lack of spatial resolution due to sensitivity effects may result in clinical misinterpretation. The manufacturers should be urged to supply more precise information relative to the sample volume size.

Blood Flow Velocity↗

PubMed1995

Sample matrix effects in micellar electrokinetic capillary electrophoresis.

Several factors related to sample matrix which can influence peak height in micellar electrokinetic capillary chromatography were studied. The ionic strength of the sample did not affect greatly the peak height. High concentration of surfactants or organic solvents in the sample decreased the peak height. On the other hand, using a surfactant in the sample different from the one in the electrophoresis buffer or the addition of polyethylene glycol to the sample enhanced slightly the peak height. A high surfactant concentration in the buffer increased the migration time as well as the plate number and the peak height. Matrix effects are more profound with large than with small sample injections. In general, the effect of sample matrix in MECC is much less than that observed in capillary zone electrophoresis. It is recommended to prepare the standards in the same matrix as that of the sample or to add the analytes directly to the sample to avoid any bias in the results.

Electrophoresis, Capillary↗

PubMed1994

Individualization of fresh and stored human urine samples by PGM1- and Gc-subtyping.

After 50- to 200-fold concentration by ultrafiltration, 56 fresh urine samples from healthy individuals (26 men, 30 women) and eight samples from corpses were subjected to isoelectrofocusing methods. All the urine samples tested could be correctly typed in both the phosphoglucomatase 1 (PGM1) and Gc system when compared to reference blood samples. The activity of urinary PGM1 revealed intraindividual and interindividual variations. To our knowledge this is the first report of PGM1 detection in urine. A systematic storage experiment over a period of 6 months was carried out at different temperatures (-20 degrees C, 4 degrees C, 20 degrees C); furthermore, aging of urine samples from 4 months to 4 years was investigated. The heterogeneous typing results were as follows. For Gc: after a storage period of 6 months positive results could be obtained in approximately 40% of those samples that were stored frozen (-20 degrees C) or in a refrigerator (4 degrees C). Some samples, however, showed negative analyses already after a 1 month storage period. At room temperature positive results could be achieved up to 3 months. Additional bands can appear in pherograms of urine samples stored at room temperature or in a refrigerator; they may cause misinterpretation, dependent on the original Gc-type. The maximum storage time compatible with successful Gc-typing was 1 year. For PGM1: this polymorphism could be regularly detected up to 1 week, and in some cases up to 1 month, in urine samples stored at 4 degrees C. The PGM1 activity gradually decreased; there were no additional or variant bands.

Female↗

PubMed2005

Concentration and characteristics of depleted uranium in water, air and biological samples collected in Serbia and Montenegro.

During the Balkan conflicts, in 1995 and 1999, depleted uranium (DU) rounds were employed and were left in the battlefield. Health concern is related to the risk arising from contamination of the environment with DU penetrators and dust. In order to evaluate the impact of DU on the environment and population in Serbia and Montenegro, radiological surveys of DU in water, air and biological samples were carried out over the period 27 October-5 November 2001. The uranium isotopic concentrations in biological samples collected in Serbia and Montenegro, mainly lichens and barks, were found to be in the range of 0.67-704 Bqkg(-1) for (238)U, 0.48-93.9 Bqkg(-1) for (234)U and 0.02-12.2 Bqkg(-1) for (235)U, showing uranium levels to be higher than in the samples collected at the control sites. Moreover, (236)U was detectable in some of the samples. The isotopic ratios of (234)U/(238)U showed DU to be detectable in many biological samples at all examined sites, especially in Montenegro, indicating widespread ground-surface DU contamination, albeit at very low level. The uranium isotopic concentrations in air obtained from the air filter samples collected in Serbia and Montenegro were found to be in the range of 1.99-42.1 microBqm(-3) for (238)U, 0.96-38.0 microBqm(-3) for (234)U, and 0.05-1.83 microBqm(-3) for (235)U, being in the typical range of natural uranium values. Thus said, most of the air samples are DU positive, this fact agreeing well with the widespread DU contamination detected in the biological samples. The uranium concentrations in water samples collected in Serbia and Montenegro were found to be in the range of 0.40-21.9 mBql(-1) for (238)U, 0.27-28.1 mBql(-1) for (234)U, and 0.01-0.88 mBql(-1) for (235)U, these values being much lower than those in mineral water found in central Italy and below the WHO guideline for drinking water. From a radiotoxicological point of view, at this moment there is no significant radiological risk related to these investigated sites in terms of possible DU contamination of water, air and/or plants.

Air Pollutants, Radioactive↗

PubMed2004

Determination of tridemorph and other fungicide residues in fruit samples by liquid chromatography-electrospray tandem mass spectrometry.

A rapid and sensitive liquid chromatography-electrospray ionization-tandem mass spectrometry (LC-ESI-MS-MS) method for the determination of tridemorph and other pre- and post-harvest fungicides (carbendazim, thiabendazole, imazalil, propiconazole and bitertanol) in banana and orange samples has been developed and validated. The sample preparation was a simple extraction step with acetone using a high-speed blender prior to the injection of the five-fold diluted extract into the LC system with no other previous sample pre-treatment. Quantification was carried out using a matrix matched calibration curve which was linear in the range of 1-100 ng ml(-1) for all the compounds. The limit of quantification was 0.05 mg kg(-1) for all studied compounds, whereas limits of detection ranged between 0.005 and 0.025 mg kg(-1) (0.01 mg kg(-1) for tridemorph). Recoveries for tridemorph from spiked banana and orange samples at 0.05 and 1 mg kg(-1) were satisfactory, with values between 83 and 99% and relative standard deviations (R.S.D.s) lower than 13% (n = 5). For the other fungicides, recoveries between 75 and 95% with R.S.D.s lower than 12% were obtained. The developed method has been applied to the determination of selected fungicides in real samples of bananas and oranges from different origin. Thiabendazole and imazalil have been detected in almost all orange samples analyzed, and in around of 30% of banana samples. Bitertanol residues exceeded the maximum residue level (0.05 mg kg(-1)) in three banana samples while tridemorph was only detected in one sample.

Calibration↗

PubMed2004

Sensitive trace enrichment of environmental andiandrogen vinclozolin from natural waters and sediment samples using hollow-fiber liquid-phase microextraction.

The presence of vinclozolin in the environment as far as the endocrine disruption effects in biota are concerned has raised interest in the environmental fate of this compound. In this respect, the present study attempts to investigate the feasibility of applying a novel quantitative method, liquid-phase microextraction (LPME), so as to determine this environmental andiandrogen in environmental samples such as water and sediment samples. The technique involved the use of a small amount (3 microL) of organic solvent impregnated in a hollow fiber membrane, which was attached to the needle of a conventional GC syringe. The extracted samples were analyzed by gas chromatography coupled with electron-capture detection. Experimental LPME conditions such as extraction solvent, stirring rate, content of NaCl and pH were tested. Once LPME was optimized, the performance of the proposed technique was evaluated for the determination of vinclozolin in different types of natural water samples. The recovery of spiked water samples was from 80 to 99%. The procedure was adequate for quantification of vinclozolin in waters at levels of 0.010 to 50 microg/L (r> 0.994) with a detection limit of 0.001 microg/L (S/N= 3). Natural sediment samples from the Aliakmonas River area (Macedonia, Greece) spiked with the target andiandrogen compound were liquid-liquid extracted and analyzed by the methodology developed in this work. No significant interferences from the samples matrix were noticed, indicating that the reported methodology is an innovative tactic for sample preparation in sediment analysis, with a considerable improvement in the achieved detection limits. The results demonstrated that apart from analyte enrichment, the proposed LPME procedure also serves as clean-up method and could be successfully performed to determine trace amounts of vinclozolin in water and sediment samples.

Androgen Antagonists↗

PubMed2005

Analysis of perfluorooctanesulfonate and related fluorochemicals in water and biological tissue samples by liquid chromatography-ion trap mass spectrometry.

A method for the determination of perfluorinated compounds (PFCs) in various water and biological tissue samples was developed and validated. The contents of selected PFCs (i.e., perfluorooctanesulfonate (PFOS), perfluorooctanoate (PFOA) and perfluorodecanoate (PFDA)) in water samples were extracted by the C(18) solid-phase extraction (SPE). The biological tissue samples (frozen-dried fish and oysters) were simply extracted by liquid-solid extraction with MTBE and adding tetrabutylammonium hydrogensulfate (TBA) as an ion-pairing reagent. The analytes were then identified and quantitated by liquid chromatography-ion trap negative electrospray mass spectrometry (LC-ESI ion-trap-MS). Limits of quantitation (LOQ) were established between 0.5 and 6 ng/l in 250 ml of water sample, while 5-50 ng/g (dry weight) for biological tissue sample. Intrabatch and interbatch precision with their accuracy at two concentration levels were also investigated. Precision for these three PFCs, as indicated by RSD, proved to be less than 11 and 17%, respectively. The total contents of PFOA, PFOS and PFDA were detected in concentrations of up to 400 ng/l in various water samples, while up to 1,100 ng/g in fish and oyster samples. PFOA and PFDA was the major PFCs detected in water samples and biological tissue samples, respectively.

Alkanesulfonic Acids↗

PubMed2006

Diffusive sampling of methylene chloride with solid phase microextraction.

This study examined the characteristics of a solid phase microextraction (SPME) assembly as a passive sampler to determine the short-term exposure level (STEL) of methylene chloride. Two types of SPME fibers and six sampling-related factors were chosen and nested in an L(18) Taguchi's orthogonal array. Samples were thermally desorpted and analyzed by gas chromatograph equipped with an electron capture detector (GC/ECD). The use of 85-mum Carboxen/polydimethylsiloxane (Car/PDMS) fibers resulted in greater adsorbed mass, which was highly correlated with the product of concentration and sampling time (r>0.99, p<0.0001), than 85-microm polyacrylate fibers. The sampling rate (SR) of the 85-microm Carboxen/polydimethylsiloxane fibers was not significantly affected by variations in relative humidity (0-80%) and coexistent toluene (none to 100 ppm). Variance of sampling rate was predominantly attributed to the diffusive path length (86.4%) and sampling time (5.7%). With diffusive paths of 3, 10 and 15 mm, the sampling rates of 85-microm Carboxen/polydimethylsiloxane fibers for methylene chloride were 1.4 x 10(-2), 7.7 x 10(-3) and 5.1 x1 0(-3)mL min(-1), respectively. The measured sampling rates were greater than the theoretical values, and decreased with increment of sampling time until they came to constant.

Chromatography, Gas↗

PubMed2005

An algorithmic approach to understand trace elemental homeostasis in serum samples of Parkinson disease.

A classical problem in neurological disorders is to understand the progression of disorder and define the trace elements (metals) which play a role in deviating a sample from normal to an abnormal state, which implies the need to create a reference knowledge base (KB) employing the control samples drawn from normal/healthy set in the context of the said neurological disorder, and in sequel to analytically understand the deviations in the cases of disorders/abnormalities/unhealthy samples. Hence building up a computational model involves mining the healthy control samples to create a suitable reference KB and designing an algorithm for estimating the deviation in case of unhealthy samples. This leads to realizing an algorithmic cognition-recognition model, where the cognition stage establishes a reference model of a normal/healthy class and the recognition stage involves discriminating whether a given test sample belongs to a normal class or not. Further if the sample belongs to a specified reference base (normal) then the requirement is to understand how strong the affiliation is, and if otherwise (abnormal) how far away the sample is from the said reference base. In this paper, an exploratory data analysis based model is proposed to carry out such estimation analysis by designing distribution and parametric models for the reference base. Further, the knowledge of the reference base in case of the distribution model is expressed in terms of zones with each zone carrying a weightage factor. Different distance measures are utilized for the subsequent affiliation analysis (City block with distribution model and Doyle's with Parametric model). Results of an experimental study based on the database of trace elemental analysis in human serum samples from control and Parkinson's neurological disorder are presented to corroborate the performance of the computational algorithm.

Algorithms↗

PubMed2006

The role of Pipelle Mark II sampling in endometrial disease diagnosis.

OBJECTIVE: To evaluate the feasibility and accuracy of Pipelle Mark II sampling (designed for combined cytology and histology testing) in the diagnosis of endometrial disease. MATERIALS AND METHODS: A 97 women with abnormal uterine bleeding or intrauterine lesions on ultrasound examination underwent Pipelle Mark II endometrial sampling, followed by diagnostic hysteroscopy. The adequacy of endometrial samples obtained for cytological and histological analysis was assessed. A correlation was established between endometrial cytology, histology and diagnostic hysteroscopy results. Where discrepancies were found, they were compared with the histological results obtained from operative hysteroscopy. RESULTS: The tissue samples obtained for cytological and histological diagnoses were insufficient in 14.4% and 11.3% of patients, respectively. The opposite was found in the group of postmenopausal women (N=52): the tissue samples for cytological and histological diagnoses were insufficient in only 3.8% and 15.4% of cases, respectively. The cytological results corroborated diagnostic hysteroscopy findings and histological results in all cases but 3 (3.6%). Only two cases of endometrial carcinoma were reported in this group of patients, and they were both detected by all three methods. The rate of false positives with endometrial cytological sampling was 3.6%. There were no false negatives. CONCLUSION: Pipelle Mark II endometrial sampling is feasible. It provides adequate samples for histological and/or cytological analysis and reliable results. It reduces the rate of false negative results for endometrial cancer. Pipelle Mark II sampling is particularly useful in postmenopausal women and in women with endometrial atrophy. Other larger studies are necessary to evaluate the efficiency of Pipelle Mark II.

Adult↗

PubMed2005

Continued axillary sampling is unnecessary and provides no further information to sentinel node biopsy in staging breast cancer.

INTRODUCTION: Sentinel lymph node biopsy (SLNB) has become increasingly accepted as a diagnostic method to stage the axilla in breast cancer, selecting women with a positive sentinel node for completion axillary clearance. As SLNB became established, many surgeons supplemented SLNB to sample a minimum of four lymph nodes, on the assumption that the four-node technique is supported by randomised trial data. We hypothesised that the practice of undirected sampling to supplement SLNB adds little information to the status of the residual axilla. METHODS: One hundred and sixty-five patients with early breast cancer were studied. Following successful identification of the sentinel node, 84 women had completion axillary dissection and 81 women had an axillary sample with at least four nodes available for pathological assessment. RESULTS: Following successful identification of the sentinel node in 165 patients, the false negative rate (FNR) was 2/44=4.5% (95% CI 0.6-15.5), sensitivity 42/44=95.5% (84.5-99.4) and negative predictive value (NPV) 121/123=98.4% (94.2-99.8). In the axillary dissection cohort, the FNR was 2/26=7.7% (0.9-25.1), sensitivity 24/26=92.3% (74.9-99.1) and NPV 58/60=96.7% (88.5-100). In the axillary sample group, the FNR was 0/18=0% (0-18.5), sensitivity 18/18=100% (81.5-100) and NPV 63/63=100% (94.3-100). The SLNB was the only positive node in 12/26 (46.2%) in the axillary dissection group and 10/18 (55.6%) in the axillary sampling group. There was no patient in the axillary sampling group where the sample node was positive and the sentinel node negative. CONCLUSION: Once SLNB is validated within the multidisciplinary unit, undirected sampling of the axilla following identification of the sentinel node(s) is unnecessary. The additional sampling of non-sentinel nodes has no role to play either in the assessment of a potential false negative SLNB nor as predictive information on the status of the residual axillary nodes.

Adult↗

PubMed2004

Aqueous sample in an EPR cavity: sensitivity considerations.

The radial mode matching (RMM) method has been used to calculate accurately the microwave field distribution of the TE(011) mode in a spherical EPR cavity containing a linear aqueous sample, in order to understand in detail the factors affecting sensitivity in EPR measurements at X band. Specific details of the experiment were included in the calculations, such as the cavity geometry, the presence of a quartz dewar, the size of the aqueous sample, and the sample's dielectric properties. From the field distribution, several key physical parameters were calculated, including cavity Q, filling factor, mean microwave magnetic field at the sample, and cavity efficiency parameter Lambda. The dependence of EPR signal intensity on sample diameter for a cylindrical aqueous sample was calculated and measured experimentally for non-saturated and half-saturated samples. The optimal aqueous sample diameter was determined for both cases. The impact of sample temperature, conductivity, and cavity Q on sensitivity of EPR is discussed.

Algorithms↗

PubMed2006

Analysis of RF heating and sample stability in aligned static solid-state NMR spectroscopy.

Sample instability during solid-state NMR experiments frequently arises due to RF heating in aligned samples of hydrated lipid bilayers. A new, simple approach for estimating sample temperature is used to show that, at 9.4 T, sample heating depends mostly on (1)H decoupling power rather than on (15)N irradiation in PISEMA experiments. Such heating for different sample preparations, including lipid composition, salt concentration and hydration level was assessed and the hydration level was found to be the primary parameter correlated with sample heating. The contribution to RF heating from the dielectric loss appears to be dominant under our experimental conditions. The heat generated by a single scan was approximately calculated from the Q values of the probe, to be a 1.7 degrees C elevation per single pulse sequence iteration under typical sample conditions. The steady-state sample temperature during PISEMA experiments can be estimated based on the method presented here, which correlates the loss factor with the temperature rise induced by the RF heating of the sample.

Hot Temperature↗

PubMed2004

Application of the heteroduplex mobility assay (HMA) for the investigation of the genomic diversity among noroviruses in environmental samples.

Recent studies have demonstrated the widespread contamination of river and seawater with noroviruses (NV), often with more than one strain. The heteroduplex mobility assay (HMA) in which amplicons from study samples are hybridised (by denaturing and reannealing) to amplicons from reference strains and resolved by electrophoresis, has the potential to provide a simple and rapid means to identify samples containing multiple NV strains and to establish the diversity of strains within that sample. PCR amplicons from environmental samples that were tested directly in the HMA assay were shown to contain more than one strain. In order to evaluate HMA for investigations of NV diversity in environmental samples, amplicons from three representative samples were cloned and, for each, 20 amplicons derived from individual clones were analysed by HMA. Between two and six different HMA profiles were demonstrated among clones from a single sample indicating the extent of NV diversity in the sample. Sequence analysis confirmed the relationship of HMA profile and NV 'genotype'. Far greater diversity was seen among Genogroup (G) II (Ni/E3) amplicons than Genogroup (G) I (Ando/E3) amplicons (generated from the RNA dependent RNA polymerase region of the ORF1 of noroviruses), which often contained only a single strain, which is reflective of the greater prevalence of GII NVs over GI NVs. Overall, four GII and four GI strains were identified in these environmental water/sewage samples.

Base Sequence↗

PubMed2006

Sampling properties of homozygosity-based statistics for linkage disequilibrium.

Homozygosity-based statistics such as Ohta's identity-in-state (IIS) excess offer the potential to measure linkage disequilibrium for multiallelic loci in small samples. However, previous observations have suggested that for independent loci, in small samples these statistics might produce values that more frequently lie on one side rather than on the other side of zero. Here we investigate the sampling properties of the IIS excess. We find that for any pair of independent polymorphic loci, as sample size n approaches infinity, the sampling distribution of the IIS excess approaches a normal distribution. For large samples, the IIS excess tends towards symmetry around zero, and the probabilities of positive and of negative IIS excess both approach 1/2. Surprisingly, however, we also find that for sufficiently large n, independent loci can be chosen so that the probability of a sample having positive IIS excess is arbitrarily close to either 0 or 1. The results are applied to interpretation of data from human populations, and we conclude that before employing homozygosity-based statistics to measure LD in a particular sample, especially for loci with either very small or very large homozygosities, it is useful to verify that loci with the observed homozygosity values are not likely to produce a large bias in IIS excess in samples of the given size.

Algorithms↗

PubMed2004

Sampling frequency and accuracy of SPM flux estimates in two contrasted drainage basins.

The present paper is based on discharges and suspended particulate matter concentrations from a 9-years high-resolution database for the Garonne River (large plain river) covering contrasted hydrologic years, and a 12-months high frequency sampling for the Nivelle River (small mountainous river). Annual SPM fluxes in the Garonne River range from 0.6 x 10(6) t year(-1) (1997) to 3.9 x 10(6) t year(-1) (1996). In contrast, the Nivelle River transported 11 x 10(3) t year(-1) from December 1995 to December 1996. From the long-term observation of the Garonne River an empirical relation between SPM* (discharge-weighted mean annual SPM concentrations) and annual discharge was established. This relation allows estimating annual SPM fluxes for the Garonne River with less than 30% deviation from reference values for the whole range of mean annual discharge observed during the past decade. Specific (=area-normalized) annual SPM fluxes (YSPM) range from 11 to 74 t km(-2) year(-1) for the Garonne River. Comparison of these results with YSPM of the Nivelle River (69 t km(-2) year(-1) in 1996) suggests that interannual hydrological variations may have a greater impact on fluvial SPM transport than basin-specific parameters. By extracting individual SPM concentrations and corresponding discharge values from the database, different sampling frequencies were simulated and resulting SPM fluxes were then compared to reference fluxes derived from the complete database. If a deviation of simulated flux estimates from reference fluxes lower than +/-20% is accepted, the Garonne River (large plain river) must be sampled at least every 3 days (10 samples per month) and the Nivelle River every 7 h (approx. 100 samples per month). For the Garonne River this minimum sampling frequency is valid for all contrasted hydrologic years of the observation period. Below these minimum sampling frequencies, annual SPM flux estimates may greatly differ from reference fluxes (up to 200%) and there is high probability of systematic underestimation. Consequently, annual SPM flux estimates for the Garonne River derived from the empirical relation (SPM*-annual discharge) are likely to be more satisfactory (errors <30%) than estimates based on sampling frequencies lower than the minimum frequency. These findings underline the need of adapted sampling strategies for erosion assessment, reliable chemical (e.g. nutrients and pollutants) mass balances and characterisation of fluvial transport mechanisms in the world's contrasted watersheds.

Journal Article↗

PubMed2006

Sampling challenges posed by continental-scale soil landscape modeling.

Limited research exists to guide the development of continental-scale field sampling approaches. We developed a method to compare different sampling schemes designed for continental-scale environmental analysis. Using simulated annealing, we produced hypothetical soil property surfaces for the conterminous United States. The surfaces exhibited varying degrees of polygonality and conditioning by existing soil datasets. Differences in mean between a gridded sample and a polygon-centered sample were evaluated using randomization and other statistical tests. We saw a weak evidence in support of the hypothesis that if a polygonal structure exists in a surface being sampled, then it should be utilized during the actual sampling routine. We saw a somewhat stronger evidence for the hypothesis that differences in local sample density across a continental trend surface can lead to significant sampling bias. Ultimately, the success of different sampling strategies designed for use in continental-scale environmental analysis will largely depend on the ability to anticipate the spatial variability of the variable being measured.

Environment Design↗