Ensembles of protein termini and specific proteolytic signatures as candidate biomarkers of disease

Early accurate diagnosis and personalized treatment are essential in order to treat complex or fatal diseases such as cancer and autoimmune, cardiovascular and neurodegenerative diseases. To realize this vision, new diagnostic and prognostic biomarkers are urgently required. MS-based proteomics is the most promising approach for protein biomarker identification, but suffers in clinical translation of biomarker candidates that show only quantitative differences from normal tissue. Indeed, success in translating proteomic data to biomarkers in the clinic has been disappointing. Here, we propose that protein termini provide a new opportunity for biomarker discovery due to qualitative differences in intact and new protein termini between diseased and normal tissues. Altered proteolysis occurs in most pathologies. Disease- and process-specific protein modifications, including proteolytic processing and subsequent modification of the terminal amino acids, frequently lead to altered protein activity that plays key roles in the disease process. Thus, mapping of ensembles of characteristic protein termini provides a proteolytic signature of high information content that shows both quantitative and most importantly qualitative differences in different diseases and stage of disease. These unique protein biomarkers have the added benefit of being mechanistically informative by revealing the activity state of the bioactive protein. Moreover, proteome-wide isolation of protein termini leads to generalized sample simplification, thereby enabling up to three orders of magnitude lower LODs compared to traditional shotgun proteomic approaches. We introduce the potential of protein termini for biomarker discovery, briefly review methods enabling large-scale studies of protein termini, and discuss how these may be integrated into a termini-oriented biomarker discovery pipeline from discovery to clinical application.     

Determining the Number of Clusters by Sampling With Replacement.

A split-sample replication criterion originally proposed by J. E. Overall and K. N. Magee (1992) as a stopping rule for hierarchical cluster analysis is applied to multiple data sets generated by sampling with replacement from an original simulated primary data set. An investigation of the validity of this bootstrap procedure was undertaken using different combinations of the true number of latent populations, degrees of overlap, and sample sizes. The bootstrap procedure enhanced the accuracy of identifying the true number of latent populations under virtually all conditions. Increasing the size of the resampled data sets relative to the size of the primary data set further increased accuracy. A computer program to implement the bootstrap stopping rule is made available via a referenced Web site. (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Comparative evaluation of two models for estimating sample sizes for tests on trends across repeated measurements

The emotional content of stimuli can enhance memory for those stimuli. This process may occur via an interaction with systems responsible for perception and memory or via the addition of distinct brain regions specialized for emotion which augment mnemonic processing. We performed an 15O PET study to identify neuroanatomical systems which encode visual stimuli with strong negative emotional valence compared to stimuli with neutral valence. Subjects also performed a recognition memory task for these same images, mixed with distracters of similar emotional valence. The experimental design permitted us to independently test effects of emotional content and recognition memory on regional activity. We found activity in the left amygdaloid complex associated with the encoding of emotional stimuli, although this activation appeared early in the scanning session and was not detectable during recognition memory. Visual recognition memory recruited the right middle frontal gyrus and the superior anterior cingulate cortex for both negative and neutral stimuli. An interaction occurred between emotional content and recognition in the lingual gyrus, where greater activation occurred during recognition of negative images compared to recognition of neutral images. Instead of distinct neuroanatomical systems for emotion augmenting memory, we found that emotionally salient stimuli appeared to enhance processing of early sensory input during visual recognition.     

Midterm feedback from students: Its relationship to instructional improvement and students' cognitive and affective outcomes.

Feedback from student ratings collected at midterm resulted in (a) more favorable student ratings at the end of the term, (b) better final examination scores, and (c) more favorable affective outcomes. Ss were the 931 students in 30 sections of a course in computer programming. Randomly selected instructors were given feedback from midterm ratings and met with the authors to discuss the ratings and strategies for improvement. Ss in the feedback sections were similar to other Ss in terms of pretest scores and midterm ratings. These findings and a review of the literature suggest that feedback from student ratings, particularly when coupled with a frank discussion of their implications with an external consultant, can be an effective intervention for improving teaching effectiveness. (13 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

A novel organ culture method to study the function of human odontoblasts in vitro: gelatinase expression by odontoblasts is differentially regulated by TGF-beta1

Odontoblasts cannot be cultured by traditional cell culture methods, thus restricting in vitro studies. Here we present an organ culture method for human odonto-blasts that utilizes the pulp chamber as a culture crucible. Crowns of human third molars were dissected, pulp was gently removed, and the odontoblasts attached to and in the walls of the pulp chambers were cultured in serum-free OPTI-MEM medium, or DMEM/Ham's F12 medium containing 10% serum. Pulp tissues were cultured separately. Cell content and morphology were analyzed by SEM, and the removed pulps were examined by light microscopy. Proteins secreted into the medium with or without TGF-beta1 supplementation were metabolically labeled with [35S]methionine, and the total protein content was assessed by TCA precipitation and SDS-PAGE/fluorography. To assess the role of gelatinolytic enzymes on dentin matrix remodeling, we used enzymography to analyze the effect of TGF-beta1 on gelatinase A and B expression. SEM revealed odontoblasts in pulp chambers after 5 days of culture, with only few or no fibroblasts, and no alterations in the odontoblast cell morphology or differences between the cells cultured in serum-free and serum-containing media. Rarely were any odontoblasts present in pulp tissue. Radiolabeling revealed protein synthesis and secretion until day 6 in both the odontoblast and pulp cultures, with no marked differences between TGF-beta1-treated and control cultures. The level of gelatinase A remained constant up to 7 days, while gelatinase B expression was always low and decreased with time in culture. However, gelatinase B levels were markedly increased upon TGF-beta1 treatment of cells and remained high to day 7. The results suggest that this method provides a novel technique for the study of human odontoblasts in vitro and that odontoblasts can be cultured even in serum-free conditions.     

Computer simulation of alternative sampling strategies to estimate risk of infection from Cryptosporidium

Microbial growth, sensory and chemical changes and composition of gas atmosphere were studied in vacuum packed (VP) and modified atmosphere packed (MAP) cod fillets stored at 0 degree C. Contrary to previous studies, coccobacilli and pleomorphic Gram-negative microorganisms (2-4 by 2-5 microns) and not Shewanella putrefaciens were found most likely to be the main spoilage organisms. These microorganisms, which may be Photobacterium phosphoreum, can explain the short shelf-life extension of VP and MAP fish products compared to meat products. It is suggested that they may inhibit the typical H2S-producing fish spoilage bacteria, S. putrefaciens, as the maximum concentration of H2S-producing bacteria found in MAP fish products is very low. Compared to VP, a shelf-life extension of 6-7 days was obtained with 48% CO2 in MAP. However, with pure CO2 the shelf life was only extended by 2-3 days. Poor texture and high drip loss indicated that the shelf life of these fillets was limited by chemical reactions and not only by microbial activity.     

Decision rules for phenomenological classification of psychiatric patients.

Used cluster analysis and related numerical taxonomy methods to identify 8 distinct phenomenological types in the psychiatric population, and prototype patterns for the types are described in terms of the Brief Psychiatric Rating Scale (BPRS) profiles. Numerical methods are provided for classifying individual patients based on similarity to the prototype patterns. Patients can also be classified operationally by simple decision rules involving 2-point code typing of BPRS profile patterns. (15 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)     

Students' evaluations of instruction: A longitudinal study of their stability.

Investigated the long-term stability of students' evaluations of instructional effectiveness. Ss were 1,374 undergraduate and graduate business administration majors from 100 classes who completed their programs at a comprehensive state university between 1974 and 1977. Each S provided course and instructor evaluations at the end of each class and again at least 1 yr after program completion. Results show large and significant correlations (median r?=?.83) between end-of-term and retrospective ratings (relative agreement). Differences between the 2 sets of ratings (absolute agreement) were small; the median rating was 6.63 for retrospective ratings and 6.61 for end-of-term ratings. Separate analyses showed relative and absolute agreement to be consistent in quantitative and nonquantitative courses taught at both graduate and undergraduate levels. These findings demonstrate that students' evaluations collected at the end of a course are remarkably similar to the retrospective ratings provided by the same students several years later. (15 ref) (PsycINFO Database Record (c) 2010 APA, all rights reserved)