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Supplementary Table 2

Supplementary Table 1

Supplementary Table 5

Tumors undergo dynamic immunoediting as part of a process that balances immunologic sensing of emerging neoantigens and evasion from immune responses. Tumor-infiltrating lymphocytes (TIL) comprise heterogeneous subsets of peripheral T cells characterized by diverse functional differentiation states and dependence on T-cell receptor (TCR) specificity gained through recombination events during their development. We hypothesized that within the tumor microenvironment (TME), an antigenic milieu and immunologic interface, tumor-infiltrating peripheral T cells could reexpress key elements of the TCR recombination machinery, namely, Rag1 and Rag2 recombinases and Tdt polymerase, as a potential mechanism involved in the revision of TCR specificity. Using two syngeneic invasive breast cancer transplantable models, 4T1 and TS/A, we observed that Rag1, Rag2, and Dntt in situ mRNA expression characterized rare tumor-infiltrating T cells. In situ expression of the transcripts was increased in coisogenic Mlh1-deficient tumors, characterized by genomic overinstability, and was also modulated by PD-1 immune-checkpoint blockade. Through immunolocalization and mRNA hybridization analyses, we detected the presence of rare TDT+RAG1/2+ cells populating primary tumors and draining lymph nodes in human invasive breast cancer. Analysis of harmonized single-cell RNA-sequencing data sets of human cancers identified a very small fraction of tumor-associated T cells, characterized by the expression of recombination/revision machinery transcripts, which on pseudotemporal ordering corresponded to differentiated effector T cells. We offer thought-provoking evidence of a TIL microniche marked by rare transcripts involved in TCR shaping.

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Breast implant-associated anaplastic large-cell lymphoma (BI-ALCL) is an uncommon peripheral T cell lymphoma usually presenting as a delayed peri-implant effusion. Chronic inflammation elicited by the implant has been implicated in its pathogenesis. Infection or implant rupture may also be responsible for late seromas. Cytomorphological examination coupled with CD30 immunostaining and eventual T-cell clonality assessment are essential for BI-ALCL diagnosis. However, some benign effusions may also contain an oligo/monoclonal expansion of CD30 + cells that can make the diagnosis challenging. Since cytokines are key mediators of inflammation, we applied a multiplexed immuno-based assay to BI-ALCL seromas and to different types of reactive seromas to look for a potential diagnostic BI-ALCL-associated cytokine profile. We found that BI-ALCL is characterized by a Th2-type cytokine milieu associated with significant high levels of IL-10, IL-13 and Eotaxin which discriminate BI-ALCL from all types of reactive seroma. Moreover, we found a cutoff of IL10/IL-6 ratio of 0.104 is associated with specificity of 100% and sensitivity of 83% in recognizing BI-ALCL effusions. This study identifies promising biomarkers for initial screening of late seromas that can facilitate early diagnosis of BI-ALCL. Electronic supplementary material The online version of this article (10.1007/s00262-020-02778-3) contains supplementary material, which is available to authorized users.

This study aims to replicate the analysis of the relationship between earnings quality and cost of equity in the Italian context, a context characterized by high ownership concentration and weak investor protection dominated by the type II agency problem. We hypothesize a different intensity of the earnings quality–cost of equity relation between concentrated-held firms and dispersed-held ones. The analysis is based on a sample of 774 firm-year observations from 128 Italian nonfinancial listed firms, from 2011 to 2017. Empirical results confirm the existence of a negative relationship between earnings quality and cost of equity. Moreover, findings show that in Italy, this relation is stronger for firms with concentrated ownership and weaker for firms with more dispersed ownership. Consistent with our hypothesis, this finding suggests that ownership structure affects the sensitivity of the earnings quality–cost of equity relationship.

Tumors undergo dynamic immunoediting as part of a process that balances immunologic sensing of emerging neoantigens and evasion from immune responses. Tumor-infiltrating lymphocytes (TIL) comprise heterogeneous subsets of peripheral T cells characterized by diverse functional differentiation states and dependence on T-cell receptor (TCR) specificity gained through recombination events during their development. We hypothesized that within the tumor microenvironment (TME), an antigenic milieu and immunologic interface, tumor-infiltrating peripheral T cells could reexpress key elements of the TCR recombination machinery, namely, Rag1 and Rag2 recombinases and Tdt polymerase, as a potential mechanism involved in the revision of TCR specificity. Using two syngeneic invasive breast cancer transplantable models, 4T1 and TS/A, we observed that Rag1, Rag2, and Dntt in situ mRNA expression characterized rare tumor-infiltrating T cells. In situ expression of the transcripts was increased in coisogenic Mlh1-deficient tumors, characterized by genomic overinstability, and was also modulated by PD-1 immune-checkpoint blockade. Through immunolocalization and mRNA hybridization analyses, we detected the presence of rare TDT+RAG1/2+ cells populating primary tumors and draining lymph nodes in human invasive breast cancer. Analysis of harmonized single-cell RNA-sequencing data sets of human cancers identified a very small fraction of tumor-associated T cells, characterized by the expression of recombination/revision machinery transcripts, which on pseudotemporal ordering corresponded to differentiated effector T cells. We offer thought-provoking evidence of a TIL microniche marked by rare transcripts involved in TCR shaping.

Gastroesophageal reflux disease (GERD) is a common digestive disorder that causes esophagitis and injuries to the esophageal mucosa. GERD symptoms are recurrent during pregnancy and their treatment is focused on lifestyle changes and nonprescription medicines. The aim of this study was to characterize the mechanism of action of a new patented medical device, an oral formulation containing hyaluronic acid, rice extract, and amino acids dispersed in a bioadhesive polymer matrix, by assessing its protective effects in in vitro and ex vivo models of esophageal mucosa damage. Acidic bile salts and pepsin cocktail (BSC) added to CP-A and COLO-680 N esophagus cells were used as an in vitro GERD model to evaluate the binding capacities, anti-inflammatory effects and reparative properties of the investigational product (IP) in comparison to a viscous control. Our results showed that the IP prevents cell permeability and tight junction dysfunction induced by BSC. Furthermore, the IP was also able to down-regulate IL-6 and IL-8 mRNA expression induced by BSC stimulation and to promote tissue repair and wound healing. The results were confirmed by ex vivo experiments in excised rat esophagi through the quantification of Evans Blue permeability assay. These experiments provided evidence that the IP is able to bind to the human esophagus cells, preventing the damage caused by gastroesophageal reflux, showing potential anti-irritative, soothing, and reparative properties.

Honey bee mating is difficult to control as it occurs in flight, several kilometers away from the hive of origin of both queens and drones. In recent years, there has been an increase in the introduction into Italy of queen bees and swarms originating from interracial crossings (especially those known as “Buckfast”), or belonging to non-native subspecies. Consequently, there is a strong need to establish areas suitable for controlled mating. The Italian national beekeeping registry (BDNA) has been recently set up to monitor the position of apiaries and movement of hives, with the purpose of economic and sanitary protection and improvement of bee heritage and food safety. The BDNA was, thus, deemed a suitable tool to explore the availability of areas that could be used as mating stations. Specific criteria, such as not be classified as wetlands, altitude below 1500 m a.s.l., distance of at least 6000 m from an apiary, and distance of at least 1500 m from the national terrestrial border, were selected for defining the mating stations. Furthermore, all the remaining Italian national territory was considered suitable for settlement of mating stations, including towns, industrial settlements, and roads. Based on these criteria, the following methodological framework was applied: (1) collection of the required data (i.e., apiaries coordinates, geospatial data on soil classification, geospatial data on terrain altitude, Italian boundary geospatial data), (2) calculation for the excluded areas according with the criteria listed above, (3) calculation of the mating areas by means of the difference between the entire Italian territory and the excluded areas. The database of BDNA was used to identify them. Appropriate databases and software were used to exclude the areas of the Italian national territory that did not fulfill the established criteria. In this paper, we report the procedure applied to identify on maps the areas suitable for controlled mating of queen bees in the Italian national territory based on data currently available in the BDNA.

The definition of antipower introduced by Fici et al. (ICALP 2016) captures the notion of being the opposite of a power: a sequence of k pairwise distinct blocks of the same length. Recently, Alamro et al. (CPM 2019) defined a string to have an antiperiod if it is a prefix of an antipower, and gave complexity bounds for the offline computation of the minimum antiperiod and all the antiperiods of a word. In this paper, we address the same problems in the online setting. Our solutions rely on new arrays that compactly and incrementally store antiperiods and antipowers as the word grows, obtaining in the process this information for all the word’s prefixes. We show how to compute those arrays online in \(O(n\log n)\) space, \(O(n\log n)\) time, and \(o(n^\epsilon )\) delay per character, for any constant \(\epsilon >0\). Running times are worst-case and hold with high probability. We also discuss more space-efficient solutions returning the correct result with high probability, and small data structures to support random access to those arrays.

Kinetics of coordination of Pd(II) by the macrocyclic porphyrin 5,10,15,20-tetrakis(1-methyl-4-pyridyl)porphyrin (H2P4+) is investigated and confirms quantitative formation of a planar PdP4+ complex at room temperature (formation rate 0.19 M-1 s-1 at 25 °C, 0.2 M NaCl, pH 3). Then, the binding ability to DNA of the pre-formed PdP4+ complex is analysed. To achieve this aim, spectrophotometry, spectrofluorometry and viscometry are used. Thermodynamic parameters for binding, obtained by the temperature dependence of the equilibrium constants, are ?H = –71 kJ mol-1 and ?S = -134 J mol-1 K-1. These values, being both highly negative, agree with full PdP4+ intercalation into DNA. Moreover, kinetics of the binding reaction is analysed by the T-jump technique (reaction times in the 1–5 ms range). Experiments on the porphyrin ligand retention on negative SDS and positive DTAC micellar surfaces are also done. Taken altogether, these data provide mechanistic details on complex formation and on DNA binding and relevant energies and driving forces. It is found that interaction between PdP4+ and base pairs is very strong (Kabs DNA = 8.0 × 105 M-1 at 25 °C, 1.0 M NaCl), not only owing to the high positive charge borne by the complex, but also to the contribution of high hydrophobicity of the porphyrin ring. In the dye/DNA complex, PdP4+ is buried into the helix, as confirmed also by fluorescence quenching tests. Both presence and type of metal ion play a major role, as lower affinity and lower induced helix conformation changes are found in the case of the H2P4+/DNA and CuP4+/DNA systems. © 2017, Springer-Verlag GmbH Austria. Consejería de Educación, Junta de Castilla y León: BU042U16 PRA_2017_28 OSLC-2012-007 Ministerio de Economía y Competitividad: CTQ2014-58,812-C2-2-R Acknowledgements The financial support by PRA 2017 of the University of Pisa—Project PRA_2017_28, from ‘‘la Caixa’’ Foundation (Project OSLC-2012-007), MINECO—Spain (CTQ2014-58,812-C2-2-R, FEDER Funds) and Junta de Castilla y León (BU042U16, FEDER Funds) is gratefully acknowledged.

An important problem in network analysis is understanding how much nodes are important in order to “propagate” the information across the input network. To this aim, many centrality measures have been proposed in the literature and our main goal here is that of providing an overview of the most important of them. In particular, we distinguish centrality measures based on walks computation from those based on shortest-paths computation. We also provide some examples in order to clarify how these measures can be calculated, with special attention to Degree Centrality, Closeness Centrality and Betweennes Centrality.