The Experts below are selected from a list of 151908 Experts worldwide ranked by ideXlab platform

Francis Martin - One of the best experts on this subject based on the ideXlab platform.

  • subtle effects of environmental stress observed in the early life stages of the common frog rana temporaria
    Scientific Reports, 2017
    Co-Authors: Rebecca J Strong, Francis Martin, Kevin C Jones, Richard F Shore, Crispin J Halsall
    Abstract:

    Worldwide amphibian populations are declining due to habitat loss, disease and pollution. Vulnerability to environmental contaminants such as pesticides will be dependent on the species, the sensitivity of the ontogenic life stage and hence the timing of exposure and the exposure pathway. Herein we investigated the biochemical tissue ‘fingerprint’ in spawn and early-stage tadpoles of the Common frog, Rana temporaria, using attenuated total reflection-Fourier-transform infrared (Atr-Ftir) Spectroscopy with the objective of observing differences in the biochemical constituents of the respective amphibian tissues due to varying water quality in urban and agricultural ponds. Our results demonstrate that levels of stress (marked by biochemical constituents such as glycogen that are involved in compensatory metabolic mechanisms) can be observed in tadpoles present in the pond most impacted by pollution (nutrients and pesticides), but large annual variability masked any inter-site differences in the frog spawn. Atr-Ftir Spectroscopy is capable of detecting differences in tadpoles that are present in selected ponds with different levels of environmental perturbation and thus serves as a rapid and cost effective tool in assessing stress-related effects of pollution in a vulnerable class of organism.

  • perfluoroalkylated substance effects in xenopus laevis a6 kidney epithelial cells determined by atr ftir Spectroscopy and chemometric analysis
    Chemical Research in Toxicology, 2016
    Co-Authors: Eva Gorrochategui, Silvia Lacorte, Roma Tauler, Francis Martin
    Abstract:

    The effects of four perfluoroalkylated substances (PFASs), namely, perfluorobutanesulfonate (PFBS), perfluorooctanoic acid (PFOA), perfluorooctanesulfonate (PFOS), and perfluorononanoic acid (PFNA) were assessed in Xenopus laevis A6 kidney epithelial cells by attenuated total reflection Fourier-transform infrared (Atr-Ftir) Spectroscopy and chemometric analysis. Principal component analysis–linear discriminant analysis (PCA-LDA) was used to visualize wavenumber-related alterations and ANOVA-simultaneous component analysis (ASCA) allowed data processing considering the underlying experimental design. Both analyses evidenced a higher impact of low-dose PFAS-treatments (10–9 M) on A6 cells forming monolayers, while there was a larger influence of high-dose PFAS-treatments (10–5 M) on A6 cells differentiated into dome structures. The observed dose–response PFAS-induced effects were to some extent related to their cytotoxicity: the EC50-values of most influential PFAS-treatments increased (PFOS < PFNA < PFOA ≪...

  • atr ftir Spectroscopy coupled with chemometric analysis discriminates normal borderline and malignant ovarian tissue classifying subtypes of human cancer
    Analyst, 2016
    Co-Authors: Georgios Theophilou, Helen F Stringfellow, Pierre L Martinhirsch, Kassio M G Lima, Francis Martin
    Abstract:

    Surgical management of ovarian tumours largely depends on their histo-pathological diagnosis. Currently, screening for ovarian malignancy with tumour markers in conjunction with radiological investigations has a low specificity for discriminating benign from malignant tumours. Also, pre-operative biopsy of ovarian masses increases the risk of intra-peritoneal dissemination of malignancy. Intra-operative frozen section, although sufficiently accurate in differentiating tumours according to their histological type, increases operation times. This results in increased surgery-related risks to the patient and additional burden to resource allocation. We set out to determine whether attenuated total reflection Fourier-transform infrared (Atr-Ftir) Spectroscopy, combined with chemometric analysis can be applied to discriminate between normal, borderline and malignant ovarian tumours and classify ovarian carcinoma subtypes according to the unique spectral signatures of their molecular composition. Formalin-fixed, paraffin-embedded ovarian tissue blocks were de-waxed, mounted on Low-E slides and desiccated before being analysed using Atr-Ftir Spectroscopy. Chemometric analysis in the form of principal component analysis (PCA), successive projection algorithm (SPA) and genetic algorithm (GA), followed by linear discriminant analysis (LDA) of the obtained spectra revealed clear segregation between benign versus borderline versus malignant tumours as well as segregation between different histological tumour subtypes, when these approaches are used in combination. Atr-Ftir Spectroscopy coupled with chemometric analysis has the potential to provide a novel diagnostic approach in the accurate diagnosis of ovarian tumours assisting surgical decision making to avoid under-treatment or over-treatment, with minimal impact to the patient.

  • segregation of ovarian cancer stage exploiting spectral biomarkers derived from blood plasma or serum analysis atr ftir Spectroscopy coupled with variable selection methods
    Biotechnology Progress, 2015
    Co-Authors: Pierre L Martinhirsch, Kassio M G Lima, Ketan Gajjar, Francis Martin
    Abstract:

    Ovarian cancer is a solid tumor and a leading cause of mortality. Diagnostic tools for the detection of early stage (stage I) ovarian cancer are urgently needed. For this purpose, attenuated total reflection Fourier-transform infrared Spectroscopy (Atr-Ftir) coupled with variable selection methods, successive projection algorithm or genetic algorithm (GA) combined with linear discriminant analysis (LDA), were employed to identify spectral biomarkers in blood plasma or serum samples for accurate diagnosis of different stages of ovarian cancer, histological type and segregation based on age. Three spectral datasets (stage I vs. stage II-IV; serous vs. non-serous carcinoma; and, ≤60 years vs. >60 years) were processed: sensitivity and specificity required for real-world diagnosis of ovarian cancer was achieved. Toward segregating stage I vs. stage II-IV, sensitivity and specificity (plasma blood) of 100% was achieved using a GA-LDA model with 33 wavenumbers. For serous vs. non-serous category (plasma blood), the sensitivity and specificity levels, using 29 wavenumbers by GA-LDA, were remarkable (up to 94%). For ≤60 years and >60 years categories (plasma blood), the sensitivity and specificity, using 42 wavenumbers by GA-LDA, gave complete accuracy (100%). For serum samples, sensitivity and specificity results gave relatively high accuracy (up to 91.6% stage I vs. stage II-IV; up to 93.0% serous vs. non-serous; and, up to 96.0% ≤60 years vs. >60 years) using several wavenumbers. These findings justify a prospective population-based assessment of biomarkers signatures using Atr-Ftir Spectroscopy as a screening tool for stage of ovarian cancer.

  • fourier transform infrared Spectroscopy coupled with a classification machine for the analysis of blood plasma or serum a novel diagnostic approach for ovarian cancer
    Analyst, 2013
    Co-Authors: Helen F Stringfellow, Pierre L Martinhirsch, Ketan Gajjar, Julio Trevisan, Gemma Owens, Patrick J Keating, N Wood, Francis Martin
    Abstract:

    Currently available screening tests do not deliver the required sensitivity and specificity for accurate diagnosis of ovarian or endometrial cancer. Infrared (IR) Spectroscopy of blood plasma or serum is a rapid, versatile, and relatively non-invasive approach which could characterize biomolecular alterations due to cancer and has potential to be utilized as a screening or diagnostic tool. In the past, no such approach has been investigated for its applicability in screening and/or diagnosis of gynaecological cancers. We set out to determine whether attenuated total reflection Fourier-transform IR (Atr-Ftir) Spectroscopy coupled with a proposed classification machine could be applied to IR spectra obtained from plasma and serum for accurate class prediction (cancer vs. normal). Plasma and serum samples were obtained from ovarian cancer cases (n = 30), endometrial cancer cases (n = 30) and non-cancer controls (n = 30), and subjected to Atr-Ftir Spectroscopy. Four derived datasets were processed to estimate the real-world diagnosis of ovarian and endometrial cancer. Classification results for ovarian cancer were remarkable (up to 96.7%), whereas endometrial cancer was classified with a relatively high accuracy (up to 81.7%). The results from different combinations of feature extraction and classification methods, and also classifier ensembles, were compared. No single classification system performed best for all different datasets. This demonstrates the need for a framework that can accommodate a diverse set of analytical methods in order to be adaptable to different datasets. This pilot study suggests that Atr-Ftir Spectroscopy of blood is a robust tool for accurate diagnosis, and carries the potential to be utilized as a screening test for ovarian cancer in primary care settings. The proposed classification machine is a powerful tool which could be applied to classify the vibrational Spectroscopy data of different biological systems (e.g., tissue, urine, saliva), with their potential application in clinical practice.

Peter R Rich - One of the best experts on this subject based on the ideXlab platform.

  • molecular recognition between protein and nicotinamide dinucleotide in intact proton translocating transhydrogenase studied by atr ftir Spectroscopy
    Journal of the American Chemical Society, 2006
    Co-Authors: Masayo Iwaki, Peter R Rich, Nick P J Cotton, Philip G Quirk, Baz J Jackson
    Abstract:

    Nicotinamide dinucleotide binding to transhydrogenase purified from Escherichia coli was investigated by attenuated total reflectance-Fourier transform infrared (Atr-Ftir) Spectroscopy. Detergent-free transhydrogenase was deposited as a thin film on an ATR prism, and spectra were recorded during perfusion with buffers in the presence and absence of dinucleotide (NADP+, NADPH, NAD+, or NADH) in both H2O and D2O media. IR spectral changes were attributable to the bound dinucleotides and to changes in the protein itself. The dissociation constant of NADPH was estimated to be approximately 5 μM from a titration of the magnitude of the IR changes against the nucleotide concentration. IR spectra of related model compounds were used to assign principle bands of the dinucleotides. This information was combined with IR data on amino acids and with protein crystallographic data to identify interactions between specific parts of the dinucleotides and their binding sites in the protein. Several IR bands of bound nucl...

  • direct observation of redox linked histidine protonation changes in the iron sulfur protein of the cytochrome bc1 complex by atr ftir Spectroscopy
    Biochemistry, 2005
    Co-Authors: Masayo Iwaki, Artur Osyczka, Leslie P Dutton, Gregory Yakovlev, Judy Hirst, Douglas Marshall, Peter R Rich
    Abstract:

    The redox-linked protonation chemistry of the iron−sulfur protein (ISP) of the cytochrome bc1 complex was studied by analysis of the pH dependencies of redox difference spectra using perfusion/electrochemically induced attenuated total reflection-Fourier transform infrared (Atr-Ftir) Spectroscopy. The ISP of Rhodobacter capsulatus within the intact cytochrome bc1 complex was analyzed in a mutant form in which the midpoint potential of cytochrome c1 was lower than that of the ISP. This was compared to a soluble domain of the ISP from the bovine bc1 complex. Spectra of in situ bacterial and isolated bovine proteins differ markedly only in part of their amide I regions with the in situ protein having additional pH-dependent component(s). Apart from this, both in situ and isolated proteins exhibited the same pH-dependent IR features in reduced minus oxidized difference spectra. Specifically, at high pH, a strong H/D insensitive negative band appeared at 1447/1450 cm-1, together with a peak at 1310 cm-1, the c...

  • atr ftir Spectroscopy studies of iron sulfur protein and cytochrome c1 in the rhodobacter capsulatus cytochrome bc1 complex
    Biochemistry, 2004
    Co-Authors: Masayo Iwaki, Artur Osyczka, Christopher C Moser, Leslie P Dutton, Peter R Rich
    Abstract:

    Redox transitions in the Rhodobacter capsulatus cytochrome bc1 complex were investigated by perfusion-induced attenuated total reflection-Fourier transform infrared (Atr-Ftir) Spectroscopy combined with synchronous visible Spectroscopy, in both the wild type and a cytochrome c1 point mutant, M183K, in which the midpoint potential of heme was lowered from the wild-type value of 320 mV to 60 mV. Overall redox difference spectra of the wild type and M183K mutant were essentially identical, indicating that the mutation did not cause any major structural perturbation. Spectra were compared with data on the bovine bc1 complex, and tentative assignments of several bands could be made by comparison with available data on model compounds and crystallographic structures. The bacterial spectra showed contributions from ubiquinone that were much larger than in the bovine enzyme, arising from additional bound and adventitious ubiquinone. The M183K mutant enabled selective reduction of the iron−sulfur protein which in ...

Fethi Caglar - One of the best experts on this subject based on the ideXlab platform.

  • attenuated total reflectance fourier transform infrared atr ftir Spectroscopy combined with chemometrics for rapid determination of cold pressed wheat germ oil adulteration
    Food Analytical Methods, 2019
    Co-Authors: Fatma Nur Arslan, Fethi Caglar
    Abstract:

    This paper describes the feasibility of attenuated total reflectance–Fourier transform infrared (ATR–FTIR) Spectroscopy combined with multivariate data analyses for rapid determination of cold-pressed wheat germ oil (WGO) adulteration. Thirty-six pure edible oils, as well as 216 binary blends of WGO adulterated with cheaper refined oils, sunflower (SFO), and soybean oil (SBO) (1–50%) were analyzed by using ATR–FTIR Spectroscopy in combination with PCA, LDA, SIMCA, and PLSR analyses. SIMCA models provide excellent classification for pure cold-pressed WGO and refined edible oil samples, with 95% significance level. The classification limits for detection of SFO and SBO adulterations in WGO were below 1%. Furthermore, a total of 100% of studied samples were correctly classified on the basis of their origin in calibration and in cross-validation by LDA models. Under the optimum conditions, the PLS–R plots of actual versus predicted values exhibited high linearity (R2 > 0.9990). The content of SFO and SBO adulterants has been successively quantified using PLSR at levels < 0.56% and < 0.99% in an unknown mixture. RMSEC and RMSECV values for the binary mixtures of WGO–SFO were between 0.56–1.98% and 0.68–4.46%, for the binary mixtures of WGO–SBO were between 0.99–1.77% and 1.09–5.12%, respectively.

Masayo Iwaki - One of the best experts on this subject based on the ideXlab platform.

  • molecular recognition between protein and nicotinamide dinucleotide in intact proton translocating transhydrogenase studied by atr ftir Spectroscopy
    Journal of the American Chemical Society, 2006
    Co-Authors: Masayo Iwaki, Peter R Rich, Nick P J Cotton, Philip G Quirk, Baz J Jackson
    Abstract:

    Nicotinamide dinucleotide binding to transhydrogenase purified from Escherichia coli was investigated by attenuated total reflectance-Fourier transform infrared (Atr-Ftir) Spectroscopy. Detergent-free transhydrogenase was deposited as a thin film on an ATR prism, and spectra were recorded during perfusion with buffers in the presence and absence of dinucleotide (NADP+, NADPH, NAD+, or NADH) in both H2O and D2O media. IR spectral changes were attributable to the bound dinucleotides and to changes in the protein itself. The dissociation constant of NADPH was estimated to be approximately 5 μM from a titration of the magnitude of the IR changes against the nucleotide concentration. IR spectra of related model compounds were used to assign principle bands of the dinucleotides. This information was combined with IR data on amino acids and with protein crystallographic data to identify interactions between specific parts of the dinucleotides and their binding sites in the protein. Several IR bands of bound nucl...

  • direct observation of redox linked histidine protonation changes in the iron sulfur protein of the cytochrome bc1 complex by atr ftir Spectroscopy
    Biochemistry, 2005
    Co-Authors: Masayo Iwaki, Artur Osyczka, Leslie P Dutton, Gregory Yakovlev, Judy Hirst, Douglas Marshall, Peter R Rich
    Abstract:

    The redox-linked protonation chemistry of the iron−sulfur protein (ISP) of the cytochrome bc1 complex was studied by analysis of the pH dependencies of redox difference spectra using perfusion/electrochemically induced attenuated total reflection-Fourier transform infrared (Atr-Ftir) Spectroscopy. The ISP of Rhodobacter capsulatus within the intact cytochrome bc1 complex was analyzed in a mutant form in which the midpoint potential of cytochrome c1 was lower than that of the ISP. This was compared to a soluble domain of the ISP from the bovine bc1 complex. Spectra of in situ bacterial and isolated bovine proteins differ markedly only in part of their amide I regions with the in situ protein having additional pH-dependent component(s). Apart from this, both in situ and isolated proteins exhibited the same pH-dependent IR features in reduced minus oxidized difference spectra. Specifically, at high pH, a strong H/D insensitive negative band appeared at 1447/1450 cm-1, together with a peak at 1310 cm-1, the c...

  • atr ftir Spectroscopy studies of iron sulfur protein and cytochrome c1 in the rhodobacter capsulatus cytochrome bc1 complex
    Biochemistry, 2004
    Co-Authors: Masayo Iwaki, Artur Osyczka, Christopher C Moser, Leslie P Dutton, Peter R Rich
    Abstract:

    Redox transitions in the Rhodobacter capsulatus cytochrome bc1 complex were investigated by perfusion-induced attenuated total reflection-Fourier transform infrared (Atr-Ftir) Spectroscopy combined with synchronous visible Spectroscopy, in both the wild type and a cytochrome c1 point mutant, M183K, in which the midpoint potential of heme was lowered from the wild-type value of 320 mV to 60 mV. Overall redox difference spectra of the wild type and M183K mutant were essentially identical, indicating that the mutation did not cause any major structural perturbation. Spectra were compared with data on the bovine bc1 complex, and tentative assignments of several bands could be made by comparison with available data on model compounds and crystallographic structures. The bacterial spectra showed contributions from ubiquinone that were much larger than in the bovine enzyme, arising from additional bound and adventitious ubiquinone. The M183K mutant enabled selective reduction of the iron−sulfur protein which in ...

Ketan Gajjar - One of the best experts on this subject based on the ideXlab platform.

  • segregation of ovarian cancer stage exploiting spectral biomarkers derived from blood plasma or serum analysis atr ftir Spectroscopy coupled with variable selection methods
    Biotechnology Progress, 2015
    Co-Authors: Pierre L Martinhirsch, Kassio M G Lima, Ketan Gajjar, Francis Martin
    Abstract:

    Ovarian cancer is a solid tumor and a leading cause of mortality. Diagnostic tools for the detection of early stage (stage I) ovarian cancer are urgently needed. For this purpose, attenuated total reflection Fourier-transform infrared Spectroscopy (Atr-Ftir) coupled with variable selection methods, successive projection algorithm or genetic algorithm (GA) combined with linear discriminant analysis (LDA), were employed to identify spectral biomarkers in blood plasma or serum samples for accurate diagnosis of different stages of ovarian cancer, histological type and segregation based on age. Three spectral datasets (stage I vs. stage II-IV; serous vs. non-serous carcinoma; and, ≤60 years vs. >60 years) were processed: sensitivity and specificity required for real-world diagnosis of ovarian cancer was achieved. Toward segregating stage I vs. stage II-IV, sensitivity and specificity (plasma blood) of 100% was achieved using a GA-LDA model with 33 wavenumbers. For serous vs. non-serous category (plasma blood), the sensitivity and specificity levels, using 29 wavenumbers by GA-LDA, were remarkable (up to 94%). For ≤60 years and >60 years categories (plasma blood), the sensitivity and specificity, using 42 wavenumbers by GA-LDA, gave complete accuracy (100%). For serum samples, sensitivity and specificity results gave relatively high accuracy (up to 91.6% stage I vs. stage II-IV; up to 93.0% serous vs. non-serous; and, up to 96.0% ≤60 years vs. >60 years) using several wavenumbers. These findings justify a prospective population-based assessment of biomarkers signatures using Atr-Ftir Spectroscopy as a screening tool for stage of ovarian cancer.

  • classification of cervical cytology for human papilloma virus hpv infection using bioSpectroscopy and variable selection techniques
    Analytical Methods, 2014
    Co-Authors: Kassio M G Lima, Ketan Gajjar, George Valasoulis, Maria Nasioutziki, Maria Kyrgiou, Petros Karakitsos, Evangelos Paraskevaidis, Pierre Martin L Hirsch
    Abstract:

    Cervical cancer is the second most common cancer in women worldwide. We set out to determine whether attenuated total reflection Fourier-transform infrared (Atr-Ftir) Spectroscopy combined with principal component analysis–linear discriminant analysis (PCA–LDA) or, variable selection techniques employing successive projection algorithm or genetic algorithm (GA) could classify cervical cytology according to human papilloma virus (HPV) infection [high-risk (hr) vs. low-risk (lr)]. Histopathological categories for squamous intraepithelial lesion (SIL) were segregated into grades (low-grade vs. high-grade) of cervical intraepithelial neoplasia (CIN) expressing different HPV infection (16/18, 31/35 or HPV Others). Risk assessment for HPV infection was investigated using age (≤29 years vs. >30 years) as the distinguishing factor. Liquid-based cytology (LBC) samples (n = 350) were collected and interrogated employing Atr-Ftir Spectroscopy. Accuracy test results including sensitivity and specificity were determined. Sensitivity in hrHPV category was high (≈87%) using a GA–LDA model with 28 wavenumbers. Sensitivity and specificity results for >30 years for HPV, using 28 wavenumbers by GA–LDA, were 70% and 67%, respectively. For normal cervical cytology, accuracy results for ≤29 years and >30 years were high (up to 81%) using a GA–LDA model with 27 variables. For the low-grade cervical cytology dataset, 83% specificity for ≤29 years was achieved using a GA–LDA model with 33 wavenumbers. HPV16/18 vs. HPV31/35 vs. HPV Others were segregated with 85% sensitivity employing a GA–LDA model with 33 wavenumbers. We show that Atr-Ftir Spectroscopy of cervical cytology combined with variable selection techniques is a powerful tool for HPV classification, which would have important implications for the triaging of patients.

  • fourier transform infrared Spectroscopy coupled with a classification machine for the analysis of blood plasma or serum a novel diagnostic approach for ovarian cancer
    Analyst, 2013
    Co-Authors: Helen F Stringfellow, Pierre L Martinhirsch, Ketan Gajjar, Julio Trevisan, Gemma Owens, Patrick J Keating, N Wood, Francis Martin
    Abstract:

    Currently available screening tests do not deliver the required sensitivity and specificity for accurate diagnosis of ovarian or endometrial cancer. Infrared (IR) Spectroscopy of blood plasma or serum is a rapid, versatile, and relatively non-invasive approach which could characterize biomolecular alterations due to cancer and has potential to be utilized as a screening or diagnostic tool. In the past, no such approach has been investigated for its applicability in screening and/or diagnosis of gynaecological cancers. We set out to determine whether attenuated total reflection Fourier-transform IR (Atr-Ftir) Spectroscopy coupled with a proposed classification machine could be applied to IR spectra obtained from plasma and serum for accurate class prediction (cancer vs. normal). Plasma and serum samples were obtained from ovarian cancer cases (n = 30), endometrial cancer cases (n = 30) and non-cancer controls (n = 30), and subjected to Atr-Ftir Spectroscopy. Four derived datasets were processed to estimate the real-world diagnosis of ovarian and endometrial cancer. Classification results for ovarian cancer were remarkable (up to 96.7%), whereas endometrial cancer was classified with a relatively high accuracy (up to 81.7%). The results from different combinations of feature extraction and classification methods, and also classifier ensembles, were compared. No single classification system performed best for all different datasets. This demonstrates the need for a framework that can accommodate a diverse set of analytical methods in order to be adaptable to different datasets. This pilot study suggests that Atr-Ftir Spectroscopy of blood is a robust tool for accurate diagnosis, and carries the potential to be utilized as a screening test for ovarian cancer in primary care settings. The proposed classification machine is a powerful tool which could be applied to classify the vibrational Spectroscopy data of different biological systems (e.g., tissue, urine, saliva), with their potential application in clinical practice.