Spontaneous symmetry breaking of binary fields in a nonlinear double-well structure

We introduce a one-dimensional two-component system with the self-focusing cubic nonlinearity concentrated at a symmetric set of two spots. Effects of the spontaneous symmetry breaking (SSB) of localized modes were previously studied in the single-component version of this system. In this work, we study the evolution (in the configuration space of the system) and SSB scenarios for two-component modes of three generic types, as concerns the spatial symmetry of each component: symmetric-symmetric (Sm-Sm), antisymmetric-antisymmetric (AS-AS), and symmetric-antisymmetric (S-AS) ones. In the limit case of the nonlinear potential represented by two $$-functions, solutions are obtained in a semi-analytical form. They feature novel properties, in comparison with the previously studied single-component model. In particular, the SSB of antisymmetric modes is possible solely in the two-component system, and, obviously, S-AS states exist only in the two-component system too. In the general case of the symmetric pair of finite-width nonlinear potential wells, evolution scenarios are very complex. In this case, new results are reported, first, for the single-component model. These are pairs of broken-antisymmetry modes, and of twin-peak symmetric ones, which are generated by saddle-mode bifurcations separated from the transformations previously studied in the the single-component setting. With regard to these findings, complex scenarios of the evolution of the two-component solution families are realized in terms of links connecting pairs of modes of three simplest types: (A) two-component ones with unbroken symmetries; (B) single-component modes featuring density peaks in both potential wells; (C) single-component modes which are trapped, essentially, in a single well.Comment: 22 pages, 18 figures; Physica D, in pres

Beliefs, benefits, barriers, attitude, intake and knowledge about peanuts and tree nuts among WIC participants in eastern North Carolina

The objective of this study was to assess beliefs (e.g. advantages, disadvantages, benefits, barriers) and knowledge about eating peanuts and tree nuts. Personal interviews based on the Theory of Planned Behavior were conducted to elicit beliefs about eating nuts. Then, a cross-sectional survey was administered to WIC participants from one county in North Carolina. One-hundred-twenty-four WIC participants (mean (SD) age=28.39 (8.09) completed the study. Most were Caucasian (51.6%) females (96%). About one third believed that eating nuts may help to lower cholesterol level. However, only about one forth believed that nuts can lower a risk of a heart attack or diabetes. More than one third believed that eating nuts will cause weight gain. The knowledge of respondents' about nutrient content of nuts was low with correct answers to most questions about 20% or below. The mean (SD) positive attitude, negative attitude, benefits and barriers scores, based on a range from 1 to 5, were 2.53 (0.91), 3.25 (0.89), 2.97 (0.85) and 2.90 (0.76), respectively. WIC participants' beliefs regarding the health effects of nuts are inconsistent with the most recent research findings. They are in a need to education about benefits of eating nuts

Bayesian Matrix Completion for Hypothesis Testing

High-throughput screening (HTS) is a well-established technology that rapidly and efficiently screens thousands of chemicals for potential toxicity. Massive testing using HTS primarily aims to differentiate active vs inactive chemicals for different types of biological endpoints. However, even using high-throughput technology, it is not feasible to test all possible combinations of chemicals and assay endpoints, resulting in a majority of missing combinations. Our goal is to derive posterior probabilities of activity for each chemical by assay endpoint combination, addressing the sparsity of HTS data. We propose a Bayesian hierarchical framework, which borrows information across different chemicals and assay endpoints in a low-dimensional latent space. This framework facilitates out-of-sample prediction of bioactivity potential for new chemicals not yet tested. Furthermore, this paper makes a novel attempt in toxicology to simultaneously model heteroscedastic errors as well as a nonparametric mean function. It leads to a broader definition of activity whose need has been suggested by toxicologists. Simulation studies demonstrate that our approach shows superior performance with more realistic inferences on activity than current standard methods. Application to an HTS data set identifies chemicals that are most likely active for two disease outcomes: neurodevelopmental disorders and obesity. Code is available on Github

Fast Growth Increases the Selective Advantage of a Mutation Arising Recurrently during Evolution under Metal Limitation

Understanding the evolution of biological systems requires untangling the molecular mechanisms that connect genetic and environmental variations to their physiological consequences. Metal limitation across many environments, ranging from pathogens in the human body to phytoplankton in the oceans, imposes strong selection for improved metal acquisition systems. In this study, we uncovered the genetic and physiological basis of adaptation to metal limitation using experimental populations of Methylobacterium extorquens AM1 evolved in metal-deficient growth media. We identified a transposition mutation arising recurrently in 30 of 32 independent populations that utilized methanol as a carbon source, but not in any of the 8 that utilized only succinate. These parallel insertion events increased expression of a novel transporter system that enhanced cobalt uptake. Such ability ensured the production of vitamin B12, a cobalt-containing cofactor, to sustain two vitamin B12–dependent enzymatic reactions essential to methanol, but not succinate, metabolism. Interestingly, this mutation provided higher selective advantages under genetic backgrounds or incubation temperatures that permit faster growth, indicating growth-rate–dependent epistatic and genotype-by-environment interactions. Our results link beneficial mutations emerging in a metal-limiting environment to their physiological basis in carbon metabolism, suggest that certain molecular features may promote the emergence of parallel mutations, and indicate that the selective advantages of some mutations depend generically upon changes in growth rate that can stem from either genetic or environmental influences

A year of genomic surveillance reveals how the SARS-CoV-2 pandemic unfolded in Africa.

The progression of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic in Africa has so far been heterogeneous, and the full impact is not yet well understood. In this study, we describe the genomic epidemiology using a dataset of 8746 genomes from 33 African countries and two overseas territories. We show that the epidemics in most countries were initiated by importations predominantly from Europe, which diminished after the early introduction of international travel restrictions. As the pandemic progressed, ongoing transmission in many countries and increasing mobility led to the emergence and spread within the continent of many variants of concern and interest, such as B.1.351, B.1.525, A.23.1, and C.1.1. Although distorted by low sampling numbers and blind spots, the findings highlight that Africa must not be left behind in the global pandemic response, otherwise it could become a source for new variants

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance.

Investment in severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing in Africa over the past year has led to a major increase in the number of sequences that have been generated and used to track the pandemic on the continent, a number that now exceeds 100,000 genomes. Our results show an increase in the number of African countries that are able to sequence domestically and highlight that local sequencing enables faster turnaround times and more-regular routine surveillance. Despite limitations of low testing proportions, findings from this genomic surveillance study underscore the heterogeneous nature of the pandemic and illuminate the distinct dispersal dynamics of variants of concern-particularly Alpha, Beta, Delta, and Omicron-on the continent. Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve while the continent faces many emerging and reemerging infectious disease threats. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

The evolving SARS-CoV-2 epidemic in Africa: Insights from rapidly expanding genomic surveillance

INTRODUCTION Investment in Africa over the past year with regard to severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) sequencing has led to a massive increase in the number of sequences, which, to date, exceeds 100,000 sequences generated to track the pandemic on the continent. These sequences have profoundly affected how public health officials in Africa have navigated the COVID-19 pandemic. RATIONALE We demonstrate how the first 100,000 SARS-CoV-2 sequences from Africa have helped monitor the epidemic on the continent, how genomic surveillance expanded over the course of the pandemic, and how we adapted our sequencing methods to deal with an evolving virus. Finally, we also examine how viral lineages have spread across the continent in a phylogeographic framework to gain insights into the underlying temporal and spatial transmission dynamics for several variants of concern (VOCs). RESULTS Our results indicate that the number of countries in Africa that can sequence the virus within their own borders is growing and that this is coupled with a shorter turnaround time from the time of sampling to sequence submission. Ongoing evolution necessitated the continual updating of primer sets, and, as a result, eight primer sets were designed in tandem with viral evolution and used to ensure effective sequencing of the virus. The pandemic unfolded through multiple waves of infection that were each driven by distinct genetic lineages, with B.1-like ancestral strains associated with the first pandemic wave of infections in 2020. Successive waves on the continent were fueled by different VOCs, with Alpha and Beta cocirculating in distinct spatial patterns during the second wave and Delta and Omicron affecting the whole continent during the third and fourth waves, respectively. Phylogeographic reconstruction points toward distinct differences in viral importation and exportation patterns associated with the Alpha, Beta, Delta, and Omicron variants and subvariants, when considering both Africa versus the rest of the world and viral dissemination within the continent. Our epidemiological and phylogenetic inferences therefore underscore the heterogeneous nature of the pandemic on the continent and highlight key insights and challenges, for instance, recognizing the limitations of low testing proportions. We also highlight the early warning capacity that genomic surveillance in Africa has had for the rest of the world with the detection of new lineages and variants, the most recent being the characterization of various Omicron subvariants. CONCLUSION Sustained investment for diagnostics and genomic surveillance in Africa is needed as the virus continues to evolve. This is important not only to help combat SARS-CoV-2 on the continent but also because it can be used as a platform to help address the many emerging and reemerging infectious disease threats in Africa. In particular, capacity building for local sequencing within countries or within the continent should be prioritized because this is generally associated with shorter turnaround times, providing the most benefit to local public health authorities tasked with pandemic response and mitigation and allowing for the fastest reaction to localized outbreaks. These investments are crucial for pandemic preparedness and response and will serve the health of the continent well into the 21st century

Beliefs benefits barriers attitude intake and knowledge about peanuts and tree nuts among WIC participants in eastern North Carolina

The objective of this study was to assess beliefs (e.g. advantages disadvantages benefits barriers) and knowledge about eating peanuts and tree nuts. Personal interviews based on the Theory of Planned Behavior were conducted to elicit beliefs about eating nuts. Then a cross-sectional survey was administered to WIC participants from one county in North Carolina. One-hundred-twenty-four WIC participants (mean (SD) age=28.39 (8.09) completed the study. Most were Caucasian (51.6%) females (96%). About one third believed that eating nuts may help to lower cholesterol level. However only about one forth believed that nuts can lower a risk of a heart attack or diabetes. More than one third believed that eating nuts will cause weight gain. The knowledge of respondents' about nutrient content of nuts was low with correct answers to most questions about 20% or below. The mean (SD) positive attitude negative attitude benefits and barriers scores based on a range from 1 to 5 were 2.53 (0.91) 3.25 (0.89) 2.97 (0.85) and 2.90 (0.76) respectively. WIC participants' beliefs regarding the health effects of nuts are inconsistent with the most recent research findings. They are in a need to education about benefits of eating nuts