Rational points on 3-folds with nef anti-canonical class over finite fields

We prove that a geometrically integral smooth 3-fold $X$ with nef anti-canonical class and negative Kodaira dimension over a finite field $\mathbb{F}_q$ of characteristic $p>5$ and cardinality $q=p^e > 19$ has a rational point. Additionally, under the same assumptions on $p$ and $q$, we show that a 3-fold $X$ with trivial canonical class and non-zero first Betti number $b_1(X) \neq 0$ has a rational point. Our techniques rely on the Minimal Model Program to establish several structure results for generalized log Calabi--Yau 3-fold pairs over perfect fields.Comment: 27 pages, comments are welcom

Searching COVID-19 clinical research using graphical abstracts

Objective. Graphical abstracts are small graphs of concepts that visually summarize the main findings of scientific articles. While graphical abstracts are customarily used in scientific publications to anticipate and summarize their main results, we propose them as a means for expressing graph searches over existing literature. Materials and methods. We consider the COVID-19 Open Research Dataset (CORD-19), a corpus of more than one million abstracts; each of them is described as a graph of co-occurring ontological terms, selected from the Unified Medical Language System (UMLS) and the Ontology of Coronavirus Infectious Disease (CIDO). Graphical abstracts are also expressed as graphs of ontological terms, possibly augmented by utility terms describing their interactions (e.g., "associated with", "increases", "induces"). We build a co-occurrence network of concepts mentioned in the corpus; we then identify the best matches of graphical abstracts on the network. We exploit graph database technology and shortest-path queries. Results. We build a large co-occurrence network, consisting of 128,249 entities and 47,198,965 relationships. A well-designed interface allows users to explore the network by formulating or adapting queries in the form of an abstract; it produces a bibliography of publications, globally ranked; each publication is further associated with the specific parts of the abstract that it explains, thereby allowing the user to understand each aspect of the matching. Discussion and Conclusion. Our approach supports the process of scientific hypothesis formulation and evidence search; it can be reapplied to any scientific domain, although our mastering of UMLS makes it most suited to clinical domains.Comment: 12 pages, 6 figure

Exploring the evolution of research topics during the COVID-19 pandemic

The COVID-19 pandemic has changed the research agendas of most scientific communities, resulting in an overwhelming production of research articles in a variety of domains, including medicine, virology, epidemiology, economy, psychology, and so on. Several open-access corpora and literature hubs were established; among them, the COVID-19 Open Research Dataset (CORD-19) has systematically gathered scientific contributions for 2.5 years, by collecting and indexing over one million articles. Here, we present the CORD-19 Topic Visualizer (CORToViz), a method and associated visualization tool for inspecting the CORD-19 textual corpus of scientific abstracts. Our method is based upon a careful selection of up-to-date technologies (including large language models), resulting in an architecture for clustering articles along orthogonal dimensions and extraction techniques for temporal topic mining. Topic inspection is supported by an interactive dashboard, providing fast, one-click visualization of topic contents as word clouds and topic trends as time series, equipped with easy-to-drive statistical testing for analyzing the significance of topic emergence along arbitrarily selected time windows. The processes of data preparation and results visualization are completely general and virtually applicable to any corpus of textual documents - thus suited for effective adaptation to other contexts.Comment: 16 pages, 6 figures, 1 tabl

Arithmetic and geometric deformations of 3-folds

We show that mixed-characteristic and equi-characteristic small deformations of 3-dimensional canonical (resp. terminal) singularities with perfect residue field of characteristic $p>5$ are canonical (resp. terminal). We discuss applications to arithmetic and geometric families of 3-dimensional Fano varieties and minimal models with canonical singularities. Our results are contingent upon the existence of log resolutions of 4-folds.Comment: v3: 19 pages, minor corrections. To appear in Bull. London Math. So

Conceptual modeling for genomics: Building an integrated repository of open data

Many repositories of open data for genomics, collected by world-wide consortia, are important enablers of biological research; moreover, all experimental datasets leading to publications in genomics must be deposited to public repositories and made available to the research community. These datasets are typically used by biologists for validating or enriching their experiments; their content is documented by metadata. However, emphasis on data sharing is not matched by accuracy in data documentation; metadata are not standardized across the sources and often unstructured and incomplete. In this paper, we propose a conceptual model of genomic metadata, whose purpose is to query the underlying data sources for locating relevant experimental datasets. First, we analyze the most typical metadata attributes of genomic sources and define their semantic properties. Then, we use a top-down method for building a global-as-view integrated schema, by abstracting the most important conceptual properties of genomic sources. Finally, we describe the validation of the conceptual model by mapping it to three well-known data sources: TCGA, ENCODE, and Gene Expression Omnibus

Functional measures and food webs of high elevation springs in the Swiss alps

Abstract.: We examined the ecosystem functioning and food webs of high elevation springs in or near the Swiss National Park. Springs originated from silicate or carbonate geologies and were near or above treeline. One iron-sulphur and three temporary springs were also included in the study. Ecosystem function was assessed in four springs via measures of bacterial abundance, sediment respiration, nutrient uptake, and ecosystem metabolism. Food webs were assessed in all 20 springs using nutrient content (C, N, P) and stable isotopes of carbon and nitrogen. Bacteria counts ranged from 1.8 to 3.4×108 cells mL−1 sediment with no significant differences between sites. Sediment respiration rates ranged from 0.13 to 0.46mg O2 h−1 and did not differ between springs. Uptake lengths for N ranged from 11 to 63 m, and for phosphorus from 4 to 60 m. Nitrogen uptake rates (U) ranged from 57 to 266μg m−2 h−1 and those for P from 0.11 to 4.2μg m−2 h−1. Gross primary production (GPP) ranged from 0.7 to 7.1 g O2 m−2 d−1, but reached values of 59.1-70.9 g O2m−2 d−1 in the iron-sulphur spring. Ecosystem respiration (ER) ranged from 1.3 to 10.3 g O2m−2 d−1, but was 91.1-101.8 g O2m−2 d−1 in the ironsulphur spring. All four springs were net-heterotrophic with production to respiration ratios (P/R) ranging from 0.48 to 0.72. The percentage C, N, and P varied significantly among the different food web compartments. The molar ratios (C:P,C:N,N:P) of the different nutrients were consistent within compartments, although varying among the different compartments. Stable isotope signatures (δ13C, d15N) were related to the specific spring types, although food webs were relatively simple with most benthic invertebrates showing omnivory. Riparian spiders partially used aquatic insects in the diet. The results suggest that these alpine springs are complex but functionally similar to forested headwater streams with simple food web

CONFRONTO NUMERICO E SPERIMENTALE TRA LA VERSIONE RIVETTATA E INCOLLATA DI UNA GIUNZIONE MECCANICA

Le giunzioni metalliche incollate offrono diversi vantaggi nei confronti dei tradizionali collegamenti meccanici (rivettatura, bullonatura, ecc.), tuttavia richiedono un’estensiva caratterizzazione meccanica al fine di garantire un’adeguata affidabilità delle strutture in cui vengono inserite. In questo lavoro si presentano i risultati delle prove sperimentali e delle simulazioni numeriche condotte nell’ambito della riprogettazione di una giunzione rivettata di un componente reale, sfruttando la tecnologia dell’incollaggio. L’adesivo usato è una resina epossidica bicomponente, caratterizzata attraverso una campagna di prove sperimentali e simulazioni numeriche, su provini di tipo single-lap e T-peel. Si presenta quindi un confronto, sia numerico che sperimentale, delle prestazioni meccaniche della giunzione rivettata con l’analoga giunzione incollata. I risultati hanno evidenziato un sostanziale miglioramento in termini di rigidezza e resistenza con l’uso della tecnica dell’incollaggio

PG-Triggers: Triggers for Property Graphs

Graph databases are emerging as the leading data management technology for storing large knowledge graphs; significant efforts are ongoing to produce new standards (such as the Graph Query Language, GQL), as well as enrich them with properties, types, schemas, and keys. In this article, we propose PG-Triggers, a complete proposal for adding triggers to Property Graphs, along the direction marked by the SQL3 Standard. We define the syntax and semantics of PG-Triggers and then illustrate how they can be implemented on top of Neo4j, one of the most popular graph databases. In particular, we introduce a syntax-directed translation from PG-Triggers into Neo4j, which makes use of the so-called APOC triggers; APOC is a community-contributed library for augmenting the Cypher query language supported by Neo4j. We also illustrate the use of PG-Triggers through a life science application inspired by the COVID-19 pandemic. The main result of this article is proposing reactive aspects within graph databases as first-class citizens, so as to turn them into an ideal infrastructure for supporting reactive knowledge management.Comment: 12 pages, 4 figures, 3 table

Expressing Biological Problems with Logical Reasoning Languages

Biology represents a very challenging domain that is typically tackled by experts in the field, with few or no interactions with the Web knowledge and rules interoperation community. However, there has been a considerable growth of data regarding biological aspects in the last decades. Moreover, the COVID-19 pandemic has traced an unprecedented point in history, where tons of information have been collected in laboratories worldwide and deposited into open data banks. Inspired by the current needs and backed by a solid knowledge base (our extensional knowledge source) called CoV2K, we propose to express and resolve a series of problems related to the SARS-CoV-2 virus and its interpretation. We formulate our queries as rules in Vadalog (our knowledge representation and reasoning language) and input them to its related logic-based reasoning system. Four cases are presented that allow to explore 1) variants effects and how they are explained in scientific literature; 2) the most typical mutations of a variant; 3) the most likely acquisition of a new mutation by a given variant and the associated reported effects; 4) the most relevant mutations of the virus according to the community. Expressing biological problems using a logic formalism is a major challenge, due to the intrinsic complexity of the domain. The four use cases show that a logical formalism is effective in expressing relevant problems for understanding the current evolution of SARS-CoV-2 variants, an essential aspect of the COVID-19 pandemic

A Comprehensive Approach for the Conceptual Modeling of Genomic Data

The human genome is traditionally represented as a DNA sequence of three billion base pairs. However, its intricacies are captured by many more complex signals, representing DNA variations, the expression of gene activity, or DNA’s structural rearrangements; a rich set of data formats is used to represent such signals. Different conceptual models explain such elaborate structure and behavior. Among them, the Conceptual Schema of the Human Genome (CSG) provides a concept-oriented, top-down representation of the genome behavior – independent of data formats. The Genomic Conceptual Model (GCM) instead provides a data-oriented, bottom-up representation, targeting a well-organized, unified description of these formats. We hereby propose to join these two approaches to achieve a more complete vision, linking (1) a concepts layer, describing genome elements and their conceptual connections, with (2) a data layer, describing datasets derived from genome sequencing with specific technologies. The link is established when specific genomic data types are chosen in the data layer, thereby triggering the selection of a view in the concepts layer. The benefit is mutual, as data records can be semantically described by high-level concepts and exploit their links. In turn, the continuously evolving abstract model can be extended thanks to the input provided by real datasets. As a result, it will be possible to express queries that employ a holistic conceptual perspective on the genome, directly translated onto data-oriented terms and organization. The approach is here exemplified using the DNA variation data type but is applicable to all genomic information