Role of artificial intelligence and vibrational spectroscopy in cancer diagnostics

ABSTRACT

Introduction

Raman and Infrared spectroscopic techniques are being used for the analysis of different types of cancers and other biological molecules. It is possible to identify cancers from normal tissues both in fresh and fixed tissues. These techniques can be used not only for the early diagnosis of cancer but also for monitoring the progression of the disease. Furthermore, chemical pathways to the progression of the disease process can be understood and followed.     

Lightweight Raman spectroscope using time-correlated photon-counting detection

Raman spectroscopy is an important tool in understanding chemical components of various materials. However, the excessive weight and energy consumption of a conventional CCD-based Raman spectrometer forbids its applications under extreme conditions, including unmanned aircraft vehicles (UAVs) and Mars/Moon rovers. In this article, we present a highly sensitive, shot-noise–limited, and ruggedized Raman signal acquisition using a time-correlated photon-counting system. Compared with conventional Raman spectrometers, over 95% weight, 65% energy consumption, and 70% cost could be removed through this design. This technique allows space- and UAV-based Raman spectrometers to robustly perform hyperspectral Raman acquisitions without excessive energy consumption.Raman spectroscopy is a valuable tool for probing chemical composition. It is widely applied in chemical analysis of molecular species and structures of chemical bonds (1, 2), and is therefore widely extended to the fields of biomedical imaging (e.g., refs. 3–5), material science (e.g., ref. 6), and remote sensing (e.g., ref. 7). Comparing with other molecular-specific imaging techniques, Raman spectroscopy provides a label-free contrast mechanism, which is intrinsically induced by the molecules contained in the sample. Relying on internal properties of molecules, investigators can avoid complicated sample preparation processes and molecular-specific labeling, etc. In many imaging/sensing applications, Raman spectroscopy often provides superior molecular specificity, imaging speed, and spectral resolution, and is usually considered as an emerging imaging technique (8, 9). However, despite decades of intensive study, Raman spectroscopy is still not widely applicable in space-based detection systems including unmanned aircraft vehicles (UAVs) and Mars/Moon rovers. This is mainly due to two hurdles: the unacceptable heavy weight of conventional spectrometers, and the excessive energy consumption by the entire system, especially the CCD camera.In typical laboratory-based Raman spectroscope setups, a beam of light is focused onto the sample. The scattered photons are then collected by a condenser lens and sent into a spectrometer. A diffractive grating is usually used to induce a spatial dispersion of the Raman peaks into different wavelengths. A CCD camera is used as the detector. In this sense, a correspondence between the CCD pixel and Raman shift can be established, and the Raman peaks are recognized and recorded.However, when extending this approach to field circumstances (e.g., space-based vehicles or UAVs), several key limitations emerge. First, due to the tiny angular dispersion provided by diffractive gratings, a long optical propagation length is required to create sufficient spatial dispersion. This is usually not allowed in space-based vehicles. Moreover, this long propagation length, together with any possible moving parts contained in the grating-based spectrometers, is unable to tolerate excessive vibrations during the launching/landing process of a space-based vehicle. Furthermore, the excessive energy consumption for the CCD cameras, especially for the cooling process, is usually not affordable by UAVs or space-based vehicles/rovers. Finally, the weight of the spectrometer is also a problem (10–12).To overcome these difficulties, investigators invented and used several different approaches. For example, to remove the diffraction grating, Lewis et al. (13) and several other investigators (14, 15) adopted acoustooptic tunable filters (AOTFs). In this solution, an acoustic-optical (AO) device was applied as a tunable-wavelength filter/switch. By tuning the rf driving frequency, the diffraction window of the AO devices could be controlled according to the phase-matching condition (16, 17). Because AOTF only allows one wavelength to transmit at a time, single-point detectors, including photomultiplier tubes (PMTs) and avalanche photodiodes (APDs), could replace the CCD detectors. In this way, the total weight and energy consumption of the system could be substantially reduced. However, the angular dispersion provided by AOTFs is usually very tiny. To acquire a sufficient spatial dispersion, its output still needs a relatively long propagation length in free space. When working under environments with excessive vibrations, the mechanical stability of this solution may be problematic. The all-fiber optical spectrometers reported by Redding et al. (18) are another viable solution to remove the diffractive grating. In this approach, a multimode fiber was used to produce wavelength-dependent sparkle patterns. By recognizing the output pattern of the multimode fiber, the wavelength can be acquired. Additionally, surface-enhanced Raman scattering is also a possible solution in fabricating lightweight Raman spectroscopes (e.g., refs. 19, 20). The enhanced Raman signal strength enables noncooled CCD camera/photodiode detectors to be implemented as signal receivers. However, this solution may not be suitable for remote-sensing applications, as it requires investigators to directly manipulate the sample and decorate it with nanoparticles. Besides the aforementioned approaches, random Raman lasing is an emerging technique which may be suitable for remote chemical identification (7), as it would guarantee the signal brightness and detection efficiency (see Fig. 1).Open in a separate windowFig. 1.Weight and energy consumption are two major factors limiting broad applications of sensitive spectroscopic techniques for UAVs and Mars/Moon rovers.In this article, we report yet another approach for building lightweight Raman spectroscopes. We address the two main hurdles––a relatively heavy spectrometer and an excessive energy consumption––by reinventing the way that the Raman signal can be collected and analyzed. Short light pulses propagate in dispersive mediums in a fashion that is equivalent to how a light beam diffracts (21–24). In this study, we direct the collected Raman signal into a dispersive single-mode optical fiber. In this way, the Raman peaks at different wavelengths can be separated in the time domain (25). By using a time-gated APD or a PMT in combination with time-correlated detection, we are able to achieve highly sensitive signal detection. We note that similar approaches have been introduced elsewhere in the field of telecommunication (e.g., refs. 23, 26–28). For example, coherent time-stretch transformation has been applied in capturing high-speed rf signals in real time. By slowing down the analog electrical signals before digitization, coherent time-stretch transformation is capable of extending the bandwidth and resolution of analog to digital converters (27–29). This concept has also been implemented in fabricating temporal lenses and prisms in the field of all-optical signal processing (23). These temporal optical components substantially extended the applicability of integrated optical waveguide components (26).Fig. 2 illustrates the concept of time–frequency duality used in this study. Fig. 2 (Left) shows the wavelength–time distribution of the Raman signal before sending it into the dispersive medium, whereas Fig. 2 (Right) portrays the same relationship after propagating through a sufficiently long distance in the dispersive medium. In the case described on the left, the Raman peaks can be separated in the frequency domain, but are mixed in the time domain. After propagating in a sufficiently long dispersive medium, the peaks with different frequencies are temporally separated. The red line on the right illustrates a typical dispersion law.Open in a separate windowFig. 2.Physics of time–frequency duality. (Left) Time–frequency distribution of the signal excited by a short laser pulse; projection on the y axis provides Raman spectrum. (Right) Distribution of the same signal after transmitting through the dispersive medium.Fig. 3 schematically illustrates the experimental setup in this study. To practically implement the time-gated Raman detection, we used a time-correlated single-photon-counting (TCSPC) system (Becker & Hickl, model SPC-150) with a multichannel plate photomultiplier tube (MCP-PMT, Hamamatsu Corp., model R3809U-50) with a transit time spread (TTS) of 25 ps. An APD (Becker & Hickl, model APM-400, TTS = 40 ps) was also implemented in some experiments during this study. To create sufficient chromatic dispersion and avoid modal dispersion, we selected a 400-m-long single-mode fiber (Fibercore Inc., model SM600, ∼6 g in weight). The pump laser was focused on the sample by an objective lens (Edmund Inc., N.A. = 0.4). The transmitted radiation was collected by an identical objective lens and directed into the single-mode fiber by another focusing lens. To avoid any possible fiber-induced Raman/fluorescence background resulting by the excitation laser, we blocked the 532-nm pulses using two 532-nm notch filters (OD = 4, Edmund Inc.) and one long-pass filter (OD ≥ 6, cut-on wavelength: 537.3 nm, Edmund Inc.). The fluorescence backgrounds originated by Raman pulses, due to their long lifetime and low strength, will not affect our measurements. The output signal of the fiber was collimated and sent into both the MCP-PMT/APD and a conventional spectrometer (InSpectrum 300, Acton Inc.), respectively. In addition, a small portion of the pump laser was sent to trigger the TCSPC card. An appropriate delay line was applied in the detection. The detection lasted for 60 ns after the excitation pulse (532 nm). Thus, the nominal temporal interval for each channel (4,096 channels in total) was ∼15 ps, which defined the temporal resolution for this setup.Open in a separate windowFig. 3.Basic experimental setup. Here a 532-nm picosecond laser, which was generated from a home-built 100-kHz Nd:YVO₄ laser, was directed and focused to the sample. The transmitted light was collected and directed to a 400-m-long single-mode fiber (Fibercore Inc., model SM600). The output signal of the single-mode fiber was sent to the MCP-PMT or the APD. The time-resolved signal is measured by the TCSPC card.     

New optical technologies for earlier endoscopic diagnosis of premalignant gastrointestinal lesions

Gastrointestinal malignancies continue to be the second leading cause of cancer-related deaths in the developed world. The early detection and treatment of gastrointestinal preneoplasms has been demonstrated to significantly improve patient survival. Conventional screening tools include standard white light endoscopy (WLE) and frequent surveillance with biopsy. Well-defined endoscopic surveillance biopsy protocols aimed at early detection of dysplasia and malignancy have been undertaken for groups at high risk. Unfortunately, the poor sensitivity associated with WLE is a significant limitation. In this regard, major efforts continue in the development and evaluation of alternative diagnostic techniques. This review will focus on notable developments made at the forefront of research in modern gastrointestinal endoscopy based on novel optical endoscopic modalities, which rely on the interactions of light with tissues. Here we present the 'state - of - the - art' in fluorescence endoscopic imaging and spectroscopy, Raman spectroscopy, optical coherence tomography, light scattering spectroscopy, chromoendoscopy, confocal fluorescence endoscopy, and immunofluorescence endoscopy. These new developments may offer significant improvements in the diagnosis of early lesions by allowing for targeted mucosal excisional biopsies, and perhaps may even provide 'optical biopsies' of equivalent histological accuracy. This enhancement of the endoscopist's ability to detect subtle preneoplastic changes in the gastrointestional mucosa in real time and improved staging of lesions could lead to curative endoscopic ablation of these lesions and, in the long term, improve patient survival and quality of life.     

乳腺纤维腺瘤表面增强拉曼光谱学特点及其临床意义

目的：采用壳层隔绝纳米粒子增强拉曼光谱(SHINRES)检测乳腺纤维腺瘤和正常乳腺组织,通过探讨乳腺纤维腺瘤光谱学特点,探讨乳腺纤维腺瘤的生物学特征和鉴别方法。方法：收集乳腺外科手术患者的乳腺组织冰冻切片,共26例,均为女性,年龄19~59岁,乳腺纤维腺瘤17例,正常乳腺组织9例。冰冻切片解冻后先行普通拉曼光谱检测,加壳层隔绝纳米粒子(SHINs)后再次检测。共收集了243个拉曼光谱和273个SHINRES光谱,所有的光谱均进行基线修正拟合,再将所有的光谱用Adjacent-Averaging算法进行15点平滑。结果：普通拉曼光谱检测,正常乳腺组织特征峰出现在1 090、1 157、1 262、1 300、1 442、1 658、1 745和1 874 cm^-1;
在加入SHINs后,少数特征峰的峰位出现2~3 cm-1位移,其中1 090和1 157 cm^-1相对强度明显增加,出现1 496 cm-1特征峰。纤维腺瘤主要的特征峰出现在751、880、930、1 157、1 262、1 442、1 579、1 658和1 745 cm^-1,其中主导的特征峰应归属为脂类,但可见蛋白酰胺Ⅰ带特征峰。结论：拉曼光谱能够发现乳腺正常组织和纤维腺瘤组织中明显的蛋白酰胺Ⅰ带特征峰的差异。利用SHINs对不同类型的乳腺组织最大增强的特征峰不同以及特征峰的最大增强倍数不同,可
以区分乳腺纤维腺瘤和正常乳腺组织。
     

Formation of Iron Sulfides on Carbon Steel in a Specific Cement Grout Designed for Radioactive Waste Repository and Associated Corrosion Mechanisms

Carbon steel coupons were buried in a specific low-pH cement grout designed for radioactive waste disposal and left 6 months in anoxic conditions at 80 °C. The corrosion product layers were analyzed by µ-Raman spectroscopy, XRD, and SEM. They proved to be mainly composed of iron sulfides, with magnetite as a minor phase, mixed with components of the grout. Average corrosion rates were estimated by weight loss measurements between 3 and 6 µm yr⁻¹. Corrosion profiles revealed local degradations with a depth up to 10 µm. It is assumed that the heterogeneity of the corrosion product layer, mainly composed of conductive compounds (FeS, Fe₃S₄, and Fe₃O₄), promotes the persistence of corrosion cells that may lead to locally aggravated degradations of the metal. New cement grouts, characterized by a slightly higher pH and a lower sulfide concentration, should then be designed for the considered application.     

Coupling Raman,Brillouin and Nd3+ Photo Luminescence Spectroscopy to Distinguish the Effect of Uniaxial Stress from Cooling Rate on Soda–Lime Silicate Glass

Evolution of spectroscopic properties of a soda–lime silicate glass with different thermal history and under applied uniaxial stress was investigated using Raman and Brillouin spectroscopies as well as Nd³⁺ photoluminescence techniques. Samples of soda–lime silicate with a cooling rate from 6 × 10⁻⁴ to 650 K/min were prepared either by controlled cooling from the melt using a differential scanning calorimeter or by a conventional annealing procedure. Uniaxial stress effects in a range from 0 to −1.3 GPa were investigated in situ by compression of the glass cylinders. The spectroscopic observations of rearrangements in the network structure were related to the set cooling rates or the applied uniaxial stress to calculate an interrelated set of calibrations. Comparing the results from Raman and Brillouin spectroscopy with Nd³⁺ photoluminescence analysis, we find a linear dependence that can be used to identify uniaxial stress and cooling rate in any given combination concurrently. The interrelated calibrations and linear dependence models are established and evaluated, and equations relating the change of glass network due to effects of cooling rate or uniaxial stress are given.     

Crystal structure of aldoxime dehydratase and its catalytic mechanism involved in carbon-nitrogen triple-bond synthesis

Aldoxime dehydratase (OxdA), which is a unique heme protein, catalyzes the dehydration of an aldoxime to a nitrile even in the presence of water in the reaction mixture. Unlike the utilization of H₂O₂ or O₂ as a mediator of catalysis by other heme-containing enzymes (e.g., P450), OxdA is notable for the direct binding of a substrate to the heme iron. Here, we determined the crystal structure of OxdA. We then constructed OxdA mutants in which each of the polar amino acids lying within ∼6 Å of the iron atom of the heme was converted to alanine. Among the purified mutant OxdAs, S219A had completely lost and R178A exhibited a reduction in the activity. Together with this finding, the crystal structural analysis of OxdA and spectroscopic and electrostatic potential analyses of the wild-type and mutant OxdAs suggest that S219 plays a key role in the catalysis, forming a hydrogen bond with the substrate. Based on the spatial arrangement of the OxdA active site and the results of a series of mutagenesis experiments, we propose the detailed catalytic mechanism of general aldoxime dehydratases: (i) S219 stabilizes the hydroxy group of the substrate to increase its basicity; (ii) H320 acts as an acid-base catalyst; and (iii) R178 stabilizes the heme, and would donate a proton to and accept one from H320.     

A Critical Comparison of Some Raman Spectroscopic Techniques for Studies of Human Stratum Corneum

This study evaluates a variety of techniques and sampling conditions for Raman spectroscopic investigations of human stratum corneum. Using a Fourier-transform Raman system and samples of stratum corneum in vitro, we demonstrated minimal inter- and intracadaver variations in molecular vibrations. We have also shown Raman spectroscopy to be relatively insensitive to the hydration state of human stratum corneum, indicating that the technique should be valuable for monitoring the transdermal delivery of drugs from aqueous solutions. The stability of human stratum corneum to near-infrared laser excitation was verified by spectral collection for approximately 1 hr. We have also compared FT-Raman spectra from human stratum corneum in vitro and in vivo. Of the different types of Raman instruments used in this study (visible-light excitation microprobe, visible-light excitation macroscopic sampling, and Fourier-transform Raman), the FT-Raman system provided good-quality spectra with high sample throughput, but systems using visible-light excitation should provide unique information for use in specialist applications.     

Investigation of the effect of simulated lens yellowing, transparency loss and refractive error on in vivo resonance Raman spectroscopy

PURPOSE: To separately investigate the impact of simulated age-related lens yellowing, transparency loss and refractive error on measurements of macular pigment (MP) using resonance Raman spectroscopy. METHODS: Two healthy young subjects with clear media underwent Raman spectroscopy under the following conditions: age-related lens yellowing was simulated using seven broad-band yellow filters with transmittance at 488 nm ranging from 0.54 to 0.90; cataract was simulated using five white filters of increasing opacity (scatter filters), the transmittance of which ranged from 0.42 to 0.86, each of which reduced peak contrast sensitivity by approximately 0.1 log units over the previous filter. Refractive error up to +6.25 D was achieved using soft contact lenses. RESULTS: The Raman signal declined steadily to an average value of 43% of the starting value with the densest yellow filter in place. The white scatter filters produced a progressive linear reduction in signal resulting in almost complete signal loss with the densest filter. Refractive error resulted in an initial slight improvement in Raman count up to a value of +2.00 D followed by a decline thereafter. CONCLUSIONS: These results imply that lens yellowing and increasing scatter has an influence on the Raman signal and suggest that studies using this technology to estimate MP levels in older populations should carefully account for the status of the lens.