The Bregman chord divergence

Distances are fundamental primitives whose choice significantly impacts the performances of algorithms in machine learning and signal processing. However selecting the most appropriate distance for a given task is an endeavor. Instead of testing one by one the entries of an ever-expanding dictionary of {\em ad hoc} distances, one rather prefers to consider parametric classes of distances that are exhaustively characterized by axioms derived from first principles. Bregman divergences are such a class. However fine-tuning a Bregman divergence is delicate since it requires to smoothly adjust a functional generator. In this work, we propose an extension of Bregman divergences called the Bregman chord divergences. This new class of distances does not require gradient calculations, uses two scalar parameters that can be easily tailored in applications, and generalizes asymptotically Bregman divergences.Comment: 10 page

Contributions of genetic and non‐genetic sources to variation in cooperative behaviour in a cooperative mammal

This is the author accepted manuscript. the final version is available from Wiley via the DOI in this recordData archiving: Data and code for reproducing the main analyses are available through the Dryad Digital Repository database (https://doi.org/10.5061/dryad.cfxpnvx68). The data and code for the meta-analysis of heritability estimates of selected traits in wild mammals are available in Files S3–S5.The evolution of cooperative behavior is a major area of research among evolutionary biologists and behavioral ecologists, yet there are few estimates of its heritability or its evolutionary potential, and long-term studies of identifiable individuals are required to disentangle genetic and nongenetic components of cooperative behavior. Here, we use long-term data on over 1800 individually recognizable wild meerkats (Suricata suricatta) collected over 30 years and a multigenerational genetic pedigree to partition phenotypic variation in three cooperative behaviors (babysitting, pup feeding, and sentinel behavior) into individual, additive genetic, and other sources, and to assess their repeatability and heritability. In addition to strong effects of sex, age, and dominance status, we found significant repeatability in individual contributions to all three types of cooperative behavior both within and across breeding seasons. Like most other studies of the heritability of social behavior, we found that the heritability of cooperative behavior was low. However, our analysis suggests that a substantial component of the repeatable individual differences in cooperative behavior that we observed was a consequence of additive genetic variation. Our results consequently indicate that cooperative behavior can respond to selection, and suggest scope for further exploration of the genetic basis of social behaviorEuropean Union Horizon 2020Human Frontier Science ProgramUniversity of Zurich.Swiss National Science FoundationMammal Research Institute at the University of Pretoria, South Afric

Silicon-based spin and charge quantum computation

Silicon-based quantum-computer architectures have attracted attention because of their promise for scalability and their potential for synergetically utilizing the available resources associated with the existing Si technology infrastructure. Electronic and nuclear spins of shallow donors (e.g. phosphorus) in Si are ideal candidates for qubits in such proposals due to the relatively long spin coherence times. For these spin qubits, donor electron charge manipulation by external gates is a key ingredient for control and read-out of single-qubit operations, while shallow donor exchange gates are frequently invoked to perform two-qubit operations. More recently, charge qubits based on tunnel coupling in P$_2^+$ substitutional molecular ions in Si have also been proposed. We discuss the feasibility of the building blocks involved in shallow donor quantum computation in silicon, taking into account the peculiarities of silicon electronic structure, in particular the six degenerate states at the conduction band edge. We show that quantum interference among these states does not significantly affect operations involving a single donor, but leads to fast oscillations in electron exchange coupling and on tunnel-coupling strength when the donor pair relative position is changed on a lattice-parameter scale. These studies illustrate the considerable potential as well as the tremendous challenges posed by donor spin and charge as candidates for qubits in silicon.Comment: Review paper (invited) - to appear in Annals of the Brazilian Academy of Science

A synthesis of bacterial and archaeal phenotypic trait data.

A synthesis of phenotypic and quantitative genomic traits is provided for bacteria and archaea, in the form of a scripted, reproducible workflow that standardizes and merges 26 sources. The resulting unified dataset covers 14 phenotypic traits, 5 quantitative genomic traits, and 4 environmental characteristics for approximately 170,000 strain-level and 15,000 species-aggregated records. It spans all habitats including soils, marine and fresh waters and sediments, host-associated and thermal. Trait data can find use in clarifying major dimensions of ecological strategy variation across species. They can also be used in conjunction with species and abundance sampling to characterize trait mixtures in communities and responses of traits along environmental gradients

Author Correction to: The VAR2CSA malaria protein efficiently retrieves circulating tumor cells in an EpCAM-independent manner (Nature Communications, (2018), 9, 1, (3279), 10.1038/s41467-018-05793-2)

This Article contained an error in the consent of some of the patients used in Figure 4. Following an institute-led investigation within BARTS Cancer Institute post-publication, no documentation of informed consent from the nine lung cancer patients whose blood samples were used in this research project could be recovered and therefore, this data have been removed from the published article.The patients and their families were informed of the original error and apologies were made.The following changes have been made to the paper to remove all mention of the lung cancer samples and the data associated with them.In the abstract, the sentence ‘We show that rVAR2 efficiently captures CTCs from hepatic, lung, pancreatic, and prostate carcinomapatients with minimal contamination of peripheral blood mononuclear cells.’ has been changed to read ‘We show that rVAR2 efficiently captures CTCs from hepatic, pancreatic, and prostate carcinoma patients with minimal contamination of peripheral blood mononuclear cells

What drives sound symbolism? Different acoustic cues underlie sound-size and sound-shape mappings

Sound symbolism refers to the non-arbitrary mappings that exist between phonetic properties of speech sounds and their meaning. Despite there being an extensive literature on the topic, the acoustic features and psychological mechanisms that give rise to sound symbolism are not, as yet, altogether clear. The present study was designed to investigate whether different sets of acoustic cues predict size and shape symbolism, respectively. In two experiments, participants judged whether a given consonant-vowel speech sound was large or small, round or angular, using a size or shape scale. Visual size judgments were predicted by vowel formant F1 in combination with F2, and by vowel duration. Visual shape judgments were, however, predicted by formants F2 and F3. Size and shape symbolism were thus not induced by a common mechanism, but rather were distinctly affected by acoustic properties of speech sounds. These findings portray sound symbolism as a process that is not based merely on broad categorical contrasts, such as round/unround and front/back vowels. Rather, individuals seem to base their sound-symbolic judgments on specific sets of acoustic cues, extracted from speech sounds, which vary across judgment dimensions

Persistence in diving American mink

Background American mink forage on land and in water, with aquatic prey often constituting a large proportion of their diet. Their long, thin body shape and relatively poor insulation make them vulnerable to heat loss, particularly in water, yet some individuals dive over 100 times a day. At the level of individual dives, previous research found no difference in dive depth or duration, or the total number of dives per day between seasons, but mink did appear to make more dives per active hour in winter than in summer. There was also no difference in the depth or duration of individual dives between the sexes, but there was some evidence that females made more dives per day than males. However, because individual mink dives tend to be extremely short in duration, persistence (quantified as the number of consecutive dives performed) may be a more appropriate metric with which to compare diving behaviour under different scenarios. Results Mink performed up to 28 consecutive dives, and dived continually for up to 36 min. Periods of more loosely aggregated diving (termed ‘aquatic activity sessions’) comprised up to 80 dives, carried out over up to 162.8 min. Contrary to our predictions, persistence was inversely proportional to body weight, with small animals more persistent than large ones, and (for females, but not for males) increased with decreasing temperature. For both sexes, persistence was greater during the day than during the night. Conclusions The observed body weight effect may point to inter-sexual niche partitioning, since in mink the smallest animals are females and the largest are males. The results may equally point to individual specialism’s, since persistence was also highly variable among individuals. Given the energetic costs involved, the extreme persistence of some animals observed in winter suggests that the costs of occasional prolonged activity in cold water are outweighed by the energetic gains. Analysing dive persistence can provide information on an animal’s physical capabilities for performing multiple dives and may reveal how such behaviour is affected by different conditions. Further development of monitoring and biologging methodology to allow quantification of hunting success, and thus the rewards obtained under alternative scenarios, would be insightful

A combined prediction strategy increases identification of peptides bound with high affinity and stability to porcine MHC class I molecules SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01

Affinity and stability of peptides bound by major histocompatibility complex (MHC) class I molecules are important factors in presentation of peptides to cytotoxic T lymphocytes (CTLs). In silico prediction methods of peptide-MHC binding followed by experimental analysis of peptide-MHC interactions constitute an attractive protocol to select target peptides from the vast pool of viral proteome peptides. We have earlier reported the peptide binding motif of the porcine MHC-I molecules SLA-1*04:01 and SLA-2*04:01, identified by an ELISA affinity-based positional scanning combinatorial peptide library (PSCPL) approach. Here, we report the peptide binding motif of SLA-3*04:01 and combine two prediction methods and analysis of both peptide binding affinity and stability of peptide-MHC complexes to improve rational peptide selection. Using a peptide prediction strategy combining PSCPL binding matrices and in silico prediction algorithms (NetMHCpan), peptide ligands from a repository of 8900 peptides were predicted for binding to SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01 and validated by affinity and stability assays. From the pool of predicted peptides for SLA-1*04:01, SLA-2*04:01, and SLA-3*04:01, a total of 71, 28, and 38 % were binders with affinities below 500 nM, respectively. Comparison of peptide-SLA binding affinity and complex stability showed that peptides of high affinity generally, but not always, produce complexes of high stability. In conclusion, we demonstrate how state-of-the-art prediction and in vitro immunology tools in combination can be used for accurate selection of peptides for MHC class I binding, hence providing an expansion of the field of peptide-MHC analysis also to include pigs as a livestock experimental model.Fil: Pedersen, Lasse Eggers. Technical University of Denmark; DinamarcaFil: Rasmussen, Michael. Universidad de Copenhagen; DinamarcaFil: Harndahl, Mikkel. Universidad de Copenhagen; DinamarcaFil: Nielsen, Morten. Technical University of Denmark; Dinamarca. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús) | Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas (subsede Chascomús); ArgentinaFil: Buus, Søren. Universidad de Copenhagen; DinamarcaFil: Jungersen, Gregers. Technical University of Denmark; Dinamarc