Mutation model for nucleotide sequences based on crystal basis

A nucleotides sequence is identified, in the two (four) letters alphabet, by the the labels of a vector state of an irreducible representation of U_q(sl(2)) (U_q(sl(2) + sl(2))), in the limit q -> 0. A master equation for the distribution function is written, where the intensity of the one-spin flip is assumed to depend from the variation of the labels of the state. In the two letters approximation, the numerically computed equilibrium distribution for short sequences is nicely fitted by a Yule distribution, which is the observed distribution of the ranked short oligonucleotides frequency in DNA. The four letter alphabet description, applied to the codons, is able to reproduce the form of the fitted rank ordered usage frequencies distribution.Comment: 27 pages, 9 figure

The Mystery of Two Straight Lines in Bacterial Genome Statistics. Release 2007

In special coordinates (codon position--specific nucleotide frequencies) bacterial genomes form two straight lines in 9-dimensional space: one line for eubacterial genomes, another for archaeal genomes. All the 348 distinct bacterial genomes available in Genbank in April 2007, belong to these lines with high accuracy. The main challenge now is to explain the observed high accuracy. The new phenomenon of complementary symmetry for codon position--specific nucleotide frequencies is observed. The results of analysis of several codon usage models are presented. We demonstrate that the mean--field approximation, which is also known as context--free, or complete independence model, or Segre variety, can serve as a reasonable approximation to the real codon usage. The first two principal components of codon usage correlate strongly with genomic G+C content and the optimal growth temperature respectively. The variation of codon usage along the third component is related to the curvature of the mean-field approximation. First three eigenvalues in codon usage PCA explain 59.1%, 7.8% and 4.7% of variation. The eubacterial and archaeal genomes codon usage is clearly distributed along two third order curves with genomic G+C content as a parameter.Comment: Significantly extended version with new data for all the 348 distinct bacterial genomes available in Genbank in April 200

Development of a WiFi-based telemetry system for ULM flight testing

LAUREA MAGISTRALELa tesi presenta il lavoro di sviluppo di un sistema di telemetria del tutto automatico per il download e la visualizzazione in tempo reale dei dati di volo acquisiti dalla suite "Mnemosine MkV" installata a bordo del velivolo. La possibilità di monitorare i vari parametri di volo istantaneamente garantisce un livello di sicurezza elevato per l’intero team di test al lavoro. Dal 2005 il DSTA-Polimi ha iniziato lo sviluppo di una suite di sensori per l’acquisizione di dati di volo chiamato Mnemosine. Il sistema è progettato in particolare per quei velivoli che appartengono alla classe Ultra Light Machines. Dopo qualche anno di sviluppo e prove sul campo, il sistema ha ora raggiunto la quinta generazione chiamata Mnemosine MkV. Tramite l’impiego di un posizionatore motorizzato e di due antenne WiFi è stata costruita un’antenna direzionale, da disporre all’aperto, in grado di "inseguire" il velivolo nel cielo e poter scaricare i dati anche nel momento in cui la distanza tra l’aereo e le antenne è elevata. Una volta acquisiti i dati provenienti dal velivolo, essi vengono trasmessi, sempre via radio, al PC della stazione di terra situato in ambiente protetto; sarà questo, attraverso i dati GPS del velivolo e dell’antenna direzionale, ad aggiornare il movimento del posizionatore e quindi continuare a garantire il collegamento bordo-terra. L’analisi dei dati, acquisiti in condizioni reali durante diversi test svolti a Maggio 2015, hanno permesso di identificare buoni margini di miglioramento che, se studiati in modo approfondito, potranno incrementare la performance dell’intero sistema di telemetria.The thesis presents the development of an all automatic telemetry system for a real-time download and visualization of flight data acquired from the "Mnemosine MkV" system installed inside the aircraft. The possibility to control instantly the various flight parameters guarantees a high security level for the entire test staff team. Since 2005 DSTA-Polimi has begun the development of a sensors suite for the flight data acquisition called "Mnemosine". The system had been designed especially for those aircraft that belong to the Ultra Light Machines class. After few years of development and field tests, the system has now reached the fifth generation called "Mnemosine MkV". Thanks to the use of a motorized positioner and two WiFi antennas, a steerable antenna station has been developed to be able to "chase" the aircraft in the sky and download flight data also when there is a high distance between the aircraft and the WiFi antennas. The steerable antenna station has been designed in order to be installed in the open air. Once the flight data are acquired, these ones are transmitted, always through a radio link, to the Ground Station PC located in a protected environment. The Ground Station PC will update the positioner angles in order to guarantee the onboard-ground link integrity thanks to the aircraft GPS and the steerable antenna station data. The data analysis, which were acquired in real conditions during the different flight tests undertaken in May 2015, have permitted the identification of positive improvement margins that, if studied in an accurate manner, should increase the performances of the entire telemetry system

HDV can constrain HBV genetic evolution in hbsag: Implications for the identification of innovative pharmacological targets

Chronic HBV + HDV infection is associated with greater risk of liver fibrosis, earlier hepatic decompensation, and liver cirrhosis hepatocellular carcinoma compared to HBV mono-infection. However, to-date no direct anti-HDV drugs are available in clinical practice. Here, we identified conserved and variable regions in HBsAg and HDAg domains in HBV + HDV infection, a critical finding for the design of innovative therapeutic agents. The extent of amino-acid variability was measured by Shannon-Entropy (Sn) in HBsAg genotype-D sequences from 31 HBV + HDV infected and 62 HBV mono-infected patients (comparable for demographics and virological-parameters), and in 47 HDAg genotype-1 sequences. Positions with Sn = 0 were defined as conserved. The percentage of conserved HBsAg-positions was significantly higher in HBV + HDV infection than HBV mono-infection (p = 0.001). Results were confirmed after stratification for HBeAg-status and patients’ age. A Sn = 0 at specific positions in the C-terminus HBsAg were correlated with higher HDV-RNA, suggesting that conservation of these positions can preserve HDV-fitness. Conversely, HDAg was characterized by a lower percentage of conserved-residues than HBsAg (p < 0.001), indicating higher functional plasticity. Furthermore, specific HDAg-mutations were significantly correlated with higher HDV-RNA, suggesting a role in conferring HDV replicative-advantage. Among HDAg-domains, only the virus-assembly signal exhibited a high genetic conservation (75% of conserved-residues). In conclusion, HDV can constrain HBsAg genetic evolution to preserve its fitness. The identification of conserved regions in HDAg poses the basis for designing innovative targets against HDV-infection

The probability subjective view: developing teachers’ knowledge to give sense to students’ productions

International audienc

Prospective teachers' interpretative knowledge: giving sense to subtraction algorithms

The process of interpretation and assessment of students’ mathematical productions represents a crucial aspect of teachers’ practices. In such processes, teachers rely on the so-called interpretative knowledge, which includes particular aspects of their mathematical and pedagogical knowledge, their view of mathematics, and their values. In this paper, we analyze and discuss prospective primary teachers’ interpretative knowledge gained through their assessment of different subtraction algorithms

HBeAg Levels Vary across the Different Stages of HBV Infection According to the Extent of Immunological Pressure and Are Associated with Therapeutic Outcome in the Setting of Immunosuppression-Driven HBV Reactivation

HBeAg is a marker of HBV-activity, and HBeAg-loss predicts a favorable clinical outcome. Here, we characterize HBeAg-levels across different phases of HBV infection, their correlation with virological/biochemical markers and the virological response to anti-HBV therapy. Quantitative HBeAg (qHBeAg, DiaSorin) is assessed in 101 HBeAg+ patients: 20 with acute-infection, 20 with chronic infection, 32 with chronic hepatitis and 29 with immunosuppression-driven HBV-reactivation (HBV-R). A total of 15/29 patients with HBV-R are monitored for &gt; 12 months after starting TDF/ETV. qHBeAg is higher in immunosuppression-driven HBV-R (median[IQR]:930[206-1945]PEIU/mL) and declines in chronic hepatitis (481[28-1393]PEIU/mL, p = 0.03), suggesting HBeAg production, modulated by the extent of immunological pressure. This is reinforced by the negative correlation between qHBeAg and ALT in acute infection (Rho = -0.66, p = 0.006) and chronic hepatitis (Rho = -0.35; p = 0.05). Interestingly, qHBeAg strongly and positively correlates with qHBsAg across the study groups, suggesting cccDNA as a major source of both proteins in the setting of HBeAg positivity (with limited contribution of integrated HBV-DNA to HBsAg production). Focusing on 15 patients with HBV-R starting TDF/ETV, virological suppression and HBeAg-loss are achieved in 60% and 53.3%. Notably, the combination of qHBeAg &gt; 2000 PEIU/mL + qHBsAg &gt; 52,000 IU/mL at HBV-R is the only factor predicting no HBeAg loss (HBeAg loss: 0% with vs. 72.7% without qHBeAg &gt; 2000 PEIU/mL + qHBsAg &gt; 52,000 IU/mL, p = 0.03). In conclusion, qHBeAg varies over the natural course of HBV infection, according to the extent of immunological pressure. In the setting of HBV-R, qHBeAg could be useful in predicting the treatment response under immunosuppression

Universality and Shannon entropy of codon usage

The distribution functions of the codon usage probabilities, computed over all the available GenBank data, for 40 eukaryotic biological species and 5 chloroplasts, do not follow a Zipf law, but are best fitted by the sum of a constant, an exponential and a linear function in the rank of usage. For mitochondriae the analysis is not conclusive. A quantum-mechanics-inspired model is proposed to describe the observed behaviour. These functions are characterized by parameters that strongly depend on the total GC content of the coding regions of biological species. It is predicted that the codon usage is the same in all exonic genes with the same GC content. The Shannon entropy for codons, also strongly depending on the exonic GC content, is computed.Comment: Latex 25 pages, 21 figure