Invariant Causal Set Covering Machines

Rule-based models, such as decision trees, appeal to practitioners due to their interpretable nature. However, the learning algorithms that produce such models are often vulnerable to spurious associations and thus, they are not guaranteed to extract causally-relevant insights. In this work, we build on ideas from the invariant causal prediction literature to propose Invariant Causal Set Covering Machines, an extension of the classical Set Covering Machine algorithm for conjunctions/disjunctions of binary-valued rules that provably avoids spurious associations. We demonstrate both theoretically and empirically that our method can identify the causal parents of a variable of interest in polynomial time

Complete genome sequence of Streptococcus thermophilus SMQ-301, a model strain for phage-host interactions

Streptococcus thermophilus is used by the dairy industry to manufacture yogurt and several cheeses. Using PacBio and Illumina platforms, we sequenced the genome of S. thermophilus SMQ-301, the host of several virulent phages. The genome is composed of 1,861,792 bp and contains 2,037 genes, 67 tRNAs, and 18 rRNAs

Serratia marcescens sch909 as reservoir and source of genetic elements related to wide dissemination of antimicrobial resistance mechanisms

Serratia marcescens SCH909 is a multidrug resistant strain isolated in 1988 harboring three class 1 integrons. We wondered if these integrons were retained over time and if there were other antimicrobial resistant determinants contributing to its multidrug resistant profile. Genomic analysis showed a fourth multidrug resistance integron, a Tn7 transposon with dfrA1-sat2-ybeA-ybfA-ybfB-ybgA gene cassettes in the variable region. Insertion sequences were involved in the genesis of novel composite transposons in the L4 subtype plasmid pSCH909, such as Tn6824 carrying an arsenic regulon and two head to head class 1 integrons surrounded by two complete IS1. Remarkably, a novel chromosomal genomic island, SmaR, was identified, closely related to Multiple Antimicrobial Resistance Regions (MARR), usually found in AbaR0-type and AbGRI2-0 from global clones of Acinetobacter baumannii, and in M-type plasmids circulating in Enterobacteriaceae. Maintenance studies showed that the three class 1 integrons were maintained over 1 month without antimicrobial pressure. Since S. marcescens is considered a relevant nosocomial pathogen that can have a wide range of niches - human, plant, animal, soil and inanimate surfaces, our findings support the ability of this species to capture, maintain and spread a broad variety of antimicrobial resistance elements.Fil: Gambino, Anahí Samanta. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Déraspe, Maxime. Laval University; CanadáFil: Alvarez, Verónica Elizabeth. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Quiroga, María Paula. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; ArgentinaFil: Corbeil, Jacques. Laval University; CanadáFil: Roy, Paul H.. Laval University; CanadáFil: Centron, Daniela. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Houssay. Instituto de Investigaciones en Microbiología y Parasitología Médica. Universidad de Buenos Aires. Facultad de Medicina. Instituto de Investigaciones en Microbiología y Parasitología Médica; Argentin

Predictive computational phenotyping and biomarker discovery using reference-free genome comparisons

The antibiotic susceptibility data for the Clostridium difficile genomes. (XLSX 20.2 kb

First complete genome sequence of Staphylococcus xylosus, a meat starter culture and a host to propagate Staphylococcus aureus phages

Staphylococcus xylosus is a bacterial species used in meat fermentation and a commensal microorganism found on animals. We present the first complete circular genome from this species. The genome is composed of 2,757,557 bp, with a GC content of 32.9%, and contains 2,514 genes and 79 structural RNAs