Prognostic factors in prostate cancer

Prognostic factors in organ confined prostate cancer will reflect survival after surgical radical prostatectomy. Gleason score, tumour volume, surgical margins and Ki-67 index have the most significant prognosticators. Also the origins from the transitional zone, p53 status in cancer tissue, stage, and aneuploidy have shown prognostic significance. Progression-associated features include Gleason score, stage, and capsular invasion, but PSA is also highly significant. Progression can also be predicted with biological markers (E-cadherin, microvessel density, and aneuploidy) with high level of significance. Other prognostic features of clinical or PSA-associated progression include age, IGF-1, p27, and Ki-67. In patients who were treated with radiotherapy the survival was potentially predictable with age, race and p53, but available research on other markers is limited. The most significant published survival-associated prognosticators of prostate cancer with extension outside prostate are microvessel density and total blood PSA. However, survival can potentially be predicted by other markers like androgen receptor, and Ki-67-positive cell fraction. In advanced prostate cancer nuclear morphometry and Gleason score are the most highly significant progression-associated prognosticators. In conclusion, Gleason score, capsular invasion, blood PSA, stage, and aneuploidy are the best markers of progression in organ confined disease. Other biological markers are less important. In advanced disease Gleason score and nuclear morphometry can be used as predictors of progression. Compound prognostic factors based on combinations of single prognosticators, or on gene expression profiles (tested by DNA arrays) are promising, but clinically relevant data is still lacking

Constructing Periodic Phase Space Orbits from <i>ab Initio</i> Molecular Dynamics Trajectories to Analyze Vibrational Spectra: Case Study of the Zundel (H₅O₂⁺) Cation

A method of analysis is introduced to probe the spectral features obtained from <i>ab initio</i> molecular dynamics simulations. Here, the instantaneous mass-weighted velocities are projected onto irreducible representations constructed from discrete time translation groups comprising operations that invoke the time-domain symmetries (or periodic phase space orbits) reflected in the spectra. The projected velocities are decomposed using singular value decomposition (SVD) to construct a set of “modes” pertaining to a given frequency domain. These modes now include all anharmonicities, as sampled during the dynamics simulations. In this approach, the underlying motions are probed in a manner invariant with respect to coordinate transformations, operations being performed along the time axis rather than coordinate axes, making the analysis independent of choice of reference frame. The method is used to probe the underlying motions responsible for the doublet at ∼1000 cm^–1 in the vibrational spectrum of the H₅O₂⁺, Zundel cation. The associated analysis results are confirmed by projecting the Fourier transformed velocities onto the harmonic normal mode coordinates and a set of mass-weighted, symmetrized Jacobi coordinates. It is found that the two peaks of the doublet are described and differentiated by their respective contributions from the proton transfer, water–water stretch, and water wag coordinates, as these are defined. Temperature dependent effects are also briefly noted