Browse
Submit Data
Databases
API
Help

Dataset Information

0 Views

0 Connections

0 Citations

0 Reanalyses

0 Downloads

Omics score: 0

Intrinsic near-infrared spectroscopic markers of breast tumors.

ABSTRACT: We have discovered quantitative optical biomarkers unique to cancer by developing a double-differential spectroscopic analysis method for near-infrared (NIR, 650-1000 nm) spectra acquired non-invasively from breast tumors. These biomarkers are characterized by specific NIR absorption bands. The double-differential method removes patient specific variations in molecular composition which are not related to cancer, and reveals these specific cancer biomarkers. Based on the spectral regions of absorption, we identify these biomarkers with lipids that are present in tumors either in different abundance than in the normal breast or new lipid components that are generated by tumor metabolism. Furthermore, the O-H overtone regions (980-1000 nm) show distinct variations in the tumor as compared to the normal breast. To quantify spectral variation in the absorption bands, we constructed the Specific Tumor Component (STC) index. In a pilot study of 12 cancer patients we found 100% sensitivity and 100% specificity for lesion identification. The STC index, combined with other previously described tissue optical indices, further improves the diagnostic power of NIR for breast cancer detection.

SUBMITTER: Kukreti S

PROVIDER: S-EPMC2732199 | biostudies-other | 2008

REPOSITORIES: biostudies-other

ACCESS DATA

Json Xml

Similar Datasets

Environmentally-Controlled Near Infrared Spectroscopic Imaging of Bone Water.

Project description:We have designed an environmentally-controlled chamber for near infrared spectroscopic imaging (NIRSI) to monitor changes in cortical bone water content, an emerging biomarker related to bone quality assessment. The chamber is required to ensure repeatable spectroscopic measurements of tissues without the influence of atmospheric moisture. A calibration curve to predict gravimetric water content from human cadaveric cortical bone was created using NIRSI data obtained at six different lyophilization time points. Partial least squares (PLS) models successfully predicted bone water content that ranged from 0-10% (R = 0.96, p < 0.05, root mean square error of prediction (RMSEP) = 7.39%), as well as in the physiologic range of 4-10% of wet tissue weight (R = 0.87, p < 0.05, RMSEP = 14.5%). Similar results were obtained with univariate and bivariate regression models for prediction of water in the 0-10% range. Further, we identified two new NIR bone absorbances, at 6560 cm-1 and 6688 cm-1, associated with water and collagen respectively. Such data will be useful in pre-clinical studies that investigate changes in bone quality with disease, aging and with therapeutic use.

| S-EPMC6629628 | biostudies-literature

Hydration of LiOH and LiCl-Near-Infrared Spectroscopic Analysis.

Project description:The hydration behavior of LiOH, LiOH·H2O, and LiCl was observed by near-infrared (NIR) spectroscopy. Anhydrous LiOH showed two absorption bands at 7340 and 7171 cm-1. These NIR bands were assigned to the first overtone of surface hydroxyls and interlayer hydroxyls of LiOH, respectively. LiOH·H2O showed two absorption bands at 7137 and 6970 cm-1. These NIR bands were assigned to the first overtone of interlayer hydroxyls and H2O molecules coordinated with Li+, respectively. The interlayer OH- and the coordinated H2O of LiOH·H2O were not modified even when the LiOH·H2O was exposed to air. In contrast, anhydrous LiOH was slowly hydrated for several hours, to form LiOH·H2O under ambient conditions (RH 60%). Kinetic analysis showed that the hydration of the interlayer OH- of LiOH proceeded as a second-order reaction, indicating the formation of intermediate species-[Li(H2O) x (OH)4]3- (x = 1 or 2). However, the hydration of the LiOH surface did not follow a second-order reaction because the chemisorption of H2O molecules onto the defect sites of the LiOH surface does not need to crossover the energy barrier. Furthermore, we succeeded in observing the hydration of deliquescent LiCl, including the formation of LiCl solution for several minutes by NIR spectroscopy.

| S-EPMC8655917 | biostudies-literature

Near infrared fluorescent imaging of choline kinase alpha expression and inhibition in breast tumors.

Project description:Choline kinase alpha (ChoKα) overexpression is associated with an aggressive tumor phenotype. ChoKα inhibitors induce apoptosis in tumors, however validation of their specificity is difficult in vivo. We report the use of optical imaging to assess ChoKα status in cells and in vivo using JAS239, a carbocyanine-based ChoKα inhibitor with inherent near infrared fluorescence. JAS239 attenuated choline phosphorylation and viability in a panel of human breast cancer cell lines. Antibody blockade prevented cellular retention of JAS239 indicating direct interaction with ChoKα independent of the choline transporters and catabolic choline pathways. In mice bearing orthotopic MCF7 breast xenografts, optical imaging with JAS239 distinguished tumors overexpressing ChoKα from their empty vector counterparts and delineated tumor margins. Pharmacological inhibition of ChoK by the established inhibitor MN58b led to a growth inhibition in 4175-Luc+ tumors that was accompanied by concomitant reduction in JAS239 uptake and decreased total choline metabolite levels as measured using magnetic resonance spectroscopy. At higher therapeutic doses, JAS239 was as effective as MN58b at arresting tumor growth and inducing apoptosis in MDA-MB-231 tumors, significantly reducing tumor choline below baseline levels without observable systemic toxicity. These data introduce a new method to monitor therapeutically effective inhibitors of choline metabolism in breast cancer using a small molecule companion diagnostic.

| S-EPMC5369982 | biostudies-literature

Infrared-spectroscopic, dynamic near-field microscopy of living cells and nanoparticles in water.

Project description:Infrared fingerprint spectra can reveal the chemical nature of materials down to 20-nm detail, far below the diffraction limit, when probed by scattering-type scanning near-field optical microscopy (s-SNOM). But this was impossible with living cells or aqueous processes as in corrosion, due to water-related absorption and tip contamination. Here, we demonstrate infrared s-SNOM of water-suspended objects by probing them through a 10-nm thick SiN membrane. This separator stretches freely over up to 250 µm, providing an upper, stable surface to the scanning tip, while its lower surface is in contact with the liquid and localises adhering objects. We present its proof-of-principle applicability in biology by observing simply drop-casted, living E. coli in nutrient medium, as well as living A549 cancer cells, as they divide, move and develop rich sub-cellular morphology and adhesion patterns, at 150 nm resolution. Their infrared spectra reveal the local abundances of water, proteins, and lipids within a depth of ca. 100 nm below the SiN membrane, as we verify by analysing well-defined, suspended polymer spheres and through model calculations. SiN-membrane based s-SNOM thus establishes a novel tool of live cell nano-imaging that returns structure, dynamics and chemical composition. This method should benefit the nanoscale analysis of any aqueous system, from physics to medicine.

| S-EPMC8576021 | biostudies-literature

Enhanced visible/near-infrared spectroscopic data for prediction of quality attributes in Cucurbitaceae commodities.

Project description:Spectra data of 300 samples from 6 Cucurbitaceae commodities, including zucchini, bitter gourd, ridge gourd, melon, chayote, and cucumber, were recorded using a handheld visible/near-infrared (Vis/NIR) instrument. Vis/NIR data were obtained in the form of absorbance spectra data at a wavelength of 381-1065 nm. The spectral data has the potential to be reused to predict quality attributes in the form of soluble solids and water content on several Cucurbitaceae commodities. The accuracy of the Vis/NIR calibration model can be increased by applying spectra preprocessing, for example, second derivative savitzky-golay (dg2). The calibration model was developed using the principal component regression (PCR) method on RAW and dg2 spectra. The enhanced Vis/NIR dataset can be used to evaluate the inner quality attributes of intact fruits in a rapid, non-destructive manner.

| S-EPMC8551409 | biostudies-literature

Non-destructive and rapid evaluation of aflatoxins in brown rice by using near-infrared and mid-infrared spectroscopic techniques.

Project description:The applicability of near-infrared (NIR) and mid-infrared (MIR) spectroscopy combined with chemometrics was explored in this study to develop rapid, low-cost and non-destructive spectroscopic methods for classification and quantification of aflatoxins in brown rice. A total of 132 brown rice samples within the aflatoxin concentration range of 0-2435.8 ?g/kg were prepared by artificially inoculated with A. flavus and A. parasiticus strains of fungus. For the classification of samples at varying levels of aflatoxin B1, the linear discriminant analysis model obtained correct classification rate of 96.9 and 90.6% for NIR and MIR spectroscopy, respectively. For the simultaneous determination of aflatoxins B1, B2, G1, G2 and the total aflatoxins, partial least squares regression also showed good predictive accuracy for both NIR (rv = 0.936-0.973, RPD = 2.5-4.0) and MIR spectroscopy (rv = 0.922-0.970, RPD = 2.5-4.0). The overall results indicated that the two spectroscopic techniques offered the feasibility to be used as alternative tools for rapid detection of various aflatoxin contaminations in grain.

| S-EPMC5821677 | biostudies-literature

In vivo near-infrared imaging of ErbB2 expressing breast tumors with dual-axes confocal endomicroscopy using a targeted peptide.

Project description:ErbB2 expression in early breast cancer can predict tumor aggressiveness and clinical outcomes in large patient populations. Accurate assessment with physical biopsy and conventional pathology can be limited by tumor heterogeneity. We aim to demonstrate real-time optical sectioning using a near-infrared labeled ErbB2 peptide that generates tumor-specific contrast in human xenograft breast tumors in vivo. We used IRDye800CW as the fluorophore, validated performance characteristics for specific peptide binding to cells in vitro, and investigated peak peptide uptake in tumors using photoacoustic tomography. We performed real-time optical imaging using a handheld dual-axes confocal fluorescence endomicroscope that collects light off-axis to reduce tissue scattering for greater imaging depths. Optical sections in either the vertical or horizontal plane were collected with sub-cellular resolution. Also, we found significantly greater peptide binding to pre-clinical xenograft breast cancer in vivo and to human specimens of invasive ductal carcinoma that express ErbB2 ex vivo. We used a scrambled peptide for control. Peptide biodistribution showed high tumor uptake by comparison with other organs to support safety. This novel integrated imaging strategy is promising for visualizing ErbB2 expression in breast tumors and serve as an adjunct during surgery to improve diagnostic accuracy, identify tumor margins, and stage early cancers.

| S-EPMC5663926 | biostudies-literature

Near-infrared-to-visible highly selective thermal emitters based on an intrinsic semiconductor.

Project description:Control of the thermal emission spectra of emitters will result in improved energy utilization efficiency in a broad range of fields, including lighting, energy harvesting, and sensing. In particular, it is challenging to realize a highly selective thermal emitter in the near-infrared-to-visible range, in which unwanted thermal emission spectral components at longer wavelengths are significantly suppressed, whereas strong emission in the near-infrared-to-visible range is retained. To achieve this, we propose an emitter based on interband transitions in a nanostructured intrinsic semiconductor. The electron thermal fluctuations are first limited to the higher-frequency side of the spectrum, above the semiconductor bandgap, and are then enhanced by the photonic resonance of the structure. Theoretical calculations indicate that optimized intrinsic Si rod-array emitters with a rod radius of 105 nm can convert 59% of the input power into emission of wavelengths shorter than 1100 nm at 1400 K. It is also theoretically indicated that emitters with a rod radius of 190 nm can convert 84% of the input power into emission of <1800-nm wavelength at 1400 K. Experimentally, we fabricated a Si rod-array emitter that exhibited a high peak emissivity of 0.77 at a wavelength of 790 nm and a very low background emissivity of <0.02 to 0.05 at 1100 to 7000 nm, under operation at 1273 K. Use of a nanostructured intrinsic semiconductor that can withstand high temperatures is promising for the development of highly efficient thermal emitters operating in the near-infrared-to-visible range.

| S-EPMC5182050 | biostudies-literature

Ultra-narrow-band near-infrared thermal exciton radiation in intrinsic one-dimensional semiconductors.

Project description:Thermal radiation is the most primitive light emission phenomenon of materials. Broadband radiation from red-hot materials is well known as the kick-starter phenomenon of modern quantum physics in the early twentieth century; even nowadays, its artificial control plays a central role in modern science and technology. Herein, we report the fundamental thermal radiation properties of intrinsic one-dimensional semiconductors and metals, which have not been elucidated because of significant technical challenges. We observed narrow-band near-infrared radiation from semiconducting single-walled carbon nanotubes at 1000-2000 K in contrast to its broadband metallic counterpart. We confirm that the ultra-narrow-band radiation is enabled by the thermal generation of excitons that are hydrogen-like neutral exotic atoms comprising mutually bound electrons and holes. Our findings uncover the robust quantum correlations in intrinsic one-dimensional semiconductors even at 2000 K; additionally, the findings provide an opportunity for excitonic optothermal engineering toward the realization of efficient thermophotovoltaic energy harvesting.

| S-EPMC6081476 | biostudies-literature

Fully Integrated Ultrathin Solid Immersion Grating Microspectrometer for Handheld Visible and Near-Infrared Spectroscopic Applications.

Project description:Despite advances in microfabrication, compact spectrometers still face challenges in shrinking their size without sacrificing optical performance. Here, the solid immersion grating microspectrometer (SIG-µSPEC) for high spectral resolution in a broad operational wavelength range is reported. The spectroscopic module incorporates a silicon microslit, index-matched lens, plane mirrors, solid immersion grating (SIG), and a CMOS line sensor within a small form factor. The SIG facilitates high angular dispersion of light on a planar focal plane, resulting in an average spectral resolution of 5.8 nm, with over 76% maximum sensitivity from 400 to 800 nm. SIG-µSPEC measures the spectral reflectance of fruits at different ripening stages, clearly revealing changes in the chlorophyll absorption band. The measured spectrum is further utilized for the precise prediction of the soluble solid content (SSC) levels, achieving a high correlation (R2 = 0.91) and a ratio of prediction-to-deviation of 2.36. This compact microspectrometer holds the potential for precise and non-invasive spectral analysis across point-of-care fields.

| S-EPMC10700170 | biostudies-literature

OmicsDI is part of the ELIXIR infrastructure

OmicsDI is an Elixir interoperability service. Learn more ›

Tweets

OmicsDI Databases

PRIDE
PeptideAtlas
MassIVE
JPOST Repository
Physiome Model Repository

EGA
EVA
ENA
LINCS
PAXDB
Cell Collective

MetaboLights
Metabolomics Workbench
MetabolomeExpress
GNPS
BioModels
FAIRDOMHub

ArrayExpress
dbGaP
ExpressionAtlas
GEO
NODE

Information

Databases
Help
API
Contact us
Code on GitHub
Terms of use
Submit Data