Andrea Barucci

Cancer is the second leading cause of death globally. Early diagnosis can allow intervention to reduce mortality but due to cancer complex structure and spatial heterogeneity among different tumors and within each lesion, it is difficult to differentiate it from healthy tissue using conventional imaging techniques. Quantification of its complexity can be a prognostic tool for fighting this disease. In recent years, clinical imaging allows this quantification thanks to Radiomics, which extracts features from images. In this study, Fractal Dimension (FD) and Lacunarity $(\pmb{L})$ in computed tomography (CT) and magnetic resonance (MR) images for different kinds of cancer were examined using box counting method. Our aim is to highlight the potentiality of features based on fractal analysis, in order to obtain new indicators able to detect tumor spatial complexity and heterogeneity. The results indicated that both FD and $\pmb{L}$ show problems linked to the lack of connection between complexity estimated with Radiomics and the underlying biological model.

Optical fibre nanotips are the key components in many applications such as nanoscale imaging and sensing. In this paper we describe and study a dynamic chemical etching method for the fabrication of optical nanoprobes. Our method allows controlling the shape and roughness of a fibre optical nanoprobe, by a combination of mechanical movements coupled to chemical etching. The stripped distal end of an optical fibre-end is dipped into a vial containing an aqueous hydrofluoric acid solution covered with a protection layer. The vial and the optical fibre are connected to different motors allowing them to rotate independently around the fibre and the vial axis respectively. The basic idea of our method is to use rotation movements to generate different kind of flows inside the vial, which will lead to different kind of shapes and surface characteristics of the obtained nanoprobes. Different regimes can be generated by changing the ratio between the angular velocities and the ratio between the radii of optical fibre and vial, ranging from laminar flow to the onset of chaotic flow (Taylor-Couette flow theory). Computational fluid dynamic analysis show that different flow regimes correspond to different shear forces acting on the forming nanotip, in agreement with experimental results.

The well-known enhancement effect of surface-enhanced Raman spectroscopy (SERS) is associated with the presence of metallic nanostructures at the substrate surface. Different bottom-up and top-down processes have been proposed to impart the substrate with such a nanostructured layer. The former approaches are low cost but may suffer from reusability and stability. The latter strategies are expensive, time consuming and require special equipment that complicate the fabrication process. Here, we present the possibility to obtain stable and reusable SERS substrates by a low-cost silver-sodium ion-exchange process in soda-lime glass microrods. The microrods were obtained by cutting the tip of the ion-exchanged soda-lime fiber, resulting in disks of about few millimeters in length and one hundred microns in diameter. A thermal annealing post-process was applied to trigger the reduction of Ag+ ions into nanoparticles (AgNPs) within the ion-exchanged glass microrods. Afterwards, ion-exchange and thermal treatments were carefully tuned to assure the presence of silver NPs exposed on the surface of the microrods, without using any chemical etching. An AFM analysis confirmed the presence of AgNPs with size of tens of nm on the surface of the fiber probe. A SERS affinity bioassay was developed on the probe with the final aim of detecting microRNA fragments acting as biomarkers of different diseases. Specifically a DNA hybridization assay was built up by anchoring a molecular beacon containing a Raman tag on the Ag surface via thiol chemistry. Initial SERS experiments confirmed the presence of the beacon on the NPs embedded on the microrods surface, as monitored by detecting main spectral bands ascribed to the oligonucleotide chain. Finally, the ability of the platform to interact with the target microRNA sequence was assessed. The analysis was repeated on a number of miRNA sequences differing from the target to evaluate the specificity of the proposed assay.

Prostate Cancer (PCa) is among of the tumors with highest incidence in men. Diagnosis of PCa is usually based on different techniques as digital rectal examination, prostate-specific antigen (PSA), transrectal ultrasonography, Magnetic Resonance Imaging (MRI) and transrectal biopsy. Thanks to its intrinsic ability to obtain anatomical, functional and molecular information, MRI is one of the most spread and powerful tools to diagnosis and staging of PCa. In particular, Diffusion-Weighted Imaging (DWI) MRI technique allows to obtain images with contrast depending on the microscopic mobility of water molecules in tissue, probing the microscopic structure. Moreover, from DWI images is possible to quantify the Apparent Diffusion Coefficient of water (ADC) using different diffusion models, as “Mono-exponential”, “Bi-exponential”, “Kurtosis”, “Gamma distribution” and “Stretched exponential”, all of them based on different assumptions on the water mobility in the tissue microenvironment. Despite that the diagnostic and prognostic power of some of these models be known, a clear connection with the physical, biological and physiological underlying features is lacking. In this work we will review all these models, showing results for patients suffering PCa, for which we have a complete clinical picture thanks to transrectal biopsy and other examinations.

An optical resonator like a fiber ring (FR) or a whispering gallery mode (WGM) resonator with two couplers along its loop is referred to be in the add-drop configuration, in analogy with the add-drop multiplexer in telecom networks. Both for practical applications as well as in several fundamental studies involving high-Q resonators, this configuration is of great interest and the assessment of the intrinsic properties of the resonator and of its interaction with the coupling systems is extremely important. We developed an original method able to fully characterize high-Q resonators in an add-drop configuration. The method is based on the study of the two cavity ringdown (CRD) signals, which are produced at the transmission and drop ports by wavelength sweeping a resonance in a time interval comparable with the photon cavity lifetime. All the resonator parameters can be assessed with a single set of simultaneous measurements. We implemented the model describing the two CRD profiles from which a best fit process of the measured profiles allows deducing the key parameters. We successfully validated the model with an experiment based on a FR resonator of known characteristics. Finally, we fully characterized a high-Q, home-made, MgF2 WGM disk resonator in the add-drop configuration, assessing its intrinsic and coupling parameters.

Coating of high-Q whispering gallery mode micro-resonators is typically performed in order to add the functionalities of the coating material to the unique properties of this type of resonators. Silica microspheres or microtoroids are typically used as high-Q cavity substrate on which a functional film is deposited. In order to effectively exploit the coating properties a critical step is the efficient excitation of WGMs mainly contained inside the deposited layer. We developed a simple method able to assess whether or not these modes are selectively excited. The method is based on monitoring the thermal shift of the excited resonance, which uniquely depends on the thermo-optic coefficient and on the thermal expansion coefficient of the material in which the mode is embedded. We applied this technique to the case of a SU-8 layer deposited on a silica microsphere. Main tests were performed around the wavelength of 770 nm because of potential application in biochemical sensing requiri...

Magnetic resonance imaging technique known as DWI (diffusion-weighted imaging) allows measurement of water diffusivity on a pixel basis for evaluating pathology throughout the body and is now routinely incorporated into many body MRI protocols, mainly in oncology. Indeed water molecules motion reflects the interactions with other molecules, membranes, cells, and in general the interactions with the environment. Microstructural changes as e.g. cellular organization and/or integrity then affect the motion of water molecules, and consequently alter the water diffusion properties measured by DWI. Then DWI technique can be used to extract information about tissue organization at the cellular level indirectly from water motion. In general the signal intensity in DWI can be quantified by using a parameter known as ADC (Apparent Diffusion Coefficient) emphasizing that it is not the real diffusion coefficient, which is a measure of the average water molecular motion. In the simplest models, ...

We implement a mathematical model able to predict the amplitude variation of the optical field inside a coupled highQ resonator as a function of the scanning wavelength. Similarly to a Fabry-Perot cavity with its two highly reflecting mirrors, the resonator has two fiber based tap couplers. By fitting experimental data with this model, it is possible to determine the physical characteristics of the resonator, such as Q-factor, coupling coefficients, and coupling regimes. In order to test our modelling tool we applied it to characterize a fiber ring resonator in add-drop configuration. We also perform preliminary test on a high-Q whispering gallery mode optical disk resonators.

The aim of this thesis is to make quantitative MRS a more valuable and attractive tool for daily clinical routine use. In the first part of this thesis we will give a brief overview of clinical proton MRS, discussing some common clinical MRS problems. In the second part we will focus on developing a standard protocol to confront the accuracy of different MR scanners from different vendors, analyzing water signals with the open source software package jMRUI – v5.0. Then we will discuss some examples of T1, T2 estimation of water and metabolites at the 3T MR scanner of A.O.U. Meyer using the Siemens phantom aimed to quantitation of metabolites concentration. Some examples of quantitation coming from S.G.D. and S.M.N. hospital will be described too. In the final part some examples of in vivo prostate cancer spectroscopic data analysis will be described, illustrating the potential of MRS, the differences between Philips data analysis software and jMRUI-v5.0, and showing the problems in ...

Optical fibre micro/nano tips (OFTs), defined here as tapered fibres with a waist diameter ranging from a few microns to tens of nanometres and different tip angles (i.e., from tens of degrees to fractions of degrees), represent extremely versatile tools that have attracted growing interest during these last decades in many areas of photonics. The field of applications can range from physical and chemical/biochemical sensing—also at the intracellular levels—to the development of near-field probes for microscope imaging (i.e., scanning near-field optical microscopy (SNOM)) and optical interrogation systems, up to optical devices for trapping and manipulating microparticles (i.e., optical tweezers). All these applications rely on the ability to fabricate OFTs, tailoring some of their features according to the requirements determined by the specific application. In this review, starting from a short overview of the main fabrication methods used for the realisation of these optical micr...

Whispering Gallery Mode (WGM) micro-resonators like microspheres or microtoroids are typically used as high-Q cavity substrate on which a functional film coating is deposited. In order to exploit the coating properties a critical step is the efficient excitation of WGMs mainly contained inside the deposited layer. We developed a simple method able to assess whether or not these modes are selectively excited. The method is based on monitoring the thermal shift of the excited resonance, which uniquely depends on the thermo-optic coefficient and on the thermal expansion coefficient of the material in which the mode is embedded.

We report efficient generation of nonlinear phenomena related to third order optical non-linear susceptibility χ(3) interactions in resonant silica microspheres and microbubbles in the regime of normal dispersion. The interactions here reported are: Stimulated Raman Scattering (SRS), and four wave mixing processes comprising Stimulated Anti-stokes Raman Scattering (SARS) and comb generation. Unusually strong anti-Stokes components and extraordinarily symmetric spectra have been observed. Resonant SARS and SRS corresponding to different Raman bands were also observed. The lack of correlation between stimulated anti-stokes and stokes scattering spectra indicates that the signal has to be resonant with the cavity.

In order to optimize the performance of an optical microbubble resonator (OMBR) as biosensor, the chemical functionalization of its inner surface plays a key role. Here we report on a spatially selective photo – chemical procedure able to bind fluorescent biomolecules only in correspondence of the OMBR inner surface. This abruptly reduces the occurrence of an undesired specific biochemical bond event all along the microfluidic section of the device. The evidence of this method, which maintains high Q factor (> 105) for the OMBR in buffer solution, is proved by fluorescence microscopy and real time measurement of the resonance broadening.

Recently, optical micro-bubble resonators (OMBRs) have gained an increasing interest in many fields of photonics thanks to their particular properties. These hollow microstructures can be suitable for the realization of label – free optical biosensors by combining the whispering gallery mode (WGM) resonator properties with the intrinsic capability of integrated microfluidics. In fact, the WGMs are morphology-dependent modes: any change on the OMBR inner surface (due to chemical and/or biochemical binding) causes a shift of the resonance position and reduces the Q factor value of the cavity. By measuring this shift, it is possible to obtain information on the concentration of the analyte to be detected. A crucial step for the development of an OMBR-based biosensor is constituted by the functionalization of its inner surface. In this work we report on the development of a physical and chemical process able to guarantee a good homogeneity of the deposed bio-layer and, contemporary, to preserve a high quality factor Q of the cavity. The OMBR capability of working as bioassay was proved by different optical techniques, such as the real time measurement of the resonance broadening after each functionalization step and fluorescence microscopy.

The objective of this work is to show the application of a Deep Learning algorithm able to operate the segmentation of ancient Egyptian hieroglyphs present in an image, with the ambition to be as versatile as possible despite the variability of the image source. The problem is quite complex, the main obstacles being the considerable amount of different classes of existing hieroglyphs, the differences related to the hand of the scribe as well as the great differences among the various supports, such as papyri, stone or wood, where they are written. Furthermore, as in all archaeological finds, damage to the supports are frequent, with the consequence that hieroglyphs can be partially corrupted. In order to face this challenging problem, we leverage on the well-known Detectron2 platform, developed by the Facebook AI Research Group, focusing on the Mask R-CNN architecture to perform segmentation of image instances. Likewise, for several machine learning studies, one of the hardest chall...

Cavity resonant enhanced stimulated Raman scattering (SRS), four-wave mixing, and broadband hyper-parametric oscillation in silica microbubble whispering gallery mode resonators (WGMR) in forward and backward directions are reported in this Letter. We show that microbubbles can operate not only in a highly ideal two-photon emission regime, but also generate combs, both natively and multi-mode spaced. The nonlinear process is phase matched because of the interaction of different mode families of the resonator.

Optical fiber sensors, thanks to their compactness, fast response and real-time measurements, have a large impact in the fields of life science research, drug discovery and medical diagnostics. In recent years, advances in nanotechnology have resulted in the development of nanotools, capable of entering the single cell, resulting in new nanobiosensors useful for the detection of biomolecules inside living cells. In this paper, we provide an application of a nanotip coupled with molecular beacons (MBs) for the detection of DNA. The MBs were characterized by hybridization studies with a complementary target to prove their functionality both free in solution and immobilized onto a solid support. The solid support chosen as substrate for the immobilization of the MBs was a 30 nm tapered tip of an optical fiber, fabricated by chemical etching. With this set-up promising results were obtained and a limit of detection (LOD) of 0.57 nM was reached, opening up the possibility of using the proposed nanotip to detect mRNAs inside the cytoplasm of living cells.

ABSTRACT Nanoprobe tips are key components in many applications such as scanning probe microscopes, nanoscale imaging, nanofabrication and sensing. This paper describes a dynamic chemical etching method for the fabrication of optical nanoprobes. The tips are produced by mechanically rotating and dipping a silica optical fibre in a chemical etching solution (aqueous hydrofluoric acid) covered with a protection layer. Using different dynamic regimes of the mechanical movements during the chemical etching process, it is possible to vary the cone angle, the shape, and the roughness of the nanoprobes. It is found that the tip profiles are determined by the nonlinear dynamic evolution of the meniscus of the etchant near the fibre. Computational fluid dynamic simulations have been performed, showing that different flow regimes correspond to different shear forces acting on the forming nanotip, in agreement with experimental results. With this method, a high yield of reproducible nanotips can be obtained, thus overcoming the drawbacks of conventional etching techniques. Typical tip features are short taper length (∼200 μm), large cone angle (up to 40°), and small probe tip dimension (less than 30 nm).

The aim of this report is to describe and explore the potential of Radiomics in the framework of the activities developed at the “Nello Carrara” Institute of Applied Physics (IFAC), which is part of the National Research Council (CNR), in collaboration with USL Toscana Centro.
The possibility of a more quantitative study of imaging data emerged during the work of specialization thesis in medical physics of one of the authors [1, 2]. The thesis subsequently led to the IRINA project (“Imaging molecolare di risonanza magnetica della biodistribuzione di nanoparticelle e vettori cellulari per applicazioni teranostiche” – Biodistribution of nanoparticles and cellular vehickles using biomolecular magnetic resonance imaging for theranostics applications) [2, Appendix 5] on the use of nanoparticles as a new theranostics agents in the context of multiparametric magnetic resonance imaging (MRI).
During the thesis work, we developed novel quantitative imaging methodologies [131], with a focus on clinical applications of MRI spectroscopy [1]. In the IRINA project we have extended the MRI techniques involved, studying different diffusion models, new algorithms for spectroscopy data analysis, techniques for data and image analysis, applications of these techniques to database of patients beginning to face the problem of Big Data in medicine, coming at the end to the concept of Radiomics.
Radiomics can be described as a process designed to extract a large number of quantitative features from digital images, place these data in shared databases, and subsequently mine the data for hypothesis generation, testing, or both. Radiomics is designed to develop decision support tools, therefore requiring the combination of radiomic data with other patient characteristics in order to increase the power of the decision support models [80].
All the activities have been divided between basic, clinical research, and clinical practice, and focused on quantitative MRI data using a translational approach.
This report provides a general introduction to Radiomics, introduces an example application on multiparametric Magnetic Resonance Imaging (mpMRI) for Prostate Cancer (PCa), and presents the workflow that we implemented in our projects.
In this report we describe Radiomics, reviewing its applications in general, but focusing on the case of Prostate Cancer (PCa) studied with the multiparametric Magnetic Resonance Imaging (mpMRI). Then we will describe the implementation of the radiomic workflow in the framework of our projects.
Prostate cancer was selected as a target of our study, following our first work on quantitative imaging [1, 2], but especially thanks to the collaboration with the Diagnostic Department of Santa Maria Nuova Hospital, which is a regional reference center for this disease [128, 129, 130].
In our study we have two objectives related to precision medicine: first the implementation of the radiomic workflow in clinical practice as a reproducible and robust clinical tool, and second, a study of the correlation of Radiomics with clinical and genomics data.
The discipline connecting tumor morphology described by Radiomics and its genome described by genomic data is called “Radiogenomics”, and it has the potential to derive the “radio phenotypes” that both correlate to and complement existing validated genomic risk stratification biomarkers [17, 18, 66, 80].
A robust clinical implementation of Radiogenomics could allow an effective personalization of the therapy (precision medicine) thanks to a better patient’s stratification.