Raman fiber-optical method for colon cancer detection: Cross-validation and outlier identification approach.

Endoscopy plays a major role in early recognition of cancer which is not externally accessible and therewith in increasing the survival rate. Raman spectroscopic fiber-optical approaches can help to decrease the impact on the patient, increase objectivity in tissue characterization, reduce expenses and provide a significant time advantage in endoscopy. In gastroenterology an early recognition of malign and precursor lesions is relevant. Instantaneous and precise differentiation between adenomas as precursor lesions for cancer and hyperplastic polyps on the one hand and between high and low-risk alterations on the other hand is important. Raman fiber-optical measurements of colon biopsy samples taken during colonoscopy were carried out during a clinical study, and samples of adenocarcinoma (22), tubular adenomas (141), hyperplastic polyps (79) and normal tissue (101) from 151 patients were analyzed. This allows us to focus on the bioinformatic analysis and to set stage for Raman endoscopic measurements. Since spectral differences between normal and cancerous biopsy samples are small, special care has to be taken in data analysis. Using a leave-one-patient-out cross-validation scheme, three different outlier identification methods were investigated to decrease the influence of systematic errors, like a residual risk in misplacement of the sample and spectral dilution of marker bands (esp. cancerous tissue) and therewith optimize the experimental design. Furthermore other validations methods like leave-one-sample-out and leave-one-spectrum-out cross-validation schemes were compared with leave-one-patient-out cross-validation. High-risk lesions were differentiated from low-risk lesions with a sensitivity of 79%, specificity of 74% and an accuracy of 77%, cancer and normal tissue with a sensitivity of 79%, specificity of 83% and an accuracy of 81%. Additionally applied outlier identification enabled us to improve the recognition of neoplastic biopsy samples.

Local Mode Analysis: Decoding IR Spectra by Visualizing Molecular Details.

Integration of experimental and computational approaches to investigate chemical reactions in proteins has proven to be very successful. Experimentally, time-resolved FTIR difference-spectroscopy monitors chemical reactions at atomic detail. To decode detailed structural information encoded in IR spectra, QM/MM calculations are performed. Here, we present a novel method which we call local mode analysis (LMA) for calculating IR spectra and assigning spectral IR-bands on the basis of movements of nuclei and partial charges from just a single QM/MM trajectory. Through LMA the decoding of IR spectra no longer requires several simulations or optimizations. The novel approach correlates the motions of atoms of a single simulation with the corresponding IR bands and provides direct access to the structural information encoded in IR spectra. Either the contributions of a particular atom or atom group to the complete IR spectrum of the molecule are visualized, or an IR-band is selected to visualize the corresponding structural motions. Thus, LMA decodes the detailed information contained in IR spectra and provides an intuitive approach for structural biologists and biochemists. The unique feature of LMA is the bidirectional analysis connecting structural details to spectral features and vice versa spectral features to molecular motions.

Virtual staining of colon cancer tissue by label-free Raman micro-spectroscopy.

The great capability of the label-free classification of tissue via vibrational spectroscopy, like Raman or infrared imaging, is shown in numerous publications (review: Diem et al., J. Biophotonics, 2013, 6, 855-886). Herein, we present a new approach, virtual staining, that improves the Raman spectral histopathology (SHP) images of colorectal cancer tissue by combining the integrated Raman intensity image in the C-H stretching region (2800-3050 cm-1) with the pseudo-colour Raman image. This allows the display of fine structures such as the filamentous composition of muscle tissue. The morphology of the virtually stained images is in agreement with the gold standard in medical diagnosis, the haematoxylin-eosin staining. The virtual staining image also represents the whole biochemical fingerprint, and several tissue components including carcinoma were identified automatically with high sensitivity and specificity. For fast tissue classifications, a similar approach was applied on coherent anti-Stokes Raman scattering (CARS) spectral data that is faster and therefore potentially more suitable for clinical applications.

Femtochemistry of norrish type-I reactions: I. Experimental and theoretical studies of acetone and related ketones on the S1 surface.

The dissociation dynamics of two acetone isotopomers ([D0 ]- and [D6 ]acetone) after 93 kcal mol(-1) (307 nm) excitation to the S1 (n,π*) state have been investigated using femtosecond pump-probe mass spectrometry. We found that the nuclear motions of the molecule on the S1 surface involve two time scales. The initial femtosecond motion corresponds to the dephasing of the wave packet out of the Franck-Condon region on the S1 surface. For longer times, the direct observation of the build-up of the acetyl radical confirms that the S1 α-cleavage dynamics of acetone is on the nanosecond time scale. Density functional theory and ab initio calculations have been carried out to characterize the potential energy surfaces for the S0 , S1 , and T1 states of acetone and six other related aliphatic ketones. For acetone, the S1 energy barrier along the single α-positioned carbon-carbon (α-CC) bond-dissociation coordinate (to reach the S0 /S1 conical intersection) was calculated to be 18 kcal mol(-1) (∼110 kcal mol(-1) above the S0 minimum) for the first step of the nonconcerted α-CC bond cleavage; the concerted path is energetically unfavorable, consistent with experiments. The S1 barrier heights for other aliphatic ketones were found to be substantially lower than that of acetone by methyl substitutions at the α-position. The α-CC bond dissociation energy barrier of acetone on the T1 surface was calculated to be only 5 kcal mol(-1) (∼90 kcal mol(-1) above the S0 minimum), which is substantially lower than the barrier on the S1 surface. Based on the calculations, the α-cleavage reaction mechanism of acetone occurring on the S0 , S1 , and T1 surfaces can be better understood via a simple physical picture within the framework of valence-bond theory. The theoretical calculations support the conclusion that the observed nanosecond-scale S1 dynamics of acetone below the barrier is governed by a rate-limiting S1 →T1 intersystem crossing process followed by α-cleavage on the T1 surface. However, at high energies, the α-cleavage can proceed by barrier crossing on the S1 surface, a situation which is demonstrated for cyclobutanone in the accompanying paper.

Femtochemistry of Norrish type-I reactions: II. The anomalous predissociation dynamics of cyclobutanone on the S1 surface.

The anomalous nonradiative dynamics for three cyclobutanone isotopomers ([D0 ]-, 3,3-[D2 ]-, and 2,2,4,4-[D4 ]cyclobutanone) have been investigated using femtosecond (fs) time-resolved mass spectrometry. We have found that the internal motions of the molecules in the S1 state above the dissociation threshold involve two time scales. The fast motion has a time constant of <50 fs, while the slow motion has a time constant of 5.0±1.0, 9.0±1.5, and 6.8±1.0 ps for the [D0 ], [D2 ], and [D4 ] species, respectively. Density functional theory and ab initio calculations have been performed to characterize the potential energy surfaces for the S0 , S1 (n,π*), and T1 (n,π*) states. The dynamic picture for bond breakage is the following: The fast motion represents the rapid dephasing of the initial wave packet out of the Franck-Condon region, whereas the slow motion reflects the α-cleavage dynamics of the Norrish type-I reaction. The redistribution of the internal energy from the initially activated out-of-plane bending modes into the in-plane ring-opening reaction coordinate defines the time scale for intramolecular vibrational energy redistribution (IVR), and the observed picosecond-scale (ps) decay gives the rate of IVR/bond cleavage across the barrier. The observed prominent isotope effect for both [D2 ] and [D4 ] isotopomers imply the significance of the ring-puckering and the CO out-of-plane wagging motions to the S1 α-cleavage dynamics. The ethylene and ketene (C2 products)-as well as CO and cyclopropane (C3 products)-product ratios can be understood by the involvement of an S0 /S1 conical intersection revealed in our calculations. This proposed dynamic picture for the photochemistry of cyclobutanone on the S1 surface can account not only for the abnormally sharp decrease in fluorescence quantum yield and lifetime but also for the dramatic change in the C3 :C2 product ratio as a function of increasing excitation energy, as reported by Lee and co-workers (J. C. Hemminger, E. K. C. Lee, J. Chem. Phys. 1972, 56, 5284-5295; K. Y. Tang, E. K. C. Lee, J. Phys. Chem. 1976, 80, 1833-1836).