Identifying Lepton Reconstruction Failures in the CMS detector for a Disappearing Tracks Search

A brief overview of the CMS experiment at the LHC and of related experimental particle physics is given. A recently published search at CMS for beyond the Standard Model long lived particles that have a 'disappearing tracks' signature is summarized. A method utilized in the search, names 'fiducial maps', which addressed lepton reconstruction inefficiencies of the CMS detector is studied in more detail, and solutions are proposed to replace it for electrons and muons independently. For electrons, a deep learning classifier is developed to identify electron tracks that fail to be reconstructed as electrons by the CMS software. This is shown to improve the reach of the search by reducing the electron background by $20 \pm 5$% compared to the fiducial maps; the classifier also retains $6-15$% more signal, except for the longest Higgsino lifetime studied in the search, for which the fiducial map is shown to have slightly better performance. Similarly, a deep learning classifier is developed to identify muon tracks that fail the CMS reconstruction. The classifier identifies $28 \pm 3$% of isolated tag and probe muons that failed the reconstruction; however, this classifier is not able to identify the muons that pass the full selections of this search.No embargoAcademic Major: MathematicsAcademic Major: Physic

Eliciting the Functional Taxonomy from protein annotations and taxa

The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules

Rapid SARS-CoV-2 intra-host and within-household emergence of novel haplotypes

In February 2020, the municipality of Vo’, a small town near Padua (Italy) was quarantined due to the first coronavirus disease 19 (COVID-19)-related death detected in Italy. To investigate the viral prevalence and clinical features, the entire population was swab tested in two sequential surveys. Here we report the analysis of 87 viral genomes, which revealed that the unique ancestor haplotype introduced in Vo’ belongs to lineage B, carrying the mutations G11083T and G26144T. The viral sequences allowed us to investigate the viral evolution while being transmitted within and across households and the effectiveness of the non-pharmaceutical interventions implemented in Vo’. We report, for the first time, evidence that novel viral haplotypes can naturally arise intra-host within an interval as short as two weeks, in approximately 30% of the infected individuals, regardless of symptom severity or immune system deficiencies. Moreover, both phylogenetic and minimum spanning network analyses converge on the hypothesis that the viral sequences evolved from a unique common ancestor haplotype that was carried by an index case. The lockdown extinguished both the viral spread and the emergence of new variant

Enhancing protein function prediction with taxonomic constraints - The Argot2.5 web server

Argot2.5 (Annotation Retrieval of Gene Ontology Terms) is a web server designed to predict protein function. It is an updated version of the previous Argot2 enriched with new features in order to enhance its usability and its overall performance. The algorithmic strategy exploits the grouping of Gene Ontology terms by means of semantic similarity to infer protein function. The tool has been challenged over two independent benchmarks and compared to Argot2, PANNZER, and a baseline method relying on BLAST, proving to obtain a better performance thanks to the contribution of some key interventions in critical steps of the working pipeline. The most effective changes regard: (a) the selection of the input data from sequence similarity searches performed against a clustered version of UniProt databank and a remodeling of the weights given to Pfam hits, (b) the application of taxonomic constraints to filter out annotations that cannot be applied to proteins belonging to the species under investigation. The taxonomic rules are derived from our in-house developed tool, FunTaxIS, that extends those provided by the Gene Ontology consortium. The web server is free for academic users and is available online at http://www.medcomp.medicina.unipd.it/Argot2-5/

Prone versus sitting position in pediatric low-grade posterior fossa tumors

The choice between sitting and prone position to access the infratentorial space in a suboccipital craniotomy is still a matter of debate. The comparisons in terms of complications and outcome of both positions are scarce, and the pediatric population is indeed more infrequent in these in scientific reviews. In this paper, we assess intraoperative and postoperative complications and neurological outcome in pediatric patients undergoing posterior cranial fossa surgery for pilocytic astrocytoma in sitting and prone position respectively

Pathway Inspector: a pathway based web application for RNAseq analysis of model and non-model organisms

Pathway Inspector is an easy-to-use web application helping researchers to find patterns of expression in complex RNAseq experiments. The tool combines two standard approaches for RNAseq analysis: the identification of differentially expressed genes and a topology-based analysis of enriched pathways. Pathway Inspector is equipped with ad-hoc interactive graphical interfaces simplifying the discovery of modulated pathways and the integration of the differentially expressed genes in the corresponding pathway topology

Reducing bias in RNA sequencing data: a novel approach to compute counts

Background: In the last decade, Next-Generation Sequencing technologies have been extensively applied to quantitative transcriptomics, making RNA sequencing a valuable alternative to microarrays for measuring and comparing gene transcription levels. Although several methods have been proposed to provide an unbiased estimate of transcript abundances through data normalization, all of them are based on an initial count of the total number of reads mapping on each transcript. This procedure, in principle robust to random noise, is actually errorprone if reads are not uniformly distributed along sequences, as happens indeed due to sequencing errors and ambiguity in read mapping. Here we propose a new approach, called maxcounts, to quantify the expression assigned to an exon as the maximum of its per-base counts, and we assess its performance in comparison with the standard approach described above, which considers the total number of reads aligned to an exon. The two measures are compared using multiple data sets and considering several evaluation criteria: independence from gene-specific covariates, such as exon length and GC-content, accuracy and precision in the quantification of true concentrations and robustness of measurements to variations of alignments quality. Results: Both measures show high accuracy and low dependency on GC-content. However, maxcounts expression quantification is less biased towards long exons with respect to the standard approach. Moreover, it shows lower technical variability at low expressions and is more robust to variations in the quality of alignments. Conclusions: In summary, we confirm that counts computed with the standard approach depend on the length of the feature they are summarized on, and are sensitive to the non-uniform distribution of reads along transcripts. On the opposite, maxcounts are robust to biases due to the non-uniformity distribution of reads and are characterized by a lower technical variability. Hence, we propose maxcounts as an alternative approach for quantitative RNA-sequencing applications

Ca’ Granda, <i>Hortus simplicium</i>: Restoring an Ancient Medicinal Garden of XV–XIX Century in Milan (Italy)

This work is based on the study of 150 majolica vases dated back to the mid XVII century that once preserved medicinal remedies prepared in the ancient Pharmacy annexed to the Ospedale Maggiore Ca’ Granda in Milan (Lombardy, Italy). The Hortus simplicium was created in 1641 as a source of plant-based ingredients for those remedies. The main objective of the present work is to lay the knowledge base for the restoration of the ancient Garden for educational and informative purposes. Therefore, the following complementary phases were carried out: (i) the analysis of the inscriptions on the jars, along with the survey on historical medical texts, allowing for the positive identification of the plant ingredients of the remedies and their ancient use as medicines; (ii) the bibliographic research in modern pharmacological literature in order to validate or refute the historical uses; (iii) the realization of the checklist of plants potentially present in cultivation at the ancient Garden, concurrently with the comparison with the results of a previous in situ archaeobotanical study concerning pollen grains. For the species selection, considerations were made also regarding drug amounts in the remedies and pedoclimatic conditions of the study area. Out of the 150 vases, 108 contained plant-based remedies, corresponding to 148 taxa. The remedies mainly treated gastrointestinal and respiratory disorders. At least one of the medicinal uses was validated in scientific literature for 112 out of the 148 examined species. Finally, a checklist of 40 taxa, presumably hosted in the Hortus simplicium, was assembled

Ca’ Granda, Hortus simplicium: Restoring an Ancient Medicinal Garden of XV–XIX Century in Milan (Italy)

This work is based on the study of 150 majolica vases dated back to the mid XVII century that once preserved medicinal remedies prepared in the ancient Pharmacy annexed to the Ospedale Maggiore Ca’ Granda in Milan (Lombardy, Italy). The Hortus simplicium was created in 1641 as a source of plant-based ingredients for those remedies. The main objective of the present work is to lay the knowledge base for the restoration of the ancient Garden for educational and informative purposes. Therefore, the following complementary phases were carried out: (i) the analysis of the inscriptions on the jars, along with the survey on historical medical texts, allowing for the positive identification of the plant ingredients of the remedies and their ancient use as medicines; (ii) the bibliographic research in modern pharmacological literature in order to validate or refute the historical uses; (iii) the realization of the checklist of plants potentially present in cultivation at the ancient Garden, concurrently with the comparison with the results of a previous in situ archaeobotanical study concerning pollen grains. For the species selection, considerations were made also regarding drug amounts in the remedies and pedoclimatic conditions of the study area. Out of the 150 vases, 108 contained plant-based remedies, corresponding to 148 taxa. The remedies mainly treated gastrointestinal and respiratory disorders. At least one of the medicinal uses was validated in scientific literature for 112 out of the 148 examined species. Finally, a checklist of 40 taxa, presumably hosted in the Hortus simplicium, was assembled