Multivariate analysis of cartilage degradation using the support vector machine algorithm.

An important limitation in MRI studies of early osteoarthritis is that measured MRI parameters exhibit substantial overlap between different degrees of cartilage degradation. We investigated whether multivariate support vector machine analysis would permit improved tissue characterization. Bovine nasal cartilage samples were subjected to pathomimetic degradation and their T(1), T(2), magnetization transfer rate (k(m) ), and apparent diffusion coefficient (ADC) were measured. Support vector machine analysis performed using certain parameter combinations exhibited particularly favorable classification properties. The areas under the receiver operating characteristic (ROC) curve for detection of extensive and mild degradation were 1.00 and 0.94, respectively, using the set (T(1), k(m), ADC), compared with 0.97 and 0.60 using T(1), the best univariate classifier. Furthermore, a degradation probability for each sample, derived from the support vector machine formalism using the parameter set (T(1), k(m), ADC), demonstrated much stronger correlations (r(2) = 0.79-0.88) with direct measurements of tissue biochemical components than did even the best-performing individual MRI parameter, T(1) (r(2) = 0.53-0.64). These results, combined with our previous investigation of Gaussian cluster-based tissue discrimination, indicate that the combinations (T(1), k(m)) and (T(1), k(m), ADC) may emerge as particularly useful for characterization of early cartilage degradation.

Compatibility of superparamagnetic iron oxide nanoparticle labeling for ¹H MRI cell tracking with ³¹P MRS for bioenergetic measurements.

Labeling of cells with superparamagnetic iron oxide nanoparticles permits cell tracking by (1)H MRI while (31)P MRS allows non-invasive evaluation of cellular bioenergetics. We evaluated the compatibility of these two techniques by obtaining (31)P NMR spectra of iron-labeled and unlabeled immobilized C2C12 myoblast cells in vitro. Broadened but usable (31)P spectra were obtained and peak area ratios of resonances corresponding to intracellular metabolites showed no significant differences between labeled and unlabeled cell populations. We conclude that (31)P NMR spectra can be obtained from cells labeled with sufficient iron to permit visualization by (1)H imaging protocols and that these spectra have sufficient quality to be used to assess metabolic status. This result introduces the possibility of using localized (31)P MRS to evaluate the viability of iron-labeled therapeutic cells as well as surrounding host tissue in vivo.

Nature of the nucleosomal barrier to RNA polymerase II.

In the cell, RNA polymerase II (pol II) efficiently transcribes DNA packaged into nucleosomes, but in vitro encounters with the nucleosomes induce catalytic inactivation (arrest) of the pol II core enzyme. To determine potential mechanisms making nucleosomes transparent to transcription in vivo, we analyzed the nature of the nucleosome-induced arrest. We found that the arrests have been detected mostly at positions of strong intrinsic pause sites of DNA. The transient pausing makes pol II vulnerable to arrest, which involves backtracking of the elongation complex for a considerable distance on DNA. The histone-DNA contacts reestablished in front of pol II stabilize backtracked conformation of the polymerase. In agreement with this mechanism, blocking of backtracking prevents nucleosome-induced arrest. Transcript cleavage factor TFIIS reactivates the backtracked complexes and promotes pol II transcription through the nucleosome. Our findings establish the crucial role of elongation factors that suppress pol II pausing and backtracking for transcription in the context of chromatin.