Rapid detection of serological biomarkers in gallbladder carcinoma using fourier transform infrared spectroscopy combined with machine learning

Gallbladder cancer (GBC) is the most common malignant tumour of the biliary tract. GBC is difficult to diagnose and treat at an early stage because of the lack of effective serum markers and typical symptoms, resulting in low survival rates. This study aimed to investigate the applicability of dried serum Fourier-transform infrared (FTIR) spectroscopy combined with machine learning algorithms to correctly differentiate patients with GBC from patients with gallbladder disease (GBD), cholangiocarcinoma (CCA), hepatocellular carcinoma (HCC) and healthy individuals. The differentiation between healthy individuals and GBC serum was better using principal component analysis (PCA) and linear discriminant analysis (LDA) for six spectral regions, especially in the protein (1710-1475 cm^-1) and combined (1710-1475 + 1354-980 cm^-1) region. However, the PCA-LDA model poorly differentiated GBC from GBD, CCA, and HCC in serum spectra. We evaluated the PCA- LDA, PCA-support vector machine (SVM), and radial basis kernel function support vector machine (RBF-SVM) models for GBC diagnosis and found that the RBF-SVM model performed the best, with 88.24-95% accuracy, 95.83% sensitivity, and 78.38-94.44% specificity in the 1710-1475 + 1354-980 cm^-1 region. This study demonstrated that serum FTIR spectroscopy combined with the RBF-SVM algorithm has great clinical potential for GBC screening.

Robotic radical cystectomy - more precision needed?

PURPOSE OF REVIEW

Recently, several trials as well as registry-data analyses investigating the role of robot-assisted radical cystectomy with extra or intracorporal urinary diversion were completed and follow up matured. This review aims to comment on the current evidence-based findings and interpret the future role of the robotic approach as a part of the treatment of bladder cancer.

RECENT FINDINGS

Numerous trials and registry-data analyses revealed no significant differences in progression-free and overall survival after open radical cystectomy or robot-assisted radical cystectomy irrespective of urinary diversion. Perioperative parameters, especially intraoperative blood loss, transfusions, thromboembolic events, wound infections and hospitalization were significantly increased in open radical cystectomy. Patients' convalescence, and especially early postsurgical quality of life, was improved by the robotic approach. The highly demanding surgery itself displayed by a flat learning curve required more than 130 surgeries per institution to reach a stable plateau of complications. The performance of high-quality radical cystectomy irrespective of the approach was significantly increased in high-volume centres. Local recurrence occurs in 11% after radical cystectomy. Current research focuses on intraoperatively usable detection methods and instruments to minimize the risk of residual tumour cells.

SUMMARY

Taken together, the total intracorporal approach in radical cystectomy holds the potential to improve perioperative parameters and reduces hospitalization without impairing oncological performance of the procedure. To provide best results for the patient radical cystectomy and especially the technically challenging total intracorporal procedure will gain importance in bladder cancer treatment but should be limited to high-volume centres.

Effect of Maltodextrin and Soy Protein Isolate on the Physicochemical and Flow Properties of Button Mushroom Powder

In this investigation, the effect of different drying techniques, such as freeze-drying and cabinet drying, with two different carrier agents, such as maltodextrin (MD) and soy protein isolate (SPI), at different levels (10, 15, and 20%) on button mushrooms has been revealed. The results showed that the button mushroom powders (BMPs) formulated with SPI as a carrier agent had significantly higher powder yield, hygroscopicity, L *, a *, and b * values, whereas BMP formulated with MD had significantly higher water activity, solubility index, tapped density, bulk density, and flowability. The highest retention of bioactive compounds was reported in freeze-dried mushroom powder compared to cabinet dried powder using SPI as a carrier agent. Fourier transform infrared (FTIR) analysis confirmed that certain additional peaks were produced in the mushroom button powder-containing SPI (1,035-3,271 cm-1) and MD (930-3,220 cm-1). Thus, the results revealed that SPI showed promising results for formulating the BMP using the freeze-drying technique.

PCR-RFLP and FTIR-based detection of high-risk human papilloma virus for cervical cancer screening and prevention

Background

Approximately 70% of cervical carcinoma cases show the presence of high-risk Human Papilloma Virus (HPV), especially HPV-16 and HPV-18, and can be used to stratify high risk patients from low risk and healthy. Currently, molecular biology techniques such as polymerase chain reaction (PCR) are used to identify the presence of virus in patient samples. While the methodology is highly sensitive, it is labor intensive and time-consuming. Alternative techniques, such as vibrational spectroscopy, has been suggested as a possible rapid alternative. Therefore, in this study, we evaluate the efficiency of cervical fluid Fourier Transform Infrared spectroscopy (FTIR) in patient risk stratification informed by PCR.

Methods

Cervical fluid samples (n = 91) were obtained from patients who have undergone routine Papanicolaou (Pap) test. Viral genome was identified and classified as high/low-risk by PCR-Restriction Fragment Length Polymorphism (PCR-RFLP). FTIR spectra were acquired from samples identified by PCR-RFLP as No-HPV (n = 10), high-risk HPV (n = 7), and low-risk HPV (n = 7).

Results

Of the 91 samples, was detected the viral genome by PCR in 36 samples. Of these 36 samples, nine samples were identified to contain high-risk HPV (HR-HPV) and nine samples were found to have low-risk HPV (LR-HPV). The FTIR spectra acquired from No-HPV, LR-HPV, and HR-HPV showed differences in 1069, 1437, 1555, 1647, 2840, 2919, and 3287 cm^-1 bands. Principal Component Analysis (PCA) showed distinct clusters for No-HPV and HR-HPV and No-HPV and LR-HPV, but there was significant overlap in the clusters of HR-HPV and LR-HPV. PCA-Linear Discriminant Analysis (PC-LDA) after Leave One Out Cross Validation (LOOCV) classified No-HPV from HR-HPV and No-HPV from LR-HPV with 100% efficiency in the 1400-1800 cm^-1 spectral range. LOOCV classifications for LR-HPV and HR-HPV from each other were 71 and 75%, respectively, in the 2800-3400 cm^-1 spectral range.

Conclusions

The results highlight the high sensitivity of PCR-RFLP in HPV identification and show that FTIR can classify samples identified as healthy, low, and high-risk samples by PCR-RFLP.

General significance

We show the possibility of using FTIR for initial cervical cancer risk stratification followed by detailed PCR-RFLP investigations for suspect cases.

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Molecular biology showed high sensitivity and specificity in HPV detection compared with cytological analysis.

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PCR-RFLP technique identify high-risk variants of HPV can significantly assist in the prevention of cervical cancer.

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PC-LDA and LOOCV classified normal from high-risk HPV and normal from low-risk HPV with 100% efficiency.

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FTIR can be used for initial cervical cancer risk stratification followed by more detailed investigations by PCR-RFLP.

Biophysical characterization of structural and conformational changes in methylmethane sulfonate modified DNA leading to the frizzled backbone structure and strand breaks in DNA

Methyl methanesulfonate (MMS) is a highly toxic DNA-alkylating agent that has a potential to damage the structural integrity of DNA. This work employed multiple biophysical and computational methods to report the MMS mediated structural alterations in the DNA (MMS-DNA). Spectroscopic techniques and gel electrophoresis studies revealed MMS induced exposure of chromophoric groups of DNA; methylation mediated anti→syn conformational change, DNA fragmentation and reduced nucleic acid stability. MMS induced single-stranded regions in the DNA were observed in nuclease S1 assay. FT-IR results indicated MMS mediated loss of the assigned peaks for DNA, partial loss of C-O ribose, loss of deoxyribose region, C-O stretching and bending of the C-OH groups of hexose sugar, a progressive shift in the assigned guanine and adenine peaks, loss of thymine peak, base stacking and presence of C-O-H vibrations of glucose and fructose, indicating direct strand breaks in DNA due to backbone loss. Isothermal titration calorimetry showed MMS-DNA interaction as exothermic with moderate affinity. Dynamic light scattering studies pointed towards methylation followed by the generation of single-stranded regions. Electron microscopy pictured the loss of alignment in parallel base pairs and showed the formation of fibrous aggregates in MMS-DNA. Molecular docking found MMS in close contact with the ribose sugar of DNA backbone having non-bonded interactions. Molecular dynamic simulations confirmed that MMS is capable of interacting with DNA at two levels, one at the level of nitrogenous bases and another at the DNA backbone. The study offers insights into the molecular interaction of MMS and DNA.Communicated by Ramaswamy H. Sarma.

Investigation of human pancreatic cancer tissues by Fourier Transform Infrared Hyperspectral Imaging

Fourier-transform infrared hyperspectral imaging (FTIR-HSI) provides hyperspectral images containing both morphological and chemical information. It is widely applied in the biomedical field to detect tumor lesions, even at the early stage, by identifying specific spectral biomarkers. Pancreatic neoplasms present different prognoses and are not always easily classified by conventional analyses. In this study, tissue samples with diagnosis of pancreatic ductal adenocarcinoma and pancreatic neuroendocrine tumor were analyzed by FTIR-HSI and the spectral data compared with those from healthy and dysplastic samples. Multivariate/univariate approaches were complemented to hyperspectral images, and definite spectral markers of the different lesions identified. The malignant lesions were recognizable both from healthy/dysplastic pancreatic tissues (high values of phospholipids and triglycerides with shorter, more branched and less unsaturated alkyl chains) and between each other (different amounts of total lipids, phosphates and carbohydrates). These findings highlight different metabolic pathways characterizing the different samples, well detectable by FTIR-HSI.

Molecular detection of HPV and FT-IR spectroscopy analysis in women with normal cervical cytology

BACKGROUND

The increase in the incidence of Cervical Cancer in the female population worldwide has been an issue that deserves further attention from the scientific community. Several studies have already proven the relationship of its development with the molecular mechanisms that Human Papillomavirus (HPV) induces in cervical cells. The gene amplification provided by molecular biology techniques has been used as the gold standard diagnostic method of this virus because of its high specificity and sensitivity.However, the high investments associated with the acquisition of reagents, equipment and labor demonstrate the need for the development of more accessible techniques that present the same accuracy. FT-IR spectroscopy has been studied as an inexpensive and easily accessible technology that can provide the differentiation of malignant and benign cells. This study aimed to demonstrate the effectiveness and sensitivity of molecular analysis by PCR in relation to cytological analysis and to evaluate the sensitivity of FT-IR spectroscopy in the diagnosis of HPV for cervical cancer prevention.

METHODS

Cervical fluid samples obtained from 50 patients with absence of cellular lesion by cytological analysis were analyzed by molecular and spectroscopic analyzes. Oncotic colpocitology analysis was performed by the Papanicolaou staining, amplification of the L1 viral gene by PCR was performed using primers MY09 and MY11 and biochemical analysis of the fluids by FT-IR was performed using the Spectrum 400 system equipped with a microscope.

RESULTS

Of the 50 patients without evident morphological alteration of the cells, seven were diagnosed by molecular analysis as positive for presence of HPV. Principal component analysis of spectroscopy was not able to separate the negative samples from the HPV positive samples and, therefore, did not present as an effective diagnostic technique.

CONCLUSIONS

We highlight the efficacy, sensitivity and specificity of molecular biology by PCR in the identification of the virus and we emphasize that more studies should be used for the application of FT-IR spectroscopy in the diagnosis of this infection and its application in the prevention of cervical cancer.

VIS-NIR spectral signature and quantitative analysis of HeLa and DU145 cell line

Cancer is increasing in incidence and the leading cause of death worldwide. Controlling and reducing cancer requires early detection and technique to accurately detect and quantify predictive biomarkers. Optical spectroscopy has shown promising non-destructive ability to display distinctive spectral characteristics between cancerous and normal tissues from different part of human organ. Nonetheless, not many information is available on spectroscopic properties of cancer cell lines. In this research, the visible-near infrared (VIS-NIR) absorbance spectroscopy measurement of cultured cervical cancer (HeLa) and prostate cancer cells (DU145) lines has been performed to develop spectral signature of cancer cells and to generate algorithm to quantify cancer cells. Spectroscopic measurement on mouse skin fibroblast (L929) was also taken for comparative purposes. In visible region, the raw cells' spectra do not produce any noticeable peak absorbance that provides information on color because the medium used for cells is colorless and transparent. NIR wavelength between 950 and 975 nm exhibit significant peak due to water absorbance by the medium. Development of spectral signature for the cells through the application of regression technique significantly enhances the diverse characteristics between L929, HeLa and DU145. The application of multiple linear regression allows high measurement accuracy of the cells with coefficient of determination above 0.94.

Vibrational Spectroscopy Fingerprinting in Medicine: from Molecular to Clinical Practice

In the last two decades, Fourier Transform Infrared (FTIR) and Raman spectroscopies turn out to be valuable tools, capable of providing fingerprint-type information on the composition and structural conformation of specific molecular species. Vibrational spectroscopy's multiple features, namely highly sensitive to changes at the molecular level, noninvasive, nondestructive, reagent-free, and waste-free analysis, illustrate the potential in biomedical field. In light of this, the current work features recent data and major trends in spectroscopic analyses going from in vivo measurements up to ex vivo extracted and processed materials. The ability to offer insights into the structural variations underpinning pathogenesis of diseases could provide a platform for disease diagnosis and therapy effectiveness evaluation as a future standard clinical tool.

Human papillomavirus detection using PCR and ATR-FTIR for cervical cancer screening

The human papillomavirus (HPV) genital infection is considered one of the most common sexually transmitted diseases worldwide, and has been associated with cervical cancer. The objective of this study was to investigate the efficacy of the diagnostic methods: polymerase chain reaction (PCR) and Fourier transform infrared (FTIR) equipped with an ATR (Attenuated Total Reflectance) unit (Pike Tech) spectroscopy, to diagnose HPV infection in women undergoing gynecological examination. Seventeen patients (41.46%) of the 41 patients analyzed were diagnosed with exophytic/condyloma acuminate lesions by clinical analysis, 29 patients (70.7%) (G1 group) of the 41 patients, showed positive result for HPV cell injury by oncotic colpocitology and 12 patients (29.3%) (G2 group), presented negative result for cellular lesion and absence of clinical HPV lesion. Four samples were obtained per patient, which were submitted oncotic colpocitology analysis (Papanicolau staining, two samples), PCR (one sample) and ATR-FTIR analysis (one sample). L1 gene was amplified by PCR technique with specific GP5+/GP6+ and MY09/MY11 primers. PCR results were uniformly positive for presence of HPV in all analyzed samples. Multivariate analysis of ATR-FTIR spectra suggests no significant biochemical changes between groups and no clustering formed, concurring with results of PCR. This study suggests that PCR and ATR-FTIR are highly sensitive technique for HPV detection.

Ultra-filtration of human serum for improved quantitative analysis of low molecular weight biomarkers using ATR-IR spectroscopy

Monitoring of changes in the concentrations of the low molecular weight constituents enhanced by abundant proteins depletion.

Diagnosing clean margins through Raman spectroscopy in human and animal mammary tumour surgery: a short review

Breast cancer frequency in human and other mammal female populations has worryingly increased lately. The acute necessity for taxonomy of the aetiological factors along with seeking for new diagnostic tools and therapy procedures aimed at reducing mortality have yielded in an intense research effort worldwide. Surgery is a regular method to counteract extensive development of breast cancer and prevent metastases provided that negative surgical margins are achieved. This highly technical challenge requires fast, extremely sensitive and selective discrimination between malignant and benign tissues even down to molecular level. The particular advantages of Raman spectroscopy, such as high chemical specificity, and the ability to measure raw samples and optical responses in the visible or near-infrared spectral range, have recently recommended it as a means with elevated potential in precise diagnostic in oncology surgery. This review spans mainly the latter 10 years of exceptional efforts of scientists implementing Raman spectroscopy as a nearly real-time diagnostic tool for clean margins assessment in mastectomy and lumpectomy. Although greatly contributing to medical discoveries for the wealth of humanity, animals as patients have benefitted less from advances in surgery diagnostic using Raman spectroscopy. This work also dedicates a few lines to applications of surface enhanced Raman spectroscopy in veterinary oncological surgery.

Vibrational spectroscopic methods for cytology and cellular research

The use of vibrational spectroscopy, FTIR and Raman, for cytology and cellular research has the potential to revolutionise the approach to cellular analysis. Vibrational spectroscopy is non-destructive, simple to operate and provides direct information. Importantly it does not require expensive exogenous labels that may affect the chemistry of the cell under analysis. In addition, the advent of spectroscopic microscopes provides the ability to image cells and acquire spectra with a subcellular resolution. This introductory review focuses on recent developments within this fast paced field and highlights potential for the future use of FTIR and Raman spectroscopy. We particularly focus on the development of live cell research and the new technologies and methodologies that have enabled this.

Comparison of FTIR transmission and transfection substrates for canine liver cancer detection

FTIR spectroscopy is a widely used technique that provides insights into disease processes at the molecular level.