Vortex knots in a Bose-Einstein condensate

We present a method for numerically building a vortex knot state in the superfluid wave-function of a Bose-Einstein condensate. We integrate in time the governing Gross-Pitaevskii equation to determine evolution and stability of the two (topologically) simplest vortex knots which can be wrapped over a torus. We find that the velocity of a vortex knot depends on the ratio of poloidal and toroidal radius: for smaller ratio, the knot travels faster. Finally, we show how unstable vortex knots break up into vortex rings.Comment: 18 pages, 15 figures, 1 tabl

Taxonomy Based on Science is Necessary for Global Conservation

Taxonomy is a scientific discipline that has provided the universal naming and classification system of biodiversity for centuries and continues effectively to accommodate new knowledge. A recent publication by Garnett and Christidis (Garnett ST, Christidis L. Taxonomy anarchy hampers conservation. Nature. 2017; 546(7656):25±27. https://doi.org/10.1038/546025a) expressed concerns regarding the difficulty that taxonomic changes represent for conservation efforts and proposed the establishment of a system to govern taxonomic changes. Their proposal to restrict the freedom of taxonomic action through governing subcommittees that would review taxonomic papers for compliance and their assertion that the scientific community\u27s failure to govern taxonomy threatens the effectiveness of global efforts to halt biodiversity loss, damages the credibility of science, and is expensive to society are flawed in many respects. They also assert that the lack of governance of taxonomy damages conservation efforts, harms the credibility of science, and is costly to society. Despite its fairly recent release, Garnett and Christidis\u27 proposition has already been rejected by a number of colleagues. Herein, we contribute to the conversation between taxonomists and conservation biologists aiming to clarify some misunderstandings and issues in the proposition by Garnett and Christidis. Placing governance over the science of taxonomy blurs the distinction between taxonomy and nomenclature. Garnett and Christidis’s proposal is far-reaching but represents a narrow perspective of taxonomy, as utilized by conservation, and reflects an increasingly broad misunderstanding throughout biology of the scientific basis of taxonomy, formalized nomenclature, and the relationship between them. This trend may have resulted from the attenuation of instruction in taxonomic principles and, in particular, nomenclature at many universities, in part because of a shift in research priorities away from taxonomy. Garnett and Christidis assert that an “assumption that species are fixed entities underpins every international agreement on biodiversity conservation.” This assumption demonstrates a fundamental misunderstanding of taxonomy and the evolving view of what species represent. The essential features of science include documenting natural patterns and processes, developing and testing hypotheses, and refining existing ideas and descriptions of nature based on new data and insights. Taxonomy, the science of recognizing and delimiting species, adheres to these fundamental principles. Discoveries of new organisms together with advances in methodology continue unabated, leading to a constant reevaluation of the boundaries between taxonomic entities. Species (and higher taxa) comprise related organisms that may be clustered together differently depending on which sets of criteria are emphasized. Hey et al. acknowledge “the inherent ambiguity of species in nature” but point out that “species-related research and conservation efforts can proceed without suffering from, and without fear of, the ambiguity of species.” Through taxonomic research, our understanding of biodiversity and classifications of living organisms will continue to progress. Any system that restricts such progress runs counter to basic scientific principles, which rely on peer review and subsequent acceptance or rejection by the community, rather than third-party regulation. Thiele and Yeates cautioned that such a system “could lead to authoritarianism and a stifling of innovative taxonomic viewpoints. No other hypothesis-driven field of science would accept such a straitjacket”. Taxonomy and associated nomenclature are not without problems. Even with a common set of facts, alternative interpretations of how to classify organisms can lead to differing classifications. However, the science of taxonomy is increasingly rigorous, which can improve the foundation for targeted legislative action regarding species. Taxonomic instability does not affect all taxonomic groups equally. Garnett and Christidis provide examples from mammals and birds, which collectively represent a small fraction

Intermittent dislocation flow in viscoplastic deformation

The viscoplastic deformation (creep) of crystalline materials under constant stress involves the motion of a large number of interacting dislocations. Analytical methods and sophisticated `dislocation-dynamics' simulations have proved very effective in the study of dislocation patterning, and have led to macroscopic constitutive laws of plastic deformation. Yet, a statistical analysis of the dynamics of an assembly of interacting dislocations has not hitherto been performed. Here we report acoustic emission measurements on stressed ice single crystals, the results of which indicate that dislocations move in a scale-free intermittent fashion. This result is confirmed by numerical simulations of a model of interacting dislocations that successfully reproduces the main features of the experiment. We find that dislocations generate a slowly evolving configuration landscape which coexists with rapid collective rearrangements. These rearrangements involve a comparatively small fraction of the dislocations and lead to an intermittent behavior of the net plastic response. This basic dynamical picture appears to be a generic feature in the deformation of many other materials. Moreover, it should provide a framework for discussing fundamental aspects of plasticity, that goes beyond standard mean-field approaches that see plastic deformation as a smooth laminar flow

Most Common Single-Nucleotide Polymorphisms Associated With Rheumatoid Arthritis in Persons of European Ancestry Confer Risk of Rheumatoid Arthritis in African Americans

Objective. Large-scale genetic association studies have identified \u3e20 rheumatoid arthritis (RA) risk alleles among individuals of European ancestry. The influence of these risk alleles has not been comprehensively studied in African Americans. We therefore sought to examine whether these validated RA risk alleles are associated with RA risk in an African American population. Methods. Twenty-seven candidate single-nucleotide polymorphisms (SNPs) were genotyped in 556 autoantibody-positive African Americans with RA and 791 healthy African American control subjects. Odds ratios (ORs) and 95% confidence intervals (95% CIs) for each SNP were compared with previously published ORs for RA patients of European ancestry. We then calculated a composite genetic risk score (GRS) for each individual based on the sum of all risk alleles. Results. Overlap of the ORs and 95% CIs between the European and African American populations was observed for 24 of the 27 candidate SNPs. Conversely, 3 of the 27 SNPs (CCR6 rs3093023, TAGAP rs394581, and TNFAIP3 rs6920220) demonstrated ORs in the opposite direction from those reported for RA patients of European ancestry. The GRS analysis indicated a small but highly significant probability that African American patients relative to control subjects were enriched for the risk alleles validated in European RA patients (P = 0.00005). Conclusion. The majority of RA risk alleles previously validated for RA patients of European ancestry showed similar ORs in our population of African Americans with RA. Furthermore, the aggregate GRS supports the hypothesis that these SNPs are risk alleles for RA in the African American population. Future large-scale genetic studies are needed to validate these risk alleles and identify novel RA risk alleles in African Americans

Excess ribosomal protein production unbalances translation in a model of Fragile X Syndrome

Dysregulated protein synthesis is a core pathogenic mechanism in Fragile X Syndrome (FX). The mGluR Theory of FX predicts that pathological synaptic changes arise from the excessive translation of mRNAs downstream of mGlu1/5 activation. Here, we use a combination of CA1 pyramidal neuron-specific TRAP-seq and proteomics to identify the overtranslating mRNAs supporting exaggerated mGlu1/5 -induced long-term synaptic depression (mGluR-LTD) in the FX mouse model (Fmr1−/y). Our results identify a significant increase in the translation of ribosomal proteins (RPs) upon mGlu1/5 stimulation that coincides with a reduced translation of long mRNAs encoding synaptic proteins. These changes are mimicked and occluded in Fmr1−/y neurons. Inhibiting RP translation significantly impairs mGluR-LTD and prevents the length-dependent shift in the translating population. Together, these results suggest that pathological changes in FX result from a length-dependent alteration in the translating population that is supported by excessive RP translation

How not to describe a species: lessons from a tangle of anacondas (Boidae: Eunectes Wagler, 1830)

A recent revision of the anacondas (Serpentes: Boidae: Eunectes), with the description of a new species of green anaconda, generated extensive publicity, but also provoked considerable controversy due to inadequacies of the evidence used and errors in nomenclature. We here use the case of this problematic publication to: (i) highlight common issues affecting species delimitations, especially an over-reliance on mitochondrial DNA data, and reiterate best practices; (ii) reanalyse the data available for anacondas to establish the true current state of knowledge and to highlight lines of further research; and (iii) analyse the nomenclatural history and status of the genus. While our analysis reveals significant morphological variation in both green and yellow anacondas, denser sampling and an analysis of informative nuclear markers are required for meaningful species delimitation in Eunectes. Tracing the history of name-bearing types establishes Trinidad as the type locality for Boa murina Linnaeus, 1758 and allows identification of the extant lectotype for the species. Finally, we emphasize the responsibility of both journals and authors to ensure that published taxonomic work meets the burden of evidence required to substantiate new species descriptions and that species are named in compliance with the rules of zoological nomenclature

Evolutionary and functional history of the Escherichia coli K1 capsule

Escherichia coli is a leading cause of invasive bacterial infections in humans. Capsule polysaccharide has an important role in bacterial pathogenesis, and the K1 capsule has been firmly established as one of the most potent capsule types in E. coli through its association with severe infections. However, little is known about its distribution, evolution and functions across the E. coli phylogeny, which is fundamental to elucidating its role in the expansion of successful lineages. Using systematic surveys of invasive E. coli isolates, we show that the K1-cps locus is present in a quarter of bloodstream infection isolates and has emerged in at least four different extraintestinal pathogenic E. coli (ExPEC) phylogroups independently in the last 500 years. Phenotypic assessment demonstrates that K1 capsule synthesis enhances E. coli survival in human serum independent of genetic background, and that therapeutic targeting of the K1 capsule re-sensitizes E. coli from distinct genetic backgrounds to human serum. Our study highlights that assessing the evolutionary and functional properties of bacterial virulence factors at population levels is important to better monitor and predict the emergence of virulent clones, and to also inform therapies and preventive medicine to effectively control bacterial infections whilst significantly lowering antibiotic usage

Priorities for health economic methodological research: Results of an expert consultation

Background: The importance of economic evaluation in decision making is growing with increasing budgetary pressures on health systems. Diverse economic evidence is available for a range of interventions across national contexts within Europe, but little attention has been given to identifying evidence gaps that, if filled, could contribute to more efficient allocation of resources. One objective of the Research Agenda for Health Economic Evaluation project is to determine the most important methodological evidence gaps for the ten highest burden conditions in the European Union (EU), and to suggest ways of filling these gaps. Methods: The highest burden conditions in the EU by Disability Adjusted Life Years were determined using the Global Burden of Disease study. Clinical interventions were identified for each condition based on published guidelines, and economic evaluations indexed in MEDLINE were mapped to each intervention. A panel of public health and health economics experts discussed the evidence during a workshop and identified evidence gaps. Results: The literature analysis contributed to identifying cross-cutting methodological and technical issues, which were considered by the expert panel to derive methodological research priorities. Conclusions: The panel suggests a research agenda for health economics which incorporates the use of real-world evidence in the assessment of new and existing interventions; increased understanding of cost-effectiveness according to patient characteristics beyond the “-omics” approach to inform both investment and disinvestment decisions; methods for assessment of complex interventions; improved cross-talk between economic evaluations from health and other sectors; early health technology assessment; and standardized, transferable approaches to economic modeling