Evaluation of the effect of chance correlations on variable selection using Partial Least Squares -Discriminant Analysis
Variable subset selection is often mandatory in high throughput metabolomics and proteomics. However, depending on the variable to sample ratio there is a significant susceptibility of variable selection towards chance correlations. The evaluation of the predictive capabilities of PLSDA models estimated by cross-validation after feature selection provides overly optimistic results if the selection is performed on the entire set and no external validation set is available. In this work, a simulation of the statistical null hypothesis is proposed to test whether the discrimination capability of a PLSDA model after variable selection estimated by cross-validation is statistically higher than t…
Atmospheric compensation in Fourier transform infrared (FT-IR) spectra of clinical samples.
A new method is proposed for the elimination of the spectral contribution of two atmospheric gases (CO2 and H2O) in Fourier transform infrared (FT-IR) spectra of clinical samples. The algorithm is based on the measurement of reference spectra of H2O followed by an automatic calculation of the spectral contribution of the above-mentioned gases to the sample spectra. Then this contribution is compensated by spectral subtraction. Attenuated total reflectance FT-IR spectra of serum and urine samples in the presence of atmospheric gases were corrected and compared with spectra obtained with an N2 purge. Visual inspection of the spectra as well as calculated noise levels confirmed that the metho…
Inside Cover: Red Blood Cells Polarize Green Laser Light Revealing Hemoglobin′s Enhanced Non-Fundamental Raman Modes (ChemPhysChem 18/2014)
Addressing Delicate and Variable Cancer Morphology in Spectral Histopathology Using Canine Visceral Hemangiosarcoma
Spectral histopathology has shown promise for the classification and diagnosis of tumors with defined morphology, but application in tumors with variable or diffuse morphologies is yet to be investigated. To address this gap, we evaluated the application of Fourier transform infrared (FTIR) imaging as an accessory diagnostic tool for canine hemangiosarcoma (HSA), a vascular endothelial cell cancer that is difficult to diagnose. To preserve the delicate vascular tumor tissue structure, and potential classification of single endothelial cells, paraffin removal was not performed, and a partial least square discrimination analysis (PLSDA) and Random Forest (RF) models to classify different tiss…
ATR-Spin: an open-source 3D printed device for direct cytocentrifugation onto attenuated total reflectance crystals.
Infrared Spectroscopy (IR) enables the direct and rapid characterization of cells at the molecular level. Achieving a rapid and consistent cell preparation is critical for the development of Point-of-Care diagnostics for cell analysis. Here we introduce an open-source, 3D printed device for integrating the isolation, preconcentration, and measurement of attenuated total reflectance IR spectra of cells from biofluids. The tool comprises a disposable card for cytocentrifugation, equipped with magnets, which allows reproducible integration into the pathlength of the IR spectrophotometer. Preliminary results using cell media containing A459 cells indicate that this system enables a qualitative …
Synthesis and Biological Evaluation of Combretastatin A-4 and Three Combretastatin-Based Hybrids
The syntheses of combretastatin A-4 from gallic acid and of three combretastatin-based hybrids are described. Starting from commercial gallic acid, the phosphonium salt (3,4,5-trimethoxybenzylphosphonium bromide) is synthesized and coupled, through a Wittig reaction, with several aldehydes, including methoxymethyl-protected isovanillin, the aldehyde γ-bicyclohomofarnesal having a labdane skeleton, 3-(3-pyridyl) propanal, and furfural. The biological properties of the cis-coupled compounds as cytotoxic, antiviral and antifungal agents are also reported. In addition, pyrogallol, gallic and 3,4,5-trimethoxybenzoic acids have been studied biologically.
Detection of batch effects in liquid chromatography-mass spectrometry metabolomic data using guided principal component analysis.
Metabolomics based on liquid chromatography-mass spectrometry (LC-MS) is a powerful tool for studying dynamic responses of biological systems to different physiological or pathological conditions. Differences in the instrumental response within and between batches introduce unwanted and uncontrolled data variation that should be removed to extract useful information. This work exploits a recently developed method for the identification of batch effects in high throughput genomic data based on the calculation of a delta statistic through principal component analysis (PCA) and guided PCA. Its applicability to LC-MS metabolomic data was tested on two real examples. The first example involved t…
Data set: Towards a rapid screening of liver grafts at the operating room using mid-infrared spectroscopy
The estimation of steatosis in a liver graft is mandatory prior to liver transplantation, as the risk of graft failure increases with the level of infiltrated fat. However, the assessment of liver steatosis before transplantation is typically based on a qualitative or semi-quantitative characterization by visual inspection and palpation, and histological analysis. Thus, there is an unmet need for transplantation surgeons to have access to a diagnostic tool enabling an in situ fast classification of grafts prior extraction. In this study, we have assessed an Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopic method compatible with the requirements of an operation…
Determination of biochemical parameters in human serum by near-infrared spectroscopy
NIR offers multiple advantages for serum analysis, permitting a fast and direct determination of several parameters simultaneously, with low sample handling and without the need for reagents during the measurement step. The aim of this paper was to provide an evaluation of this technique in a real world scale, for the simultaneous determination of several parameters and based on a considerable number of samples. Direct near infrared (NIR) absorbance measurements were used to determine the concentration of clinical parameters in human serum that are required in routine biochemical tests. Total protein, albumin, total cholesterol, high-density lipoprotein (HDL cholesterol), low-density lipopr…
Determination of lidocaine in urine at low ppm levels using dispersive microextraction and attenuated total reflectance–Fourier transform infrared measurements of dry films
Abstract IR spectra provide valuable information about biological systems and can be obtained with compactable and affordable instruments, but the lack of sensitivity of this technique hampers its use in the determination of drugs in clinical fluids. Taking lidocaine as a target molecule, in this paper we introduced a methodology for determining drugs in urine samples using infrared spectroscopy. The lack of sensitivity of the IR was compensated with the combination of an effective and straightforward dispersive liquid–liquid microextraction and the measurement of the dry film of the organic extracts through attenuated total reflectance (ATR). The method developed improves the sensitivity b…
Data set: Towards a rapid screening of liver grafts at the operating room using mid-infrared spectroscopy
The estimation of steatosis in a liver graft is mandatory prior to liver transplantation, as the risk of graft failure increases with the level of infiltrated fat. However, the assessment of liver steatosis before transplantation is typically based on a qualitative or semi-quantitative characterization by visual inspection and palpation, and histological analysis. Thus, there is an unmet need for transplantation surgeons to have access to a diagnostic tool enabling an in situ fast classification of grafts prior extraction. In this study, we have assessed an Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopic method compatible with the requirements of an operation…
Evaluation of infrared spectroscopy as a screening tool for serum analysis
Abstract The application of attenuated total reflectance Fourier transform infrared (ATR-FT-IR) spectroscopy to the determination of clinical parameters in serum using partial least squares (PLS) has been evaluated as a point-of-care diagnostic tool. In this study the effect of using an increased size of the calibration set and the influence of the origin of samples and their interyear variation on the prediction capability of the method were considered. PLS-ATR-FT-IR provides a green, fast and cheap point-of-care tool for the determination of total protein. Albumin, glucose, urea, HDL, LDL and total cholesterol were predicted with relative errors between 15 and 32%. The analytical predicti…
Red Blood Cells Polarize Green Laser Light Revealing Hemoglobin's Enhanced Non-Fundamental Raman Modes
In general, the first overtone modes produce weak bands that appear at approximately twice the wavenumber value of the fundamental transitions in vibrational spectra. Here, we report the existence of a series of enhanced non-fundamental bands in resonance Raman (RR) spectra recorded for hemoglobin (Hb) inside the highly concentrated heme environment of the red blood cell (RBC) by exciting with a 514.5 nm laser line. Such bands are most intense when detecting parallel-polarized light. The enhancement is explained through excitonic theory invoking a type C scattering mechanism and bands have been assigned to overtone and combination bands based on symmetry arguments and polarization measureme…
Modified locally weighted—Partial least squares regression improving clinical predictions from infrared spectra of human serum samples
Locally weighted partial least squares regression (LW-PLSR) has been applied to the determination of four clinical parameters in human serum samples (total protein, triglyceride, glucose and urea contents) by Fourier transform infrared (FTIR) spectroscopy. Classical LW-PLSR models were constructed using different spectral regions. For the selection of parameters by LW-PLSR modeling, a multi-parametric study was carried out employing the minimum root-mean square error of cross validation (RMSCV) as objective function. In order to overcome the effect of strong matrix interferences on the predictive accuracy of LW-PLSR models, this work focuses on sample selection. Accordingly, a novel strateg…
Short syntheses of (+)-ferruginol from (+)-dehydroabietylamine
Short syntheses of bioactive (+)-ferruginol in five or six synthetic steps starting from commercially available (+)-dehydroabietylamine are described. The oxygenated function at C12 was introduced via a Friedel–Crafts acylation of N-phthaloyldehydroabietylamine followed by Baeyer–Villiger oxidation. Then, overall deprotection of functional groups, reductive deamination or biomimetic oxidative deamination, and final Wolff–Kishner reduction provided (+)-ferruginol in 21 and 23% overall yields, respectively.
Towards a Rapid Screening of Liver Grafts at the Operating Room Using Mid-Infrared Spectroscopy
The estimation of steatosis in a liver graft is mandatory prior to liver transplantation, as the risk of graft failure increases with the level of infiltrated fat. However, the assessment of liver steatosis before transplantation is typically based on a qualitative or semiquantitative characterization by visual inspection and palpation and histological analysis. Thus, there is an unmet need for transplantation surgeons to have access to a diagnostic tool enabling an in situ fast classification of grafts prior to extraction. In this study, we have assessed an attenuated total reflection-Fourier transform infrared (ATR-FTIR) spectroscopic method compatible with the requirements of an operatio…
ATR-FTIR spectroscopy as a quality control system for monitoring the storage of blood products
Blood screening is a fundamental part of disease diagnosis and monitoring health. Attenuated total reflectance Fourier transform infrared (ATR-FTIR) spectroscopy offers an innovative solution to streamlining the process, especially for multianalyte detection in aqueous samples. However, samples always undergo a storage phase before they are processed for testing and blood transfusion. In this study, we investigated the effect of standard storage procedures on the macromolecular composition of whole blood, and plasma collected in blood tubes for diagnostic purposes and initial screening of blood products. Periphery blood samples were collected from 10 volunteers and then stored for 14 days a…
Infrared-based quantification of clinical parameters
Abstract Infrared (IR) spectroscopy has become a promising technique for the analysis of clinical samples, and IR-based diagnosis is already a well-established technique in the academic field. This review aims to report the methodologies proposed for IR quantification of different analytes and parameters in a variety of clinical samples; including: liquids, such as whole blood, serum, plasma, urine, human milk, amniotic fluid and cerebrospinal fluid; solids, such as urinary stones, skin, hair and lips; breath; or, microscopic quantifications on tissues. For the application of IR spectroscopy to the clinical field, we also discuss: the benefits, which make IR spectroscopy ideally suited to m…
Towards the determination of isoprene in human breath using substrate-integrated hollow waveguide mid-infrared sensors
Selected volatile organic compounds (VOCs) in breath may be considered biomarkers if they are indicative of distinct diseases or disease states. Given the inherent molecular selectivity of vibrational spectroscopy, infrared sensing technologies appear ideally suitable for the determination of endogenous VOCs in breath. The aim of this study was to determine that mid-infrared (MIR; 3-20 µm) gas phase sensing is capable of determining isoprene in exhaled breath as an exemplary medically relevant VOC by hyphenating novel substrate-integrated hollow waveguides (iHWG) with a likewise miniaturized preconcentration system. A compact preconcentrator column for sampling isoprene from exhaled breath …
Towards the Point of Care and Noninvasive Classification of Bladder Cancer from Urine Sediment Infrared Spectroscopy. Spectral differentiation of normal, abnormal and cancer patients
Abstract Bladder cancer (BC) is the 9th cancer cause of death and one of most cost-intensive in the world. The diagnostic tools are still not at all satisfactory. Herein we evaluated the potential of infrared spectroscopy to detect molecular changes that precede and accompany the carcinogenesis in voided urine sediment. We collected 165 samples from patients being diagnosed for BC and measured them with attenuated total reflectance Fourier transformed infrared spectroscopy (ATR FTIR). Samples were primarily divided into three groups according to cytology that indicated the presence of normal, abnormal and cancer cells. ATR FTIR spectra of sediments were analyzed with the use of partial leas…
Assessment of the statistical significance of classifications in infrared spectroscopy based diagnostic models.
Fourier transform infrared (IR) spectroscopy in combination with multivariate data analysis is a versatile tool that can be applied to disease diagnosis. However, a rigorous validation of the obtained models is necessary in order to obtain robust results. This work evaluates the advantages of the use of permutation testing for determining the statistical significance of the misclassification errors obtained from IR based diagnostic models through cross validation (CV). The model performance, estimated by CV, is compared to a distribution of CV-performance values obtained using randomly permuted class labels. The distribution of ‘random CV-values’ is considered as a null distribution and use…
Materials and methods of signal enhancement for spectroscopic whole blood analysis: Novel research overview
Abstract The early diagnosis of diseases is crucial for reducing morbidity and mortality and also for improving the quality of treatment process. Among various biological samples used to follow up the concentrations of disease markers, whole blood sensing can efficiently decrease analysis time by means of introducing methods with no pretreatment. In addition, the direct detection of markers in whole blood facilitates testing procedure and minimize the possibility of the loss of analytes in the process. Therefore, the assay of unprocessed whole blood is becoming increasingly important in clinical diagnostics and biomedical research. Incorporation of new advanced materials plays a major role …
Infrared biospectroscopy for a fast qualitative evaluation of sample preparation in metabolomics.
Liquid chromatography-mass spectrometry (LC-MS) has been increasingly used in biomedicine to study the dynamic metabolomic responses of biological systems under different physiological or pathological conditions. To obtain an integrated snapshot of the system, metabolomic methods in biomedicine typically analyze biofluids (e.g. plasma) that require clean-up before being injected into LC-MS systems. However, high resolution LC-MS is costly in terms of resources required for sample and data analysis and care must be taken to prevent chemical (e.g. ion suppression) or statistical artifacts. Because of that, the effect of sample preparation on the metabolomic profile during metabolomic method d…
Chemometric determination of lipidic parameters in serum using ATR measurements of dry films of solvent extracts
Attenuated total reflectance (ATR) infrared spectroscopy of dried organic extracts of serum samples has been evaluated as a fast method for the determination of triglycerides, cholesterol, high density lipoprotein (HDL) and low density lipoprotein (LDL). After careful selection of solvents based on green parameters, serum samples were extracted using hexane-isopropanol and ethyl acetate-ethanol mixtures. Microscopy studies and comparison with standard spectra were performed in order to investigate whether the proposed methodology is suitable for the quantification of lipids in serum samples. The results of these preliminary studies confirmed that the variations in the IR spectra of sample e…
Synthesis and biological evaluation of dehydroabietic acid derivatives.
A series of C18-oxygenated derivatives of dehydroabietic acid were synthesized from commercial abietic acid and evaluated for their cytotoxic, antimycotic, and antiviral activities.
Infrared based saliva screening test for COVID‐19
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has resulted in an unprecedented need for diagnostic testing that is critical in controlling the spread of COVID-19. We propose a portable infrared spectrometer with purpose-built transflection accessory for rapid point-of-care detection of COVID-19 markers in saliva. Initially, purified virion particles were characterized with Raman spectroscopy, synchrotron infrared (IR) and AFM-IR. A data set comprising 171 transflection infrared spectra from 29 subjects testing positive for SARS-CoV-2 by RT-qPCR and 28 testing negative, was modeled using Monte Carlo Double Cross Validation with 50 randomized test and model sets. The testing se…
Data set: Towards a rapid screening of liver grafts at the operating room using mid-infrared spectroscopy
The estimation of steatosis in a liver graft is mandatory prior to liver transplantation, as the risk of graft failure increases with the level of infiltrated fat. However, the assessment of liver steatosis before transplantation is typically based on a qualitative or semi-quantitative characterization by visual inspection and palpation, and histological analysis. Thus, there is an unmet need for transplantation surgeons to have access to a diagnostic tool enabling an in situ fast classification of grafts prior extraction. In this study, we have assessed an Attenuated Total Reflection-Fourier Transform Infrared (ATR-FTIR) spectroscopic method compatible with the requirements of an operation…
Analysis of multi-source metabolomic data using joint and individual variation explained (JIVE).
Metabolic profiling is increasingly being used for understanding biological processes but there is no single analytical technique that provides a complete quantitative or qualitative profiling of the metabolome. Data fusion (i.e. joint analysis of data from multiple sources) has the potential to circumvent this issue facilitating knowledge discovery and reliable biomarker identification. Another field of application of data fusion is the simultaneous analysis of metabolomic changes through several biofluids or tissues. However, metabolomics typically deals with large datasets, with hundreds to thousands of variables and the identification of shared and individual factors or structures acros…
Comparison of transflection and transmission FTIR imaging measurements performed on differentially fixed tissue sections
The widespread and cost-effective use of transflection substrates in Fourier transform infrared (FTIR) imaging of clinical samples is affected by the presence of artefacts including the electric field standing wave (EFSW) and contributions from light dispersion. For IR-based diagnostics, the manifestation of undesirable artifacts can distort the spectra and lead to erroneous diagnosis. Nevertheless, there is no clear consensus in the literature about the degree of influence of these effects. The aim of this work is to contribute to this discussion by comparing transflection and transmission images of the same tissue. For this purpose two adjacent sections of the same tissue (lymphoma sample…
Cytotoxic, immunomodulatory, antimycotic, and antiviral activities of semisynthetic 14-hydroxyabietane derivatives and triptoquinone C-4 epimers
A series of C14-hydroxy derivatives of dehydroabietic acid were synthesised from commercial abietic acid and evaluated for their cytotoxic, antimycotic, and antiviral activities. From these C14-hydroxy derivatives, triptoquinone C-4 epimers were obtained and their immunomodulatory activity was additionally evaluated. None of the tested compounds showed antiviral activity against herpes simplex virus type 1 (HHV-1), and nor did they display antimycotic activity against certain Aspergillus, spp. except for one compound, abieta-8,11,13-trien-14,18-diol. Interestingly, two triptoquinone epimers showed cytotoxic activity, and one of them induced mitochondrial potential loss, DNA damage and cell …
ATR-FTIR spectroscopy for the routine quality control of exosome isolations
Abstract Exosomes are nanosized vesicles containing specific cargos of DNA, RNA, proteins, metabolites, and intracellular and membrane lipids. Exosome isolation needs to be optimized carefully depending on the type of biofluid and tissue and the retrieved exosomes need to be characterized. The main objective of this study was to determine the feasibility of a multimodal analysis of Attenuated Total Reflectance – Fourier Transform Infrared (ATR-FTIR) spectroscopy and UPLC–QqTOF-MSMS for the development of a routine quality control tool of isolated exosomes and the rapid characterization of their lipid profiles and total protein content. Using human milk as model example, exosomes were isolat…