Bayesian estimation of fold-changes in the analysis of gene expression: the PFOLD algorithm.

A general and detailed noise model for the DNA microarray measurement of gene expression is presented and used to derive a Bayesian estimation scheme for expression ratios, implemented in a program called PFOLD, which provides not only an estimate of the fold-change in gene expression, but also confidence limits for the change and a P-value quantifying the significance of the change. Although the focus is on oligonucleotide microarray technologies, the scheme can also be applied to cDNA based technologies if parameters for the noise model are provided. The model unifies estimation for all signals in that it provides a seamless transition from very low to very high signal-to-noise ratios, an essential feature for current microarray technologies for which the median signal-to-noise ratios are always moderate. The dual use, as decision statistics in a two-dimensional space, of the P-value and the fold-change is shown to be effective in the ubiquitous problem of detecting changing genes against a background of unchanging genes, leading to markedly higher sensitivities, at equal selectivity, than detection and selection based on the fold-change alone, a current practice until now.     

Performance and limitations of positron emission tomography (PET) scanners for imaging very low activity sources

Emerging applications for positron emission tomography (PET) may require the ability to image very low activity source distributions in the body. The performance of clinical PET scanners in the regime where activity in the field of view is <1 MBq has not previously been explored. In this study, we compared the counting rate performance of two clinical PET/CT scanners, the Siemens Biograph Reveal 16 scanner which is based on lutetium oxyorthosilicate (LSO) detectors and the GE Discovery-ST scanner which is based on bismuth germanate (BGO) detectors using a modified National Electrical Manufacturers Association (NEMA) NU 2-2007 protocol. Across the activity range studied (2–100 kBq/mL in a 5.5 mL line source in the NEMA scatter phantom), the BGO-based scanner significantly outperformed the LSO-based scanner. This was largely due to the effect of background counts emanating from naturally occurring but radioactive ¹⁷⁶Lu within the LSO detector material, which dominates the observed counting rate at the lowest activities. Increasing the lower energy threshold from 350 keV to 425 keV in an attempt to reduce this background did not significantly improve the measured NECR performance. The measured singles rate due to ¹⁷⁶Lu emissions within the scanner energy window was also found to be dependent on temperature, and to be affected by the operation of the CT component, making approaches to correct or compensate for the background more challenging. We conclude that for PET studies in a very low activity range, BGO-based scanners are likely to have better performance because of the lack of significant background.     

High sensitivity multianalyte immunoassay using covalent DNA-labeled antibodies and polymerase chain reaction.

A multianalyte immunoassay for simultaneous detection of three analytes (hTSH, hCG and beta-Gal) has been demonstrated using DNA-labeled antibodies and polymerase chain reaction (PCR) for amplification of assay response. The labeled antibodies were prepared by covalently coupling uniquely designed DNA oligonucleotides to each of the analyte-specific monoclonal antibodies. Each of the DNA oligonucleotide labels contained the same primer sequences to facilitate co-amplification by a single primer pair. Assays were performed using a two-antibody sandwich assay format and a mixture of the three DNA-labeled antibodies. Dose-response relationships for each analyte were demonstrated. Analytes were detected at sensitivities exceeding those of conventional enzyme immunoassays by approximately three orders of magnitude. Detection limits for hTSH, beta-Gal and hCG were respectively 1 x 10(-19), 1 x 10(-17) and 1 x 10(-17) mol. Given the enormous amplification afforded by PCR and the existing capability to differentiate DNA based on size or sequence differences, the use of DNA-labeled antibodies could provide the basis for the simultaneous detection of many analytes at sensitivities greater than those of existing antigen detection systems. These findings in concert with previous reports suggest this hybrid technology could provide a new generation of ultra-sensitive multianalyte immunoassays.     

Objective quality evaluation of fluorescence images to optimize automatic image acquisition.

BACKGROUND: Because different spectral sensitivities of human eye and image sensor lead to different perception of fluorescence signals, data generation is an important step in image analysis, because following work steps depend on it. METHODS: We developed a method to determine image parameters allowing an objective appraisal of quality of image data as well as a separation of object and background. RESULTS: Calculated parameters can be used for an automated adjustment of camera parameters in image analysis systems. DISCUSSION: Our approach for objective adjusted data generation achieves an improvement of analysis quality.     

Inactivation action spectra of Bacillus subtilis spores with monochromatic soft X rays (0.1-0.6 nm) of synchrotron radiation.

Five types of Bacillus subtilis spores differing in DNA repair and recombinational capacities were exposed in vacuum to monochromatic soft X rays from synchrotron radiation. The inactivation rate constants were obtained from exposure-survival curves upon irradiations at 12 wavelengths in the range of 0.1000 nm (12.40 keV) to 0.6000 nm (2.066 keV). Spores of two repair-deficient strains, UVS (uvrA ssp) and UVP (uvrA ssp polA), exhibited almost equal sensitivities to those of wild-type UVR+, while those of two recombination-deficient strains, RCE (recE) and RCF (recF), exhibited higher sensitivities in the whole wavelength range. This suggested that the repair of DNA damage produced by soft X rays was dependent on the recombinational capabilities. Inactivation action spectra based on photon fluence showed that the effectiveness of the radiation increased as the wavelengths became longer. Abrupt changes in the effectiveness occurred around the wavelengths corresponding to the absorption edges of K-shell electrons of phosphorus and calcium. In both cases, the sensitivity was the highest at the wavelengths of the resonance absorption peak, the next highest at those of the higher energy, and the lowest at the lower energy. Mass energy absorption coefficients of spores were obtained from the transmission of a flake made of spores. They were used to derive inactivation action spectra based on absorbed doses. In these spectra, basal levels of the sensitivity seemed constant, and enhancements of the sensitivity were observed consistent with the absorption by calcium and phosphorus. Thus calcium and phosphorus atoms were the predominant targets for the absorption events leading to the inactivation of spores in the wavelength range examined.     

Alamethicin-induced pore formation in biological membranes.

The effects of alamethicin on the membrane barrier function of rabbit erythrocytes, human platelets and sarcoplasmic reticulum vesicles, as well as on that of brain microsomes and liver mitochondria of the rat were compared. An upset of the barrier function was observed for plasma membranes of brain microsomes as well as for erythrocyte and platelet membranes at alamethicin concentrations ranging between 25-80 micrograms/ml. The membrane barrier functions of sarcoplasmic reticulum vesicles, of endoplasmic reticulum vesicles of rat brain microsomes, and of liver mitochondria were disturbed at 3-7 micrograms/ml alamethicin. The different sensitivities of plasma and intracellular membranes to alamethicin were supposed to be due to the presence of considerable quantities of cholesterol in plasma membranes as well as to peculiarities of their protein compositions.     

Detection by bismuth staining of highly phosphorylated nucleo-proteins in plants. Determination of its specificity by X-ray microanalysis,SDS-PAGE and immunological analysis

Summary— Staining with bismuth salts after glutaraldehyde fixation is a very useful technique for preferential detection of phosphorylated nucleoproteins in mammalians and insects. In the present work we report an adaptation of this method for plant nuclei: staining with bismuth salts either in tissue blocks before embedding, or on thin sections of acrylic resin. Both procedures are highly reproducible and give the same pattern of staining in the nuclei in situ or isolated at the electron microscope. The specificity of bismuth binding to the dense nucleolar fibrillar component and interchromatin granules is proven by X-ray microanalysis. The nuclear proteins which bind bismuth have been identified by bismuth and immunostains of blots from total nuclear proteins. This technique is a very useful and specific cytochemical tool for studying nuclear organization and functions in plants.     

A high-power vircator operating as an X-ray bremsstrahlung generator

Avircator capable of generating high-power X-ray pulses due to the multiple transitions of electrons through a thin anode foil transparent to X radiation has been created and put into operation for the first time. The vircator is created on the basis of a direct-action electron accelerator supplied from an inductive energy storage operating with a plasma opening switch. Self-consistent two-dimensional simulations of the electron beam dynamics in the vircator chamber are performed, and the spectra of the generated microwave radiation are determined. Self-consistent one-dimensional simulations of the beam dynamics with allowance for electron scattering in the foil were also carried out, and the X-ray bremsstrahlung spectra were measured. Results are presented from the first experiments on the generation of X-ray bremsstrahlung in vircators with thin (10 μm) and thick (100 μm) tantalum anode foils. For a thin foil, the X-ray (E _γ>30 keV) dose is eight times as high as that for a thick foil and the average photon energy is 30 keV (against 80 keV for a thick foil). __________ Translated from Fizika Plazmy, Vol. 30, No. 9, 2004, pp. 828–834. Original Russian Text Copyright ￠ 2004 by Selemir, Dubinov, Ryaslov, Kargin, Efimova, Loyko.     

Levofloxacin- vs. ranitidine bismuth citrate-containing therapy after H. pylori treatment failure

AIM: Ranitidine bismuth citrate and levofloxacin-based regimen may be an alternative to quadruple therapy after Helicobacter pylori eradication failure. Our aim was to compare two 7-day triple second-line regimens containing ranitidine bismuth citrate or levofloxacin. METHODS: Patients in whom a first eradication trial with omeprazole-clarithromycin-amoxicillin had failed were randomized to receive 7-day treatment with: 1, ranitidine bismuth citrate (400 mg b.i.d.), tetracycline (500 mg q.i.d.), and metronidazole (250 mg q.i.d.), or 2, levofloxacin (500 mg b.i.d.), amoxicillin (1 g b.i.d.), and omeprazole (20 mg b.i.d.). Cure rates were evaluated by (13)C-urea breath test. RESULTS: One-hundred patients were included: 50 received the ranitidine bismuth citrate regimen, and 50 the levofloxacin one. Groups were comparable in terms of demographic variables. Two percent of the patients (one in each group) did not return for follow up. Compliance was similar in both groups (90% took all the medications correctly). Side-effects (only mild/moderate) in the two groups were also comparable (38% with ranitidine bismuth citrate and 36% with levofloxacin). Per-protocol cure rates were 69% (95% CI = 54-80%) in the ranitidine bismuth citrate group, and 71% (57-82%) in the levofloxacin one. Intention-to-treat cure rates were, respectively, 68% (59-79%) and 68% (59-79%) (nonstatistically significant differences). CONCLUSIONS: Both 7-day ranitidine bismuth citrate- and levofloxacin-containing second-line regimens represent alternatives to quadruple therapy in patients with previous omeprazole-clarithromycin-amoxicillin failure.     

X-ray enabled detection and eradication of circulating tumor cells with nanoparticles

The early detection and eradication of circulating tumor cells (CTCs) play an important role in cancer metastasis management. This paper describes a new nanoparticle-enabled technique for integrated enrichment, detection and killing of CTCs by using magnetic nanoparticles and bismuth nanoparticles, X-ray fluorescence spectrometry, and X-ray radiation. The nanoparticles are modified with tumor targeting agents and conjugated with tumor cells through folate receptors over-expressed on cancer cells. A permanent micro-magnet is used to collect CTCs suspended inside a flowing medium that contains phosphate buffered saline (PBS) or whole blood. The characteristic X-ray emissions from collected bismuth nanoparticles, upon excitation with collimated X-rays, are used to detect CTCs. Results show that the method is capable of selectively detecting CTCs at concentrations ranging from 100-100,000cells/mL in the buffer solution, with a detection limit of ～100CTCs/mL. Moreover, the dose of primary X-rays can be enhanced to kill the localized CTCs by radiation induced DNA damage, with minimal invasiveness, thus making in vivo personalized CTC management possible.     

The optical sensitivity of compound eyes: theory and experiment compared

The Land sensitivity equation is a well-known tool for comparing optical performance between eyes. Despite this, the equation has never been experimentally tested. Here, we present, to our knowledge, the first experimental validation of the equation. We have investigated different insect species active at different intensities, and possessing different types of compound eyes, to compare ratios of calculated sensitivities to ratios determined experimentally. Experimental optical sensitivities were measured by adjusting the intensity of an external light source until photoreceptors in the different eyes produced roughly equal numbers of photon responses ('bumps') per second. The sensitivity ratios obtained in this manner agree well with those obtained using the equation. We conclude that the Land equation remains an excellent tool for comparing sensitivities between different eyes.     

Third generation oral contraceptives and risk of venous thromboembolic disorders: an international case-control study. Transnational Research Group on Oral Contraceptives and the Health of Young Women.

OBJECTIVE--To test whether use of combined oral contraceptives containing third generation progestogens is associated with altered risk of venous thromboembolism. DESIGN--Matched case-control study. SETTING--10 centres in Germany and United Kingdom. SUBJECTS--Cases were 471 women aged 16-44 who had a venous thromboembolism. Controls were 1772 women (at least 3 controls per case) unaffected by venous thromboembolism who were matched with corresponding case for age and for hospital or community setting. MAIN OUTCOME MEASURES--Odds ratios derived with stratified analyses and unconditional logistic regression to adjust for potential confounding variables. RESULTS--Odds ratios (95% confidence intervals) for venous thromboembolism were: for any oral contraceptives versus no use, 4.0 (3.1 to 5.3); for second generation products (low dose ethinyl-oestradiol, no gestodene or desogestrel) versus no use, 3.2 (2.3 to 4.3); for third generation products (low dose ethinyloestradiol, gestodene or desogestrel) versus no use, 4.8 (3.4 to 6.7); for third generation products versus second generation products, 1.5 (1.1 to 2.1); for products containing gestodene versus second generation products, 1.5 (1.0 to 2.2); and for products containing desogestrel versus second generation products, 1.5 (1.1 to 2.2). Probability of death due to venous thromboembolism for women using third generation products is about 20 per million users per year, for women using second generation products it is about 14 per million users per year, and for non-users it is five per million per year. CONCLUSIONS--Risk of venous thromboembolism was slightly increased in users of third generation oral contraceptives compared with users of second generation products.     

On-line detection of nitric oxide formation in liquid aqueous phase by electron paramagnetic resonance spectroscopy.

A method for the detection of the nitric oxide radical (NO) in oxygen-containing aqueous solution by means of electron paramagnetic resonance spectroscopy (EPR) is described. NO evolving from the spontaneous decomposition of 3-morpholinosydnonimine (SIN-1) was trapped by Fe(2+)-diethyldithiocarbamate (DETC) complex dissolved in yeast cell membranes. The resulting mononitrosyl-Fe(2+)-(DETC)2 complex was stable and exhibited a characteristic EPR signal at g perpendicular = 2.04 and g parallel = 2.02 with an unresolved triplet hyperfine structure at g perpendicular in frozen solution and an isotropic triplet signal at gav = 2.03 at 37 degrees C. The amount of NO trapped was calculated from the amplitude of one of the triplet lines calibrated by means of a dinitrosyl-Fe(2+)-thiosulfate standard. The lower detection limit of NO was 0.5 nmol/(ml x h) due to a low background NO signal. The upper detection limit was about 10 nmol NO/40 mg traps (DETC-loaded yeast cells), because of saturation of traps. The trapping efficiency approached 60% under anaerobic conditions and with low concentrations of SIN-1, but decreased progressively with higher concentrations and in the presence of oxygen. Nitrite (up to 0.1 mM) did not increase the background NO level. The sensitivity was sufficient to follow the rate of NO release from SIN-1 on-line at 37 degrees C in a flat quartz cuvette. The time course of NO release detected by EPR spectrometry correlated with the time course of nitrite accumulation measured by diazotation. In conclusion, this method will permit the on-line detection of NO formation from endogenous and pharmacological sources in oxygen-containing aqueous media.     

Amplification of microsphere-based microarrays using catalyzed reporter deposition

Assay sensitivities using three fluorescent signal generation schemes were evaluated on the Luminex flow cytometer. Following microsphere capture of antigen by immobilized antibodies, bound targets were quantified by use of (1) Cy3-labeled "tracer" antibodies (30min total time), (2) biotinylated tracers followed by streptavidin-R-phycoerythrin (60min total time), or (3) biotinylated tracers followed by avidin-peroxidase conjugates and tyramide signal amplification (TSA; 90min total time). Use of TSA for signal generation in three individual toxin assays improved performance up to 100-fold over Cy3-antibody-based detection, and while streptavidin-R-phycoerythrin provided equivalent sensitivities, TSA produced dramatic increases at low concentrations simplifying positive sample identification. Detection limits for TSA-interrogated assays for ricin, cholera toxin, and staphylococcal enterotoxin B were 64pg/ml, 4pg/ml, and 0.1ng/ml, respectively, using optimized conjugates; analogous detection limits for Cy3-antibody-interrogated assays were 8ng/ml, 1ng/ml, and 1ng/ml, respectively. No improvement was observed in botulinum toxoid A assays when TSA amplification was used. As unique preferences for specific avidin-peroxidase conjugates were observed in the individual assays, improvements in multiplexed assays utilizing a single conjugate were significantly lower (3-10-fold improvements). Furthermore, increases in variability resulted in poorer performance of TSA-interrogated assays for botulinum toxoid, indicating that assay-specific optimization should be performed, especially prior to multiplexing.     

Auger effects on bromo-deoxyuridine-monophosphate irradiated with monochromatic X-rays around bromine K-absorption edge

Summary In order to study the enhanced effect by Auger cascade, samples of bromo-deoxyuridine-monophosphate (Br-dUMP) in aqueous solutions were irradiated with monochromatic X-rays at 13.49 keV and 13.43 keV, just above and below the K-absorption edge of bromine, using synchrotron radiation as a source. Radiolytic products such as deoxyuridine-monophosphate (dUMP), uracil and bromo-uracil (Br-uracil) were isolated using high performance liquid chromatography. Their amounts were quantitatively analysed as a function of the absorbed dose in the solutions containing Br-dUMP for the energy of the X-rays.G values for these products were calculated on the basis of the absorbed energy. As the results, the ratios of G values of radiolytic products from Br-dUMP between X-rays of 13.49 keV and 13.43 keV were 2.2 for dUMP, 1.02 for Br-uracil and 1.23 for uracil, suggesting clearly the energy dependent enhancement. On the other hand, little significant difference between X-rays of 13.49 keV and 13.43 keV was observed for theG values of uracil released from dUMP irradiated in aqueous solutions. It seemed to confirm that the Auger electrons from K-shell of bromine atoms might play the main role for energy-dependent enhancement at induction of these radiolytic products.     

Low-LET microbeam investigation of the track-end dependence of electron-induced damage in normal human diploid fibroblasts

Using a pulsed electron beam, we investigated the dependence of micronucleus formation on the incident electron energy in AG01522 human diploid fibroblasts after nontargeted irradiations at 25 and 80 keV. Examining the dose response, we found that 25 keV electrons are more effective than 80 keV electrons at producing biological damage for a given dose. Our results demonstrating the induction of micronuclei as a function of incident electron energy offer direct support for the hypothesis that the electron track end is responsible for the biological damage occurring in the cell.     

Induced synthesis of chromochelatin, the low molecular weight bismuth-binding protein in rat kidneys.

Bismuth administered subcutaneously to rats as BiCl3 is deposited in the kidneys, where it is bound to two classes of proteins: one of high molecular weight and a fraction of molecular weight approx. 7500 (chromochelatin). The latter fraction prevails on repeated exposure to bismuth. The bismuth-binding protein is heterogenous and using polyacrylamide gel may be divided into three fractions of which all contain bismuth and copper. In parallel with increasing concentration of chromochelatin due to bismuth administration, the incorporation of L-[35S]cysteine is elevated in all three fractions. The incorporation is augmented especially if repeated administration of bismuth is applied. Cycloheximide (CH) completely abolishes the inducing effect of bismuth on the incorporation of L-[35S]cysteine into chromochelatin both following single and repeated administration of bismuth. Actinomycin D (AcD) eliminates the incorporation only in the case of single dose of bismuth. The obtained results suggest that the elevation of chromochelatin levels in the kidney following administration of bismuth is due to the induction of the de novo protein synthesis.     

Waist circumference action levels in the identification of cardiovascular risk factors: prevalence study in a random sample.

OBJECTIVE--To determine the frequency of cardiovascular risk factors in people categorised by previously defined "action levels" of waist circumference. DESIGN--Prevalence study in a random population sample. SETTING--Netherlands. SUBJECTS--2183 men and 2698 women aged 20-59 years selected at random from the civil registry of Amsterdam and Maastricht. MAIN OUTCOME MEASURES--Waist circumference, waist to hip ratio, body mass index (weight (kg)/height (m2)), total plasma cholesterol concentration, high density lipoprotein cholesterol concentration, blood pressure, age, and lifestyle. RESULTS--A waist circumference exceeding 94 cm in men and 80 cm in women correctly identified subjects with body mass index of > or = 25 and waist to hip ratios > or = 0.95 in men and > or = 0.80 in women with a sensitivity and specificity of > or = 96%. Men and women with at least one cardiovascular risk factor (total cholesterol > or = 6.5 mmol/l, high density lipoprotein cholesterol < or = 0.9 mmol/l, systolic blood pressure > or = 160 mm Hg, diastolic blood pressure > or = 95 mm Hg) were identified with sensitivities of 57% and 67% and specificities of 72% and 62% respectively. Compared with those with waist measurements below action levels, age and lifestyle adjusted odds ratios for having at least one risk factor were 2.2 (95% confidence interval 1.8 to 2.8) in men with a waist measurement of 94-102 cm and 1.6 (1.3 to 2.1) in women with a waist measurement of 80-88 cm. In men and women with larger waist measurements these age and lifestyle adjusted odds ratios were 4.6 (3.5 to 6.0) and 2.6 (2.0 to 3.2) respectively. CONCLUSIONS--Larger waist circumference identifies people at increased cardiovascular risks.     

ESR spin trapping of hydroxyl radicals in aqueous solution irradiated with high-LET carbon-ion beams

The aim of this study was to quantify the hydroxyl radicals (*OH) produced when aqueous solutions are decomposed by high-linear energy transfer (LET) 290 MeV/nucleon carbon-ion beams using an electron spin resonance (ESR) spectrometer. Aerated cell culture medium containing 200 mM 5,5-dimethyl-1-pyrroline-N-oxide (DMPO) was irradiated with doses of 0 to 20 Gy with an LET of 20 to 90 keV/ micro m. We were able to obtain ESR spectra 10 min after irradiation, and the formation of *OH and hydrogen atoms was confirmed by radiolysis of deuterium oxide and ethanol containing DMPO. Our results showed that the yield of *OH by carbon-ion radiolysis increased in proportion to the absorbed dose over the range of 0 to 20 Gy. Furthermore, we discovered that the yield of *OH decreased linearity as LET increased logarithmically from 20 to 90 keV/ micro m. The generation of *OH by carbon-ion radiolysis at LETs of 20, 40, 60, 80 and 90 keV/ micro m was 64, 58, 52, 49 and 50%, respectively, of that for low-LET X radiolysis. These unique findings provide a further understanding of the indirect effect of high-LET radiation.     

Selective determination of arginine-containing and tyrosine-containing peptides using capillary electrophoresis and laser-induced fluorescence detection.

The use of two different amino acid-selective fluorogenic reagents for the derivatization of peptides is investigated. One such scheme utilizes a selective reaction of benzoin with the guanidine moiety to derivatize arginine residues occurring in a peptide. The second scheme involves the formylation of tyrosine, followed by reaction with 4-methoxy-1,2-phenylenediamine. The use of capillary electrophoresis and laser-induced fluorescence detection allows enhanced efficiencies and sensitivities to be obtained for the separations of either arginine- or tyrosine-containing peptides. A helium-cadmium laser (325 nm) is ideally suited for the laser-based detection system due to a close match of the excitation maxima of derivatized peptides from both reactions. A detection limit of 270 amol is achieved for model arginine-containing peptides, while the detection limit for model tyrosine-containing peptides is measured at 390 amol. Both derivatization reactions are found to be useful for high-sensitivity peptide mapping applications in which only the peptides containing the derivatized amino acids are detected.