Skeletal Markers of Activity: Methodological and Interpretative Reflections after the study of the whole Frassetto Sassari identified skeletal collection

Entheses (skeletal attachment sites of muscles and ligaments) and their pathologic modifications (enthesopathies) have long been used as skeletal markers of activity in bioarchaeological (reconstruction of past populations lifestyle) and forensic (personal identification) contexts. However, a functional interpretation of these markers have to deal critically with the multifactorial etiology of the same. Factors such as sex, age, genetic factors, mechanical stress, metabolic conditions, etc.. can compete to produce the observed morphological variability at each attachment site. The aim of this thesis has drawn on the ongoing debate about the informativeness of entheseal modifications as skeletal markers of activity and represent a deepening of the actual knowledge about the relationship between these characters and sex, age and physical activity. For this purpose, the whole "Frassetto” identified skeletal collection of Sassari (Sardinia, Italy) was analyzed. The collection includes the skeletal remains of about 600 individuals died in the late 19th and early 20th century for whom information regarding sex, age at death and, in many cases the occupation are known The results obtained highlight the great age importance on the entheseal modifications. The differences observed between sexes may reflect differences in the level or type of activity performed in life, but could also be related to a different bone tissue response to mechanical stress due to hormonal factors and different growth rates. The role of biomechanical stress related to professional activities remains doubtful. This is probably partly attributable to the analyzed sample characteristics (preponderance of farmers compared with other professions, different mean age of the considered professional subsamples), which has hampered the analysis of samples homogenous with regard to age, which is very influential on the entheses and enthesopathies expression.

Modelli Digitali e Archivi di Progetto. Sistemi integrati di documentazione per l'architettura.

Le tecniche dell'informazione e i metodi della comunicazione hanno modificato il modo di redigere documenti destinati a trasmettere la conoscenza, in un processo che è a tutt'oggi in corso di evoluzione. Anche l'attività progettuale in ingegneria ed architettura, pure in un settore caratterizzato da una notevole inerzia metodologica e restio all'innovazione quale è quello dell'industria edilizia, ha conosciuto profonde trasformazioni in ragione delle nuove espressioni tecnologiche. Da tempo l'informazione necessaria per realizzare un edificio, dai disegni che lo rappresentano sino ai documenti che ne indicano le modalità costruttive, può essere gestita in maniera centralizzata mediante un unico archivio di progetto denominato IPDB (Integrated Project DataBase) pur essendone stata recentemente introdotta sul mercato una variante più operativa chiamata BIM (Building Information Modelling). Tuttavia l'industrializzazione del progetto che questi strumenti esplicano non rende conto appieno di tutti gli aspetti che vedono la realizzazione dell'opera architettonica come collettore di conoscenze proprie di una cultura progettuale che, particolarmente in Italia, è radicata nel tempo. La semantica della rappresentazione digitale è volta alla perequazione degli elementi costitutivi del progetto con l'obiettivo di catalogarne le sole caratteristiche fabbricative. L'analisi della letteratura scientifica pertinente alla materia mostra come non sia possibile attribuire ai metodi ed ai software presenti sul mercato la valenza di raccoglitori omnicomprensivi di informazione: questo approccio olistico costituisce invece il fondamento della modellazione integrata intesa come originale processo di rappresentazione della conoscenza, ordinata secondo il paradigma delle "scatole cinesi", modello evolvente che unifica linguaggi appartenenti ai differenti attori compartecipanti nei settori impiantistici, strutturali e della visualizzazione avanzata. Evidenziando criticamente i pregi e i limiti operativi derivanti dalla modellazione integrata, la componente sperimentale della ricerca è stata articolata con l'approfondimento di esperienze condotte in contesti accademici e professionali. Il risultato conseguito ha coniugato le tecniche di rilevamento alle potenzialità di "modelli tridimensionali intelligenti", dotati cioè di criteri discriminanti per la valutazione del relazionamento topologico dei componenti con l'insieme globale.

Valorizzazione di cartografia storica attraverso moderne tecniche geomatiche: recupero metrico, elaborazione e consultazione in ambiente digitale

“Cartographic heritage” is different from “cartographic history”. The second term refers to the study of the development of surveying and drawing techniques related to maps, through time, i.e. through different types of cultural environment which were background for the creation of maps. The first term concerns the whole amount of ancient maps, together with these different types of cultural environment, which the history has brought us and which we perceive as cultural values to be preserved and made available to many users (public, institutions, experts). Unfortunately, ancient maps often suffer preservation problems of their analog support, mostly due to aging. Today, metric recovery in digital form and digital processing of historical cartography allow preserving map heritage. Moreover, modern geomatic techniques give us new chances of using historical information, which would be unachievable on analog supports. In this PhD thesis, the whole digital processing of recovery and elaboration of ancient cartography is reported, with a special emphasis on the use of digital tools in preservation and elaboration of cartographic heritage. It is possible to divide the workflow into three main steps, that reflect the chapter structure of the thesis itself: • map acquisition: conversion of the ancient map support from analog to digital, by means of high resolution scanning or 3D surveying (digital photogrammetry or laser scanning techniques); this process must be performed carefully, with special instruments, in order to reduce deformation as much as possible; • map georeferencing: reproducing in the digital image the native metric content of the map, or even improving it by selecting a large number of still existing ground control points; this way it is possible to understand the projection features of the historical map, as well as to evaluate and represent the degree of deformation induced by the old type of cartographic transformation (that can be unknown to us), by surveying errors or by support deformation, usually all errors of too high value with respect to our standards; • data elaboration and management in a digital environment, by means of modern software tools: vectorization, giving the map a new and more attractive graphic view (for instance, by creating a 3D model), superimposing it on current base maps, comparing it to other maps, and finally inserting it in GIS or WebGIS environment as a specific layer. The study is supported by some case histories, each of them interesting from the point of view of one digital cartographic elaboration step at least. The ancient maps taken into account are the following ones: • three maps of the Po river delta, made at the end of the XVI century by a famous land-surveyor, Ottavio Fabri (he is single author in the first map, co-author with Gerolamo Pontara in the second map, co-author with Bonajuto Lorini and others in the third map), who wrote a methodological textbook where he explains a new topographical instrument, the squadra mobile (mobile square) invented and used by himself; today all maps are preserved in the State Archive of Venice; • the Ichnoscenografia of Bologna by Filippo de’ Gnudi, made in the 1702 and today preserved in the Archiginnasio Library of Bologna; it is a scenographic view of the city, captured in a bird’s eye flight, but also with an icnographic value, as the author himself declares; • the map of Bologna by the periti Gregorio Monari and Antonio Laghi, the first map of the city derived from a systematic survey, even though it was made only ten years later (1711–1712) than the map by de’ Gnudi; in this map the scenographic view was abandoned, in favor of a more correct representation by means of orthogonal projection; today the map is preserved in the State Archive of Bologna; • the Gregorian Cadastre of Bologna, made in 1831 and updated until 1927, now preserved in the State Archive of Bologna; it is composed by 140 maps and 12 brogliardi (register volumes). In particular, the three maps of the Po river delta and the Cadastre were studied with respect to their acquisition procedure. Moreover, the first maps were analyzed from the georeferencing point of view, and the Cadastre was analyzed with respect to a possible GIS insertion. Finally, the Ichnoscenografia was used to illustrate a possible application of digital elaboration, such as 3D modeling. Last but not least, we must not forget that the study of an ancient map should start, whenever possible, from the consultation of the precious original analogical document; analysis by means of current digital techniques allow us new research opportunities in a rich and modern multidisciplinary context.

Biomechanics of sprint running: a methodological contribution

Sports biomechanics describes human movement from a performance enhancement and an injury reduction perspective. In this respect, the purpose of sports scientists is to support coaches and physicians with reliable information about athletes’ technique. The lack of methods allowing for in-field athlete evaluation as well as for accurate joint force estimates represents, to date, the main limitation to this purpose. The investigations illustrated in the present thesis aimed at providing a contribution towards the development of the above mentioned methods. Two complementary approaches were adopted: a Low Resolution Approach – related to performance assessment – where the use of wearable inertial measurement units is exploited during different phases of sprint running, and a High Resolution Approach – related to joint kinetics estimate for injury prevention – where subject-specific, non-rigid constraints for knee joint kinematic modelling used in multi-body optimization techniques are defined. Results obtained using the Low Resolution Approach indicated that, due to their portability and inexpensiveness, inertial measurement systems are a valid alternative to laboratory-based instrumentation for in-field performance evaluation of sprint running. Using acceleration and angular velocity data, the following quantities were estimated: trunk inclination and angular velocity, instantaneous horizontal velocity and displacement of a point approximating the centre of mass, and stride and support phase durations. As concerns the High Resolution Approach, results indicated that the length of the anterior cruciate and lateral collateral ligaments decreased, while that of the deep bundle of the medial collateral ligament increased significantly during flexion. Variations of the posterior cruciate and the superficial bundle of the medial collateral ligament lengths were concealed by the experimental indeterminacy. A mathematical model was provided that allowed the estimate of subject-specific ligament lengths as a function of knee flexion and that can be integrated in a multi-body optimization procedure.

Methodological improvement of 3D fluoroscopic analysis for the robust quantification of 3D kinematics of human joints

3D video-fluoroscopy is an accurate but cumbersome technique to estimate natural or prosthetic human joint kinematics. This dissertation proposes innovative methodologies to improve the 3D fluoroscopic analysis reliability and usability. Being based on direct radiographic imaging of the joint, and avoiding soft tissue artefact that limits the accuracy of skin marker based techniques, the fluoroscopic analysis has a potential accuracy of the order of mm/deg or better. It can provide fundamental informations for clinical and methodological applications, but, notwithstanding the number of methodological protocols proposed in the literature, time consuming user interaction is exploited to obtain consistent results. The user-dependency prevented a reliable quantification of the actual accuracy and precision of the methods, and, consequently, slowed down the translation to the clinical practice. The objective of the present work was to speed up this process introducing methodological improvements in the analysis. In the thesis, the fluoroscopic analysis was characterized in depth, in order to evaluate its pros and cons, and to provide reliable solutions to overcome its limitations. To this aim, an analytical approach was followed. The major sources of error were isolated with in-silico preliminary studies as: (a) geometric distortion and calibration errors, (b) 2D images and 3D models resolutions, (c) incorrect contour extraction, (d) bone model symmetries, (e) optimization algorithm limitations, (f) user errors. The effect of each criticality was quantified, and verified with an in-vivo preliminary study on the elbow joint. The dominant source of error was identified in the limited extent of the convergence domain for the local optimization algorithms, which forced the user to manually specify the starting pose for the estimating process. To solve this problem, two different approaches were followed: to increase the optimal pose convergence basin, the local approach used sequential alignments of the 6 degrees of freedom in order of sensitivity, or a geometrical feature-based estimation of the initial conditions for the optimization; the global approach used an unsupervised memetic algorithm to optimally explore the search domain. The performances of the technique were evaluated with a series of in-silico studies and validated in-vitro with a phantom based comparison with a radiostereometric gold-standard. The accuracy of the method is joint-dependent, and for the intact knee joint, the new unsupervised algorithm guaranteed a maximum error lower than 0.5 mm for in-plane translations, 10 mm for out-of-plane translation, and of 3 deg for rotations in a mono-planar setup; and lower than 0.5 mm for translations and 1 deg for rotations in a bi-planar setups. The bi-planar setup is best suited when accurate results are needed, such as for methodological research studies. The mono-planar analysis may be enough for clinical application when the analysis time and cost may be an issue. A further reduction of the user interaction was obtained for prosthetic joints kinematics. A mixed region-growing and level-set segmentation method was proposed and halved the analysis time, delegating the computational burden to the machine. In-silico and in-vivo studies demonstrated that the reliability of the new semiautomatic method was comparable to a user defined manual gold-standard. The improved fluoroscopic analysis was finally applied to a first in-vivo methodological study on the foot kinematics. Preliminary evaluations showed that the presented methodology represents a feasible gold-standard for the validation of skin marker based foot kinematics protocols.

Hsp90 characterization and inhibition: a multi-methodological study

Many physiological and pathological processes are mediated by the activity of proteins assembled in homo and/or hetero-oligomers. The correct recognition and association of these proteins into a functional complex is a key step determining the fate of the whole pathway. This has led to an increasing interest in selecting molecules able to modulate/inhibit these protein-protein interactions. In particular, our research was focused on Heat Shock Protein 90 (Hsp90), responsible for the activation and maturation and disposition of many client proteins [1], [2] [3]. Circular Dichroism (CD) spectroscopy, Surface Plasmon Resonance (SPR) and Affinity Capillary Electrophoresis (ACE) were used to characterize the Hsp90 target and, furthermore, its inhibition process via C-terminal domain driven by the small molecule Coumermycin A1. Circular Dichroism was used as powerful technique to characterize Hsp90 and its co-chaperone Hop in solution for secondary structure content, stability to different pHs, temperatures and solvents. Furthermore, CD was used to characterize ATP but, unfortunately, we were not able to monitor an interaction between ATP and Hsp90. The utility of SPR technology, on the other hand, arises from the possibility of immobilizing the protein on a chip through its N-terminal domain to later study the interaction with small molecules able to disrupt the Hsp90 dimerization on the C-terminal domain. The protein was attached on SPR chip using the “amine coupling” chemistry so that the C-terminal domain was free to interact with Coumermycin A1. The goal of the experiment was achieved by testing a range of concentrations of the small molecule Coumermycin A1. Despite to the large difference in the molecular weight of the protein (90KDa) and the drug (1110.08 Da), we were able to calculate the affinity constant of the interaction that was found to be 11.2 µm. In order to confirm the binding constant calculated for the Hsp90 on the chip, we decided to use Capillary Electrophoresis to test the Coumermycin binding to Hsp90. First, this technique was conveniently used to characterize the Hsp90 sample in terms of composition and purity. The experimental conditions were settled on two different systems, the bared fused silica and the PVA-coated capillary. We were able to characterize the Hsp90 sample in both systems. Furthermore, we employed an application of capillary electrophoresis, the Affinity Capillary Electrophoresis (ACE), to measure and confirm the binding constant calculated for Coumermycin on Optical Biosensor. We found a KD = 19.45 µM. This result compares favorably with the KD previously obtained on biosensor. This is a promising result for the use of our novel approach to screen new potential inhibitors of Hsp90 C-terminal domain.

Export Supply Chain Organization and Food Safety and Quality Standards: a case study of the Moroccan Fruit and Vegetable Sector

Agri-food supply chains extend beyond national boundaries, partially facilitated by a policy environment that encourages more liberal international trade. Rising concentration within the downstream sector has driven a shift towards “buyer-driven” global value chains (GVCs) extending internationally with global sourcing and the emergence of multinational key economic players that compete with increase emphasis on product quality attributes. Agri-food systems are thus increasingly governed by a range of inter-related public and private standards, both of which are becoming a priori mandatory, especially in supply chains for high-value and quality-differentiated agri-food products and tend to strongly affect upstream agricultural practices, firms’ internal organization and strategic behaviour and to shape the food chain organization. Notably, increasing attention has been given to the impact of SPS measures on agri-food trade and notably on developing countries’ export performance. Food and agricultural trade is the vital link in the mutual dependency of the global trade system and developing countries. Hence, developing countries derive a substantial portion of their income from food and agricultural trade. In Morocco, fruit and vegetable (especially fresh) are the primary agricultural export. Because of the labor intensity, this sector (especially citrus and tomato) is particularly important in terms of income and employment generation, especially for the female laborers hired in the farms and packing houses. Hence, the emergence of agricultural and agrifood product safety issues and the subsequent tightening of market requirements have challenged mutual gains due to the lack of technical and financial capacities of most developing countries.

The Structure of Financial Supervision: Consolidation or Fragmentation for Financial Regulators?

This research was designed to answer the question of which direction the restructuring of financial regulators should take – consolidation or fragmentation. This research began by examining the need for financial regulation and its related costs. It then continued to describe what types of regulatory structures exist in the world; surveying the regulatory structures in 15 jurisdictions, comparing them and discussing their strengths and weaknesses. This research analyzed the possible regulatory structures using three methodological tools: Game-Theory, Institutional-Design, and Network-Effects. The incentives for regulatory action were examined in Chapter Four using game theory concepts. This chapter predicted how two regulators with overlapping supervisory mandates will behave in two different states of the world (where they can stand to benefit from regulating and where they stand to lose). The insights derived from the games described in this chapter were then used to analyze the different supervisory models that exist in the world. The problem of information-flow was discussed in Chapter Five using tools from institutional design. The idea is based on the need for the right kind of information to reach the hands of the decision maker in the shortest time possible in order to predict, mitigate or stop a financial crisis from occurring. Network effects and congestion in the context of financial regulation were discussed in Chapter Six which applied the literature referring to network effects in general in an attempt to conclude whether consolidating financial regulatory standards on a global level might also yield other positive network effects. Returning to the main research question, this research concluded that in general the fragmented model should be preferable to the consolidated model in most cases as it allows for greater diversity and information-flow. However, in cases in which close cooperation between two authorities is essential, the consolidated model should be used.

Methodological approaches to estimate human population exposure to chemical substances

The public awareness that chemical substances are present ubiquitously in the environment, can be assumed through the diet and can exhibit various health effects, is very high in Europe and Italy. National and international institutions are called to provide figures on the magnitude, frequency, and duration of the population exposure to chemicals, including both natural or anthropogenic substances, voluntarily added to consumers’ good or accidentally entering the production chains. This thesis focuses broadly on how human population exposure to chemicals can be estimated, with particular attention to the methodological approaches and specific focus on dietary exposure assessment and biomonitoring. From the results obtained in the different studies collected in this thesis, it has been pointed out that when selecting the approach to use for the estimate of the exposure to chemicals, several different aspects must be taken into account: the nature of the chemical substance, the population of interest, clarify if the objective is to assess chronic or acute exposure, and finally, take into account the quality and quantity of data available in order to specify and quantify the uncertainty of the estimate.

Essays in Macroecometrics: methodological aspects and empirical applications

In the first chapter, I develop a panel no-cointegration test which extends Pesaran, Shin and Smith (2001)'s bounds test to the panel framework by considering the individual regressions in a Seemingly Unrelated Regression (SUR) system. This allows to take into account unobserved common factors that contemporaneously affect all the units of the panel and provides, at the same time, unit-specific test statistics. Moreover, the approach is particularly suited when the number of individuals of the panel is small relatively to the number of time series observations. I develop the algorithm to implement the test and I use Monte Carlo simulation to analyze the properties of the test. The small sample properties of the test are remarkable, compared to its single equation counterpart. I illustrate the use of the test through a test of Purchasing Power Parity in a panel of EU15 countries. In the second chapter of my PhD thesis, I verify the Expectation Hypothesis of the Term Structure in the repurchasing agreements (repo) market with a new testing approach. I consider an "inexact" formulation of the EHTS, which models a time-varying component in the risk premia and I treat the interest rates as a non-stationary cointegrated system. The effect of the heteroskedasticity is controlled by means of testing procedures (bootstrap and heteroskedasticity correction) which are robust to variance and covariance shifts over time. I fi#nd that the long-run implications of EHTS are verified. A rolling window analysis clarifies that the EHTS is only rejected in periods of turbulence of #financial markets. The third chapter introduces the Stata command "bootrank" which implements the bootstrap likelihood ratio rank test algorithm developed by Cavaliere et al. (2012). The command is illustrated through an empirical application on the term structure of interest rates in the US.

An integrated system for building and running reproducible research

Our generation of computational scientists is living in an exciting time: not only do we get to pioneer important algorithms and computations, we also get to set standards on how computational research should be conducted and published. From Euclid’s reasoning and Galileo’s experiments, it took hundreds of years for the theoretical and experimental branches of science to develop standards for publication and peer review. Computational science, rightly regarded as the third branch, can walk the same road much faster. The success and credibility of science are anchored in the willingness of scientists to expose their ideas and results to independent testing and replication by other scientists. This requires the complete and open exchange of data, procedures and materials. The idea of a “replication by other scientists” in reference to computations is more commonly known as “reproducible research”. In this context the journal “EAI Endorsed Transactions on Performance & Modeling, Simulation, Experimentation and Complex Systems” had the exciting and original idea to make the scientist able to submit simultaneously the article and the computation materials (software, data, etc..) which has been used to produce the contents of the article. The goal of this procedure is to allow the scientific community to verify the content of the paper, reproducing it in the platform independently from the OS chosen, confirm or invalidate it and especially allow its reuse to reproduce new results. This procedure is therefore not helpful if there is no minimum methodological support. In fact, the raw data sets and the software are difficult to exploit without the logic that guided their use or their production. This led us to think that in addition to the data sets and the software, an additional element must be provided: the workflow that relies all of them.

[CONSORT 2010 Explanation and Elaboration: updated guidelines for reporting parallel group randomised trials (Chinese version)]

Overwhelming evidence shows the quality of reporting of randomised controlled trials (RCTs) is not optimal. Without transparent reporting, readers cannot judge the reliability and validity of trial findings nor extract information for systematic reviews. Recent methodological analyses indicate that inadequate reporting and design are associated with biased estimates of treatment effects. Such systematic error is seriously damaging to RCTs, which are considered the gold standard for evaluating interventions because of their ability to minimise or avoid bias. A group of scientists and editors developed the CONSORT (Consolidated Standards of Reporting Trials) statement to improve the quality of reporting of RCTs. It was first published in 1996 and updated in 2001. The statement consists of a checklist and flow diagram that authors can use for reporting an RCT. Many leading medical journals and major international editorial groups have endorsed the CONSORT statement. The statement facilitates critical appraisal and interpretation of RCTs. During the 2001 CONSORT revision, it became clear that explanation and elaboration of the principles underlying the CONSORT statement would help investigators and others to write or appraise trial reports. A CONSORT explanation and elaboration article was published in 2001 alongside the 2001 version of the CONSORT statement. After an expert meeting in January 2007, the CONSORT statement has been further revised and is published as the CONSORT 2010 Statement. This update improves the wording and clarity of the previous checklist and incorporates recommendations related to topics that have only recently received recognition, such as selective outcome reporting bias. This explanatory and elaboration document-intended to enhance the use, understanding, and dissemination of the CONSORT statement-has also been extensively revised. It presents the meaning and rationale for each new and updated checklist item providing examples of good reporting and, where possible, references to relevant empirical studies. Several examples of flow diagrams are included. The CONSORT 2010 Statement, this revised explanatory and elaboration document, and the associated website (www.consort-statement.org) should be helpful resources to improve reporting of randomised trials.