Innovations in Calculating Precise Nutrient Intake of Hospitalized Patients.

Obtaining a detailed assessment of a hospitalized patient's nutrient intake is often critically important to ensuring the patient's successful recovery. However, this process is often laborious and prone to error. Inaccurate nutrient intake assessments result in the inability of the healthcare team to recognize patients with developing nutritional deficits that contribute to delayed recovery and prolonged lengths of stay. This paper describes an innovative, easy to use system designed to increase the precision of calorie count reports by using a combination of photography, direct observation, and a specially developed computer program. Although the system was designed specifically for use in a Department of Veterans Affairs Hospital, it has the potential to be adapted for use in other hospital environments.

Improved signal processing and normalization for biomarker protein detection in broad-mass-range TOF mass spectra from clinical samples.

PURPOSE: To demonstrate robust detection of biomarkers in broad-mass-range TOF-MS data. EXPERIMENTAL DESIGN: Spectra were obtained for two serum protein profiling studies: (i) 2-200 kDa for 132 patients, 67 healthy and 65 diagnosed as having adult T-cell leukemia and (ii) 2-100 kDa for 140 patients, 70 pairs, each with matched prostate-specific antigen (PSA) levels and biopsy-confirmed diagnoses of one benign and one prostate cancer. Signal processing was performed on raw spectra and peak data were normalized using four methods. Feature selection was performed using Bayesian Network Analysis and a classifier was tested on withheld data. Identification of candidate biomarkers was pursued. RESULTS: Integrated peak intensities were resolved over full spectra. Normalization using local noise values was superior to global methods in reducing peak correlations, reducing replicate variability and improving feature selection stability. For the leukemia data set, potential disease biomarkers were detected and were found to be predictive for withheld data. Preliminary assignments of protein IDs were consistent with published results and LC-MS/MS identification. No prostate-specific-antigen-independent biomarkers were detected in the prostate cancer data set. CONCLUSIONS AND CLINICAL RELEVANCE: Signal processing, local signal-to-noise (SNR) normalization and Bayesian Network Analysis feature selection facilitate robust detection and identification of biomarker proteins in broad-mass-range clinical TOF-MS data.

Precision enhancement of MALDI-TOF MS using high resolution peak detection and label-free alignment.

We have developed an automated procedure for aligning peaks in multiple TOF spectra that eliminates common timing errors and small variations in spectrometer output. Our method incorporates high-resolution peak detection, re-binning, and robust linear data fitting in the time domain. This procedure aligns label-free (uncalibrated) peaks to minimize the variation in each peak's location from one spectrum to the next, while maintaining a high number of degrees of freedom. We apply our method to replicate pooled-serum spectra from multiple laboratories and increase peak precision (t/sigma(t)) to values limited only by small random errors (with sigma(t) less than one time count in 89 out of 91 instances, 13 peaks in seven datasets). The resulting high precision allowed for an order of magnitude improvement in peak m/z reproducibility. We show that the CV for m/z is 0.01% (100 ppm) for 12 out of the 13 peaks that were observed in all datasets between 2995 and 9297 Da.

Effects of gemcitabine on cis-platinum-DNA adduct formation and repair in a panel of gemcitabine and cisplatin-sensitive or -resistant human ovarian cancer cell lines.

Gemcitabine (dFdC) can increase the sensitivity of both cisplatin (CDDP)-sensitive and -resistant cell lines. It has been postulated that both formation and repair of platinum-(Pt)-DNA adducts are related to these effects. Therefore, we investigated the effects of dFdC on the formation and repair of Pt-DNA adducts in the human ovarian cancer cell line, A2780, and its CDDP- or dFdC-resistant variants, ADDP and AG6000, which have a different expression of various repair enzymes. Cells were exposed for 1 h to CDDP alone or combined with dFdC in IC50 concentrations, followed by a 1-h exposure to thiourea and, subsequently, by a drug-free period of 1, 3 or 23 h (i.e. 2, 4 or 24 h after CDPP +/- dFdC removal). Pt-DNA adducts were quantified with 32P-post-labeling. The gene expression of the repair enzymes, XPA and XRCC1, was the same in all 3 cell lines but ERCC1, ERCC3 and XPC were 2-6 times higher in AG6000 compared to A2780 cells. In contrast, both ERCC1 and ERCC3 were 10- and 1.5-fold lower in ADDP cells compared to A2780. The mismatch enzyme, MLH1, was lower in ADDP cells. At equally toxic CDDP concentrations, all cell lines formed comparable peak levels of total Pt-DNA adducts (36-48 fmol/microg DNA). However, the time at which peak levels were reached showed large variation. The repair of the adducts was very efficient in the resistant cell lines whereas, in A2780 cells, plateau levels were retained until 24 h after CDDP exposure. In A2780 cells, dFdC shifted the adduct peaks from 4 h to directly after CDDP exposure and increased peak levels by >3.9-fold. dFdC also enhanced the repair of adducts by >1.7-fold and increased the Pt-GG:Pt-AG ratio compared to CDDP alone by >1.4-fold. Overall, dFdC decreased the area under the Pt-DNA adduct-time curve (AUA0-25 h) in A2780 cells by 2.7-fold. In ADDP cells, dFdC shifted the adduct peaks from 2 to 4 h and increased them by >2.2-fold. dFdC also increased the Pt-GG:Pt-AG ratio during the repair process by 1.4-fold. Overall, dFdC increased the AUA0-25 h in ADDP cells by 1.7-fold. In AG6000 cells, dFdC increased the Pt-GG:Pt-AG ratio by 1.6-fold directly after exposure but did not clearly affect the AUA0-25 h. In conclusion, dFdC can affect both Pt-DNA adduct formation and repair, depending on the initial sensitivity of the cells.