Enhanced equivalent model algorithm for solar mirrors

The SolarPACES Reflectance Guideline provides an essential tool to obtain comparable reflectance measurements, but because of the lack of adequate commercial instrumentation, till now the exhaustive characterization of reflectance behaviour versus incidence ¿i and (half) acceptance angle ¿ is unachieved. An expert group in Task III has been working to outline some practicable solutions. The Equivalent Model Algorithm (EMA) was found quite promising: with few input data, EMA allows to predict any reflectance feature by computation. The recent availability of reliable reflectance measurements at oblique incidence made possible the refinement of EMA by analysing a representative set of commercial solar mirrors. This paper describes the new EMA for solar mirror, named EMA4SM, and reports its validation

New insights on the interaction between thiophene derivatives and Au surfaces: the case of 3,4-ethylenedioxythiophene and the relevant polymer.

The nature of the interface between electrogenerated poly(3,4-ethylenedioxythiophene) and the Au substrate is studied in detail. In particular, the adsorption of the relevant monomer, namely, 3,4-ethylenedioxythiophene, is investigated and compared with that of other thiophene derivatives. Different deposition procedures have been adopted: very thin films of the thiophene derivatives have been obtained through chemisorption processes from vapor and liquid phases, on Au polycrystalline substrates, Au nano particles possessing different size, and a Au(111) single crystal. Different techniques, operating both in situ and ex situ, have been employed for the characterization of these deposits, that is, X-ray photoemission and surface enhanced Raman spectroscopy. The results show that the poly(3,4-ethylenedioxythiophene)/metal interface is far from being simply constituted by unreacted molecules in contact with the substrate; rather, the formation of oligothiophene species and sulfur atoms at the interface has been ascertained

Human colorectal cancer: upregulation of the adaptor protein Rai in TILs leads to cell dysfunction by sustaining GSK-3 activation and PD-1 expression

Background: The immunosuppressive tumor microenvironment (TME) of colorectal cancer (CRC) is a major hurdle for immune checkpoint inhibitor-based therapies. Hence characterization of the signaling pathways driving T cell exhaustion within TME is a critical need for the discovery of novel therapeutic targets and the development of effective therapies. We previously showed that (i) the adaptor protein Rai is a negative regulator of T cell receptor signaling and T helper 1 (Th1)/Th17 cell differentiation; and (ii) Rai deficiency is implicated in the hyperactive phenotype of T cells in autoimmune diseases. Methods: The expression level of Rai was measured by qRT-PCR in paired peripheral blood T cells and T cells infiltrating tumor tissue and the normal adjacent tissue in CRC patients. The impact of hypoxia-inducible factor (HIF)-1α on Rai expression was evaluated in T cells exposed to hypoxia and by performing chromatin immunoprecipitation assays and RNA interference assays. The mechanism by which upregulation of Rai in T cells promotes T cell exhaustion were evaluated by flow cytometric, qRT-PCR and western blot analyses. Results: We show that Rai is a novel HIF-1α-responsive gene that is upregulated in tumor infiltrating lymphocytes of CRC patients compared to patient-matched circulating T cells. Rai upregulation in T cells promoted Programmed cell Death protein (PD)-1 expression and impaired antigen-dependent degranulation of CD8+ T cells by inhibiting phospho-inactivation of glycogen synthase kinase (GSK)-3, a central regulator of PD-1 expression and T cell-mediated anti-tumor immunity. Conclusions: Our data identify Rai as a hitherto unknown regulator of the TME-induced exhausted phenotype of human T cells

The SUCCESSO-TERRA project: A lesson of sustainability from the terramare culture, middle bronze age of the po plain (Northern Italy)

This backstory article deals with the SUCCESSO-TERRA Project (2017–2020), an interdisciplinary research program aiming at reconstructing the land-use transformations that occurred during the development of the Terramare culture in the southern-central Po Plain of Northern Italy. Topics include climate-environment changes, human impact and exploitation of natural resources that are interconnected topics in human ecology and environmental sciences. These topics can only be understood in a long-term perspective integrating archaeology, geology, botany and other sciences. The text includes the theoretical basis, the research strategy and the main methodological approaches given by geoarchaeology and palynology, the two research sides constituting the partnership of the project

Annotations for Rule-Based Models

The chapter reviews the syntax to store machine-readable annotations and describes the mapping between rule-based modelling entities (e.g., agents and rules) and these annotations. In particular, we review an annotation framework and the associated guidelines for annotating rule-based models of molecular interactions, encoded in the commonly used Kappa and BioNetGen languages, and present prototypes that can be used to extract and query the annotations. An ontology is used to annotate models and facilitate their description

ProKinO: An Ontology for Integrative Analysis of Protein Kinases in Cancer

Protein kinases are a large and diverse family of enzymes that are genomically altered in many human cancers. Targeted cancer genome sequencing efforts have unveiled the mutational profiles of protein kinase genes from many different cancer types. While mutational data on protein kinases is currently catalogued in various databases, integration of mutation data with other forms of data on protein kinases such as sequence, structure, function and pathway is necessary to identify and characterize key cancer causing mutations. Integrative analysis of protein kinase data, however, is a challenge because of the disparate nature of protein kinase data sources and data formats., where the mutations are spread over 82 distinct kinases. We also provide examples of how ontology-based data analysis can be used to generate testable hypotheses regarding cancer mutations.

Ontologies in Quantitative Biology: A Basis for Comparison, Integration, and Discovery

As biology is becoming a data-driven discipline, ontologies become increasingly important for systematically capturing the existing knowledge. This essay discusses current trends and how ontologies can also be used for discovery

Broadening the horizon – level 2.5 of the HUPO-PSI format for molecular interactions

BACKGROUND: Molecular interaction Information is a key resource in modern biomedical research. Publicly available data have previously been provided in a broad array of diverse formats, making access to this very difficult. The publication and wide implementation of the Human Proteome Organisation Proteomics Standards Initiative Molecular Interactions (HUPO PSI-MI) format in 2004 was a major step towards the establishment of a single, unified format by which molecular interactions should be presented, but focused purely on protein-protein interactions. RESULTS: The HUPO-PSI has further developed the PSI-MI XML schema to enable the description of interactions between a wider range of molecular types, for example nucleic acids, chemical entities, and molecular complexes. Extensive details about each supported molecular interaction can now be captured, including the biological role of each molecule within that interaction, detailed description of interacting domains, and the kinetic parameters of the interaction. The format is supported by data management and analysis tools and has been adopted by major interaction data providers. Additionally, a simpler, tab-delimited format MITAB2.5 has been developed for the benefit of users who require only minimal information in an easy to access configuration. CONCLUSION: The PSI-MI XML2.5 and MITAB2.5 formats have been jointly developed by interaction data producers and providers from both the academic and commercial sector, and are already widely implemented and well supported by an active development community. PSI-MI XML2.5 enables the description of highly detailed molecular interaction data and facilitates data exchange between databases and users without loss of information. MITAB2.5 is a simpler format appropriate for fast Perl parsing or loading into Microsoft Excel

The Botanical Record of Archaeobotany Italian Network - BRAIN: a cooperative network, database and website

The BRAIN (Botanical Records of Archaeobotany Italian Network) database and network was developed by the cooperation of archaeobotanists working on Italian archaeological sites. Examples of recent research including pollen or other plant remains in analytical and synthetic papers are reported as an exemplar reference list. This paper retraces the main steps of the creation of BRAIN, from the scientific need for the first research cooperation to the website which has a free online access since 2015

The Botanical Record of Archaeobotany Italian Network - BRAIN: a cooperative network, database and website

The BRAIN (Botanical Records of Archaeobotany Italian Network) database and network was developed by the cooperation of archaeobotanists working on Italian archaeological sites. Examples of recent research including pollen or other plant remains in analytical and synthetic papers are reported as an exemplar reference list. This paper retraces the main steps of the creation of BRAIN, from the scientific need for the first research cooperation to the website which has a free online access since 2015