Deep learning data augmentation for Raman spectroscopy cancer tissue classification.

Recently, Raman Spectroscopy (RS) was demonstrated to be a non-destructive way of cancer diagnosis, due to the uniqueness of RS measurements in revealing molecular biochemical changes between cancerous vs. normal tissues and cells. In order to design computational approaches for cancer detection, the quality and quantity of tissue samples for RS are important for accurate prediction. In reality, however, obtaining skin cancer samples is difficult and expensive due to privacy and other constraints. With a small number of samples, the training of the classifier is difficult, and often results in overfitting. Therefore, it is important to have more samples to better train classifiers for accurate cancer tissue classification. To overcome these limitations, this paper presents a novel generative adversarial network based skin cancer tissue classification framework. Specifically, we design a data augmentation module that employs a Generative Adversarial Network (GAN) to generate synthetic RS data resembling the training data classes. The original tissue samples and the generated data are concatenated to train classification modules. Experiments on real-world RS data demonstrate that (1) data augmentation can help improve skin cancer tissue classification accuracy, and (2) generative adversarial network can be used to generate reliable synthetic Raman spectroscopic data

Discovery of small molecule inhibitors of xyloglucan endotransglucosylase (XET) activity by high-throughput screening

AbstractSmall molecules (xenobiotics) that inhibit cell-wall-localised enzymes are valuable for elucidating the enzymes’ biological roles. We applied a high-throughput fluorescent dot-blot screen to search for inhibitors of Petroselinum xyloglucan endotransglucosylase (XET) activity in vitro. Of 4216 xenobiotics tested, with cellulose-bound xyloglucan as donor-substrate, 18 inhibited XET activity and 18 promoted it (especially anthraquinones and flavonoids). No compounds promoted XET in quantitative assays with (cellulose-free) soluble xyloglucan as substrate, suggesting that promotion was dependent on enzyme–cellulose interactions. With cellulose-free xyloglucan as substrate, we found 22 XET-inhibitors – especially compounds that generate singlet oxygen (1O2) e.g., riboflavin (IC50 29μM), retinoic acid, eosin (IC50 27μM) and erythrosin (IC50 36μM). The riboflavin effect was light-dependent, supporting 1O2 involvement. Other inhibitors included tannins, sulphydryl reagents and triphenylmethanes. Some inhibitors (vulpinic acid and brilliant blue G) were relatively specific to XET, affecting only two or three, respectively, of nine other wall-enzyme activities tested; others [e.g. (−)-epigallocatechin gallate and riboflavin] were non-specific. In vivo, out of eight XET-inhibitors bioassayed, erythrosin (1μM) inhibited cell expansion in Rosa and Zea cell-suspension cultures, and 40μM mycophenolic acid and (−)-epigallocatechin gallate inhibited Zea culture growth. Our work showcases a general high-throughput strategy for discovering wall-enzyme inhibitors, some being plant growth inhibitors potentially valuable as physiological tools or herbicide leads

The Mechanism of Formation of N-Formylkynurenine by Heme Dioxygenases

[Image: see text] Heme dioxygenases catalyze the oxidation of l-tryptophan to N-formylkynurenine (NFK), the first and rate-limiting step in tryptophan catabolism. Although recent progress has been made on early stages in the mechanism, there is currently no experimental data on the mechanism of product (NFK) formation. In this work, we have used mass spectrometry to examine product formation in a number of dioxygenases. In addition to NFK formation (m/z = 237), the data identify a species (m/z = 221) that is consistent with insertion of a single atom of oxygen into the substrate during O(2)-driven turnover. The fragmentation pattern for this m/z = 221 species is consistent with a cyclic amino acetal structure; independent chemical synthesis of the 3a-hydroxypyrroloindole-2-carboxylic acid compound is in agreement with this assignment. Labeling experiments with (18)O(2) confirm the origin of the oxygen atom as arising from O(2)-dependent turnover. These data suggest that the dioxygenases use a ring-opening mechanism during NFK formation, rather than Criegee or dioxetane mechanisms as previously proposed

Near threshold photochemistry of propanal: barrier height, transition state structure and product state distributions for the HCO channel

The photodissociation dynamics of propanal have been investigated at photolysis wavelengths between 300 and 327 nm. The threshold for production of HCO fragments was found to be 326.26 nm, which corresponds to 30645 cm-1 (366.6 kJ mol-1) above the zero-point of the S0 state. From known thermochemical data, this threshold lies 25.0 ± 3.6 kJ mol-1 above the bond dissociation energy. The nascent HCO rotational and translational energy distributions were determined following dissociation at threshold. The rotational population was measured as a function of N, Ka, Kc, and S. The distribution of rotational states followed a Gaussian function with an average rotational energy of 2.5 ± 0.5 kJ mol-1. The population of the near-degenerate spin-rotation states was equal, while the population in the asymmetry doublets favored the upper energy component by about 3:1. Careful measurement of the Doppler profiles of individual Ka = 0 lines in the LIF spectrum revealed that the translational energy also shows a Gaussian-like distribution with an average energy of 6.5 ± 1.0 kJ mol-1. The ethyl fragment must also have an average translational energy of 6.5 ± 1.0 kJ mol-1 and therefore an average internal energy of 9.5 kJ mol-1 is inferred. The observed energy partitioning in the fragments is consistent with a model in which the HCO rotational and translational excitation is determined mostly by the transition state geometry, a barrier on the triplet surface, and the fixed energy in the exit channel. A modified impulsive model was satisfactory in reproducing the energy deposited into the various degrees of freedom. The model implied impact parameters at infinite separation corresponding to an in-plane HCO angle of 40 and an out-of-plane angle of 60. The strongly pyramidal nature of the transition state produces more angular momentum about the b axis than the c axis, which causes the preference for the upper energy component of the asymmetry doublets.Gregory F. Metha, Andrew C. Terentis, and Scott H. Kabl

HCO (N,Ka,Kc,J) distributions from near-threshold photolysis of H2CO (J,Ka,Kc)

Copyright © 1998 American Institute of PhysicsThe dynamics of the reaction H2CO+hv(λ≈330 nm)→H+HCO have been studied following excitation of formaldehyde into the à (1A2) state, just above the dissociation threshold of the X̃(1A2) state. Formaldehyde was excited via specific J, Ka, Kc rotational states and the ensuing rotational distribution of HCO measured by fully resolving N, Ka, Kc, and J=N±S of the fragment. When only the N and Ka quantum numbers of both formaldehyde and the formyl radical are considered, the distributions are generally modeled well by phase space theory (PST). Within≈10cm-1 of the threshold, however, the PST predictions consistently exceed the experimental populations. This was accounted for by the inclusion of a centrifugal barrier in the PST model. The attractive part of the effective centrifugal potential was modeled by a dipole-induced dipole plus dispersion interaction. The barrier is weak and long range (>5 Å). Resolution of Kc in the reaction, in both parent and product, gave large deviations from the PST model. The HCO population distributions separate according to whether Kc was the upper- or lower-energy state. Additionally, the upper/lower preference was sensitive to the choice of Kc in the parent. Insufficient data are currently available to quantify this observation. The product state distribution was also found to be independent of the spin-rotation state of HCO. © 1997 American Institute of Physics.Andrew C. Terentis, Siobhan E. Waugh, Gregory F. Metha, and Scott H. Kabl

Conservation of angular momentum in polyatomic photochemical reactions: H(2)CO(v,J,Ka,Kc)->H+HCO(N,Ka,Kc,J)

Laser Techniques for State-Selected and State-to-State Chemistry IV / John W. Hepburn, Robert E. Continetti, Mark A. Johnson (eds.), pp. 36-46The photodissociation dynamics of the reaction H2CO + hv → H + HCO have been investigated just above the reaction threshold (λdiss ≈ 330 nm). Formaldehyde was excited into specific J, Ka, Kc rotational states of three vibrational levels in the à (1A2) state. Molecules in these states undergo internal conversion back to the X̃ (1A1) ground state on which the radical fragments are formed. The ensuing distribution of rotational energy in the HCO fragment was measured as a function of the N, Ka, Kc and J = N ± S quantum numbers of the fragment, and also the initial v, J, Ka, Kc quantum numbers of the parent. In a previous publication (J. Chem. Phys., in press) we investigated the dynamics of this reaction at low available energy and concluded that when only the N and Ka quantum numbers of both formaldehyde and the formyl radical are considered, the distributions are modelled well by phase space theory (PST). This is consistent with statistical dynamics on a bound, barrierless surface. Within ≈10 cm-1 of the energetic threshold, a centrifugal barrier affected the populations by inhibiting product states that require large orbital angular momentum. Resolution of Kc in the parent and product gave large deviations from the PST model, however little data were available to quantify this observation. In this work we have extended the number of initially excited H2CO levels to explore this "Kc effect" further. We find that in the HCO Ka = 1 manifold there is always a preference (up to 5:1) for HCO to be produced in either the higher energy Kc state (N1,N-1) or the lower energy state (N1,N). This preference is consistent over all N for any particular initial H2CO state but may vary for different initial states. Over the seven initial states probed here, four favoured Kc (lower) and the other three Kc (upper). A correlation between this Kc preference and the initial state was observed: odd Kc formaldehyde states produce Kc (lower) preference in HCO and vice versa for initially even Kc states. A comparison with one previous observation of this effect is presented, however no concrete explanation can be offered at this stage.Siobhan E. Waugh, Andrew C. Terentis, Gregory F. Metha and Scott H. Kabl