Infrared microspectroscopy of inflammatory process and colon tumors.

According to the last global burden of disease published by the World Health Organization, tumors were the third leading cause of death worldwide in 2004. Among the different types of tumors, colorectal cancer ranks as the fourth most lethal. To date, tumor diagnosis is based mainly on the identification of morphological changes in tissues. Considering that these changes appears after many biochemical reactions, the development of vibrational techniques may contribute to the early detection of tumors, since they are able to detect such reactions. The present study aimed to develop a methodology based on infrared microspectroscopy to characterize colon samples, providing complementary information to the pathologist and facilitating the early diagnosis of tumors. The study groups were composed by human colon samples obtained from paraffin-embedded biopsies. The groups are divided in normal (n=20), inflammation (n=17) and tumor (n=18). Two adjacent slices were acquired from each block. The first one was subjected to chemical dewaxing and H&E staining. The infrared imaging was performed on the second slice, which was not dewaxed or stained. A computational preprocessing methodology was employed to identify the paraffin in the images and to perform spectral baseline correction. Such methodology was adapted to include two types of spectral quality control. Afterwards the preprocessing step, spectra belonging to the same image were analyzed and grouped according to their biochemical similarities. One pathologist associated each obtained group with some histological structure based on the H&E stained slice. Such analysis highlighted the biochemical differences between the three studied groups. Results showed that severe inflammation presents biochemical features similar to the tumors ones, indicating that tumors can develop from inflammatory process. A spectral database was constructed containing the biochemical information identified in the previous step. Spectra obtained from new samples were confronted with the database information, leading to their classification into one of the three groups: normal, inflammation or tumor. Internal and external validation were performed based on the classification sensitivity, specificity and accuracy. Comparison between the classification results and H&E stained sections revealed some discrepancies. Some regions histologically normal were identified as inflammation by the classification algorithm. Similarly, some regions presenting inflammatory lesions in the stained section were classified into the tumor group. Such differences were considered as misclassification, but they may actually evidence that biochemical changes are in course in the analyzed sample. In the latter case, the method developed throughout this thesis would have proved able to identify early stages of inflammatory and tumor lesions. It is necessary to perform additional experiments to elucidate this discrepancy between the classification results and the morphological features. One solution would be the use of immunohistochemistry techniques with specific markers for tumor and inflammation. Another option includes the recovering of the medical records of patients who participated in this study in order to check, in later times to the biopsy collection, whether they actually developed the lesions supposedly detected in this research.

Library of medium-resolution Fiber Optic Echelle spectra of F, G, K, and M field dwarfs to giant stars

We present a library of Penn State Fiber Optic Echelle (FOE) observations of a sample of field stars with spectral types F to M and luminosity classes V to I. The spectral coverage is from 3800 to 10000 Å with a nominal resolving power of 12,000. These spectra include many of the spectral lines most widely used as optical and near-infrared indicators of chromospheric activity such as the Balmer lines (Hα to H epsilon), Ca II H & K, the Mg I b triplet, Na I D_1, D_2, He I D_3, and Ca II IRT lines. There are also a large number of photospheric lines, which can also be affected by chromospheric activity, and temperature-sensitive photospheric features such as TiO bands. The spectra have been compiled with the goal of providing a set of standards observed at medium resolution. We have extensively used such data for the study of active chromosphere stars by applying a spectral subtraction technique. However, the data set presented here can also be utilized in a wide variety of ways ranging from radial velocity templates to study of variable stars and stellar population synthesis. This library can also be used for spectral classification purposes and determination of atmospheric parameters (T_eff, log g, [Fe/H]). A digital version of all the fully reduced spectra is available via ftp and the World Wide Web (WWW) in FITS format.

Library of high-resolution UES echelle spectra of F, G, K and M field dwarf stars

We present a library of Utrecht echelle spectrograph (UES) observations of a sample of F, G, K and M field dwarf stars covering the spectral range from 4800 Å to 10600 Å with a resolution of 55000. These spectra include some of the spectral lines most widely used as optical and near-infrared indicators of chromospheric activity such as Hβ, Mg I b triplet, Na I D_1, D_2, He I D_3, Hα, and Ca II IRT lines, as well as a large number of photospheric lines which can also be affected by chromospheric activity. The spectra have been compiled with the aim of providing a set of standards observed at high-resolution to be used in the application of the spectral subtraction technique to obtain the active-chromosphere contribution to these lines in chromospherically active single and binary stars. This library can also be used for spectral classification purposes. A digital version with all the spectra is available via ftp and the World Wide Web (WWW) in both ASCII and FITS formats.

The XMM deep survey in the CDF-S. VI. Obscured AGN selected as infrared power-law galaxies

Context. Accretion onto supermassive black holes is believed to occur mostly in obscured active galactic nuclei (AGN). Such objects are proving rather elusive in surveys of distant galaxies, including those at X-ray energies. Aims. Our main goal is to determine whether the revised IRAC criteria of Donley et al. (2012, ApJ, 748, 142; objects with an infrared (IR) power-law spectral shape), are effective at selecting X-ray type-2 AGN (i.e., absorbed N_H > 10^22 cm^-2). Methods. We present the results from the X-ray spectral analysis of 147 AGN selected by cross-correlating the highest spectral quality ultra-deep XMM-Newton and the Spitzer/IRAC catalogues in the Chandra Deep Field South. Consequently it is biased towards sources with high S/N X-ray spectra. In order to measure the amount of intrinsic absorption in these sources, we adopt a simple X-ray spectral model that includes a power-law modified by intrinsic absorption at the redshift of each source and a possible soft X-ray component. Results. We find 21/147 sources to be heavily absorbed but the uncertainties in their obscuring column densities do not allow us to confirm their Compton-Thick nature without resorting to additional criteria. Although IR power-law galaxies are less numerous in our sample than IR non-power-law galaxies (60 versus 87 respectively), we find that the fraction of absorbed (N_H^intr > 10^22 cm^-2) AGN is significantly higher (at about 3 sigma level) for IR-power-law sources (similar to 2/3) than for those sources that do not meet this IR selection criteria (~1/2). This behaviour is particularly notable at low luminosities, but it appears to be present, although with a marginal significance, at all luminosities. Conclusions. We therefore conclude that the IR power-law method is efficient in finding X-ray-absorbed sources. We would then expect that the long-sought dominant population of absorbed AGN is abundant among IR power-law spectral shape sources not detected in X-rays.

Infrared identification of 2XMM J191043.4+091629.4

Context. We report the infrared identification of the X-ray source 2XMM J191043.4+091629.4, which was detected by XMM-Newton/EPIC in the vicinity of the Galactic supernova remnant W49B. Aims. The aim of this work is to establish the nature of the X-ray source 2XMM J191043.4+091629.4 studying both the infrared photometry and spectroscopy of the companion. Methods. We analysed UKIDSS images around the best position of the X-ray source and obtained spectra of the best candidate using NICS in the Telescopio Nazionale Galileo (TNG) 3.5-m telescope. We present photometric and spectroscopic TNG analyses of the infrared counterpart of the X-ray source, identifying emission lines in the K-band. The H-band spectra does not present any significant feature. Results. We have shown that the Brackett γ H i at 2.165 μm, and He i at 2.184 μm and at 2.058 μm are significantly present in the infrared spectrum. The CO bands are also absent from our spectrum. Based on these results and the X-ray characteristics of the source, we conclude that the infrared counterpart is an early B-type supergiant star with an E(B − V) = 7.6 ± 0.3 at a distance of 16.0 ± 0.5 kpc. This would be, therefore, the first high-mass X-ray binary in the Outer Arm at galactic longitudes of between 30° and 60°.

Infrared microspectroscopic mapping of the homogeneity of extruded blends: Application to starch/polyester blends

Blends of starch and a biodegradable polyester, produced by an extrusion process, which included a cross-linker/compatibilizer (maleic anhydride) and an initiator (dicumyl peroxide), were studied by infrared (IR) microspectroscopy using an attenuated total reflectance (ATR) objective. Extruded material, which had a diameter of about 3 mm, was sectioned and embedded in epoxy resin prior to IR analysis. Spectra were collected in a grid pattern across the sectioned face of the sample. Measurement of various band parameters from the spectra allowed IR maps to be constructed containing semi-quantitative information about the distribution of blend components. These maps showed the quality of the blend on a microscopic scale and showed how it varied with different concentrations of compatibilizer and initiator. (c) 2005 Elsevier Ltd. All rights reserved.

Advanced fibre gratings fabricated in standard and infrared glass fibres by ultraviolet and near-infrared-femtosecond lasers

In this thesis, I describe studies on fabrication, spectral characteristics and applications of tilted fibre gratings (TFGs) with small, large and 45° tilted structures and novel developments in fabrication of fibre Bragg gratings (FBGs) and long period gratings (LPGs) in normal silica and mid-infrared (mid-IR) glass fibres using near-IR femtosecond laser. One of the major contributions presented in this thesis is the systematic investigation of structures, inscription methods and spectral, polarisation dependent loss (PDL) and thermal characteristics of TFGs with small (<45°), large (>45°) and 45° tilted structures. I have experimentally characterised TFGs, obtaining relationships between the radiation angle, central wavelength of the radiation profile, Bragg resonance and the tilt angle, which are consistent with theoretical simulation based on the mode-coupling theory. Furthermore, thermal responses have been measured for these three types of TFGs, showing the transmission spectra of large and 45° TFGs are insensitive to the temperature change, unlike the normal and small angle tilted FBGs. Based on the distinctive optical properties, TFGs have been developed into interrogation system and sensors, which form the other significant contributions of the work presented in this thesis. The 10°-TFG based 800nm WDM interrogation system can function not just as an in-fibre spectrum analyser but also possess refractive index sensing capability. By utilising the unique polarisation properties, the 81 °-TFG based sensors are capable of sensing the transverse loading and twisting with sensitivities of 2.04pW/(kg/m) and 145.90pW/rad, repectively. The final but the most important contribution from the research work presented in this thesis is the development of novel grating inscription techniques using near-IR femtosecond laser. A number of LPGs and FBGs were successfully fabricated in normal silica and mid-IR glass fibres using point-by-point and phase-mask techniques. LPGs and 1st and 2nd order FBGs have been fabricated in these mid-IR glass fibres showing resonances covering the wavelength range from 1200 to 1700nm with the strengths up to 13dB. In addition, the thermal and strain sensitivities of these gratings have been systematically investigated. All the results from these initial but systematic works will provide useful function characteristics information for future fibre grating based devices and applications in mid-IR range.

Identification and relative quantification of tyrosine nitration in a model peptide using two-dimensional infrared spectroscopy

Nitration of tyrosine in proteins and peptides is a post-translational modification that occurs under conditions of oxidative stress. It is implicated in a variety of medical conditions, including neurodegenerative and cardiovascular diseases. However, monitoring tyrosine nitration and understanding its role in modifying biological function remains a major challenge. In this work, we investigate the use of electron-vibration-vibration (EVV) two-dimensional infrared (2DIR) spectroscopy for the study of tyrosine nitration in model peptides. We demonstrate the ability of EVV 2DIR spectroscopy to differentiate between the neutral and deprotonated states of 3-nitrotyrosine, and we characterize their spectral signatures using information obtained from quantum chemistry calculations and simulated EVV 2DIR spectra. To test the sensitivity of the technique, we use mixed-peptide samples containing various levels of tyrosine nitration, and we use mass spectrometry to independently verify the level of nitration. We conclude that EVV 2DIR spectroscopy is able to provide detailed spectroscopic information on peptide side-chain modifications and to detect nitration levels down to 1%. We further propose that lower nitration levels could be detected by introducing a resonant Raman probe step to increase the detection sensitivity of EVV 2DIR spectroscopy. (Graph Presented).

Infrared Excess sources: Compton thick QSOs, low-luminosity Seyferts or starbursts?

We explore the nature of Infrared Excess sources (IRX), which are proposed as candidates for luminous [L_X(2–10 keV) > 10^43 erg s^−1] Compton thick (NH > 2 × 1024 cm−2) QSOs at z≈ 2. Lower redshift, z≈ 1, analogues of the distant IRX population are identified by first redshifting to z= 2 the spectral energy distributions (SEDs) of all sources with secure spectroscopic redshifts in the AEGIS (6488) and the GOODS-North (1784) surveys and then selecting those that qualify as IRX sources at that redshift. A total of 19 galaxies are selected. The mean redshift of the sample is z≈ 1. We do not find strong evidence for Compton thick QSOs in the sample. For nine sources with X-ray counterparts, the X-ray spectra are consistent with Compton thin active galactic nucleus (AGN). Only three of them show tentative evidence for Compton thick obscuration. The SEDs of the X-ray undetected population are consistent with starburst activity. There is no evidence for a hot dust component at the mid-infrared associated with AGN heated dust. If the X-ray undetected sources host AGN, an upper limit of L_X(2–10 keV) = 10^43 erg s^−1 is estimated for their intrinsic luminosity. We propose that a large fraction of the z≈ 2 IRX population is not Compton thick quasi-stellar objects (QSOs) but low-luminosity [L_X(2–10 keV) < 10^43 erg s^−1], possibly Compton thin, AGN or dusty starbursts. It is shown that the decomposition of the AGN and starburst contribution to the mid-IR is essential for interpreting the nature of this population, as star formation may dominate this wavelength regime.

Local luminous infrared galaxies. I. Spatially resolved observations with the Spitzer infrared spectrograph

We present results from the Spitzer Infrared Spectrograph spectral mapping observations of 15 local luminous infrared galaxies (LIRGs). In this paper, we investigate the spatial variations of the mid-IR emission which includes fine structure lines, molecular hydrogen lines, polycyclic aromatic features (PAHs), continuum emission, and the 9.7 μm silicate feature. We also compare the nuclear and integrated spectra. We find that the star formation takes place in extended regions (several kpc) as probed by the PAH emission, as well as the [Ne II]12.81 μm and [Ne III]15.56 μm emissions. The behavior of the integrated PAH emission and 9.7 μm silicate feature is similar to that of local starburst galaxies. We also find that the minima of the [Ne III]15.56 μm/[Ne II]12.81 μm ratio tends to be located at the nuclei and its value is lower than that of H II regions in our LIRGs and nearby galaxies. It is likely that increased densities in the nuclei of LIRGs are responsible for the smaller nuclear [Ne III]15.56 μm/[Ne II]12.81 μm ratios. This includes the possibility that some of the most massive stars in the nuclei are still embedded in ultracompact H II regions. In a large fraction of our sample, the 11.3 μm PAH emission appears more extended than the dust 5.5 μm continuum emission. We find a dependency of the 11.3 μm PAH/7.7 μm PAH and [Ne II]12.81 μm/11.3 μm PAH ratios with the age of the stellar populations. Smaller and larger ratios, respectively, indicate recent star formation. The estimated warm (300 K

Local luminous infrared galaxies: Spatially resolved mid-infrared observations with Spitzer/IRS

Luminous Infrared (IR) Galaxies (LIRGs, L_IR=10^11-10 L_⨀) are an important cosmological class of galaxies as they are the main contributors to the co-moving star formation rate density of the universe at z=1. In this paper we present a guaranteed time observation (GTO) Spitzer InfraRed Spectrograph (IRS) program aimed to obtain spectral mapping of a sample of 14 local d<76Mpc LIRGs. The data cubes map, at least, the central 20arcsec X 20arcsec to 30 arcsec X 30 arcsec regions of the galaxies, and use all four IRS modules covering the full 5-38 μ m spectral range. The final goal of this project is to characterize fully the mid-IR properties of local LIRGs as a first step to understanding their more distant counterparts. In this paper we present the first results of this GTO program. The IRS spectral mapping data allow us to build spectral maps of the bright mid-IR emission lines (e.g., [Ne II] 12.81 μ m, [Ne III]15.56 μ m, [S III] 18.71 μ m, H_2 at 17 μ m), continuum, the 6.2 and 11.3 μ m polycyclic aromatic hydrocarbon (PAH) features, and the 9.7 μ m silicate feature, as well as to extract 1D spectra for regions of interest in each galaxy. The IRS data are used to obtain spatially resolved measurements of the extinction using the 9.7 μ m silicate feature, and to trace star forming regions using the neon lines and the PAH features. We also investigate a number of active galactic nuclei (AGN) indicators, including the presence of high excitation emission lines and a strong dust continuum emission at around 6 9.7 μ m . We finally use the integrated Spitzer/IRS spectra as templates of local LIRGs. We discuss several possible uses for these templates, including the calibration of the star formation rate of IR-bright galaxies at high redshift. We also predict the intensities of the brightest mid-IR emission lines for LIRGs as a function of redshift, and compare them with the expected sensitivities of future space IR missions.

X-ray analysis of local mid-infrared selected Compton-thick AGN candidates

Cosmic X-ray background synthesis models (Gilli 2007) require a significant fraction of obscured AGN, some of which are expected to be heavily obscured (Compton-thick), but the number density of observationally found obscured sources is still an open issue (Vignali 2010, 2014). This thesis work takes advantage of recent NuSTAR data and is based on a multiwavelength research approach. Gruppioni et al. 2016 compared the AGN bolometric luminosity, for a sample of local 12 micron Seyfert galaxies, derived from the SED decomposition to the same quantity obtained by the 2-10 keV luminosity (IPAC-NED). A difference up to two orders of magnitude resulted between these quantities for some sources. Thus, the intrinsic X-ray luminosity obtained correcting for the obscuration may be underestimated. In this thesis we have tested this hypothesis by re-analysing the X-ray spectra of three of the sources (UGC05101, NGC1194 and NGC3079), for which observations from NuSTAR and Chandra and/or XMM-Newton were available. This is meant to extend our analysis to energies above 10 keV and thus estimate the AGN column density as reliable as possible. For spectral fitting we made use of both the commonly used XSPEC package and the two very recent MYtorus and BNtorus physical models. The available wide bandpass allowed us to achieve new and more solid insights into the X-ray spectral properties of these sources. The measured absorption column densities are highly suggestive of heavy obscuration. Once corrected the X-ray AGN luminosity for the obscuration estimated through our spectral analysis, we compared the L(X) values in the 2-10 keV band with those derived from the MIR band, by means of the relation by Gandhi, 2009. As expected, the values derived from this relation are in good agreement with those we measured, indicating that the column densities were underestimated in the previous literature works.

Analysis of the high-resolution ro-vibrational spectrum of DC3N in the far and mid infrared regions

Cyanoacetylene HC3N is a molecule of great astronomical importance and it has been observed in many interstellar environments. Its deuterated form DC3N has been detected in number of sources from external galaxies to Galactic interstellar clouds, star-forming regions and planetary atmospheres. All these detections relied on previous laboratory investigations, which however still lack some essential information concerning its infrared spectrum. In this project, high-resolution ro-vibrational spectra of DC3N have been recorded in two energy regions: 150 – 450 cm-1 and 1800 – 2800 cm-1. In the first window the ν7← GS, 2ν7 ← ν7, ν5 ← ν7, ν5+ν7 ← 2ν7, ν6+ν7 → 2v7, 4ν7 ← 2ν7 bands have been assigned, while in the second region the three stretching fundamental bands ν1, ν2, ν3 have been observed and analysed. The 150 – 450 cm-1 region spectra have been recorded at the AILES beamline at the SOLEIL synchrotron (France), the 1800 – 2800 cm-1 spectra at the Department of Industrial Chemistry “Toso Montanari” in Bologna. In total, 2299 transitions have been assigned. Such experimental transition, together with data previously recorded for DC3N, were included in a least-squares fitting procedure from which several spectroscopic parameters have been determined with high precision and accuracy. They include rotational, vibrational and resonance constants. The spectroscopic data of DC3N have been included in a line catalog for this molecule in order to assist future astronomical observations and data interpretation. A paper which includes this research work has been published (M. Melosso, L. Bizzocchi, A. Adamczyk, E. Cane, P. Caselli, L. Colzid, L. Dorea, B. M. Giulianob, J.-C. Guillemine, M-A. Martin-Drumel, O. Piralif, A. Pietropolli Charmet , D. Prudenzano, V. M. Rivillad, F. Tamassia, Extensive ro-vibrational analysis of deuterated-cyanoacetylene (DC3N) from millimeter wavelengths to the infrared domain, Jour. of Quant. Spectr. and Rad. Tran. 254, 107221, 2020).

Analysis Of The Dna Fourier Transform-infrared Microspectroscopic Signature Using An All-reflecting Objective.

The Fourier transform-infrared (FT-IR) signature of dry samples of DNA and DNA-polypeptide complexes, as studied by IR microspectroscopy using a diamond attenuated total reflection (ATR) objective, has revealed important discriminatory characteristics relative to the PO2(-) vibrational stretchings. However, DNA IR marks that provide information on the sample's richness in hydrogen bonds have not been resolved in the spectral profiles obtained with this objective. Here we investigated the performance of an all reflecting objective (ARO) for analysis of the FT-IR signal of hydrogen bonds in DNA samples differing in base richness types (salmon testis vs calf thymus). The results obtained using the ARO indicate prominent band peaks at the spectral region representative of the vibration of nitrogenous base hydrogen bonds and of NH and NH2 groups. The band areas at this spectral region differ in agreement with the DNA base richness type when using the ARO. A peak assigned to adenine was more evident in the AT-rich salmon DNA using either the ARO or the ATR objective. It is concluded that, for the discrimination of DNA IR hydrogen bond vibrations associated with varying base type proportions, the use of an ARO is recommended.

Ihwg-μnir: A Miniaturised Near-infrared Gas Sensor Based On Substrate-integrated Hollow Waveguides Coupled To A Micro-nir-spectrophotometer.

A miniaturised gas analyser is described and evaluated based on the use of a substrate-integrated hollow waveguide (iHWG) coupled to a microsized near-infrared spectrophotometer comprising a linear variable filter and an array of InGaAs detectors. This gas sensing system was applied to analyse surrogate samples of natural fuel gas containing methane, ethane, propane and butane, quantified by using multivariate regression models based on partial least square (PLS) algorithms and Savitzky-Golay 1(st) derivative data preprocessing. The external validation of the obtained models reveals root mean square errors of prediction of 0.37, 0.36, 0.67 and 0.37% (v/v), for methane, ethane, propane and butane, respectively. The developed sensing system provides particularly rapid response times upon composition changes of the gaseous sample (approximately 2 s) due the minute volume of the iHWG-based measurement cell. The sensing system developed in this study is fully portable with a hand-held sized analyser footprint, and thus ideally suited for field analysis. Last but not least, the obtained results corroborate the potential of NIR-iHWG analysers for monitoring the quality of natural gas and petrochemical gaseous products.