The role of surface and structural similarities in the retrieval of realistic perceptual events.

This study investigated whether structural similarities (i.e. abstract frames, e.

Revealing mental representations of arithmetic word problems through false memories: New insights into semantic congruence.

What can false memories tell us about the structure of mental representations of arithmetic word problems? The semantic congruence model describes the central role of world semantics in the encoding, recoding, and solving of these problems. We propose to use memory tasks to evaluate key predictions of the semantic congruence model regarding the representations constructed when solving arithmetic word problems. We designed isomorphic word problems differing only by the world semantics imbued in their problem statement.

Neural correlates of unconventional verb extensions reveal preschoolers' analogical abilities.

In the current event-related potential (ERP) study, we assessed 4-year-olds' ability to extend verbs to new action events on the basis of abstract similarities. Participants were presented with images of actions (e.g.

Cost-based feature selection for network model choice.

Selecting a small set of informative features from a large number of possibly noisy candidates is a challenging problem with many applications in machine learning and approximate Bayesian computation. In practice, the cost of computing informative features also needs to be considered. This is particularly important for networks because the computational costs of individual features can span several orders of magnitude.

Nanoprecipitation through solvent-shifting using rapid mixing: Dispelling the Ouzo boundary to reach large solute concentrations.

Hypothesis: The addition of a non-solvent to a solute in good solvent solution leads to nanoprecipitation, which is the spontaneous formation of nanodomains. Yet, increasing solute concentration usually leads to the formation of macrodomains that quickly separate into a bulk phase, which is a severe process limitation. The corresponding concentration threshold, often termed as the Ouzo boundary, remains a mystery that could find its origin in the complex interplay between nanoprecipitation and mixing.

Scalable Approximate Bayesian Computation for Growing Network Models via Extrapolated and Sampled Summaries.

Approximate Bayesian computation (ABC) is a simulation-based likelihood-free method applicable to both model selection and parameter estimation. ABC parameter estimation requires the ability to forward simulate datasets from a candidate model, but because the sizes of the observed and simulated datasets usually need to match, this can be computationally expensive. Additionally, since ABC inference is based on comparisons of summary statistics computed on the observed and simulated data, using computationally expensive summary statistics can lead to further losses in efficiency.

Framework for assessing and easing global COVID-19 travel restrictions.

During the COVID-19 pandemic, many countries implemented international travel restrictions that aimed to contain viral spread while still allowing necessary cross-border travel for social and economic reasons. The relative effectiveness of these approaches for controlling the pandemic has gone largely unstudied. Here we developed a flexible network meta-population model to compare the effectiveness of international travel policies, with a focus on evaluating the benefit of policy coordination.

Extending approximate Bayesian computation with supervised machine learning to infer demographic history from genetic polymorphisms using DIYABC Random Forest.

Simulation-based methods such as approximate Bayesian computation (ABC) are well-adapted to the analysis of complex scenarios of populations and species genetic history. In this context, supervised machine learning (SML) methods provide attractive statistical solutions to conduct efficient inferences about scenario choice and parameter estimation. The Random Forest methodology (RF) is a powerful ensemble of SML algorithms used for classification or regression problems.

Policies for Easing COVID-19 Pandemic Travel Restrictions.

During the COVID-19 pandemic, many countries implemented international travel restrictions that aimed to contain viral spread while still allowing necessary cross-border travel for social and economic reasons. The relative effectiveness of these approaches for controlling the pandemic has gone largely unstudied. Here we developed a flexible network meta-population model to compare the effectiveness of international travel policies, with a focus on evaluating the benefit of policy coordination.

A young age of subspecific divergence in the desert locust inferred by ABC random forest.

Dating population divergence within species from molecular data and relating such dating to climatic and biogeographic changes is not trivial. Yet it can help formulating evolutionary hypotheses regarding local adaptation and future responses to changing environments. Key issues include statistical selection of a demographic and historical scenario among a set of possible scenarios, and estimation of the parameter(s) of interest under the chosen scenario.

Photochemical Methods for Peptide Macrocyclisation.

Photochemical reactions have been the subject of renewed interest over the last two decades, leading to the development of many new, diverse and powerful chemical transformations. More recently, these developments have been expanded to enable the photochemical macrocyclisation of peptides and small proteins. These constructs benefit from increased stability, structural rigidity and biological potency over their linear counterparts, providing opportunities for improved therapeutic agents.

Are Superficially Dissimilar Analogs better retrieved than Superficially Similar Disanalogs?

In the present study, we tested the assumption that structural similarity overcomes surface similarity in the retrieval of past events, by observing whether structural similarity alone is a better cue than surface similarity alone. To do so, in four story-recall experiments, we provided the participants with multiple source stories and then with a target cue story. This target cue only shared either surface or structural similarity with the source stories.

Facile and versatile solid state surface modification of silk fibroin membranes using click chemistry.

Reported is a fast and versatile protocol to surface modify pre-cast silk membranes targeting tyrosine residues. Enriched alkyne silk membranes were prepared using this method and azides possessing a range of functional groups were tethered to the membrane surface using click chemistry to give a range of water contact angles from 85 ± 3° to 34 ± 6°.

ABC random forests for Bayesian parameter inference.

Motivation: Approximate Bayesian computation (ABC) has grown into a standard methodology that manages Bayesian inference for models associated with intractable likelihood functions. Most ABC implementations require the preliminary selection of a vector of informative statistics summarizing raw data. Furthermore, in almost all existing implementations, the tolerance level that separates acceptance from rejection of simulated parameter values needs to be calibrated.

Panton-Valentine leukocidin in pediatric community-acquired Staphylococcus aureus infections.

Purpose: Panton-Valentine Leukocidin (PVL) is an exotoxin produced by strains of Staphylococcus aureus (SA). Its importance as a virulence factor is controversial. We aim to further characterize the role of PVL in pediatric community-acquired SA infections.

Epidemiological, biochemical and antimicrobial susceptibility characteristics of Streptococcus pseudoporcinus isolated in Quebec, Canada, from 1997 to 2006.

From 1997 to 2006, in the province of Quebec, Canada, 15 isolates of Streptococcus pseudoporcinus from 1 urine and 14 vaginorectal cultures were recovered from the genitourinary tract of pregnant women. All these women originated from the Caribbean or sub-Saharan Africa (P=0.00045 compared with a suitable control group).

A fatal case of Arcanobacterium pyogenes endocarditis in a man with no identified animal contact: case report and review of the literature.

Arcanobacterium pyogenes is a rare cause of infection in humans, mostly related to living in rural areas and to contacts with animals. We describe a case of fatal Arcanobacterium pyogenes endocarditis, confirmed by DNA sequencing, in a patient without typical epidemiological exposure.

Streptococcus pseudoporcinus sp. nov., a novel species isolated from the genitourinary tract of women.

Streptococcus strains from animal and human sources identified biochemically as Streptococcus porcinus were investigated by 16S rRNA gene sequencing. The nine human strains isolated between 1997 and 2005 formed a single cluster with more than 2.1% dissimilarity with S.

The N-terminal region of the CCAAT displacement protein (CDP)/Cux transcription factor functions as an autoinhibitory domain that modulates DNA binding.

The CCAAT displacement protein/Cut homeobox (CDP/Cux) transcription factor is expressed as multiple isoforms that may contain up to four DNA-binding domains: Cut repeats 1, 2, and 3 (CR1, CR2, CR3) and the Cut homeodomain (HD). The full-length protein, which contains all four DNA-binding domains, is surprisingly less efficient than the shorter isoforms in DNA binding. Using a panel of recombinant proteins expressed in mammalian or bacterial cells, we have identified a domain at the extreme N terminus of the protein that can inhibit DNA binding.

CDP/Cux stimulates transcription from the DNA polymerase alpha gene promoter.

CDP/Cux (CCAAT-displacement protein/cut homeobox) contains four DNA binding domains, namely, three Cut repeats (CR1, CR2, and CR3) and a Cut homeodomain. CCAAT-displacement activity involves rapid but transient interaction with DNA. More stable DNA binding activity is up-regulated at the G(1)/S transition and was previously shown to involve an N-terminally truncated isoform, CDP/Cux p110, that is generated by proteolytic processing.

Poly(A) polymerase I of Escherichia coli: characterization of the catalytic domain, an RNA binding site and regions for the interaction with proteins involved in mRNA degradation.

Poly(A) polymerase I (PAP I) of Escherichia coli is a member of the nucleotidyltransferase (Ntr) superfamily that includes the eukaryotic PAPs and all the known tRNA CCA-adding enzymes. Five highly conserved aspartic acids in the putative catalytic site of PAP I were changed to either alanine or proline, demonstrating their importance for polymerase activity. A glycine that is absolutely conserved in all Ntrs was also changed yielding a novel mutant protein in which ATP was wastefully hydrolysed in a primer-independent reaction.

mRNA degradation. A tale of poly(A) and multiprotein machines.

The Escherichia coli RNA degradosome is a multiprotein complex containing an endoribonuclease, polynucleotide phosphorylase and a DEAD-box RNA helicase. A related complex has been described in the spinach chloroplast. The exosome and the mtEXO complex have recently been described in yeast and it is likely that related complexes also exist in animal cells.

The Bacillus subtilis nucleotidyltransferase is a tRNA CCA-adding enzyme.

There has been increased interest in bacterial polyadenylation with the recent demonstration that 3' poly(A) tails are involved in RNA degradation. Poly(A) polymerase I (PAP I) of Escherichia coli is a member of the nucleotidyltransferase (Ntr) family that includes the functionally related tRNA CCA-adding enzymes. Thirty members of the Ntr family were detected in a search of the current database of eubacterial genomic sequences.

Ribonuclease E organizes the protein interactions in the Escherichia coli RNA degradosome.

The Escherichia coli RNA degradosome is the prototype of a recently discovered family of multiprotein machines involved in the processing and degradation of RNA. The interactions between the various protein components of the RNA degradosome were investigated by Far Western blotting, the yeast two-hybrid assay, and coimmunopurification experiments. Our results demonstrate that the carboxy-terminal half (CTH) of ribonuclease E (RNase E) contains the binding sites for the three other major degradosomal components, the DEAD-box RNA helicase RhlB, enolase, and polynucleotide phosphorylase (PNPase).

Bacterial poly(A) polymerase: an enzyme that modulates RNA stability.

We have constructed a strain that overexpresses E coli poly(A) polymerase (PAP I). The recombinant protein was soluble, and a partially purified extract had high levels of poly(A) polymerising activity. An antiserum raised against the overexpressed PAP I has permitted two types of analysis: the identification of other E coli proteins that may interact with PAP I, and the search for PAP I-like proteins in other bacteria.