A machine learning based method to detect genomic imbalances exploiting X chromosome exome reads

Whole Exome Sequencing (WES) is rapidly becoming the first-tier test in clinics, both thanks to its declining costs and the development of new platforms that help clinicians in the analysis and interpretation of SNV and InDels. However, we still know very little on how CNV detection could increase WES diagnostic yield. A plethora of exome CNV callers have been published over the years, all showing good performances towards specific CNV classes and sizes, suggesting that the combination of multiple tools is needed to obtain an overall good detection performance. Here we present TrainX, a ML-based method for calling heterozygous CNVs in WES data using EXCAVATOR2 Normalized Read Counts. We select males and females’ non pseudo-autosomal chromosome X alignments to construct our dataset and train our model, make predictions on autosomes target regions and use HMM to call CNVs. We compared TrainX against a set of CNV tools differing for the detection method (GATK4 gCNV, ExomeDepth, DECoN, CNVkit and EXCAVATOR2) and found that our algorithm outperformed them in terms of stability, as we identified both deletions and duplications with good scores (0.87 and 0.82 F1-scores respectively) and for sizes reaching the minimum resolution of 2 target regions. We also evaluated the method robustness using a set of WES and SNP array data (n=251), part of the Italian cohort of Epi25 collaborative, and were able to retrieve all clinical CNVs previously identified by the SNP array. TrainX showed good accuracy in detecting heterozygous CNVs of different sizes, making it a promising tool to use in a diagnostic setting.

La Comunità Energetica del Sud Est Europa quale fattore di stabilità nell’area Balcanica

Il lavoro cerca di valutare il possibile ruolo della Comunità Energetica del Sud Est Europa quale fattore di stabilita’ nell’area Balcanica. Il Trattato fondativo della Comunita’ assegna a questa l’obiettivo di condurre una cooperazione in campo energetico al fine diffondere istituzioni e normative condivise, quali elementi di superamento del conflitto: tuttavia, sono molti gli ostacoli posti su questo cammino sia di natura interna alla regione che esterna, per l’influenza di fattori e poteri internazionali interessati all’area. Il processo di transizione in molti dei paesi del quadrante non e’ ancora concluso e molti sono i nodi politici successivi ai processi di disgregazione della Federazione Jugoslava ancora presenti e non risolti. I progetti di corridoi energetici portati avanti dall’Unione Europea, Stati Uniti e Russia, concentrano sui Balcani un interesse sempre alto e tali attenzioni potrebbero influire sui processi d’area e sulle scelte politiche da compiersi. Sullo sfondo di tutto cio’ un altro importante fattore contribuisce alle dinamiche in corso: la crisi economica ha fatto sentire la sua presenza anche nella regione balcanica e questo crea importanti squilibri che devono essere valutati alla luce di processi di cooperazione quale quello della Comunita’ Energetica.

A holistic approach for the investigation of bee health

Despite current evidence is in strong disagreement with an emergency for the conservation of Apis mellifera, great concern is related to profitability of beekeeping operations. A growing involvement of veterinary science in addressing bee health topics will therefore be fundamental to preserve and protect the entire sector. The experiments in this thesis focused on two different and interdependent levels related to bee health: the biochemical level and the parasitological level. At the biochemical level the impact of plant protection products on bee physiology and survival was studied, elucidating synergistic interactions between poor nutrition and pesticide exposure in A. mellifera and between an insecticide and a fungicide in Osmia bicornis. Moreover, an innovative fingerprinting approach on honey bee haemolymph was applied to detect population imbalances in the hive. The control of Varroa infestations was studied both at the biochemical and parasitological level. A panel of biomarkers in honey bee haemolymph was applied to compare different mite control protocols. This resulted in relevant indications for beekeeping operations pursuing the least impact on nutritional status of the colonies. To guide the decision making of beekeepers, a new formic acid evaporator was tested in comparison with a more established one. Considering its widespread distribution in the country, efforts were directed also towards N. ceranae. In particular, the pivotal aspect of diagnosis was studied, proposing a new qPCR method to overcome some limits of the existing ones. In conclusion, this works fills some of the knowledge gaps of the beekeeping sector. However, many of them still need to be addressed and the upcoming menaces of climate change and dispersal of pathogens via globalization should be targeted by research efforts in the near future. Therefore, a multifaceted vision of bee health is of capital importance, aware of the complementarity of reductionist and holistic approaches.

Si sanctitas inter eos sit digna foedere coniugali. Gli apporti patrimoniali alla moglie superstite in età tardoantica e giustinianea

Queste ricerche si propongono di indagare gli apporti patrimoniali alla morte del marito in favore della moglie superstite, concentrandosi sulla normazione di età tardoantica e giustinianea. Vengono presi in considerazione i principali istituti giuridici che realizzavano, al momento della scomparsa dell’uomo, una cessione patrimoniale a favore della sua vedova: la successione intestata e testata della moglie superstite, la restituzione della dote e il suo lucro sulla donazione nuziale, nonché la c.d. quarta della vedova povera. Di essi si indagano i profili dei relativi regimi giuridici interessanti per il tema di indagine, soffermandosi sulla portata e le ragioni delle riforme che li hanno riguardati, le loro specifiche funzioni nel sistema di sostentamento patrimoniale della coniuge superstite, la loro interazione e integrazione reciproca, il loro ricorso nella prassi. Si giunge alla conclusione che il sistema di tutela della coniuge superstite ebbe poco a che vedere con la successione intestata. Profondamente differente il discorso per quanto attiene alla successione testata e la dote. Più circoscritti di quanto comunemente si pensi, invece, sono i termini in cui è possibile parlare di una funzione di appannaggio vedovile della donazione nuziale. Ecco dunque che, se le garanzie patrimoniali della moglie superstite si sostanziano nel testamento del marito, nella dote, nella donazione nuziale e – nel diritto ultimo e nei soli casi di estremo bisogno – nella quarta uxoria, è chiaro come la questione sia stata demandata, in gran parte, all’autoregolamentazione dei privati. Il legislatore ha saputo predisporre gli strumenti giuridici necessari, assestare gli squilibri dovuti a mutamenti economici e sociali, intervenire laddove ce ne fosse stato bisogno, ma senza invadere un campo così privato e intimo come quello delle relazioni patrimoniali tra coniugi. D’altro canto, il suo intervento non è richiesto «si sanctitas inter eos sit digna foedere coniugali».

Outcomes of global coagulation assays in patients with Philadelphia-negative myeloproliferative neoplasms with respect to genetic determinants of clonal progression

Classical myeloproliferative neoplasms (MPNs) are hematopoietic stem cell disorders that manifest with inflammation, promotion of atherosclerosis, hypercoagulability, fibrosis, and clonal evolution. The complex biological background lends itself to multi-omics studies. We have previously shown that reduced platelet fibrinogen receptor (PFR) expression may follow hyperactivation of plasma-dependent mechanisms, such as tissue factor (TF) release, unbalanced thrombin generation, involvement of protease-activated receptors (PARs). Acetylsalicylic acid (ASA) helped to restore the expression of PFRs. In this study, we enrolled 53 MPN patients, subjecting them to advanced genetic testing (panel of 30 genes in NGS), global coagulation testing (Rotational Thromboelastometry - ROTEM) and cytofluorometric determination of PFRs. ROTEM parameters appear to differ considerably depending on the type of pathology under investigation, cell count, and selected mutations. Essential thrombocythemia (ET) and CALR mutation appear to correlate with increased efficiency of both classical coagulation pathways, with significantly more contracted clot formation times (CFTs). In contrast, primary myelofibrosis (PMF) and polycythemia vera (PV) show greater imbalances in the hemostatic system. PV, probably due to its peculiar hematological features, shows a lengthening of the CFT and, at the same time, a selective contraction of parameters in INTEM with the increase of platelets and white blood cells. PMF - in contrast - seems to exploit the extrinsic pathway more to increase cell numbers. The presence of DNMT3A mutations is associated with reduced clotting time (CT) in EXTEM, while ASXL1 causes reduced maximal lysis (ML). EZH2 could be responsible for the elongation of CFT in INTEM assay. In addition, increased PFR expression is associated with history of hemorrhage and sustained CT time in FIBTEM under ASA prophylaxis. Our findings corroborate the existing models on the connection between fibrosis, genetic complexity, clonal progression, and hypercoagulability. Global coagulation assays and PFR expression are potentially useful tools for dynamic evaluation of treatments’ outcomes.