Asteroids co-orbital motion classification based on Machine Learning

In this work, we explore how to classify asteroids in co-orbital motion with a given planet using Machine Learning. We consider four different kinds of motion in mean motion resonance with the planet, nominally Tadpole, Horseshoe and Quasi-satellite, building 3 datasets defined as Real (taking the ephemerides of real asteroids from the JPL Horizons system), Ideal and Perturbed (both simulated, obtained by propagating initial conditions considering two different dynamical systems) for training and testing the Machine Learning algorithms in different conditions. The time series of the variable theta (angle related to the resonance) are studied with a data analysis pipeline defined ad hoc for the problem and composed by: data creation and annotation, time series features extraction thanks to the tsfresh package (potentially followed by selection and standardization) and the application of Machine Learning algorithms for Dimensionality Reduction and Classification. Such approach, based on features extracted from the time series, allows to work with a smaller number of data with respect to Deep Learning algorithms, also allowing to define a ranking of the importance of the features. Physical Interpretability of the features is another key point of this approach. In addition, we introduce the SHapley Additive exPlanations for Explainability technique. Different training and test sets are used, in order to understand the power and the limits of our approach. The results show how the algorithms are able to identify and classify correctly the time series, with a high degree of performance

AMS-VegBank: a new database of vegetation plots for the Italian territory

The importance of collection, storage and exchange of georeferenced vegetation plot-based data has significantly grown in the recent decades, because of the new potentialities offered by ecoinformatics. In this article we introduce the Alma Mater Studiorum – University of Bologna vegetation database (AMS-VegBank; GIVD code EU-IT-021) compiling 17,505 georeferenced vegetation-plot observations within a time span of 90 years. This database includes 337,799 occurrence data of vascular plant species, belonging to many different habitat types. The historical relevance of the presented database is highlighted by the presence of some of the most ancient vegetation-plot observations in Europe (years 1930–1938). The geographic coverage of the database is mostly for Italian territory but it includes also data from other countries. The thematic focuses represented in the database are various, such as small Mediterranean islands, the Dolomite Mountains and the Italian National Parks. The large amount of historical plots available for the country not previously included in existing databases, combined with the constant action to improve the georeferencing of existing data and the addition of new data, highlight the uniqueness of this database. AMS-VegBank represents thus an important tool for studying plant biodiversity within the context of continental and global vegetation plot databases

Thrombin promotes diet-induced obesity through fibrin-driven inflammation

Obesity promotes a chronic inflammatory and hypercoagulable state that drives cardiovascular disease, type 2 diabetes, fatty liver disease, and several cancers. Elevated thrombin activity underlies obesity-linked thromboembolic events, but the mechanistic links between the thrombin/fibrin(ogen) axis and obesity-associated pathologies are incompletely understood. In this work, immunohistochemical studies identified extravascular fibrin deposits within white adipose tissue and liver as distinct features of mice fed a high-fat diet (HFD) as well as obese patients. Fibγ390–396A mice carrying a mutant form of fibrinogen incapable of binding leukocyte αMβ2-integrin were protected from HFD-induced weight gain and elevated adiposity. Fibγ390–396A mice had markedly diminished systemic, adipose, and hepatic inflammation with reduced macrophage counts within white adipose tissue, as well as near-complete protection from development of fatty liver disease and glucose dysmetabolism. Homozygous thrombomodulin-mutant ThbdPro mice, which have elevated thrombin procoagulant function, gained more weight and developed exacerbated fatty liver disease when fed a HFD compared with WT mice. In contrast, treatment with dabigatran, a direct thrombin inhibitor, limited HFD-induced obesity development and suppressed progression of sequelae in mice with established obesity. Collectively, these data provide proof of concept that targeting thrombin or fibrin(ogen) may limit pathologies in obese patients

Location of primary tumor and benefit from anti-epidermal growth factorreceptor monoclonalantibodies in patients with RAS and BRAF wild-typemetastatic colorectal cancer

Introduction. Right- and left-sided colorectal cancers (CRCs) differ in clinical and molecular characteristics. Some retrospective analyses suggested that patients with right-sided tumors derive less benefit from anti-epidermal growth factor receptor (EGFR) antibodies; however, molecular selection in those studies was not extensive. Patients and Methods. Patients with RAS and BRAF wild-type metastatic CRC (mCRC) who were treated with single-agent anti-EGFRs or with cetuximab-irinotecan (if refractory to previous irinotecan) were included in the study. Differences in outcome between patients with right- and left-sided tumors were investigated. Results. Of 75 patients, 14 and 61 had right- and left-sided tumors, respectively. None of the right-sided tumors responded according to RECIST, compared with 24 left-sided tumors (overall response rate: 0% vs. 41%; p 5 .0032), and only 2 patients with right-sided tumors (15%) versus 47 patients with left-sided tumors (80%) achieved disease control (p, .0001). The median duration of progression-free survival was 2.3 and 6.6 months in patients with right-sided and left-sided tumors, respectively (hazard ratio: 3.97;95%confidence interval: 2.09–7.53; p,.0001). Conclusion. Patients with right-sided RAS and BRAF wild-type mCRC seemed to derive no benefit from single-agent anti- EGFRs

R1441G but not G2019S mutation enhances LRRK2 mediated Rab10 phosphorylation in human peripheral blood neutrophils

Heterozygous gain-of-kinase function variants in LRRK2 (leucine-rich repeat kinase 2) cause 1–2% of all cases of Parkinson’s disease (PD) albeit with incomplete and age-dependent penetrance. All pathogenic LRRK2 mutations reside within the two catalytic domains of LRRK2—either in its kinase domain (e.g. G2019S) with modest effect or its ROC-COR GTPase domain (e.g. R1441G/H) with large effect on LRRK2 kinase activity. We have previously reported assays to interrogate LRRK2 kinase pathway activity in human bio-samples measuring phosphorylation of its endogenous substrate Rab10, that mirrors LRRK2 kinase activation status. Here, we isolated neutrophils from fresh peripheral blood from 101 participants including 42 LRRK2 mutation carriers (21 with the G2019S and 21 with the R1441G mutations), 27 patients with idiopathic PD, and 32 controls. Using a dual approach, LRRK2 dependent Rab10 phosphorylation at Threonine 73 (pRab10(Thr73)) was measured by quantitative multiplexed immunoblotting for pRab10(Thr73)/total Rab10 as well as targeted mass-spectrometry for absolute pRab10(Thr73) occupancy. We found a significant over fourfold increase in pRab10(Thr73) phosphorylation in carriers of the LRRK2 R1441G mutation irrespective of clinical disease status. The effect of the LRRK2 G2019S mutation did not reach statistical significance. Furthermore, we show that LRRK2 phosphorylation at Serine 935 is not a marker for LRRK2 kinase activity in human neutrophils. When analysing pRab10(Thr73) phosphorylation in post-mortem brain samples, we observed overall high variability irrespective of clinical and LRRK2 mutation status and attributed this mainly to the adverse effect of the peri- and post-mortem period on the stability of posttranslational modifications such as protein phosphorylation. Overall, in vivo LRRK2 dependent pRab10(Thr73) phosphorylation in human peripheral blood neutrophils is a specific, robust and promising biomarker for significant LRRK2 kinase hyperactivation, as with the LRRK2 R1441G mutation. Additional readouts and/or assays may be needed to increase sensitivity to detect modest LRRK2 kinase activation, as with the LRRK2 G2019S mutation. Our assays could be useful for patient stratification and target engagement studies for LRRK2 kinase inhibitors. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s00401-021-02325-z

Quality assurance for automatically generated contours with additional deep learning

Objective: Deploying an automatic segmentation model in practice should require rigorous quality assurance (QA) and continuous monitoring of the model’s use and performance, particularly in high-stakes scenarios such as healthcare. Currently, however, tools to assist with QA for such models are not available to AI researchers. In this work, we build a deep learning model that estimates the quality of automatically generated contours. Methods: The model was trained to predict the segmentation quality by outputting an estimate of the Dice similarity coefficient given an image contour pair as input. Our dataset contained 60 axial T2-weighted MRI images of prostates with ground truth segmentations along with 80 automatically generated segmentation masks. The model we used was a 3D version of the EfficientDet architecture with a custom regression head. For validation, we used a fivefold cross-validation. To counteract the limitation of the small dataset, we used an extensive data augmentation scheme capable of producing virtually infinite training samples from a single ground truth label mask. In addition, we compared the results against a baseline model that only uses clinical variables for its predictions. Results: Our model achieved a mean absolute error of 0.020 ± 0.026 (2.2% mean percentage error) in estimating the Dice score, with a rank correlation of 0.42. Furthermore, the model managed to correctly identify incorrect segmentations (defined in terms of acceptable/unacceptable) 99.6% of the time. Conclusion: We believe that the trained model can be used alongside automatic segmentation tools to ensure quality and thus allow intervention to prevent undesired segmentation behavior

A Kinome RNAi Screen Identified AMPK as Promoting Poxvirus Entry through the Control of Actin Dynamics

Poxviruses include medically important human pathogens, yet little is known about the specific cellular factors essential for their replication. To identify genes essential for poxvirus infection, we used high-throughput RNA interference to screen the Drosophila kinome for factors required for vaccinia infection. We identified seven genes including the three subunits of AMPK as promoting vaccinia infection. AMPK not only facilitated infection in insect cells, but also in mammalian cells. Moreover, we found that AMPK is required for macropinocytosis, a major endocytic entry pathway for vaccinia. Furthermore, we show that AMPK contributes to other virus-independent actin-dependent processes including lamellipodia formation and wound healing, independent of the known AMPK activators LKB1 and CaMKK. Therefore, AMPK plays a highly conserved role in poxvirus infection and actin dynamics independent of its role as an energy regulator

Slégami Open Access - Manuale d'uso per ricercatori

Il seguente documento nasce nell’ambito delle attività svolte dal Gruppo di Lavoro (GdL) APRE dedicato al tema dell’Open Science e si sviluppa come un manuale d’uso per i ricercatori, con specifico riguardo all’Open Access e all’Open Data. La sua redazione ha coinvolto attivamente tutti i membri del GdL, i cui membri sono rappresentanti delle biblioteche e degli uffici di supporto alla ricerca di diverse università e centri di ricerca italiani (è possibile consultare la lista dei partecipanti nell’ultima pagina di questo documento). Il lavoro è un aggiornamento del manuale originariamente pubblicato nel 2019 e la cui prima edizione era il risultato di un lavoro svolto in 3 fasi: 1) un’iniziale raccolta delle domande più comuni poste dai ricercatori presso le strutture di supporto (siano esse biblioteche o uffici di supporto alla ricerca) degli enti partecipanti in materia di Open Access e Open Data; 2) una fase di consolidamento e classificazione delle domande raccolte in 6 categorie; 3) un’ultima fase di redazione, da parte di alcuni membri del GdL, delle risposte alle domande poste e successivamente emendate a più riprese dall’intero gruppo. Nel 2021 il GdL si è riunito nuovamente per lavorare ad un aggiornamento del manuale in ottica Horizon Europe. Seguendo lo stesso schema di lavoro in 3 fasi (raccolta, classificazione ed elaborazione), il gruppo ha identificato 76 domande aggiuntive rispetto al documento originale, le quali a loro volta sono state successivamente raggruppate e classificate in 10 categorie

AMP-Activated Kinase Restricts Rift Valley Fever Virus Infection by Inhibiting Fatty Acid Synthesis

The cell intrinsic innate immune responses provide a first line of defense against viral infection, and often function by targeting cellular pathways usurped by the virus during infection. In particular, many viruses manipulate cellular lipids to form complex structures required for viral replication, many of which are dependent on de novo fatty acid synthesis. We found that the energy regulator AMPK, which potently inhibits fatty acid synthesis, restricts infection of the Bunyavirus, Rift Valley Fever Virus (RVFV), an important re-emerging arthropod-borne human pathogen for which there are no effective vaccines or therapeutics. We show restriction of RVFV both by AMPK and its upstream activator LKB1, indicating an antiviral role for this signaling pathway. Furthermore, we found that AMPK is activated during RVFV infection, leading to the phosphorylation and inhibition of acetyl-CoA carboxylase, the first rate-limiting enzyme in fatty acid synthesis. Activating AMPK pharmacologically both restricted infection and reduced lipid levels. This restriction could be bypassed by treatment with the fatty acid palmitate, demonstrating that AMPK restricts RVFV infection through its inhibition of fatty acid biosynthesis. Lastly, we found that this pathway plays a broad role in antiviral defense since additional viruses from disparate families were also restricted by AMPK and LKB1. Therefore, AMPK is an important component of the cell intrinsic immune response that restricts infection through a novel mechanism involving the inhibition of fatty acid metabolism