From superconducting fluctuations to the bosonic limit in the response functions above the critical temperature

We investigate the density, current, and spin response functions above the critical temperature for a system of three-dimensional fermions interacting via an attractive short-range potential. In the strong-coupling (bosonic) limit of this interaction, we identify the dominant diagrammatic contributions for a ``dilute'' system of composite bosons which form as bound-fermion pairs, and compare them with the usual (Aslamazov-Larkin, Maki-Thompson, and density-of-states) terms occurring in the theory of superconducting fluctuations above the critical temperature for a clean system in the weak-coupling limit. We show that, at the zeroth order in the diluteness parameter for the composite bosons, the Aslamazov-Larkin term still represents formally the dominant contribution to the density and current response functions, while the Maki-Thompson and density-of-states terms are strongly suppressed. Corrections to the Aslamazov-Larkin term are then considered at the next order in the diluteness parameter for the composite bosons. The spin response function is also examined, and it is found to be exponentially suppressed in the bosonic limit only when appropriate sets of diagrams are considered simultaneously.Comment: 10 pages, 6 figure

Polynomial conjunctive query rewriting under unary inclusion dependencies

Ontology-based data access (OBDA) is widely accepted as an important ingredient of the new generation of information systems. In the OBDA paradigm, potentially incomplete relational data is enriched by means of ontologies, representing intensional knowledge of the application domain. We consider the problem of conjunctive query answering in OBDA. Certain ontology languages have been identified as FO-rewritable (e.g., DL-Lite and sticky-join sets of TGDs), which means that the ontology can be incorporated into the user's query, thus reducing OBDA to standard relational query evaluation. However, all known query rewriting techniques produce queries that are exponentially large in the size of the user's query, which can be a serious issue for standard relational database engines. In this paper, we present a polynomial query rewriting for conjunctive queries under unary inclusion dependencies. On the other hand, we show that binary inclusion dependencies do not admit polynomial query rewriting algorithms

Computing FO-Rewritings in EL in Practice: from Atomic to Conjunctive Queries

A prominent approach to implementing ontology-mediated queries (OMQs) is to rewrite into a first-order query, which is then executed using a conventional SQL database system. We consider the case where the ontology is formulated in the description logic EL and the actual query is a conjunctive query and show that rewritings of such OMQs can be efficiently computed in practice, in a sound and complete way. Our approach combines a reduction with a decomposed backwards chaining algorithm for OMQs that are based on the simpler atomic queries, also illuminating the relationship between first-order rewritings of OMQs based on conjunctive and on atomic queries. Experiments with real-world ontologies show promising results

Proliferation of cerebellar precursor cells is negatively regulated by nitric oxide in newborn rat.

The diffusible messenger, nitric oxide plays multiple roles in neuroprotection, neurodegeneration and brain plasticity. Its involvement in neurogenesis has been disputed, on the basis of results on models in vivo and in culture. We report here that pharmacological blockade of nitric oxide production in rat pups resulted, during a restricted time window of the first three postnatal days, in increased cerebellar proliferation rate, as assessed through tritiated thymidine or BrdU incorporation into DNA. This was accompanied by increased expression of Myc, a transcription factor essential for cerebellar development, and of the cell cycle regulating gene, cyclin D1. These effects were mediated downstream by the nitric oxide-dependent second messenger, cGMP. Schedules of pharmacological NO deprivation targeted to later developmental stages (from postnatal day 3 to 7), no longer increased proliferation, probably because of partial escape of the cGMP level from nitric oxide control. Though limited to a brief temporal window, the proliferative effect of neonatal nitric oxide deprivation could be traced into adulthood. Indeed, the number of BrdU-labeled surviving cells, most of which were of neuronal phenotype, was larger in the cerebellum of 60-day-old rats that had been subjected to NO deprivation during the first three postnatal days than in control rats. Experiments on cell cultures from neonatal cerebellum confirmed that nitric oxide deprivation stimulated proliferation of cerebellar precursor cells and that this effect was not additive with the proliferative action of sonic hedgehog peptide. The finding that nitric oxide deprivation during early cerebellar neurogenesis, stimulates a brief increase in cell proliferation may contribute to a better understanding of the controversial role of nitric oxide in brain development

Active human full-length CDKL5 produced in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125

Background: A significant fraction of the human proteome is still inaccessible to in vitro studies since the recombinant production of several proteins failed in conventional cell factories. Eukaryotic protein kinases are difficult-to-express in heterologous hosts due to folding issues both related to their catalytic and regulatory domains. Human CDKL5 belongs to this category. It is a serine/threonine protein kinase whose mutations are involved in CDKL5 Deficiency Disorder (CDD), a severe neurodevelopmental pathology still lacking a therapeutic intervention. The lack of successful CDKL5 manufacture hampered the exploitation of the otherwise highly promising enzyme replacement therapy. As almost two-thirds of the enzyme sequence is predicted to be intrinsically disordered, the recombinant product is either subjected to a massive proteolytic attack by host-encoded proteases or tends to form aggregates. Therefore, the use of an unconventional expression system can constitute a valid alternative to solve these issues. Results: Using a multiparametric approach we managed to optimize the transcription of the CDKL5 gene and the synthesis of the recombinant protein in the Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 applying a bicistronic expression strategy, whose generalization for recombinant expression in the cold has been here confirmed with the use of a fluorescent reporter. The recombinant protein largely accumulated as a full-length product in the soluble cell lysate. We also demonstrated for the first time that full-length CDKL5 produced in Antarctic bacteria is catalytically active by using two independent assays, making feasible its recovery in native conditions from bacterial lysates as an active product, a result unmet in other bacteria so far. Finally, the setup of an in cellulo kinase assay allowed us to measure the impact of several CDD missense mutations on the kinase activity, providing new information towards a better understanding of CDD pathophysiology. Conclusions: Collectively, our data indicate that P. haloplanktis TAC125 can be a valuable platform for both the preparation of soluble active human CDKL5 and the study of structural–functional relationships in wild type and mutant CDKL5 forms. Furthermore, this paper further confirms the more general potentialities of exploitation of Antarctic bacteria to produce “intractable” proteins, especially those containing large intrinsically disordered regions

Ontology-based data access with databases: a short course

Ontology-based data access (OBDA) is regarded as a key ingredient of the new generation of information systems. In the OBDA paradigm, an ontology defines a high-level global schema of (already existing) data sources and provides a vocabulary for user queries. An OBDA system rewrites such queries and ontologies into the vocabulary of the data sources and then delegates the actual query evaluation to a suitable query answering system such as a relational database management system or a datalog engine. In this chapter, we mainly focus on OBDA with the ontology language OWL 2QL, one of the three profiles of the W3C standard Web Ontology Language OWL 2, and relational databases, although other possible languages will also be discussed. We consider different types of conjunctive query rewriting and their succinctness, different architectures of OBDA systems, and give an overview of the OBDA system Ontop

Development of high-copy number plasmids in Pseudoalteromonas haloplanktis TAC125

Abstract: The Antarctic bacterium Pseudoalteromonas haloplanktis TAC125 (PhTAC125) is considered an interesting alternative host for the recombinant protein production, that can be explored when the conventional bacterial expression systems fail. Indeed, the manufacture of all the difficult-to-express proteins produced so far in this bacterial platform gave back soluble and active products. Despite these promising results, the low yield of recombinant protein production achieved is hampering the wider and industrial exploitation of this psychrophilic cell factory. All the expression plasmids developed so far in PhTAC125 are based on the origin of replication of the endogenous pMtBL plasmid and are maintained at a very low copy number. In this work, we set up an experimental strategy to select mutated OriR sequences endowed with the ability to establish recombinant plasmids at higher multiplicity per cell. The solution to this major production bottleneck was achieved by the construction of a library of psychrophilic vectors, each containing a randomly mutated version of pMtBL OriR, and its screening by fluorescence-activated cell sorting (FACS). The selected clones allowed the identification of mutated OriR sequences effective in enhancing the plasmid copy number of approximately two orders of magnitude, and the production of the recombinant green fluorescent protein was increased up to twenty times approximately. Moreover, the molecular characterization of the different mutant OriR sequences allowed us to suggest some preliminary clues on the pMtBL replication mechanism that deserve to be further investigated in the future. Key points: • Setup of an electroporation procedure for Pseudoalteromonas haloplanktis TAC125. • Two order of magnitude improvement of OriR-derived psychrophilic expression systems. • Almost twenty times enhancement in Green fluorescent protein production

Tailoring temporal description logics for reasoning over temporal conceptual models

Temporal data models have been used to describe how data can evolve in the context of temporal databases. Both the Extended Entity-Relationship (EER) model and the Unified Modelling Language (UML) have been temporally extended to design temporal databases. To automatically check quality properties of conceptual schemas various encoding to Description Logics (DLs) have been proposed in the literature. On the other hand, reasoning on temporally extended DLs turn out to be too complex for effective reasoning ranging from 2ExpTime up to undecidable languages. We propose here to temporalize the ‘light-weight’ DL-Lite logics obtaining nice computational results while still being able to represent various constraints of temporal conceptual models. In particular, we consider temporal extensions of DL-Lite^N_bool, which was shown to be adequate for capturing non-temporal conceptual models without relationship inclusion, and its fragment DL-Lite^N_core with most primitive concept inclusions, which are nevertheless enough to represent almost all types of atemporal constraints (apart from covering)