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A rapid, low-cost, sensitive, multi-cancer early detection (MCED) test would be transformational in the diagnostics field. Earlier cancer detection can increase survival rates and quality of life of patients. An effective test must accurately identify the small proportion of patients with typically non-specific symptoms who have cancer. Such symptoms do not easily segregate by organ system, necessitating a multi-cancer approach. In this large-scale study (n = 2094 patients) we applied the Dxcover® Cancer Liquid Biopsy to differentiate cancer against non-cancer patients, as well as organ specific tests to identify cancers of the brain, breast, colorectal, kidney, lung, ovary, pancreas, and prostate. The test uses Fourier transform infrared (FTIR) spectroscopy to analyze all macromolecules in a minute volume of patient serum, and machine learning algorithms to build a classifier of the resultant spectral profiles to detect cancer. This approach can be fine-tuned to maximize either sensitivity or specificity depending on the requirements from different healthcare systems and cancer diagnostic pathways. The cancer v asymptomatic non-cancer classification detected 64% of stage I cancers when specificity was 99% (overall sensitivity 56%). When tuned for higher sensitivity, this model identified 99% of stage I cancers (while specificity was 58%). When examining cancer against all non-cancer (including symptomatic patients), the sensitivity-tuned model enabled 90% sensitivity with 61% specificity, with detection rates of 93% for stage I, 84% for stage II, 92% for stage III and 95% for stage IV. For organ specific cancer classifiers, area under the receiver operating characteristic (ROC) curve values were calculated for all cancers: brain (0.90), breast (0.75), colorectal (0.91), kidney (0.91), lung (0.91), ovarian (0.86), pancreatic (0.85) and prostate (0.86). Cancer treatment is more effective when given earlier and this low-cost strategy can facilitate the requisite earlier diagnosis.

Background Diagnostic delays impact the quality of life and survival of patients with brain tumors. Earlier and expeditious diagnoses in these patients are crucial to reduce the morbidities and mortalities associated with brain tumors. A simple, rapid blood test that can be administered easily in a primary care setting to efficiently identify symptomatic patients who are most likely to have a brain tumor would enable quicker referral to brain imaging for those who need it most. Methods Blood serum samples from 603 patients were prospectively collected and analyzed. Patients either had non-specific symptoms that could be indicative of a brain tumor on presentation to the Emergency Department, or a new brain tumor diagnosis and referral to the neurosurgical unit, NHS Lothian, Scotland. Patient blood serum samples were analyzed using the Dxcover® Brain Cancer liquid biopsy. This technology utilizes infrared spectroscopy combined with a diagnostic algorithm to predict the presence of intracranial disease. Results Our liquid biopsy approach reported an area under the receiver operating characteristic curve of 0.8. The sensitivity-tuned model achieves a 96% sensitivity with 45% specificity (NPV 99.3%) and identified 100% of glioblastoma multiforme patients. When tuned for a higher specificity, the model yields a sensitivity of 47% with 90% specificity (PPV 28.4%). Conclusions This simple, non-invasive blood test facilitates the triage and radiographic diagnosis of brain tumor patients while providing reassurance to healthy patients. Minimizing time to diagnosis would facilitate the identification of brain tumor patients at an earlier stage, enabling more effective, less morbid surgical and adjuvant care.

Analytical technologies that can improve disease diagnosis are highly sought after. Current screening/diagnostic tests for several diseases are limited by their moderate diagnostic performance, invasiveness, costly and laborious methodologies or the need for multiple tests before a definitive diagnosis. Spectroscopic techniques, including infrared (IR) and Raman, have attracted great interest in the medical field, with applications expanding from early disease detection to monitoring and real-time diagnosis.\ud This review highlights applications of IR and Raman spectroscopy, with a focus on cancer and infectious diseases since 2015, and underscores the diverse sample types that can be analyzed, such as biofluids, cells and tissues. Studies involving more than 25 participants per group (disease and control group; if no control group >25 in disease group) were considered eligible, to retain the clinical focus of the paper. Following literature searches, we identified 94 spectroscopic studies on different cancers and 30 studies on infectious diseases. The review suggests that such technologies have the potential to develop into an objective, inexpensive, point-of-care test or facilitate disease diagnosis and monitoring. Up-to-date considerations for the implementation of spectroscopic techniques into a clinical setting, health economics and successful applications of vibrational spectroscopic tests in the clinical arena are also discussed.

Simple Summary Due to the non-specific symptoms of brain cancer (e.g., headaches or memory changes), gliomas will often remain undetected until they are larger or at a higher grade, reducing the patient’s likelihood of a good clinical outcome. Earlier detection and diagnosis of brain tumours is vital to improve patient outcomes, leading to safer surgeries and earlier treatments. A liquid biopsy for brain tumour would prove revolutionary however in order to detect disease earlier the liquid biopsy needs to be able to detect smaller tumours; and current liquid biopsies perform worse when detecting smaller or earlier stage tumours. Here, for the first time, we confirm the applicability of a validated spectroscopic liquid biopsy approach to detect both small and low-grade gliomas proving that the spectroscopic liquid biopsy approach is insensitive to tumour volume unlike other liquid biopsies. Abstract Background: To support the early detection and diagnosis of brain tumours we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumour diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumour genetic material) report a lower classification accuracy for early-stage tumours. In this manuscript we present an investigation into the link between brain tumour volume and liquid biopsy test performance. Methods: In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligoastrocytoma and oligodendroglioma)) tumour volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumour patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Results: Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumour volumes as small as 0.2 cm3 were correctly identified. Conclusions: Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis.

Hyperspectral imaging can generate spatial chemical information in plants. The imaging acquisition system is basically composed of a radiation source, sample stage, objective lens, spectrograph, CCD camera and a computer to store and process derived data. Most hyperspectral imaging acquisition approaches are nondestructive in nature and require minimum sample preparation, thus producing chemically rich information without modifying a sample’s features. Data processing is mainly performed via multivariate image analysis (MIA), where computed-based methods are employed for preprocessing, feature extraction and multivariate analysis towards classification. Applications vary according to the desired information of interest, but they mainly include textural analysis, chemical and biochemical analysis and plant disease identification. Successful studies in these areas reinforce the sensitivity and versatility of hyperspectral imaging in plants.

To support the early detection and diagnosis of brain tumors we have developed a rapid, cost-effective and easy to use spectroscopic liquid biopsy based on the absorbance of infrared radiation. We have previously reported highly sensitive results of our approach which can discriminate patients with a recent brain tumor diagnosis and asymptomatic controls. Other liquid biopsy approaches (e.g., based on tumor genetic material) report a lower classification accuracy for early-stage tumors. In this manuscript we present an investigation into the link between brain tumor volume and liquid biopsy test performance. In a cohort of 177 patients (90 patients with high-grade glioma (glioblastoma (GBM) or anaplastic astrocytoma), or low-grade glioma (astrocytoma, oligo-astrocytoma and oligodendroglioma)) tumor volumes were calculated from magnetic resonance imaging (MRI) investigations and patients were split into two groups depending on MRI parameters (T1 with contrast enhancement or T2/FLAIR (fluid-attenuated inversion recovery)). Using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy coupled with supervised learning methods and machine learning algorithms, 90 tumor patients were stratified against 87 control patients who displayed no symptomatic indications of cancer, and were classified as either glioma or non-glioma. Sensitivities, specificities and balanced accuracies were all greater than 88%, the area under the curve (AUC) was 0.98, and cancer patients with tumor volumes as small as 0.2 cm3 were correctly identified. Our spectroscopic liquid biopsy approach can identify gliomas that are both small and low-grade showing great promise for deployment of this technique for early detection and diagnosis. Citation Format: Alexandra Sala, Ashton G. Theakstone, Paul M. Brennan, Michael D. Jenkinson, Samantha J. Mills, Khaja Syed, Christopher Rinaldi, Yun Xu, Royston Goodacre, Holly J. Butler, David S. Palmer, Benjamin R. Smith, Matthew J. Baker. Rapid spectroscopic liquid biopsy for the early detection of brain tumors [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5923.

Diagnostic delays impact the quality of life and survival of patients with brain tumors. Earlier and expeditious diagnoses in these patients are crucial to reducing the morbidities and mortalities associated with brain tumors. A simple, rapid blood test that can be administered easily in a primary care setting to efficiently identify symptomatic patients who are most likely to have a brain tumor would enable quicker referral to brain imaging for those who need it most. Blood serum samples from 603 patients were prospectively collected and analyzed. Patients either had non-specific symptoms that could be indicative of a brain tumor on presentation to the Emergency Department, or a new brain tumor diagnosis and referral to the neurosurgical unit, NHS Lothian, Scotland. Patient blood serum samples were analyzed using the Dxcover® Brain Cancer liquid biopsy. This technology utilizes infrared spectroscopy combined with a diagnostic algorithm to predict the presence of intracranial disease. Our liquid biopsy approach reported an area under the receiver operating characteristic curve of 0.8. The sensitivity-tuned model achieves a 96% sensitivity with 45% specificity (NPV 99.3%) and identified 100% of glioblastoma multiforme patients. When tuned for a higher specificity, the model yields sensitivity of 47% with 90% specificity (PPV 28.4%). This simple, non-invasive blood test facilitates the triage and radiographic diagnosis of brain tumor patients, while providing reassurance to healthy patients. Minimizing time to diagnosis would facilitate identification of brain tumor patients at an earlier stage, enabling more effective, less morbid surgical and adjuvant care. Citation Format: James M. Cameron, Paul M. Brennan, Georgios Antoniou, Holly J. Butler, Loren Christie, Justin J.A. Conn, Tom Curran, Ewan Gray, Mark G. Hegarty, Michael Jenkinson, Daniel Orringer, David S. Palmer, Alexandra Sala, Benjamin R. Smith, Matthew J. Baker. Clinical validation of a spectroscopic liquid biopsy for early detection of brain cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 5922.

International audience; Changes in protein concentrations within human blood are used as an indicator for nutritional state, hydration and underlying illnesses. They are often measured at regular clinical appointments and the current analytical process can result in long waiting times for results and the need for return patient visits. Attenuated total reflectance – Fourier transform infrared (ATR-FTIR) spectroscopy has the ability to detect minor molecular differences, qualitatively and quantitatively, in biofluid samples, without extensive sample preparation. ATR-FTIR can return an analytical measurement almost instantaneously and therefore could be deemed as an ideal technique for monitoring molecular alterations in blood within the clinic.To determine the suitability of using ATR-FTIR spectroscopy to enable protein quantification in a clinical setting, pooled human serum samples spiked with varying concentrations of human serum albumin (HSA) and immunoglobulin G (IgG) were analysed, before analysing patient clinical samples. Using a validated partial least squares method, the spiked samples (IgG) produced a linearity as high as 0.998 and a RMSEV of 0.49 ± 0.05 mg mL−1, with the patient samples producing R2 values of 0.992 and a corresponding RMSEV of 0.66 ± 0.05 mg mL−1. This claim was validated using two blind testing models, leave one patient out cross validation and k-fold cross validation, achieving optimum linearity and RMSEV values of 0.934 and 1.99 ± 0.79 mg mL−1, respectively.This demonstrates that ATR-FTIR is able to quantify protein within clinically relevant complex matrices and concentrations, such as serum samples, rapidly and with simple sample preparation. The ability to provide a quantification step, along with rapid disease classification, from a spectroscopic signature will aid clinical translation of vibrational spectroscopy to assist with problems currently faced with patient diagnostic pathways.

Early diagnosis of brain tumours is challenging and a major unmet need. Patients with brain tumours most often present with non-specific symptoms more commonly associated with less serious diagnoses, making it difficult to determine which patients to prioritize for brain imaging. Delays in diagnosis affect timely access to treatment, with potential impacts on quality of life and survival. A test to help identify which patients with non-specific symptoms are most likely to have a brain tumour at an earlier stage would dramatically impact on patients by prioritizing demand on diagnostic imaging facilities. This clinical feasibility study of brain tumour early diagnosis was aimed at determining the accuracy of our novel spectroscopic liquid biopsy test for the triage of patients with non-specific symptoms that might be indicative of a brain tumour, for brain imaging. Patients with a suspected brain tumour based on assessment of their symptoms in primary care can be referred for open access CT scanning. Blood samples were prospectively obtained from 385 of such patients, or patients with a new brain tumour diagnosis. Samples were analysed using our spectroscopic liquid biopsy test to predict presence of disease, blinded to the brain imaging findings. The results were compared to the patient’s index brain imaging delivered as per standard care. Our test predicted the presence of glioblastoma, the most common and aggressive brain tumour, with 91% sensitivity, and all brain tumours with 81% sensitivity, and 80% specificity. Negative predictive value was 95% and positive predictive value 45%. The reported levels of diagnostic accuracy presented here have the potential to improve current symptom-based referral guidelines, and streamline assessment and diagnosis of symptomatic patients with a suspected brain tumour., Brennan et al. show a rapid, low-cost blood test can identify which patients with suspected brain tumour to prioritize for diagnostic imaging, reducing time to diagnosis. The test is more than 90% sensitive for the most aggressive tumours. Earlier diagnosis can provide health and economic benefits., Graphical Abstract Graphical Abstract

Objectives An early economic evaluation to inform the translation into clinical practice of a spectroscopic liquid biopsy for the detection of brain cancer. Two specific aims are (1) to update an existing economic model with results from a prospective study of diagnostic accuracy and (2) to explore the potential of brain tumor-type predictions to affect patient outcomes and healthcare costs. Methods A cost-effectiveness analysis from a UK NHS perspective of the use of spectroscopic liquid biopsy in primary and secondary care settings, as well as a cost–consequence analysis of the addition of tumor-type predictions was conducted. Decision tree models were constructed to represent simplified diagnostic pathways. Test diagnostic accuracy parameters were based on a prospective validation study. Four price points (GBP 50-200, EUR 57-228) for the test were considered. Results In both settings, the use of liquid biopsy produced QALY gains. In primary care, at test costs below GBP 100 (EUR 114), testing was cost saving. At GBP 100 (EUR 114) per test, the ICER was GBP 13,279 (EUR 15,145), whereas at GBP 200 (EUR 228), the ICER was GBP 78,300 (EUR 89,301). In secondary care, the ICER ranged from GBP 11,360 (EUR 12,956) to GBP 43,870 (EUR 50,034) across the range of test costs. Conclusions The results demonstrate the potential for the technology to be cost-effective in both primary and secondary care settings. Additional studies of test use in routine primary care practice are needed to resolve the remaining issues of uncertainty—prevalence in this patient population and referral behavior.

Data quality and reproducibility are vital for robust, reliable and consistent diagnostic techniques within clinical environments. Most variance within clinical laboratories occur within the pre-analytical phase, prior to obtaining and analysing data. Herein, we investigate pre-analytical considerations for the spectroscopic analysis of blood serum for the purpose of clinical diagnostics. Variables within sample collection, storage and preparation are explored in order to evaluate their effects on the spectral outcome, including; differences between sample collection tubes, centrifugal speed and time, short and long-term storage conditions, individual analyst technique, sample volumes, environment of sample batches, as well as various drying techniques. Exploratory data analysis using principal component analysis was implemented to unearth spectral variance not immediately observable. Minor spectral variations were observed within each experiment; however, these were not considered significant differences as a result of these varying experimental factors. Variation between different operator techniques when preparing samples was observed, yet can be resolved with appropriate standard operating procedures, regardless of other factors such as sample volume and storage conditions. The findings within this report suggest that experimental variations within a laboratory, or between different laboratories, does not significantly affect the spectral outcome, and with good laboratory practice and careful sample handling results should be consistent and reliable.

Fourier Transform Infrared Spectroscopy (FTIR) has been largely employed by scientific researchers to improve diagnosis and treatment of cancer, using various biofluids and tissues. The technology has proved to be easy to use, rapid and cost-effective for analysis on human blood serum to discriminate between cancer versus healthy control samples. The high sensitivity and specificity achievable during samples classification aided by machine learning algorithms, offers an opportunity to transform cancer referral pathways, as it has been demonstrated in a unique and recent prospective clinical validation study on brain tumours. We herein highlight the importance of early detection in cancer research using FTIR, discussing the technique, the suitability of serum for analysis and previous studies, with special focus on pre-clinical factors and clinical translation requirements and development.

In recent years, the diagnosis of brain tumors has been investigated with attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopy on dried human serum samples to eliminate spectral interferences of the water component, with promising results. This research evaluates ATR-FTIR on both liquid and air-dried samples to investigate "digital drying" as an alternative approach for the analysis of spectra obtained from liquid samples. Digital drying approaches, consisting of water subtraction and least-squares method, have demonstrated a greater random forest (RF) classification performance than the air-dried spectra approach when discriminating cancer vs control samples, reaching sensitivity values higher than 93.0% and specificity values higher than 83.0%. Moreover, quantum cascade laser infrared (QCL-IR) based spectroscopic imaging is utilized on liquid samples to assess the implications of a deep-penetration light source on disease classification. The RF classification of QCL-IR data has provided sensitivity and specificity amounting to 85.1% and 75.3% respectively.

Foliar application of nutrient fertilizers is standard practice in agricul- tural environments, and has been shown to increase crop yield and quality more efficiently and economically than soil-based fertilizers. The adsorption of macro- and micro-nutrients through the upper epidermis of leaves is largely species dependent; reliant upon pene- tration through the cuticle and stomata, and also upon the plant’s ability to translocate the nutrient. Herein we describe a method to observe nitrate (NO3) uptake at the adaxial leaf surface to deter- mine the efficacy of foliar fertilizers. We use Raman microspectro- scopy as a sensitive approach to monitor NO3 associated vibrational modes, complemented by ion probe measurements and measurements of leaf nutrient status using flame atomic absorption spectroscopy. The results show that NO3 uptake can be observed down to concentrations as low as 15 mM using Raman microspectro- scopy over a defined surface area, and that the rate of uptake can also be quantified using this approach. These observations could also infer information regarding the transport of other ions present in nitrate salts, such as calcium (Ca), via the indirect monitoring of NO3- specific bands. We believe that Raman microspectroscopy pro- vides a novel method for monitoring nutrient movement throughout plant tissue, and provides a potential tool for nutrient screening.

Alterations in biomolecular components in human blood are commonly used as an indication of disease states, namely differences in protein concentration. Unfortunately, conventional test kits currently employed in hospitals suffer from long time delays, meaning patients often have to wait anxiously for their test results. Vibrational spectroscopic techniques, such as infrared and Raman, have the ability to replace current practices, as they are label-free, cost-effective, easy to operate, and require minimal sample preparation. The sensitivity to subtle changes in biochemical composition makes them ideal diagnostic tools, and recent advances in technology and data analytics means bodily fluids can be analyzed rapidly and noninvasively to detect disease-related fluctuations in protein concentration. In this chapter, we outline the current clinical procedures for blood tests, examine the capability of biomedical vibrational spectroscopy for disease diagnostics and monitoring, and discuss the potentiality for the techniques to be successfully translated into the clinic.

In recent years, the application of vibrational spectroscopy in biomedical research has rapidly expanded; covering aspects of pharmaceutical development, to point-of-care technologies. Vibrational spectroscopy techniques such as Fourier-transform IR (FTIR), and Raman spectroscopy have been at the forefront of this movement, with their complementary information able to shine light onto a range of medical applications. As a relative newcomer to biomedical applications, two-dimensional (2D)-IR is also gaining traction in the field. Here we describe the recent development of these techniques as analytical tools in medical science, and their relative advancements towards the clinic.

Over a third of brain tumour patients visit their general practitioner more than five times prior to diagnosis in the UK, leading to 62% of patients being diagnosed as emergency presentations. Unfortunately, symptoms are non-specific to brain tumours, and the majority of these patients complain of headaches on multiple occasions before being referred to a neurologist. As there are currently no methods in place for the early detection of brain cancer, the affected patients' average life expectancy is reduced by 20 years. These statistics indicate that the current pathway is ineffective, and there is a vast need for a rapid diagnostic test. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy is sensitive to the hallmarks of cancer, as it analyses the full range of macromolecular classes. The combination of serum spectroscopy and advanced data analysis has previously been shown to rapidly and objectively distinguish brain tumour severity. Recently, a novel high-throughput ATR accessory has been developed, which could be cost-effective to the National Health Service in the UK, and valuable for clinical translation. In this study, 765 blood serum samples have been collected from healthy controls and patients diagnosed with various types of brain cancer, contributing to one of the largest spectroscopic studies to date. Three robust machine learning techniques - random forest, partial least squares-discriminant analysis and support vector machine - have all provided promising results. The novel high-throughput technology has been validated by separating brain cancer and non-cancer with balanced accuracies of 90% which is comparable to the traditional fixed diamond crystal methodology. Furthermore, the differentiation of brain tumour type could be useful for neurologists, as some are difficult to distinguish through medical imaging alone. For example, the highly aggressive glioblastoma multiforme and primary cerebral lymphoma can appear similar on magnetic resonance imaging (MRI) scans, thus are often misdiagnosed. Here, we report the ability of infrared spectroscopy to distinguish between glioblastoma and lymphoma patients, at a sensitivity and specificity of 90.1% and 86.3%, respectively. A reliable serum diagnostic test could avoid the need for surgery and speed up time to definitive chemotherapy and radiotherapy.

Non-specific symptoms, as well as the lack of a cost-effective test to triage patients in primary care, has resulted in increased time-to-diagnosis and a poor prognosis for brain cancer patients. A rapid, cost-effective, triage test could significantly improve this patient pathway. A blood test using attenuated total reflection (ATR)-Fourier transform infrared (FTIR) spectroscopy for the detection of brain cancer, alongside machine learning technology, is advancing towards clinical translation. However, whilst the methodology is simple and does not require extensive sample preparation, the throughput of such an approach is limited. Here we describe the development of instrumentation for the analysis of serum that is able to differentiate cancer and control patients at a sensitivity and specificity of 93.2% and 92.8%. Furthermore, preliminary data from the first prospective clinical validation study of its kind are presented, demonstrating how this innovative technology can triage patients and allow rapid access to imaging., Diagnosing brain cancer is frequently difficult and requires specialist equipment. Here, the authors develop their previous attenuated total reflectance-Fourier transform infrared spectroscopy method and incoporate the use of disposable silicon wafers for diagnosing brain cancer using serum samples.

Pre-processing is an essential step in the analysis of spectral data. Mid-IR spectroscopy of biological samples is often subject to instrumental and sample specific variances which may often conceal valuable biological information. Whilst pre-processing can effectively reduce this unwanted variance, the plethora of possible processing steps has resulted in a lack of consensus in the field, often meaning that analysis outputs are not comparable. As pre-processing is specific to the sample under investigation, here we present a systematic approach for defining the optimum pre-processing protocol for biofluid ATR-FTIR spectroscopy. Using a trial-and-error based approach and a clinically relevant dataset describing control and brain cancer patients (3,897 spectra), the effects of pre-processing permutations on subsequent classification algorithms were observed, by assessing key diagnostic performance parameters, including sensitivity and specificity. It was found that optimum diagnostic performance correlated with the use of minimal binning and baseline correction, with derivative functions improving diagnostic performance most significantly. If smoothing is required, a Sovitzky-Golay approach was the preferred option in this investigation. Heavy binning appeared to reduce classification most significantly, alongside wavelet noise reduction (filter length ≥ 6), resulting in the lowest diagnostic performances of all pre-processing permutations tested.

Simple Summary Gliomas represent the vast majority of primary brain tumours and are of significant medical importance due to the poor clinical course of affected patients. The isocitrate dehydrogenase 1 (IDH1) mutation is associated with improved prognosis, compared to patients with IDH1-wildtype lesions of the same stage. In this proof-of-concept study, Fourier transform infrared spectroscopy was used to determine the IDH1 molecular status in fixed glioma sections. Classification algorithms successfully distinguished the two IDH1 classes with high accuracies (>80%). Knowledge of the IDH1 status would be beneficial, as maximum resection may be preferred in patients with IDH1-mutant gliomas, whilst a more limited resection can be best for IDH1-wildtype gliomas. Furthermore, we examined blood serum in an attempt to identify the biomolecular alterations caused by the IDH1 mutation. Non-invasive approaches that can detect the molecular status may guide some patients to an alternative treatment prior to surgery. Abstract Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are found in a high proportion of diffuse gliomas. The presence of the IDH1 mutation is a valuable diagnostic, prognostic and predictive biomarker for the management of patients with glial tumours. Techniques involving vibrational spectroscopy, e.g., Fourier transform infrared (FTIR) spectroscopy, have previously demonstrated analytical capabilities for cancer detection, and have the potential to contribute to diagnostics. The implementation of FTIR microspectroscopy during surgical biopsy could present a fast, label-free method for molecular genetic classification. For example, the rapid determination of IDH1 status in a patient with a glioma diagnosis could inform intra-operative decision-making between alternative surgical strategies. In this study, we utilized synchrotron-based FTIR microanalysis to probe tissue microarray sections from 79 glioma patients, and distinguished the positive class (IDH1-mutated) from the IDH1-wildtype glioma, with a sensitivity and specificity of 82.4% and 83.4%, respectively. We also examined the ability of attenuated total reflection (ATR)-FTIR spectroscopy in detecting the biomolecular events and global epigenetic and metabolic changes associated with mutations in the IDH1 enzyme, in blood serum samples collected from an additional 72 brain tumour patients. Centrifugal filtration enhanced the diagnostic ability of the classification models, with balanced accuracies up to ~69%. Identification of the molecular status from blood serum prior to biopsy could further direct some patients to alternative treatment strategies.

This study tested the hypothesis that prepubertal exposure to 4-Nonylphenol (NP) affects reproductive function in male rats. Twenty-four rats at five-weeks-old were randomly divided into four groups and treated with NP at varying concentrations (0, 5, 20, and 60 mg/kg/2d) for thirty days by intra-peritoneal injection. 60 mg/kg NP induced spermatogenic degeneration and pronounced deficits in epididymal sperm count, motility and function, whereas potentially stimulatory effects were observed at 5 NP mg/kg. Moreover, 60 mg/kg NP resulted in a significant reduction in fructose, FSH and LH; induced apoptosis related to oxidative stress; inhibited mRNA and protein levels of Bcl-2 and PCNA; as well as the additional up-regulation of p53, Bax, Apaf-1, cytochrome c, cleaved-caspase-3, Fas and FasL expression. Our data suggest potentially hormetic effects of NP on spermatogenic function. High-dose NP impairs testicular development and function by reducing cell proliferation and inducing apoptosis involving oxidative stress-related p53-Bcl-2/Bax and −Fas/FasL pathways.

4-Nonylphenol (NP) is a ubiquitous environmental chemical with estrogenic activity. Our aim was to test the hypothesis that pubertal exposure to NP leads to testicular dysfunction. Herein, 24 7-week-old rats were randomly divided into four groups and treated with NP (0, 25, 50, or 100 mg/kg body weight every 2 days for 20 consecutive days) by intraperitoneal injection. Compared to untreated controls, the parameters of sperm activation rate, curvilinear velocity, average path velocity, and swimming velocity were significantly lower at doses of 100 mg/kg, while sperm morphological abnormalities were higher, indicating functional disruption and reduced fertilization potential. High exposure to NP (100 mg/kg) resulted in disordered arrangement of spermatoblasts and reduction of spermatocytes in seminiferous tubules, while tissues exhibited a marked decline in testicular fructose content and serum FSH, LH, and testosterone levels. Oxidative stress was induced by NP (50 or 100 mg/kg) as evidenced by elevated MDA, decreased SOD and GSH-Px, and inhibited antioxidant gene expression (CAT, GPx, SOD1, and CYP1B1). In addition, NP treatment decreased proportions of Ki-67-positive cells and increased apoptosis in a dose-dependent manner. Rats treated with 100 mg/kg NP exhibited significantly increased mRNA expression of caspase-1, -2, -9, and -11, decreased caspase-8 and PCNA1 mRNA expression, downregulation of Bcl-2/Bax ratios and upregulation of Fas, FasL, and p53 at the protein and mRNA levels. Taken together, NP-induced apoptosis, hormonal deficiencies, and depletion of fructose potentially impairs spermatogenesis and sperm function. p53-independent Fas/FasL-Bax/Bcl-2 pathways may be involved in NP-induced oxidative stress-related apoptosis.

Raman spectroscopy can be used to measure the chemical composition of a sample, which can in turn be used to extract biological information. Many materials have characteristic Raman spectra, which means that Raman spectroscopy has proven to be an effective analytical approach in geology, semiconductor, materials and polymer science fields. The application of Raman spectroscopy and microscopy within biology is rapidly increasing because it can provide chemical and compositional information, but it does not typically suffer from interference from water molecules. Analysis does not conventionally require extensive sample preparation; biochemical and structural information can usually be obtained without labeling. In this protocol, we aim to standardize and bring together multiple experimental approaches from key leaders in the field for obtaining Raman spectra using a microspectrometer. As examples of the range of biological samples that can be analyzed, we provide instructions for acquiring Raman spectra, maps and images for fresh plant tissue, formalin-fixed and fresh frozen mammalian tissue, fixed cells and biofluids. We explore a robust approach for sample preparation, instrumentation, acquisition parameters and data processing. By using this approach, we expect that a typical Raman experiment can be performed by a nonspecialist user to generate high-quality data for biological materials analysis.

Objectives To determine the potential costs and health benefits of a serum-based spectroscopic triage tool for brain tumours, which could be developed to reduce diagnostic delays in the current clinical pathway. Design A model-based health pre-trial economic assessment. Decision tree models were constructed based on simplified diagnostic pathways. Models were populated with parameters identified from rapid reviews of the literature and clinical expert opinion. Setting Explored as a test in both primary and secondary care (neuroimaging) in the UK health service, as well as application to the USA. Participants Calculations based on an initial cohort of 10 000 patients. In primary care, it is estimated that the volume of tests would approach 75 000 per annum. The volume of tests in secondary care is estimated at 53 000 per annum. Main outcome measures The primary outcome measure was quality-adjusted life-years (QALY), which were employed to derive incremental cost-effectiveness ratios (ICER) in a cost-effectiveness analysis. Results Results indicate that using a blood-based spectroscopic test in both scenarios has the potential to be highly cost-effective in a health technology assessment agency decision-making process, as ICERs were well below standard threshold values of £20 000–£30 000 per QALY. This test may be cost-effective in both scenarios with test sensitivities and specificities as low as 80%; however, the price of the test would need to be lower (less than approximately £40). Conclusion Use of this test as triage tool in primary care has the potential to be both more effective and cost saving for the health service. In secondary care, this test would also be deemed more effective than the current diagnostic pathway.

The complex patterns observed from evaporated liquid drops have been examined extensively over the last 20 years. Complete understanding of drop deposition is vital in many medical processes, and one which is essential to the translation of biofluid spectroscopic disease diagnostics. The promising use of spectroscopy in disease diagnosis has been hindered by the complicated patterns left by dried biological fluids which may inhibit the clinical translation of this technology. Coffee-ring formation, cracking and gelation patterns have all been observed in biofluid drops, and with surface homogeneity being a key element to many spectroscopic techniques, experimental issues have been found to arise. A better understanding of the fundamental processes involved in a drying droplet could allow efficient progression in this research field, and ultimately benefit the population with the development of a reliable cancer diagnostic.

It has recently been demonstrated that a spectroscopic test using blood-serum is able to effectively identify brain tumours in patients with sensitivities and specificities as high as 91.5% and 83% respectively. The approach employs Attenuated Total Reflectance - Fourier Transform Infrared (ATR-FTIR) spectroscopy to derive a disease specific spectroscopic signature, that using pattern recognition and machine learning algorithms is able to identify brain tumour cases. The ability to identify brain cancer cases based on serum samples alone raises the possibility of systematic screening prior to investigation with more expensive (MRI/CT imaging) and invasive (biopsy) tests. However, current methodology is currently limited to single patient analysis due to limitations in standard instrumentation. Here, we investigate the performance of a novel ATR-FTIR spectroscopic approach that allows automated, disposable, and multi-patient sampling. Our results indicate that this optimised approach is able to stratify brain tumour patients at performances equivalent to previous approaches, with sensitivities and specificities as high as 94.56% and 87.65% respectively. In advance of any prospective clinical study results being available, a cost-effectiveness analysis (CEA) was conducted to calculate the effects on health outcomes and health service costs of introducing this technology as a triage tool in primary and secondary care. Results indicate that using a serum spectroscopy test for brain tumours in both scenarios may be considered highly cost-effective in an HTA agency decision making process. Incremental cost-effectiveness ratios were well below standard threshold values of £20,000 to £30,000 per quality adjusted life year (QALY) gained used in the UK, and similar thresholds used internationally. In primary care, the test has the potential to be both more effective and cost saving for the health service.

“Large” nanoparticles potentially are a good starting point in order to derive informative NIR/IR SERS analysis of biological samples., As biospectroscopy techniques continue to be developed for screening or diagnosis within a point-of-care setting, an important development for this field will be high-throughput optimization. For many of these techniques, it is therefore necessary to adapt and develop parameters to generate a robust yet simple approach delivering high-quality spectra from biological samples. Specifically, this is important for surface-enhanced Raman spectroscopy (SERS) wherein there are multiple variables that can be optimised to achieve an enhancement of the Raman signal from a sample. One hypothesis is that “large” diameter (>100 nm) gold nanoparticles provide a greater enhancement at near-infrared (NIR) and infrared (IR) wavelengths than those

By 2050, it is estimated that the global population will have surpassed 9 billion people, presenting a significant challenge with regards to food security. In order to provide sufficient quantities of nutritious food in the future, it is necessary to improve agricultural productivity by up to 70%. Nutrient deficiencies are one particular threat to food security that can have a negative impact on crop yield and quality. Currently the standard agricultural approach to prevention is to supply an excess of macronutrient fertiliser, such as nitrate or phosphate, during crop production. However, the efficiency of this approach is poor as deficiencies of specific nutrients, such as Ca, are not prevented in this circumstance, and fertiliser use is associated with a host of adverse environmental impacts. Herein, we describe a novel method to detect Ca deficiency using synchrotron radiation-based Fourier-transform infrared (FTIR) microspectroscopy in live and fixed tissue of the model plant Commelina communis, as a precursor to targeted nutrient remediation in the field.

Spectroscopic diagnostics have been shown to be an effective tool for the analysis and discrimination of disease states from human tissue. Furthermore, Raman spectroscopic probes are of particular interest as they allow for in vivo spectroscopic diagnostics, for tasks such as the identification of tumour margins during surgery. In this study, we investigate a feature-driven approach to the classification of metastatic brain cancer, glioblastoma (GB) and non-cancer from tissue samples, and we provide a real-time feedback method for endoscopic diagnostics using sound. To do this, we first evaluate the sensitivity and specificity of three classifiers (SVM, KNN and LDA), when trained with both sub-band spectral features and principal components taken directly from Raman spectra. We demonstrate that the feature extraction approach provides an increase in classification accuracy of 26.25% for SVM and 25% for KNN. We then discuss the molecular assignment of the most salient sub-bands in the dataset. The most salient sub-band features are mapped to parameters of a frequency modulation (FM) synthesizer in order to generate audio clips from each tissue sample. Based on the properties of the sub-band features, the synthesizer was able to maintain similar sound timbres within the disease classes and provide different timbres between disease classes. This was reinforced via listening tests, in which participants were able to discriminate between classes with mean classification accuracy of 71.1%. Providing intuitive feedback via sound frees the surgeons’ visual attention to remain on the patient, allowing for greater control over diagnostic and surgical tools during surgery, and thus promoting clinical translation of spectroscopic diagnostics.

As Notch receptors have been shown to induce chemoresistance, we hypothesized that delta-like ligand-4 (DLL4), a central Notch signalling ligand, might also participate in chemoresistance in breast cancer. To investigate this issue, overexpression of DLL4 was induced by transfection with expression vectors for DLL4 in the human breast cancer cell line Michigan cancer foundation-7 (MCF-7). It was found that DLL4 could be adaptively upregulated by docetaxel (DOC) treatment in a dose-dependent manner, but Notch1 was unaffected. Overexpression of DLL4 could significantly attenuate the cytotoxic effects of DOC by increasing Bcl-2 expression, while decreasing Bax expression, apoptosis rate and DNA damage. The protective effects of DLL4 made cells acquire chemoresistance against DOC and resulted in cancer cell survival. DLL4 is normally regarded as a regulator of vascular development. Our results expanded the understanding of DLL4. Since DLL4 may play an important role in the process of acquiring chemoresistance, it may be a promising target in overcoming chemoresistance in breast cancer.

Terrestrial plants are ideal sentinels of environmental pollution, due to their sedentary nature, abundance and sensitivity to atmospheric changes. However, reliable and sensitive biomarkers of exposure have hitherto been difficult to characterise. Biospectroscopy offers a novel approach to the derivation of biomarkers in the form of discrete molecular alterations detectable within a biochemical fingerprint. We investigated the application of this approach for the identification of biomarkers for pollution exposure using the common sycamore (Acer pseudoplatanus) as a sentinel species. Attenuated total reflection Fourier-transform infrared (ATR-FTIR) spectroscopy was used to interrogate leaf tissue collected from three sites exposed to different levels of vehicle exhaust emissions. Following multivariate analysis of acquired spectra, significant biochemical alterations were detected between comparable leaves from different sites that may constitute putative biomarkers for pollution-induced stress. These included differences in carbohydrate and nucleic acid conformations, which may be indicative of sub-lethal exposure effects. We also observed several corresponding spectral alterations in both the leaves of A. pseudoplatanus exposed to ozone pollution under controlled environmental conditions and in leaves infected with the fungal pathogen Rhytisma acerinum, indicating that some stress-induced changes are conserved between different stress signatures. These similarities may be indicative of stress-induced reactive oxygen species (ROS) generation, although further work is needed to verify the precise identity of infrared biomarkers and to identify those that are specific to pollution exposure. Taken together, our data clearly demonstrate that biospectroscopy presents an effective toolkit for the utilisation of higher plants, such as A. pseudoplatanus, as sentinels of environmental pollution.

The substantial cost of substrates is an enormous obstacle in the successful translation of biospectroscopy (IR or Raman) into routine clinical/laboratory practice (screening or diagnosis). As a cheap and versatile substrate, we compared the performance of readily available aluminium (Al) foil with low-E, Au-coated and glass slides for cytological and histological specimen analysis by attenuated total reflection Fourier-transform infrared (ATR-FTIR), transflection FTIR or Raman spectroscopy. The low and almost featureless background signal of Al foil enables the acquisition of IR or Raman spectra without substrate interference or sacrificing important fingerprint biochemical information of the specimen, even for very thin samples with thicknesses down to 2 \ensuremathμm. Al foil is shown to perform as well as, if not better than, low-E or Au-coated slide, irrespective of its relatively rough surface. Although transmission FTIR is not possible on Al foil, this work demonstrates Al foil is an inexpensive, readily available and versatile substrate suitable for ATR-FTIR, transflection FTIR or Raman spectrochemical measurements of diverse biological specimens. The features of Al foil demonstrated here could promote a transition towards accessible substrates that can be readily implemented in either research or clinical settings.

4-Nonylphenol (NP) is a ubiquitous environmental chemical with estrogenic activity. Our aim was to test the hypothesis that pubertal exposure to NP leads to testicular dysfunction. Herein, 24 7-week-old rats were randomly divided into four groups and treated with NP (0, 25, 50, or 100 mg/kg body weight every 2 days for 20 consecutive days) by intraperitoneal injection. Compared to untreated controls, the parameters of sperm activation rate, curvilinear velocity, average path velocity, and swimming velocity were significantly lower at doses of 100 mg/kg, while sperm morphological abnormalities were higher, indicating functional disruption and reduced fertilization potential. High exposure to NP (100 mg/kg) resulted in disordered arrangement of spermatoblasts and reduction of spermatocytes in seminiferous tubules, while tissues exhibited a marked decline in testicular fructose content and serum FSH, LH, and testosterone levels. Oxidative stress was induced by NP (50 or 100 mg/kg) as evidenced by elevated MDA, decreased SOD and GSH-Px, and inhibited antioxidant gene expression (CAT, GPx, SOD1, and CYP1B1). In addition, NP treatment decreased proportions of Ki-67-positive cells and increased apoptosis in a dose-dependent manner. Rats treated with 100 mg/kg NP exhibited significantly increased mRNA expression of caspase-1, -2, -9, and -11, decreased caspase-8 and PCNA1 mRNA expression, downregulation of Bcl-2/Bax ratios and upregulation of Fas, FasL, and p53 at the protein and mRNA levels. Taken together, NP-induced apoptosis, hormonal deficiencies, and depletion of fructose potentially impairs spermatogenesis and sperm function. p53-independent Fas/FasL-Bax/Bcl-2 pathways may be involved in NP-induced oxidative stress-related apoptosis. © 2016 Wiley Periodicals, Inc. Environ Toxicol 32: 739-753, 2017.

IR spectroscopy is an excellent method for biological analyses. It enables the nonperturbative, label-free extraction of biochemical information and images toward diagnosis and the assessment of cell functionality. Although not strictly microscopy in the conventional sense, it allows the construction of images of tissue or cell architecture by the passing of spectral data through a variety of computational algorithms. Because such images are constructed from fingerprint spectra, the notion is that they can be an objective reflection of the underlying health status of the analyzed sample. One of the major difficulties in the field has been determining a consensus on spectral pre-processing and data analysis. This manuscript brings together as coauthors some of the leaders in this field to allow the standardization of methods and procedures for adapting a multistage approach to a methodology that can be applied to a variety of cell biological questions or used within a clinical setting for disease screening or diagnosis. We describe a protocol for collecting IR spectra and images from biological samples (e.g., fixed cytology and tissue sections, live cells or biofluids) that assesses the instrumental options available, appropriate sample preparation, different sampling modes as well as important advances in spectral data acquisition. After acquisition, data processing consists of a sequence of steps including quality control, spectral pre-processing, feature extraction and classification of the supervised or unsupervised type. A typical experiment can be completed and analyzed within hours. Example results are presented on the use of IR spectra combined with multivariate data processing.