ProMAT calibrator: A tool for reducing experimental bias in antibody microarrays

Our research group has been developing enzyme-linked immunosorbent assays (ELISA) microarray technology for the rapid and quantitative evaluation of biomarker panels. Studies using antibody microarrays are susceptible to systematic bias from the various steps in the experimental process, and these biases can mask biologically significant differences. For this reason, we have developed a calibration system that can identify and reduce systematic bias due to processing factors. Specifically, we developed a sandwich ELISA for green fluorescent protein (GFP) that is included on each chip. The GFP antigen is spiked into each biological sample or standard mixture and the resulting signal is used for calibration between chips. We developed ProMAT Calibrator, an open-source bioinformatics tool, for the rapid visualization and interpretation of the calibrator data and, if desired, data normalization. We demonstrate that data normalization using this system markedly reduces bias from processing factors. Equally useful, this calibrator system can help reveal the source of the bias, thereby facilitating the elimination of the underlying problem. ProMAT Calibrator can be downloaded at http://www.pnl.gov/statistics/ProMAT .

Mixed-effects statistical model for comparative LC-MS proteomics studies

Comparing a protein's concentrations across two or more treatments is the focus of many proteomics studies. A frequent source of measurements for these comparisons is a mass spectrometry (MS) analysis of a protein's peptide ions separated by liquid chromatography (LC) following its enzymatic digestion. Alas, LC-MS identification and quantification of equimolar peptides can vary significantly due to their unequal digestion, separation, and ionization. This unequal measurability of peptides, the largest source of LC-MS nuisance variation, stymies confident comparison of a protein's concentration across treatments. Our objective is to introduce a mixed-effects statistical model for comparative LC-MS proteomics studies. We describe LC-MS peptide abundance with a linear model featuring pivotal terms that account for unequal peptide LC-MS measurability. We advance fitting this model to an often incomplete LC-MS data set with REstricted Maximum Likelihood (REML) estimation, producing estimates of model goodness-of-fit, treatment effects, standard errors, confidence intervals, and protein relative concentrations. We illustrate the model with an experiment featuring a known dilution series of a filamentous ascomycete fungus Trichoderma reesei protein mixture. For 781 of the 1546 T. reesei proteins with sufficient data coverage, the fitted mixed-effects models capably described the LC-MS measurements. The LC-MS measurability terms effectively accounted for this major source of uncertainty. Ninety percent of the relative concentration estimates were within 0.5-fold of the true relative concentrations. Akin to the common ratio method, this model also produced biased estimates, albeit less biased. Bias decreased significantly, both absolutely and relative to the ratio method, as the number of observed peptides per protein increased. Mixed-effects statistical modeling offers a flexible, well-established methodology for comparative proteomics studies integrating common experimental designs with LC-MS sample processing plans. It favorably accounts for the unequal LC-MS measurability of peptides and produces informative quantitative comparisons of a protein's concentration across treatments with objective measures of uncertainties.

An integrated confocal and magnetic resonance microscope for cellular research

Complementary data acquired with different microscopy techniques provide a basis for establishing a more comprehensive understanding of health and disease at a cellular level, particularly when data acquired with different methodologies can be correlated in both time and space. In this Communication, a brief description of a novel instrument capable of simultaneously performing confocal optical and magnetic resonance microscopy is presented, and the first combined images of live Xenopus laevis oocytes are shown. Also, the potential benefits of combined microscopy are discussed, and it is shown that the a priori knowledge of the high-resolution optical images can be used to enhance the boundary resolution and contrast of the MR images.

Extracting and visualizing matrix-assisted laser desorption/ionization time-of-flight mass spectral fingerprints

We have developed a method for constructing and extracting matrix-assisted laser desorption/ionization (MALDI) fingerprints. This method is fully automated and statistically based, allowing a large number of spectra to be analyzed at a time in an objective manner. This method can be used to extract the fingerprint of a particular analyte from a spectrum containing multiple analytes. Therefore, this method lends itself well to real-world applications where samples to be analyzed are likely to be impure. We illustrate this method on experimental results from a series of studies of E. coli and B. atrophaeus MALDI time-of-flight mass spectrometry (TOFMS) fingerprints.

Sedation for upper gastrointestinal endoscopy: a comparison of alfentanil-midazolam and meperidine-diazepam

The authors studied the efficacy and cost of substituting sedation using midazolam and alfentanil for the existing regimen of diazepam and meperidine in patients requiring upper gastrointestinal endoscopy. Sixty consenting subjects were randomized to receive either meperidine 50 mg with diazepam approximately 90 micrograms.kg-1 (Group D) or alfentanil 250 micrograms with midazolam approximately 50 micrograms.kg-1 (Group M). Endoscope insertion time, patient acceptance, apnoeic or desaturation episodes were noted by a physician observer. Pulse oximetry was used to monitor heart rate and oxygen saturation (SpO2) during endoscopy. Subjects performed four-choice reaction time (4CRT) tests before, 30 and 60 min after endoscopy, and were assessed for nausea or dizziness and their ability to stand and walk. During endoscopy, insertion time was shorter (84 +/- 45 sec vs 122 +/- 83 sec, P < 0.03) and fewer aversive movements occurred (0.4 +/- 0.6 vs. 1.7 +/- 2.4, P < 0.005) in Group M than Group D. No subject in either group suffered any apnoea or prolonged desaturation requiring supplemental oxygen. Irrespective of treatment group, greater decreases in SpO2 (6.1 +/- 3.4% vs 3.6 +/- 2.2% P < 0.001) occurred in subjects > 45 yr of age than in subjects < or = 45 yr. During recovery 4CRT values at 30 min after endoscopy were longer (723 +/- 226 msec vs 594 +/- 139 msec, P < 0.005) in Group M than in Group D but not after 60 min. It was concluded that the small differences in endoscopy conditions and greater sedation during the first 30 min of recovery did not justify the additional cost of using midazolam and alfentnil.(ABSTRACT TRUNCATED AT 250 WORDS)

Scalloped valvulae conniventes: an endoscopic marker of celiac sprue

The finding, in a patient with celiac sprue, of a characteristic change at endoscopy (scalloping of the valvulae conniventes, event on close inspection, but forming only a mosaic pattern from a distance) led to an endoscopic survey designed to define its incidence. In a series of 28 sequential patients found to have microscopic changes characteristic of sprue on biopsy, distinctive endoscopic changes were found in 22 (in 6 of 9 with sprue in relapse, and 16 of 19 presenting with initial symptoms). The finding of the distinctive appearance provides an endoscopically recognizable pattern that can be associated with sprue. It also provides the potential for early recognition of the process in patients in whom the diagnosis might otherwise have been delayed due to a lack of substantial evolution of the usually associated symptom complex.

A new device for measuring fluctuations in plant stem diameter: Implications for monitoring plant responses : Note

An electrical device capable of continuously measuring micronsized changes in stem diameter of woody and herbaceous plants is described. Fumigation of sunflowers with automotive exhaust was used to test the ability of the device to detect short-term plant responses.

Mallory-Weiss tear. A complication of cancer chemotherapy

Since the original report by Mallory and Weiss of tears in the lower esophagus or cardia of the stomach following alcoholic debauch, there have been many other cases, associated with sundry other causes, described in the literature. Recently, a Mallory-Weiss tear was reported in a patient as a complication of cancer chemotherapy. This article describes two similar cases and suggests that the Mallory-Weiss syndrome should be included in the differential diagnosis of any patient with epigastric pain, hematemesis, or melena after chemotherapy-induced retching or vomiting.

Metronidazole: an alternate therapy for antibiotic-associated colitis

The results of treatment of 13 consecutive cases of antibiotic-associated pseudomembranous colitis with oral metronidazole are described. The diagnosis was made by typical sigmoidoscopic appearance with a confirming characteristic colonic biopsy specimen and/or stools positive for Clostridium difficile cytotoxin. All patients responded with the disappearance of diarrhea between 1 and 5 days. Two patients experienced relapse when the therapy was discontinued. Our experience with metronidazole shows that it is an effective treatment for antibiotic-associated pseudomembranous colitis. The response to metronidazole treatment compares favorably with that usually obtained with vancomycin.

Uptake of labeled palmitate by the intact liver: role of intracellular binding sites

The multiple-indicator dilution technique was utilized to examine the hepatic uptake of albumin-bound labeled palmitate from the portal vein blood of the pentobarbital-anesthetized dog, in a fasted state and after infusion of a variety of compounds that were expected to bind to Z protein, the cellular cytosolic protein binding free fatty acids, and their acyl-CoA derivatives. Analysis of the data indicates that after infusion of alpha-bromopalmitate, 16-bromo-9-hexadecenoate, and sulfobromophthalein sodium (which also bind to albumin), the palmitate label influx, efflux, and metabolic sequestration (removal of label from the pool of free fatty acids able to leave the cell) all increase and that, after infusion of flavaspidic acid, label efflux and metabolic sequestration increase. In vitro competitive binding studies carried out on the cellular cytosol indicat that the basis for the increase in efflux and metabolic sequestration is displacement of labeled palmitate from high affinity sites on the intracellular Z protein (which are presumably in equilibrium with and may be taken to be representative of other intracellular binding sites). These studies also suggest that increased uptake is due to similar displacement from high affinity sites on serum albumin.

A fibreendoscopic study of acute upper gastrointestinal hemorrhage in Nairobi, Kenya

A prospective survey of acute upper gastrointestinal hemorrhage in the major government hospital of Kenya was done using fibre-optic esophagogastroduodenoscopy. Of 66 African patients presenting with hematemesis and melena, a precise visual diagnosis was made in 89%. Duodenal ulcer was most common, accounting for 53%, but esophageal varices occurred in 20%. Gastric ulcers and esophagitis were surprisingly infrequent. There was a correlation between hemorrhage from esophageal varices and schistosomiasis distribution. Variceal bleeding occurred in a young age group (mean age 28 yr) and correlated closely with the presence of splenomegaly. These findings have implications for the diagnostic approach and management of patients from areas of endemic schistosomiasis.

Intramural esophageal bleeding in a hemodialysis patient

A case of intramural esophageal hemorrhage in a hemodialysis patient is described. The hemorrhage followed an episode of vomiting and violent retching. Spontaneous resolution occurred with conservative management. The clinical course resembled that of previous case reports of intramural esophageal hemorrhage, whether or not associated with chronic renal failure and intermittent hemodialysis.