Structural Cheminformatics for Kinase-Centric Drug Design

Drug development is a long, expensive, and iterative process with a high failure rate, while patients wait impatiently for treatment. Kinases are one of the main drug targets studied for the last decades to combat cancer, the second leading cause of death worldwide. These efforts resulted in a plethora of structural, chemical, and pharmacological kinase data, which are collected in the KLIFS database. In this thesis, we apply ideas from structural cheminformatics to the rich KLIFS dataset, aiming to provide computational tools that speed up the complex drug discovery process. We focus on methods for target prediction and fragment-based drug design that study characteristics of kinase binding sites (also called pockets). First, we introduce the concept of computational target prediction, which is vital in the early stages of drug discovery. This approach identifies biological entities such as proteins that may (i) modulate a disease of interest (targets or on-targets) or (ii) cause unwanted side effects due to their similarity to on-targets (off-targets). We focus on the research field of binding site comparison, which lacked a freely available and efficient tool to determine similarities between the highly conserved kinase pockets. We fill this gap with the novel method KiSSim, which encodes and compares spatial and physicochemical pocket properties for all kinases (kinome) that are structurally resolved. We study kinase similarities in the form of kinome-wide phylogenetic trees and detect expected and unexpected off-targets. To allow multiple perspectives on kinase similarity, we propose an automated and production-ready pipeline; user-defined kinases can be inspected complementarily based on their pocket sequence and structure (KiSSim), pocket-ligand interactions, and ligand profiles. Second, we introduce the concept of fragment-based drug design, which is useful to identify and optimize active and promising molecules (hits and leads). This approach identifies low-molecular-weight molecules (fragments) that bind weakly to a target and are then grown into larger high-affinity drug-like molecules. With the novel method KinFragLib, we provide a fragment dataset for kinases (fragment library) by viewing kinase inhibitors as combinations of fragments. Kinases have a highly conserved pocket with well-defined regions (subpockets); based on the subpockets that they occupy, we fragment kinase inhibitors in experimentally resolved protein-ligand complexes. The resulting dataset is used to generate novel kinase-focused molecules that are recombinations of the previously fragmented kinase inhibitors while considering their subpockets. The KinFragLib and KiSSim methods are published as freely available Python tools. Third, we advocate for open and reproducible research that applies FAIR principles ---data and software shall be findable, accessible, interoperable, and reusable--- and software best practices. In this context, we present the TeachOpenCADD platform that contains pipelines for computer-aided drug design. We use open source software and data to demonstrate ligand-based applications from cheminformatics and structure-based applications from structural bioinformatics. To emphasize the importance of FAIR data, we dedicate several topics to accessing life science databases such as ChEMBL, PubChem, PDB, and KLIFS. These pipelines are not only useful to novices in the field to gain domain-specific skills but can also serve as a starting point to study research questions. Furthermore, we show an example of how to build a stand-alone tool that formalizes reoccurring project-overarching tasks: OpenCADD-KLIFS offers a clean and user-friendly Python API to interact with the KLIFS database and fetch different kinase data types. This tool has been used in this thesis and beyond to support kinase-focused projects. We believe that the FAIR-based methods, tools, and pipelines presented in this thesis (i) are valuable additions to the toolbox for kinase research, (ii) provide relevant material for scientists who seek to learn, teach, or answer questions in the realm of computer-aided drug design, and (iii) contribute to making drug discovery more efficient, reproducible, and reusable

Dynamics of Hybrid Zones at a Continental Scale

Hybridization has traditionally been viewed as a happenstance that negatively impacts populations, but is now recognized as an important evolutionary mechanism that can substantially impact the evolutionary trajectories of gene pools, influence adaptive capacity, and contravene or reinforce divergence. Physiographic processes are important drivers of dispersal, alternately funneling populations into isolation, promoting divergence, or facilitating secondary contact of diverged populations, increasing the potential for hybridization. In North America, glacial-interglacial cycles and geomorphological changes have provided a dynamic backdrop over the last two million years that promoted such oscillations of population contraction and expansion. These biogeographic processes have resulted in regional hybrid zones where hybridization spans generations Herein, I explored hybrid zones in two species complexes of reptiles across Eastern, Central, and Southwestern North America. Hybrid zones can influence evolutionary trajectories, and understanding the mechanisms underlying their formation is important for defining appropriate management strategies and can help avoid actions that would inadvertently lead to new hybrid zones. Chapter I assessed differential introgression in a complex of terrestrial turtles, the American Box Turtles (Terrapene spp.), from a contemporary hybrid zone in the southeastern United States. Transcriptomic loci were correlated with environmental predictors to evaluate mechanisms engendering maladapted hybrids and adaptive introgression. Selection against hybrids predominated for inter-specifics but directional introgression did so in conspecifics. Outlier loci also primarily correlated with temperature, reflecting the temperature dependency of ectotherms and underscoring their vulnerability to climate change. Chapter II performed a robust assessment of recently developed machine learning (M-L) approaches to delimit four Terrapene species and evaluate the impact of data filtering and M-L parameter choices. Parameter selections were varied to determine their effects in resolving clusters. The results provide necessary recommendations on using M-L for species delimitation in species complexes defined by secondary contact. These data exemplify usage of M-L software in a phylogenetically complex group. Chapter III describes an R package to visualize some of the analyses from Chapter I. Current software to generate genomic clines does not include functions to visualize the results. Thus, I wrote an API (application programming interface) that does so and also performs other genomic and geographic cline-related tasks. Chapter IV examines historical and contemporary phylogeographic patterns in the Massasaugas (Sistrurus spp.), a type of dwarf rattlesnake found across the Southwest and Central Great Plains. In the Southwest, S. tergeminus tergeminus and S. t. edwardsii putatively diverged in the absence of strong physiographic barriers and physical glaciers, suggesting primary divergence. In contrast, a disjunct population of S. t. tergeminus in Missouri reflects potentially historical secondary contact with S. catenatus. These taxa represent contrasting examples of divergence resulting from alternative phylogeographic processes and contextualizes evolutionarily significant and management units. Combined, the four chapters present population genomic data to elucidate impacts of phylogeographic processes on hybrid zones at a continental scale. The data will promote effective conservation management strategies, as many species in the focal regions have been affected by anthropogenic pressures. In this sense, the results can be extrapolated to co-distributed taxa with similar phylogeographic histories

Application of computer-aided drug design for identification of P. falciparum inhibitors

Malaria is a millennia-old disease with the first recorded cases dating back to 2700 BC found in Chinese medical records, and later in other civilizations. It has claimed human lives to such an extent that there are a notable associated socio-economic consequences. Currently, according to the World Health Organization (WHO), Africa holds the highest disease burden with 94% of deaths and 82% of cases with P. falciparum having ~100% prevalence. Chemotherapy, such as artemisinin combination therapy, has been and continues to be the work horse in the fight against the disease, together with seasonal malaria chemoprevention and the use of insecticides. Natural products such as quinine and artemisinin are particularly important in terms of their antimalarial activity. The emphasis in current chemotherapy research is the need for time and cost-effective workflows focussed on new mechanisms of action (MoAs) covering the target candidate profiles (TCPs). Despite a decline in cases over the past decades with, countries increasingly becoming certified malaria free, a stalling trend has been observed in the past five years resulting in missing the 2020 Global Technical Strategy (GTS) milestones. With no effective vaccine, a reduction in funding, slower drug approval than resistance emergence from resistant and invasive vectors, and threats in diagnosis with the pfhrp2/3 gene deletion, malaria remains a major health concern. Motivated by these reasons, the primary aim of this work was a contribution to the antimalarial pipeline through in silico approaches focusing on P. falciparum. We first intended an exploration of malarial targets through a proteome scale screening on 36 targets using multiple metrics to account for the multi-objective nature of drug discovery. The continuous growth of structural data offers the ideal scenario for mining new MoAs covering antimalarials TCPs. This was combined with a repurposing strategy using a set of orally available FDA approved drugs. Further, use was made of time- and cost-effective strategies combining QVina-W efficiency metrics that integrate molecular properties, GRIM rescoring for molecular interactions and a hydrogen mass repartitioning (HMR) molecular dynamics (MD) scheme for accelerated development of antimalarials in the context of resistance. This pipeline further integrates a complex ranking for better drug-target selectivity, and normalization strategies to overcome docking scoring function bias. The different metrics, ranking, normalization strategies and their combinations were first assessed using their mean ranking error (MRE). A version combining all metrics was used to select 36 unique protein-ligand complexes, assessed in MD, with the final retention of 25. From the 16 in vitro tested hits of the 25, fingolimod, abiraterone, prazosin, and terazosin showed antiplasmodial activity with IC50 2.21, 3.37, 16.67 and 34.72 μM respectively and of these, only fingolimod was found to be not safe with respect to human cell viability. These compounds were predicted active on different molecular targets, abiraterone was predicted to interact with a putative liver-stage essential target, hence promising as a transmission-blocking agent. The pipeline had a promising 25% hit rate considering the proteome-scale and use of cost-effective approaches. Secondly, we focused on Plasmodium falciparum 1-deoxy-D-xylulose-5-phosphate reductoisomerase (PfDXR) using a more extensive screening pipeline to overcome some of the current in silico screening limitations. Starting from the ZINC lead-like library of ~3M, hierarchical ligand-based virtual screening (LBVS) and structure-based virtual screening (SBVS) approaches with molecular docking and re-scoring using eleven scoring functions (SFs) were used. Later ranking with an exponential consensus strategy was included. Selected hits were further assessed through Molecular Mechanics Poisson-Boltzmann Surface Area (MM-PBSA), advanced MD sampling in a ligand pulling simulations and (Weighted Histogram Analysis Method) WHAM analysis for umbrella sampling (US) to derive binding free energies. Four leads had better predicted affinities in US than LC5, a 280 nM potent PfDXR inhibitor with ZINC000050633276 showing a promising binding of -20.43 kcal/mol. As shown with fosmidomycin, DXR inhibition offers fast acting compounds fulfilling antimalarials TCP1. Yet, fosmidomycin has a high polarity causing its short half-life and hampering its clinical use. These leads scaffolds are different from fosmidomycin and hence may offer better pharmacokinetic and pharmacodynamic properties and may also be promising for lead optimization. A combined analysis of residues’ contributions to the free energy of binding in MM-PBSA and to steered molecular dynamics (SMD) Fmax indicated GLU233, CYS268, SER270, TRP296, and HIS341 as exploitable for compound optimization. Finally, we updated the SANCDB library with new NPs and their commercially available analogs as a solution to NP availability. The library is extended to 1005 compounds from its initial 600 compounds and the database is integrated to Mcule and Molport APIs for analogs automatic update. The new set may contribute to virtual screening and to antimalarials as the most effective ones have NP origin.Thesis (PhD) -- Faculty of Science, Biochemistry and Microbiology, 202

Investigating the evolution and ecology of obscure bacterial symbioses found in invertebrates, ciliates and algae.

Bacterial symbioses form a fundamental part of the biology of most eukaryotic lifeforms, influencing their evolution, ecology, and behaviour. Their importance has been increasingly recognised in the last few decades, aided by advances in genomic and bioinformatic methods and analyses. As with most emerging fields, most of our knowledge comes from selected ‘model’ case studies, leaving the breadth of possible symbioses poorly explored. In this thesis I utilise a combination of bioinformatics, genomics, fieldwork, and microscopy to explore obscure symbioses across invertebrates, algae, and ciliates. First, I broaden the scope of available genomic and metabolic data available for rarer symbionts in invertebrates, a group that are often studied for their heritable symbionts. I argue that the group previously called Torix Rickettsia is distinct and diverse and should be regarded as a genus with at least three species, which I name ‘Candidatus Tisiphia’. I also report the first genome for the genus ‘Candidatus Megaira’, a widely recorded but poorly understood symbiont of microeukaryotes. I then explored the distribution of various symbiotic bacteria found in ciliates and algae, two host groups that are known to have strong links to symbiotic bacteria and the origins of symbioses but are rarely examined. I show the genus ‘Ca. Megaira’ appears as a deeply diverse, multi-species group of symbionts that is deserving of family status. I find ‘Ca. Megaira’ in both algae and ciliate species and infer that they have the potential to form protective symbioses. Likewise, I find diverse Parachlamydiales in algae and ciliates and propose three new species groups to aid taxonomic clarification of these bacteria. I provide potential microeukaryotic hosts for a group that are often divorced from host species when described and propose the possibility of nutritional and protective symbioses. Lastly, I develop a potential host-symbiont study system for future functional studies. Here, I demonstrate the existence of a likely heritable Ca. Tisiphia symbiont in the mosquito Anopheles plumbeus. It represents a potentially important system for onward application in manipulation of anopheline vector populations, which are currently restricted to a single symbiont. Finally, I synthesize these findings and argue future research should focus on the phenotypes of real-world symbioses discovered within this research

DEEP LEARNING METHODS FOR PREDICTION OF AND ESCAPE FROM PROTEIN RECOGNITION

Protein interactions drive diverse processes essential to living organisms, and thus numerous biomedical applications center on understanding, predicting, and designing how proteins recognize their partners. While unfortunately the number of interactions of interest still vastly exceeds the capabilities of experimental determination methods, computational methods promise to fill the gap. My thesis pursues the development and application of computational methods for several protein interaction prediction and design tasks. First, to improve protein-glycan interaction specificity prediction, I developed GlyBERT, which learns biologically relevant glycan representations encapsulating the components most important for glycan recognition within their structures. GlyBERT encodes glycans with a branched biochemical language and employs an attention-based deep language model to embed the correlation between local and global structural contexts. This approach enables the development of predictive models from limited data, supporting applications such as lectin binding prediction. Second, to improve protein-protein interaction prediction, I developed a unified geometric deep neural network, ‘PInet’ (Protein Interface Network), which leverages the best properties of both data- and physics-driven methods, learning and utilizing models capturing both geometrical and physicochemical molecular surface complementarity. In addition to obtaining state-of-the-art performance in predicting protein-protein interactions, PInet can serve as the backbone for other protein-protein interaction modeling tasks such as binding affinity prediction. Finally, I turned from ii prediction to design, addressing two important tasks in the context of antibodyantigen recognition. The first problem is to redesign a given antigen to evade antibody recognition, e.g., to help biotherapeutics avoid pre-existing immunity or to focus vaccine responses on key portions of an antigen. The second problem is to design a panel of variants of a given antigen to use as “bait” in experimental identification of antibodies that recognize different parts of the antigen, e.g., to support classification of immune responses or to help select among different antibody candidates. I developed a geometry-based algorithm to generate variants to address these design problems, seeking to maximize utility subject to experimental constraints. During the design process, the algorithm accounts for and balances the effects of candidate mutations on antibody recognition and on antigen stability. In retrospective case studies, the algorithm demonstrated promising precision, recall, and robustness of finding good designs. This work represents the first algorithm to systematically design antigen variants for characterization and evasion of polyclonal antibody responses

Development and validation of in silico tools for efficient library design and data analysis in high throughput screening campaigns

My PhD project findings have their major application in the early phase of the drug discovery process, in particular we have developed and validated two computational tools (Molecular Assembles and LiGen) to support the hit finding and the hit to lead phases. I have reported here novel methods to first design chemical libraries optimized for HTS and then profile them for a specific target receptor or enzyme. I also analyzed the generated bio-chemical data in order to obtain robust SARs and to select the most promising hits for the follow up. The described methods support the iterative process of validated hit series optimization up to the identification of a lead. In chapter 3, Ligand generator (LiGen), a de novo tool for structure based virtual screening, is presented. The development of LiGen is a project based on a collaboration among Dompé Farmaceutici SpA, CINECA and the University of Parma. In this multidisciplinary group, the integration of different skills has allowed the development, from scratch, of a virtual screening tool, able to compete in terms of performance with long standing, well-established molecular docking tools such as Glide, Autodock and PLANTS. LiGen, using a novel docking algorithm, is able to perform ligand flexible docking without performing a conformational sampling. LiGen also has other distinctive features with respect to other molecular docking programs: • LiGen uses the inverse pharmacophore derived from the binding site to identify the putative bioactive conformation of the molecules, thus avoiding the evaluation of molecular conformations which do not match the key features of the binding site. • LiGen implemenst a de novo molecule builder based on the accurate definition of chemical rules taking account of building block (reagents) reactivity. • LiGen is natively a multi-platform C++ portable code designed for HPC applications and optimized for the most recent hardware architectures like the Xeon Phi Accelerators. Chapter 3 also reports the further development and optimization of the software starting from the results obtained in the first optimization step performed to validate the software and to derive the default parameters. In chapter 4, the application of LiGen in the discovery and optimization of novel inhibitors of the complement factor 5 receptor (C5aR) is reported. Briefly, the C5a anaphylatoxin acting on its cognate G protein-coupled receptor C5aR is a potent pronociceptive mediator in several models of inflammatory and neuropathic pain. Although there has long been interest in the identification of C5aR inhibitors, their development has been complicated, as is the case with many peptidomimetic drugs, mostly due to the poor drug-like properties of these molecules. Herein, we report the de novo design of a potent and selective C5aR noncompetitive allosteric inhibitor, DF2593A. DF2593A design was guided by the hypothesis that an allosteric site, the “minor pocket”, previously characterized in CXCR1 and CXCR2, could be functionally conserved in the GPCR class.DF2593A potently inhibited C5a-induced migration of human and rodent neutrophils in vitro. Moreover, oral administration of DF2593A effectively reduced mechanical hyperalgesia in several models of acute and chronic inflammatory and neuropathic pain in vivo, without any apparent side effects. Chapter 5 describes another tool: Molecular Assemblies (MA), a novel metrics based on a hierarchical representation of the molecule based on different representations of the scaffold of the molecule and pruning rules. The algorithm used by MA, defining a priori a metrics (a set of rules), creates a representation of the chemical structure through hierarchical decomposition of the scaffold in fragments, in a pathway invariant way (this feature is novel with respect to the other algorithms reported in literature). Such structure decomposition is applied to nine hierarchical representation of the scaffold of the reference molecule, differing for the content of structural information: atom typing and bond order (this feature is novel with respect to the other algorithms reported in literature) The algorithm (metrics) generates a multi-dimensional hierarchical representation of the molecule. This descriptor applied to a library of compounds is able to extract structural (molecule having the same scaffold, wireframe or framework) and sub structural (molecule having the same fragments in common) relations among all the molecules. At least, this method generates relations among molecules based on identities (scaffolds or fragments). Such an approach produces a unique representation of the reference chemical space not biased by the threshold used to define the similarity cut-off between two molecules. This is in contrast to other methods which generate representations based in similarities. MA procedure, retrieving all scaffold representation, fragments and fragmentation’s patterns (according to the predefined rules) from a molecule, creates a molecular descriptor useful for several cheminformatics applications: • Visualization of the chemical space. The scaffold relations (Figure 7) and the fragmentation patterns can be plotted using a network representation. The obtained graphs are useful depictions of the chemical space highlighting the relations that occur among the molecule in a two dimensional space. • Clustering of the chemical space. The relations among the molecules are based on identities. This means that the scaffold representations and their fragments can be used as a hierarchical clustering method. This descriptor produces clusters that are independent from the number and similarity among closest neighbors because belonging to a cluster is a property of the single molecule (Figure 8). This intrinsic feature makes the scaffold based clustering much faster than other methods in producing “stable” clusters in fact, adding and removing molecules increases and decreases the number of clusters while adding or removing relations among the clusters. However these changes do not affect the cluster number and the relation of the other molecules in dataset. • Generate scaffold-based fingerprints. The descriptor can be used as a fingerprint of the molecule and to generate a similarity index able to compare single molecules or also to compare the diversity of two libraries as a whole. Chapter 6 reports an application of MA in the design of a diverse drug-like scaffold based library optimized for HTS campaigns. A well designed, sizeable and properly organized chemical library is a fundamental prerequisite for any HTS project. To build a collection of chemical compounds with high chemical diversity was the aim of the Italian Drug Discovery Network (IDDN) initiative. A structurally diverse collection of about 200,000 chemical molecules was designed and built taking into account practical aspects related to experimental HTS procedures. Algorithms and procedures were developed and implemented to address compound filtering, selection, clusterization and plating. Chapter 7 collects concluding remarks and plans for the further development of the tools

Participatory analytics for transport decision-making

This thesis investigates the design and evaluation of several software platforms that facilitate participatory outcomes in transport decision-making across operational, local and strategic scales. These platforms act as instruments to explore aspects of the research question: "How can urban dashboards be contextualised, designed & evaluated in a way that is sensitive to the changing role of digital democracy, immersive technologies and the increasingly collaborative nature of planning?". The concept of participatory urban dashboards is introduced, followed by process of participatory analytics. This process involves bringing more people on board with both using the dashboard (e.g., together or collaboratively) and allowing a more general audience of citizens or stakeholders to make sense and validate what is displayed. The research is applied to the city of Sydney, Australia. Sydney is a growing, global city with a wide variety of transport infrastructure ambitions and a strong, open-data ecosystem. Sydney’s transport system underpins the case studies of the operational, local and strategic digital artefacts assessed in this research. Participatory analytics outcomes as a result of interacting with these digital prototypes are evaluated. This will, in turn, help direct research and real-life applications and development of these tools. Further, it aims to build on research gap calling for further understanding of context-specific, user-centric design and evaluation of these participatory analytics tools

Computer Aided Tools for the Design and Planning of Personalized Shoulder Arthroplasty

La artroplastia de hombro es el tercer procedimiento de reemplazo articular más común, después de la artroplastia de rodilla y cadera, y actualmentees el de más rápido crecimiento en el campo ortopédico. Las principales opciones quirúrgicas incluyen la artroplastia total de hombro (TSA), en la quese restaura la anatomía articular normal, y, para pacientes con un manguito rotador completamente desgarrado, la artroplastia inversa de hombro (RSA), en la que la bola y la cavidad de la articulación glenohumeral se cambian. A pesar del progreso reciente y los avances en el diseño, las tasas de complicaciones reportadas para RSA son más altas que las de la artroplastia de hombro convencional. Un enfoque específico para el paciente, en el que los médicos adaptan el tratamiento quirúrgico a las características del mismo y al estado preoperatorio, por ejemplo mediante implantes personalizados y planificación previa, puede ayudar a reducir los problemas postoperatorios y mejorar el resultado funcional. El objetivo principal de esta tesis es desarrollar y evaluar métodos novedosos para RSA personalizado, utilizando tecnologías asistidas por ordenador de última generación para estandarizar y automatizar las fases de diseño y planificación.Los implantes personalizados son una solución adecuada para el tratamiento de pacientes con pérdida extensa de hueso glenoideo. Sin embargo, los ingenieros clínicos se enfrentan a muchas variables en el diseño de implantes (número y tipo de tornillos, superficie de contacto, etc.) y una gran variabilidad anatómica y patológica. Actualmente, no existen herramientas objetivas para guiarlos a la hora de elegir el diseño óptimo, es decir, con suficiente estabilidad inicial del implante, lo que hace que el proceso de diseño sea tedioso, lento y dependiente del usuario. En esta tesis, se desarrolló una simulación de Virtual Bench Test (VBT) utilizando un modelo de elementos finitos para evaluar automáticamente la estabilidad inicial de los implantes de hombro personalizados. A través de un experimento de validación, se demostró que los ingenieros clínicos pueden utilizar el resultado de Virtual Bench Test como referencia para respaldar sus decisiones y adaptaciones durante el proceso de diseño del implante.Al diseñar implantes de hombro, el conocimiento de la morfología y la calidad ósea de la escápula en toda la población es fundamental. En particular, se tienen en cuenta las regiones con la mejor reserva ósea (hueso cortical) para definir la posición y orientación de los orificios de los tornillos, mientras se busca una fijación óptima. Como alternativa a las mediciones manuales, cuya generalización está limitada por el análisis de pequeños subconjuntos de pacientes potenciales, Statistical Shape Models (SSMs) se han utilizado comúnmente para describir la variabilidad de la forma dentro de una población. Sin embargo, estos SSMs normalmente no contienen información sobre el grosor cortical.Por lo tanto, se desarrolló una metodología para combinar la forma del hueso escapular y la morfología de la cortical en un SSM. Primero, se presentó y evaluó un método para estimar el espesor cortical, a partir de un análisis de perfil de Hounsfield Unit (HU). Luego, utilizando 32 escápulas sanas segmentadas manualmente, se creó y evaluó un modelo de forma estadística que incluía información de la cortical. La herramienta desarrollada se puede utilizar para implantar virtualmente un nuevo diseño y probar su congruencia dentro de una población virtual generada, reduciendo así el número de iteraciones de diseño y experimentos con cadáveres.Las mediciones del alargamiento de los músculos deltoides y del manguito rotador durante la planificación quirúrgica pueden ayudar a los médicos aseleccionar un diseño y una posición de implante adecuados. Sin embargo, tal evaluación requiere la indicación de puntos anatómicos como referencia para los puntos de unión de los músculos, un proceso que requiere mucho tiempo y depende del usuario, ya que a menudo se realiza manualmente. Además, las imágenes médicas, que se utilizan normalmente para la artroplastia de hombro,contienen en su mayoría solo el húmero proximal, lo que hace imposible indicarlos puntos de unión de los músculos que se encuentran fuera del campo de visión de la exploración. Por lo tanto, se desarrolló y evaluó un método totalmente automatizado, basado en SSM, para medir la elongación del deltoides y del manguito rotador. Su aplicabilidad clínica se demostró mediante la evaluación del rendimiento de la estimación automatizada de la elongación muscular para un conjunto de articulaciones artríticas del hombro utilizadas para la planificación preoperatoria de RSA, lo que confirma que es una herramienta adecuada para los cirujanos a la hora de evaluar y refinar las decisiones clínicas.En esta investigación, se dio un paso importante en la dirección de un enfoque más personalizado de la artroplastia inversa de hombro, en el que el manejo quirúrgico, es decir, el diseño y la posición del implante, se adapta a las características específicas del paciente y al estado preoperatorio. Al aplicar tecnologías asistidas por computadora en la práctica clínica, el proceso de diseño y planificación se puede automatizar y estandarizar, reduciendo así los costos y los plazos de entrega. Además, gracias a los métodos novedosos presentados en esta tesis, esperamos en el futuro una adopción más amplia del enfoque personalizado, con importantes beneficios tanto para los cirujanos como para los pacientes.Shoulder arthroplasty is the third most common joint replacement procedure, after knee and hip arthroplasty, and currently the most rapidly growing one in the orthopaedic field. The main surgical options include total shoulder arthroplasty (TSA), in which the normal joint anatomy is restored, and, for patients with a completely torn rotator cuff, reverse shoulder arthroplasty (RSA), in which the ball and the socket of the glenohumeral joint are switched. Despite the recent progress and advancement in design, the reported rates of complication for RSA are higher than those of conventional shoulder arthroplasty. A patient-specific approach, in which clinicians adapt the surgical management to patient characteristics and preoperative condition, e.g. through custom implants and pre-planning, can help to reduce postoperative problems and improve the functional outcome. The main goal of this thesis is to develop and evaluate novel methods for personalized RSA, using state-of-the-art computer aided technologies to standardize and automate the design and planning phases. Custom implants are a suitable solution when treating patients with extensive glenoid bone loss. However, clinical engineers are confronted with an enormous implant design space (number and type of screws, contact surface, etc.) and large anatomical and pathological variability. Currently, no objective tools exist to guide them when choosing the optimal design, i.e. with sufficient initial implant stability, thus making the design process tedious, time-consuming, and user-dependent. In this thesis, a Virtual Bench Test (VBT) simulation was developed using a finite element model to automatically evaluate the initial stability of custom shoulder implants. Through a validation experiment, it was shown that the virtual test bench output can be used by clinical engineers as a reference to support their decisions and adaptations during the implant design process. When designing shoulder implants, knowledge about bone morphology and bone quality of the scapula throughout a certain population is fundamental. In particular, regions with the best bone stock (cortical bone) are taken into account to define the position and orientation of the screw holes, while aiming for an optimal fixation. As an alternative to manual measurements, whose generalization is limited by the analysis of small sub-sets of the potential patients, Statistical Shape Models (SSMs) have been commonly used to describe shape variability within a population. However, these SSMs typically do not contain information about cortical thickness. Therefore, a methodology to combine scapular bone shape and cortex morphology in an SSM was developed. First, a method to estimate cortical thickness, starting from a profile analysis of Hounsfield Unit (HU), was presented and evaluated. Then, using 32 manually segmented healthy scapulae, a statistical shape model including cortical information was created and assessed. The developed tool can be used to virtually implant a new design and test its congruency inside a generated virtual population, thus reducing the number of design iterations and cadaver labs. Measurements of deltoid and rotator cuff muscle elongation during surgical planning can help clinicians to select a suitable implant design and position. However, such an assessment requires the indication of anatomical landmarks as a reference for the muscle attachment points, a process that is time-consuming and user-dependent, since often performed manually. Additionally, the medical images, which are normally used for shoulder arthroplasty, mostly contain only the proximal humerus, making it impossible to indicate those muscle attachment points which lie outside of the field of view of the scan. Therefore, a fully-automated method, based on SSM, for measuring deltoid and rotator cuff elongation was developed and evaluated. Its clinical applicability was demonstrated by assessing the performance of the automated muscle elongation estimation for a set of arthritic shoulder joints used for preoperative planning of RSA, thus confirming it a suitable tool for surgeons when evaluating and refining clinical decisions. In this research, a major step was taken into the direction of a more personalized approach to Reverse Shoulder Arthroplasty, in which the surgical management, i.e. implant design and position, is adapted to the patient-specific characteristics and preoperative condition. By applying computer aided technologies in the clinical practice, design and planning process can be automated and standardized, thus reducing costs and lead times. Additionally, thanks to the novel methods presented in this thesis, we expect in the future a wider adoption of the personalized approach, with important benefits both for surgeons and patients.<br /

Firefly genomes illuminate parallel origins of bioluminescence in beetles

Fireflies and their luminous courtships have inspired centuries of scientific study. Today firefly luciferase is widely used in biotechnology, but the evolutionary origin of bioluminescence within beetles remains unclear. To shed light on this long-standing question, we sequenced the genomes of two firefly species that diverged over 100 million-years-ago: the North American Photinus pyralis and Japanese Aquatica lateralis. To compare bioluminescent origins, we also sequenced the genome of a related click beetle, the Caribbean Ignelater luminosus, with bioluminescent biochemistry near-identical to fireflies, but anatomically unique light organs, suggesting the intriguing hypothesis of parallel gains of bioluminescence. Our analyses support independent gains of bioluminescence in fireflies and click beetles, and provide new insights into the genes, chemical defenses, and symbionts that evolved alongside their luminous lifestyle