Quantifying status and trends from monitoring surveys: application to Pygmy Whitefish (Prosopium coulterii) in Lake Superior

Population assessments of fish species often rely on data from surveys with different objectives such as measuring biodiversity or community dynamics. These surveys often contain spatial-temporal dependencies that can greatly influence conclusions drawn from analyses. Pygmy whitefish (PWF, Prosopium coulterii) populations in Lake Superior were recently assessed as Threatened by the Committee on the Status of Endangered Species in Canada which motivated a thorough analysis of available data to improve our understanding of its population status. The U.S. Geological Survey conducts annual bottom trawl surveys in Lake Superior that commonly captures PWF. We used these data (1989-2018) to model temporal trends in PWF biomass-density and make lake-wide population projections. We used a Bayesian approach, Integrated Nested Laplace Approximation (INLA), and compared the impact of including different random structures on model fit. Inclusion of spatial structure improved model fit and conclusions differed from models omitting random effects. PWF populations have experienced periodic fluctuations in biomass-density since 1989, though 2018 may represent the lowest density in the 30-year time series. Lake-wide biomass was estimated to be 71.5t.

The overlap gap property: A topological barrier to optimizing over random structures

The problem of optimizing over random structures emerges in many areas of science and engineering, ranging from statistical physics to machine learning and artificial intelligence. For many such structures, finding optimal solutions by means of fast algorithms is not known and often is believed not to be possible. At the same time, the formal hardness of these problems in the form of the complexity-theoretic NP-hardness is lacking. A new approach for algorithmic intractability in random structures is described in this article, which is based on the topological disconnectivity property of the set of pairwise distances of near-optimal solutions, called the Overlap Gap Property. The article demonstrates how this property 1) emerges in most models known to exhibit an apparent algorithmic hardness; 2) is consistent with the hardness/tractability phase transition for many models analyzed to the day; and, importantly, 3) allows to mathematically rigorously rule out a large class of algorithms as potential contenders, specifically the algorithms that exhibit the input stability (insensitivity).

The Role of Random Structures in Tissue Formation: From a Viewpoint of Morphogenesis in Stochastic Systems

In this article, we investigate a type of biological tissue formation system with a random structure of reaction or/and diffusion, analyzing the connection with the results obtained in [Rajapakse & Smale, 2017a] for the corresponding deterministic systems and showing the major difference from these results. Interestingly, we find a dynamical phenomenon leading to morphogenesis or emergence in such a system. Also we find their transitions in this system, while only one type of dynamical behavior occurs for the deterministic systems that satisfy typical conditions. Using the stability theory of stochastic systems, we quantitatively elucidate how such a phenomenon is emergent in complex networks with random structures. We believe that our analytical results could be beneficial to understand the underlying mechanisms of complexity-induced functions in tissue formation within real environments.

Determination of Vacancy Formation Energies in Binary UZr Alloys Using Special Quasirandom Structure Methods

The use of predictive models to examine defect production and migration in metallic systems requires a thorough understanding of the energetics of defect formation and migration. In fully miscible alloys, atomistic properties will all have a range of values that are heavily dependent on local atomic configurations. In this work we have used the atomistic simulation tool Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) to investigate the impact of first nearest neighbor configuration on vacancy formation energies at 0 K in γ-U-Zr alloys of varying Zr concentrations. The properties of randomly generated alloy microstructures were also compared with those produced as special quasi-random structures (SQS) using the “mcsqs” code within the Alloy Theoretic Automated Toolkit. Results have confirmed that local configuration can have a significant impact on measured properties and must be considered when characterizing miscible alloy systems. Results also indicated that the generation method of the random structure (i.e., via random species assignment or a method of enforced randomness) does not result in a measurable difference in average vacancy formation energies in miscible U-Zr systems.

Features of the Secondary Structure of BSA – Containing Protein Complexes, Isolated from Milk of High Temperature Processing

Present paper describes features of the component composition in the secondary structure of BSA–containing protein complexes isolated from ultra-pasteurized (UHT), sterilized (SHT) and powdered (DRY) milk. We have found β – sheets to present in all complexes investigated. However, the smallest number of such components have been revealed in samples derived from sterilized milk with less β – sheets in 1621–1626 cm–1 region. The composition study of the complexes originated from UHT milk has shown random coils to be the rarest in them. When considering the structure of the complexes isolated from powdered milk, the α – 310 – heliсes were more characteristic for such samples, then the α – helix. Moreover, during spray–drying, the number of random structures increase with a simultaneous decrease in the number of β – sheets, whereas in UHT – and SHT – processing the number of random structures is inversely proportional to the number of α – helices.

The energy-spectrum of bicompatible sequences

Background Genotype-phenotype maps provide a meaningful filtration of sequence space and RNA secondary structures are particular such phenotypes. Compatible sequences, which satisfy the base-pairing constraints of a given RNA structure, play an important role in the context of neutral evolution. Sequences that are simultaneously compatible with two given structures (bicompatible sequences), are beacons in phenotypic transitions, induced by erroneously replicating populations of RNA sequences. RNA riboswitches, which are capable of expressing two distinct secondary structures without changing the underlying sequence, are one example of bicompatible sequences in living organisms. Results We present a full loop energy model Boltzmann sampler of bicompatible sequences for pairs of structures. The sequence sampler employs a dynamic programming routine whose time complexity is polynomial when assuming the maximum number of exposed vertices, $$\kappa $$ κ , is a constant. The parameter $$\kappa $$ κ depends on the two structures and can be very large. We introduce a novel topological framework encapsulating the relations between loops that sheds light on the understanding of $$\kappa $$ κ . Based on this framework, we give an algorithm to sample sequences with minimum $$\kappa $$ κ on a particular topologically classified case as well as giving hints to the solution in the other cases. As a result, we utilize our sequence sampler to study some established riboswitches. Conclusion Our analysis of riboswitch sequences shows that a pair of structures needs to satisfy key properties in order to facilitate phenotypic transitions and that pairs of random structures are unlikely to do so. Our analysis observes a distinct signature of riboswitch sequences, suggesting a new criterion for identifying native sequences and sequences subjected to evolutionary pressure. Our free software is available at: https://github.com/FenixHuang667/Bifold.