3D high resolution Ground Penetrating Radar (GPR) survey was performed in the Crypt of the Duomo of Lecce (South Italy), built in 1114. The GPR data revealed us a stratified subsoil in which there is a distribution, with the depth, of several “remains” referable to different epochs. Here we present and discuss the experimental evidences, comparing them with the historical-archaeological documentation. We think that they constitute a valid contribution to the knowledge of the ancient stratigraphy, as well as of the Roman history of Lecce, especially because of many suppositions have not yet found a confirmation.

The increasing interest in the production and selection of aptamers for therapeutic and diagnostic applications yields many studies in recent years. Most of them investigated the production techniques, usually performed in vitro, but also the possibility of an in silico selection. Due to their specific ability of target-inhibition, some aptamers are under clinical trials, and some other were just patented by several pharmaceutical companies. However, the mechanism of aptamer-ligand formation is not completely understood. In this paper we explore the possibility to describe some topological and electrical features of the aptamer TBA alone and complexed with thrombin, its specific ligand, by using a network consisting of two different networks. The results are quite intriguing, confirming some conjectures about the different role of two cations, i.e. Na+ and K+, in stabilizing the compound. Furthermore, this study suggests the use of resistance measurements to discriminate among different affinities.

This work is a part of the MAGI5 (Medical Applications on a Grid Infrastructure Connection) experiment of the Italian INFN (Istituto Nazionale di Fisica Nucleare). A simple CAD (Computer Assisted Detection) system for juxta pleural lung nodules in CT images is presented, with the purpose of comparing different 2D concavity patching techniques and assessing the respective efficiency in locating nodules.

A fully automated and three-dimensional (3D) segmentation method for the identification of the pulmonary parenchyma in thorax X-ray computed tomography (CT) datasets is proposed. It is meant to be used as preprocessing step in the computer-assisted detection (CAD) system for malignant lung nodule detection that is being developed by the Medical Applications in a Grid Infrastructure Connection (MAGIC-5) Project. In this new approach the segmentation of the external airways (trachea and bronchi), is obtained by 3D region growing with wavefront simulation and suitable stop conditions, thus allowing an accurate handling of the hilar region, notoriously difficult to be segmented. Particular attention was also devoted to checking and solving the problem of the apparent ‘fusion’ between the lungs, caused by partialvolume effects, while 3D morphology operations ensure the accurate inclusion of all the nodules (internal, pleural, and vascular) in the segmented volume. The newalgorithm was initially developed and tested on a dataset of 130 CT scans fromthe Italung-CT trial, andwas then applied to the ANODE09-competition images (55 scans) and to the LIDC database (84 scans), giving very satisfactory results. In particular, the lung contour was adequately located in 96% of the CT scans, with incorrect segmentation of the external airways in the remaining cases. Segmentation metrics were calculated that quantitatively express the consistency between automatic and manual segmentations: themean overlap degree of the segmentationmasks is 0.96±0.02, and the mean and the maximum distance between the mask borders (averaged on the whole dataset) are 0.74±0.05 and 4.5±1.5, respectively, which confirms that the automatic segmentations quite correctly reproduce the borders traced by the radiologist. Moreover, no tissue containing internal and pleural nodules was removed in the segmentation process, so that this method proved to be fit for the use in the framework of a CAD system. Finally, in the comparison with a two-dimensional segmentation procedure, inter-slice smoothness was calculated, showing that the masks created by the 3D algorithm are significantly smoother than those calculated by the 2D-only procedure.

In cultural buildings, processes of degradation are a direct or indirect result of unsuitable environmental conditions. We studied ancient Crypts located in different sites in Italy, showing different types of decay. Some have moulds, fungi, algae and bacteria present on columns and shafts; while in others salt efflorescence is spread along the masonry and on the base of the columns. To characterize the complex interactions leading to damage in these historical buildings, microclimatic conditions were accurately monitored. In addition, non-destructive methodologies, involving biological and physico-chemical approaches, were utilized and the experimental results are compared and discussed. Then, building location, historical background, climatic characteristics, stone typology and features, natural-artificial lighting and ventilation were taken into account and correlated in order to properly understand the state of conservation and to address possible strategies for the safeguard of these Crypts.

Many deterioration processes are linked to unsuitable microclimatic condition in cultural buildings.One of the most diffused processes is soluble salts crystallization that can be accelerated in masonry structures within specific microclimatic values for different chemical compounds. In this paper, micro-climate and efflorescence diffusion were monitored over a one-year period in the Crypt of the Cathedralof Lecce (South Italy). This allowed to relate the microclimate with the efflorescence variation overtime. A three-dimensional computational fluid dynamics (CFD) model was then developed to detail thethermo-hygrometric parameters and airflow patterns responsible for salts crystallization and artworksdeterioration. Two main conditions were reproduced; one to simulate the current microclimate, whichsimulations showed to be inadequate for conservation, and the other to search for a more appropriatesolution. In both cases, summer and winter conditions were simulated and compared to find a microcli-mate able to ensure more suitable thermo-hygrometric intervals required by the constituting artworksmaterials. The results helped to suggest actions to improve maintenance of the Crypt.

A morphometric analysis of a southern European city and the derivation of relevant fluid dynamical parameters for use in urban flow and dispersion models are explained in this paper. Calculated parameters are compared with building statistics that have already been computed for parts of three northern European and two North American cities. The aim of this comparison is to identify similarities and differences between several building configurations and city types, such as building packing density, compact versus sprawling neighborhoods, regular versus irregular street orientation, etc. A novel aspect of this work is the derivation and use of digital elevation models (DEMs) for parts of a southern European city. Another novel aspect is the DEMs’ construction methodology, which is low cost, low tech, and of simple implementation. Several building morphological parameters are calculated from the urban DEMs using image processing techniques. The correctness and robustness of these techniques have been verified through a series of sensitivity tests performed on both idealized building configurations, as well as on real case DEMs, which were derived using the methodology here. In addition, the planar and frontal area indices were calculated as a function of elevation. It is argued that those indices, estimated for neighborhoods of real cities, may be used instead of the detailed building geometry within urban canopy models as those indices together synthesize the geometric features of a city. The direct application of these results will facilitate the development of fast urban flow and dispersion models.

Objectives We detail a procedure for generating a set of templates for the hippocampal region in Magnetic Resonance images, representative of the clinical conditions of the population under investigation. Methods The first step is robust standardization of the intensity scale of brain MR images, belonging to patients with different degrees of neuropathology (Alzheimer’s Disease). So similar tissues have similar intensities, even across images coming from different sources. After the automatic extraction of the hippocampal region from a large dataset of images, we address template generation, choosing by clusterization methods a small number of the extracted regions. Results We assess that template generation is largely independent on the clusterization method and on the number and the clinical condition of the patients. The templates are chosen as the most representative images in a population. The estimation of the ‘minimum’ number of templates for the hippocampal region can be proposed, using a metric based on the geometrical position of the extracted regions. Conclusions This study describes a simple and easily reproducible procedure to generate templates for the hippocampal region. It can be generalized and applied to other brain regions, which may be relevant for neuroimaging studies.

We detail a procedure for generating a set of templates for the hippocampal region in magnetic resonance (MR) images, representative of the clinical conditions of the population under investigation. METHODS: The first step is robust standardization of the intensity scale of brain MR images, belonging to patients with different degrees of neuropathology (Alzheimer's disease). So similar tissues have similar intensities, even across images coming from different sources. After the automatic extraction of the hippocampal region from a large dataset of images, we address template generation, choosing by clusterization methods a small number of the extracted regions. RESULTS: We assess that template generation is largely independent on the clusterization method and on the number and the clinical condition of the patients. The templates are chosen as the most representative images in a population. The estimation of the "minimum" number of templates for the hippocampal region can be proposed, using a metric based on the geometrical position of the extracted regions. CONCLUSIONS: This study describes a simple and easily reproducible procedure to generate templates for the hippocampal region. It can be generalized and applied to other brain regions, which may be relevant for neuroimaging studies.

Aptamers are single stranded DNA, RNA or peptide sequences having the ability to bind several specific targets (proteins, molecules as well as ions). Therefore, aptamer production and selection for therapeutic and diagnostic applications is very challenging. Usually, they are generated in vitro, although computational approaches have been recently developed for the in silico production. Despite these efforts, the mechanism of aptamer-ligand formation is not completely clear, and producing high affinity aptamers is still quite difficult. This paper aims to develop a computational model able to describe aptamer-ligand affinity. Topological tools, such as the conventional degree distribution, the rank-degree distribution (hierarchy), and the node assortativity are employed. In doing so, the macromolecules tertiary-structures are mapped into appropriate graphs. These graphs reproduce the main topological features of the macromolecules, by preserving the distances between amino acids (nucleotides). Calculations are applied to the thrombin binding aptamer (TBA), and the TBA-thrombin complex, produced in the presence of Na+ or K+. The topological analysis is able to detect several differences between complexes obtained in the presence of the two cations, as expected by previous investigations. These results support graph analysis as a novel computational tool for testing affinity. Otherwise, starting from the graphs, an electrical network can be obtained by using the specific electrical properties of amino acids and nucleobases. Therefore, a further analysis concerns with the electrical response, revealing that the resistance is sensitively affected by the presence of sodium or potassium, thus suggesting resistance as a useful physical parameter for testing binding affinity

The present work aims to gather information on the subsoil stratigraphy and identify structures of probable archaeological interest under the Crypt of Duomo of Lecce (South Italy) with Ground Penetrating Radar (GRP) techniques. The area around is highly urbanized and has been the scenario of the social and political life of the town over the centuries. The surveys revealed a stratigraphic distribution of features that could be related to different historic periods, when analysed in the light of the few occasional references available in the historical-archaeological literary sources. Here we present and discuss those findings, especially regarding the Roman period. In particular we drew our attention on the Roman “Forum” of the town, because no ruins of this structure are kept, even if many historians agree that it would have been placed in the area we investigated. These findings could lead to a better characterization of the extent and the richness of the subsoil and should ultimately be used to guide future geophysical and archaeological investigations with the aim to produce a large scale 3D reconstruction of this area of the ancient town of Lecce.

Ancient masonry structures are often damaged by soluble salt crystallization which is activated by even small microclimatic variations. Unsuitable environmental conditions can accelerate this process, affecting the type and the quantity of salts and the consequent damage to the masonry. Therefore the importance of monitoring salt diffusion to control salt crystallization and microclimate over time is widely recognized. This paper proposes an integrated monitoring methodology to obtain information on the relationship between salt efflorescence and microclimate in the Crypt of the Duomo of Lecce (South Italy). By combining Ion Chromatography, powder X-ray diffraction and Raman microscopy with environmental monitoring and deterioration maps, salt components were identified and efflorescence diffusion on masonry was monitored over time. Due to this a possible explanation for the process is finally given.

The presence of particular environmental conditions inside monumental buildings is responsible for deterioration processes. The Crypt (1114) of the Duomo in the city centre of Lecce (South-Italy) is a valuable monument with many artworks in the interior, affected by salt damage on the masonry and columns. In order to give a diagnosis of the damage, condition assessment and documentation were performed with various techniques. Here we focus on the results of a microclimatic monitoring combined with a decay mapping and Ground-Penetrating Radar (GPR) observations. The aim is to highlight the conditions that allow crystal growth and the presence of moisture sources in the subsoil, involved in the salt damage. In such a manner an explanation for crystallization and its variation over time is given.

It is known that unsuitable microclimatic conditions can raise the risk of damage in ancient monuments where even small fluctuations can activate deterioration processes, such as soluble salts crystallization. Therefore the importance to monitor the environmental conditions in cultural buildings is widely recognized. Furthermore, in the last decades, many modeling tools have been developed in order to better control the indoors in a preventive way. A microclimatic monitoring was performed over a one year period in the Crypt of the Duomo of Lecce (South Italy) where efflorescence is one of the main decay evidence. The microclimatic data were then used to develop a 3-dimensional computational fluid dynamic (CFD) model to investigate the indoor thermo-hygrometric parameters and determine the most appropriate microclimatic asset. A number of possible microclimatic scenarios, given by ventilation through the windows, were considered. The simulations allowed to establish the most suitable scenario to preserve the building limiting salt crystallization.

Aptamers are chemically produced oligonucleotides, able to bind a variety of targets such as drugs, proteins and pathogens with high sensitivity and selectivity. Therefore, aptamers are largely employed for producing label-free biosensors (aptasensors), with significant applications in diagnostics and drug delivery. In particular, the anti-thrombin aptamers are biomolecules of high interest for clinical use, because of their ability to recognize and bind the thrombin enzyme. Among them, the DNA 15-mer aptamer (TBA), has been widely explored around the possibility of using it in aptasensors. This paper proposes a microscopic model of the electrical properties of TBA and of the aptamer-thrombin complex, combining information from both structure and function, following the issues addressed in an emerging branch of electronics known as proteotronics. The theoretical results are compared and validated with measurements reported in the literature. Finally, the model suggests resistance measurements as a novel tool for testing aptamer-target affinity.

Human olfactory 17-40 and Bacteriorhodopsin are two protein receptors that received particular attention in electronics, due to the possibility of implementing nano-biodevices able to detect odours and light and thus useful for medical and green energy harvesting applications. Some recent experiments concerning the electrical responses of these receptors are reviewed. Data are interpreted in the framework of a new science exploiting the complexity in biology and biomedical engineering called proteotronics. In particular, the single protein is modelled as an impedance network whose topological properties affect the electrical response as measured by experiments.

The paper is focused on a tiSsue-Based Standardization Technique (SBST) of magnetic resonance (MR) brain images. Magnetic Resonance Imaging intensities have no fixed tissue-specific numeric meaning, even within the same MRI protocol, for the same body region, or even for images of the same patient obtained on the same scanner in different moments. This affects postprocessing tasks such as automatic segmentation or unsupervised/supervised classification methods, which strictly depend on the observed image intensities, compromising the accuracy and efficiency of many image analyses algorithms. A large number of MR images from public databases, belonging to healthy people and to patients with different degrees of neurodegenerative pathology, were employed together with synthetic MRIs. Combining both histogram and tissue-specific intensity information, a correspondence is obtained for each tissue across images. The novelty consists of computing three standardizing transformations for the three main brain tissues, for each tissue class separately. In order to create a continuous intensity mapping, spline smoothing of the overall slightly discontinuous piecewise-linear intensity transformation is performed. The robustness of the technique is assessed in a post hoc manner, by verifying that automatic segmentation of images before and after standardization gives a high overlapping (Dice index >0.9) for each tissue class, even across images coming from different sources. Furthermore, SBST efficacy is tested by evaluating if and how much it increases intertissue discrimination and by assessing gaussianity of tissue gray-level distributions before and after standardization. Some quantitative comparisons to already existing different approaches available in the literature are performed.

Robust gray-level standardization in brain Magnetic-Resonance images. G. De Nunzio1, R. Cataldo1, A. Carlà1. (1) University of Salento, Dept. of Mathematics and Physics, and INFN, Lecce Purpose: it is known that intensities in MRI do not have a fixed tissue-specific numeric meaning, even within the same MRI protocol, for the same body region, or for images of the same patient obtained on the same scanner in different moments. Consequently many problems can arise in large multi-site clinical studies, making the interpretation of results difficult or confused, or affecting post processing phases such as segmentation and registration. In spite of the fact that the lack of a standard and quantifiable interpretation compromises the precision, accuracy, and efficiency of those applications, few papers have explicitly addressed the problems. In this context, we propose a tiSsue-Based Standardization Technique (SBST) of MR brain images. Methods and materials: the system was developed and tested on a large number of images, belonging to healthy people and to patients with different degrees of neurodegenerative pathology, obtained from public databases and the clinical practice. Both histogram and tissue-specific intensity information were used, performing piecewise linear intensity transformations between images, so sharing the simplicity and robustness of landmark techniques, while remaining fully automated and quite light from the computational point of view. Results: the efficacy in minimizing the risk of “mixing” brain tissues during intensity transformations was assessed, and particular attention was devoted to a thorough examination of the benefits comparing SBST with other approaches available in the literature. Conclusion: the technique proved robust in standardizing tissues, giving similar intensities to similar tissues, even across images coming from different sources.

Le applicazioni della Fisica e dell’Informatica alla Biomedicina includono i sistemi di individuazione di patologie (CAD, Computer-Assisted Detection) basati sul trattamento di dati provenienti da esami diagnostici (in particolare ma non limitandosi alle immagini diagnostiche quali TC, RM, etc.), gli strumenti di ausilio alla chirurgia (realtà virtuale, telechirurgia), l’analisi e l’interpretazione di segnali di interesse biomedicale (per esempio segnali da elettroencefalogramma, EEG, o da elettrocardiogramma, ECG). Questo lavoro presenta una rassegna di applicazioni, in cui gli autori sono impegnati, dandone alcuni dettagli implementativi e discutendone brevemente i risultati. Le applicazioni si differenziano per il tipo di dati analizzati (serie temporali provenienti da misure EEG, oppure dati bi- o tridimensionali contenuti in immagini diagnostiche), per il distretto corporeo di intervento, le finalità, la patologia.

Crypts, mainly originating from the early Christian catacombs with the function for burial and worship, were very common in Europe during the Romanesque and Gothic periods. A lot of them suffer processes of degradation with different types of decay. Sometimes moulds, fungi, algae and bacteria are present on the shafts of the columns, sometimes salt efflorescence is spread along the masonry and on the base of the columns. Anyway both the chemical and biological alterations as well as the mechanical deterioration are strongly correlated with the changes in relative humidity and temperature, that play a key role in the activation of the damage. An environmental control, often cited as a desirable means of reducing deterioration, when incorrectly applied could exacerbate the damage. So, it is important that the environmental conditions for limiting the damage are selected on the basis of studies that accurately reflect the real situation. Here we focus on the study of some ancient Italian crypts with the aim to investigate the influence of the environment on the degradation processes, assessing possible connections between those findings and microclimatic behaviour. We detailed the change of the damage distribution both spatially and over time, making use of non-destructive methods. They consist of sampling and chemical/biologic analyses, condition assessment by environmental monitoring, image processing of photographic documentations and in situ observations. Furthermore building location, historical background, stone typology and features, natural-artificial lighting and ventilation, are taken into account. Once this had been addressed, a plausible explanation for the dynamic deterioration is given, some strategies are suggested and compared with the literature. They are both structural such as consolidation procedures, after removing contamination sources, and environmental, such as the control of indoor flow, as predicted by fluid dynamics simulations. Other possibility is to use Light Emitting Diode systems to control biodeterioration, eliminating chemicals means, such as bleach or steam, to remove growth. Keywords: Degradation; Environmental control; Thermodynamic behaviour; Fluid dynamics

The effect of ventilation strategies on the microclimate of the Crypt of Lecce Cathedral (South Italy) was modelled using computational fluid-dynamics (CFD) tools. In the ancient church deterioration mainly consists of efflorescence whose diffusion appeared to be linked to unsuitable indoor conditions. The model was validated using experimental data collected over a one year microclimatic campaign and allowed to investigate a number of possible ventilation scenarios in the Crypt. The outputs of the CFD simulations helped to establish the ventilation scenario ensuring the microclimate with the lowest gradients and the most appropriate airflows in the building. In the analysis of the results a particular attention was dedicated to the artworks location in order to avoid their decay. The research allowed to determine how to improve the indoor conditions in the Crypt controlling the ventilation to preserve the monument.