New Phylogenetic Markov Models for Inapplicable Morphological Characters.

This article proposes new Markov models for phylogenetic inference with anatomically dependent (inapplicable) morphological characters. The proposed models can explicitly model an anatomical dependency in which one or several characters are allowed to evolve only within a specific state of the hierarchically upstream character. The new models come up in two main types depending on the type of character hierarchy. The functions for constructing custom character hierarchies are provided in the R package rphenoscate. The performance of the new models is assessed using theory and simulations. This article provides practical recommendations for using the new models in Bayesian phylogenetic inference with RevBayes. [Bayesian; inapplicable characters; likelihood; Markov models; morphology; parsimony; RevBayes.].

Formalizing Invertebrate Morphological Data: A Descriptive Model for Cuticle-Based Skeleto-Muscular Systems, an Ontology for Insect Anatomy, and their Potential Applications in Biodiversity Research and Informatics.

The spectacular radiation of insects has produced a stunning diversity of phenotypes. During the past 250 years, research on insect systematics has generated hundreds of terms for naming and comparing them. In its current form, this terminological diversity is presented in natural language and lacks formalization, which prohibits computer-assisted comparison using semantic web technologies. Here we propose a Model for Describing Cuticular Anatomical Structures (MoDCAS) which incorporates structural properties and positional relationships for standardized, consistent, and reproducible descriptions of arthropod phenotypes. We applied the MoDCAS framework in creating the ontology for the Anatomy of the Insect Skeleto-Muscular system (AISM). The AISM is the first general insect ontology that aims to cover all taxa by providing generalized, fully logical, and queryable, definitions for each term. It was built using the Ontology Development Kit (ODK), which maximizes interoperability with Uberon (Uberon multispecies anatomy ontology) and other basic ontologies, enhancing the integration of insect anatomy into the broader biological sciences. A template system for adding new terms, extending, and linking the AISM to additional anatomical, phenotypic, genetic, and chemical ontologies is also introduced. The AISM is proposed as the backbone for taxon-specific insect ontologies and has potential applications spanning systematic biology and biodiversity informatics, allowing users to: 1) use controlled vocabularies and create semiautomated computer-parsable insect morphological descriptions; 2) integrate insect morphology into broader fields of research, including ontology-informed phylogenetic methods, logical homology hypothesis testing, evo-devo studies, and genotype to phenotype mapping; and 3) automate the extraction of morphological data from the literature, enabling the generation of large-scale phenomic data, by facilitating the production and testing of informatic tools able to extract, link, annotate, and process morphological data. This descriptive model and its ontological applications will allow for clear and semantically interoperable integration of arthropod phenotypes in biodiversity studies.

Novel Conductive Polymer Composite PEDOT:PSS/Bovine Serum Albumin for Microbial Bioelectrochemical Devices.

A novel conductive composite based on PEDOT:PSS, BSA, and Nafion for effective immobilization of acetic acid bacteria on graphite electrodes as part of biosensors and microbial fuel cells has been proposed. It is shown that individual components in the composite do not have a significant negative effect on the catalytic activity of microorganisms during prolonged contact. The values of heterogeneous electron transport constants in the presence of two types of water-soluble mediators were calculated. The use of the composite as part of a microbial biosensor resulted in an electrode operating for more than 140 days. Additional modification of carbon electrodes with nanomaterial allowed to increase the sensitivity to glucose from 1.48 to 2.81 µA × mM-1 × cm-2 without affecting the affinity of bacterial enzyme complexes to the substrate. Cells in the presented composite, as part of a microbial fuel cell based on electrodes from thermally expanded graphite, retained the ability to generate electricity for more than 120 days using glucose solution as well as vegetable extract solutions as carbon sources. The obtained data expand the understanding of the composition of possible matrices for the immobilization of Gluconobacter bacteria and may be useful in the development of biosensors and biofuel cells.

The Invariant Nature of a Morphological Character and Character State: Insights from Gene Regulatory Networks.

What constitutes a discrete morphological character versus character state has been long discussed in the systematics literature but the consensus on this issue is still missing. Different methods of classifying organismal features into characters and character states (CCSs) can dramatically affect the results of phylogenetic analyses. Here, I show that, in the framework of Markov models, the modular structure of the gene regulatory network (GRN) underlying trait development, and the hierarchical nature of GRN evolution, essentially remove the distinction between morphological CCS, thus endowing the CCS with an invariant property with respect to each other. This property allows the states of one character to be represented as several individual characters and vice versa. In practice, this means that a phenotype can be encoded using a set of characters or just one complex character with numerous states. The representation of a phenotype using one complex character can be implemented in Markov models of trait evolution by properly structuring transition rate matrix.

Integration of Anatomy Ontologies and Evo-Devo Using Structured Markov Models Suggests a New Framework for Modeling Discrete Phenotypic Traits.

Modeling discrete phenotypic traits for either ancestral character state reconstruction or morphology-based phylogenetic inference suffers from ambiguities of character coding, homology assessment, dependencies, and selection of adequate models. These drawbacks occur because trait evolution is driven by two key processes-hierarchical and hidden-which are not accommodated simultaneously by the available phylogenetic methods. The hierarchical process refers to the dependencies between anatomical body parts, while the hidden process refers to the evolution of gene regulatory networks (GRNs) underlying trait development. Herein, I demonstrate that these processes can be efficiently modeled using structured Markov models (SMM) equipped with hidden states, which resolves the majority of the problems associated with discrete traits. Integration of SMM with anatomy ontologies can adequately incorporate the hierarchical dependencies, while the use of the hidden states accommodates hidden evolution of GRNs and substitution rate heterogeneity. I assess the new models using simulations and theoretical synthesis. The new approach solves the long-standing "tail color problem," in which the trait is scored for species with tails of different colors or no tails. It also presents a previously unknown issue called the "two-scientist paradox," in which the nature of coding the trait and the hidden processes driving the trait's evolution are confounded; failing to account for the hidden process may result in a bias, which can be avoided by using hidden state models. All this provides a clear guideline for coding traits into characters. This article gives practical examples of using the new framework for phylogenetic inference and comparative analysis.

Experimental study of the transmission of low-frequency acoustic waves through a water-air interface.

The effect of the anomalous transparency of the water-air interface on low-frequency acoustic waves is investigated. The effect is an abnormal increase in the amount of energy that passes from water to air. This effect is manifested if the source of the acoustic waves is located at a distance less than the wavelength from the water-air interface. According to the mathematical models of Godin and Brekhovskikh, this effect is based on the properties of inhomogeneous plane waves. The results of the measurement of the pressure transmission coefficient for a spherical source are given in this article, and the conditions of the laboratory experiment are briefly described. Graphs showing the dependence of the transmission coefficient on the frequency of source radiation are provided. Oscillograms that indirectly confirm the presence of inhomogeneous plane waves are also provided. The results of the experiments are in good agreement with the theoretical calculations of Godin and Brekhovskikh. The article briefly discusses possible ways of applying the anomalous transparency effect in two real problems: transferring information from a submarine to an aircraft and monitoring underwater seismic activity.

Multigene phylogenetic analysis redefines dung beetles relationships and classification (Coleoptera: Scarabaeidae: Scarabaeinae).

BACKGROUND: Dung beetles (subfamily Scarabaeinae) are popular model organisms in ecology and developmental biology, and for the last two decades they have experienced a systematics renaissance with the adoption of modern phylogenetic approaches. Within this period 16 key phylogenies and numerous additional studies with limited scope have been published, but higher-level relationships of this pivotal group of beetles remain contentious and current classifications contain many unnatural groupings. The present study provides a robust phylogenetic framework and a revised classification of dung beetles. RESULTS: We assembled the so far largest molecular dataset for dung beetles using sequences of 8 gene regions and 547 terminals including the outgroup taxa. This dataset was analyzed using Bayesian, maximum likelihood and parsimony approaches. In order to test the sensitivity of results to different analytical treatments, we evaluated alternative partitioning schemes based on secondary structure, domains and codon position. We assessed substitution models adequacy using Bayesian framework and used these results to exclude partitions where substitution models did not adequately depict the processes that generated the data. We show that exclusion of partitions that failed the model adequacy evaluation has a potential to improve phylogenetic inference, but efficient implementation of this approach on large datasets is problematic and awaits development of new computationally advanced software. In the class Insecta it is uncommon for the results of molecular phylogenetic analysis to lead to substantial changes in classification. However, the results presented here are congruent with recent morphological studies and support the largest change in dung beetle systematics for the last 50 years. Here we propose the revision of the concepts for the tribes Deltochilini (Canthonini), Dichotomiini and Coprini; additionally, we redefine the tribe Sisyphini. We provide and illustrate synapomorphies and diagnostic characters supporting the new concepts to facilitate diagnosability of the redefined tribes. As a result of the proposed changes a large number of genera previously assigned to these tribes are now left outside the redefined tribes and are treated as incertae sedis. CONCLUSIONS: The present study redefines dung beetles classification and gives new insight into their phylogeny. It has broad implications for the systematics as well as for various ecological and evolutionary analyses in dung beetles.

Phylogenetics and biogeography of the dung beetle genus Onthophagus inferred from mitochondrial genomes.

Phylogenetic relationships of dung beetles in the tribe Onthophagini, including the species-rich, cosmopolitan genus Onthophagus, were inferred using whole mitochondrial genomes. Data were generated by shotgun sequencing of mixed genomic DNA from >100 individuals on 50% of an Illumina MiSeq flow cell. Genome assembly of the mixed reads produced contigs of 74 (nearly) complete mitogenomes. The final dataset included representatives of Onthophagus from all biogeographic regions, closely related genera of Onthophagini, and the related tribes Onitini and Oniticellini. The analysis defined four major clades of Onthophagini, which was paraphyletic for Oniticellini, with Onitini as sister group to all others. Several (sub)genera considered as members of Onthophagus in the older literature formed separate deep lineages. All New World species of Onthophagus formed a monophyletic group, and the Australian taxa are confined to a single or two closely related clades, one of which forms the sister group of the New World species. Dating the tree by constraining the basal splits with existing calibrations of Scarabaeoidea suggests an origin of Onthophagini sensu lato in the Eocene and a rapid spread from an African ancestral stock into the Oriental region, and secondarily to Australia and the Americas at about 20-24 Mya. The successful assembly of mitogenomes and the well-supported tree obtained from these sequences demonstrates the power of shotgun sequencing from total genomic DNA of species pools as an efficient tool in genus-level phylogenetics.

Towards computable taxonomic knowledge: Leveraging nanopublications for sharing new synonyms in the Madagascan genus Helictopleurus (Coleoptera, Scarabaeinae).

Background: Numerous taxonomic studies have focused on the dung beetle genus Helictopleurus d'Orbigny, 1915, endemic to Madagascar. However, this genus stilll needs a thorough revision. Semantic technologies, such as nanopublications, hold the potential to enhance taxonomy by transforming how data are published and analysed. This paper evaluates the effectiveness of nanopublications in establishing synonyms within the genus Helictopleurus. New information: In this study, we identify four new synonyms within Helictopleurus: H.rudicollis (Fairmaire, 1898) = H.hypocrita Balthasar, 1941 syn. nov.; H.vadoni Lebis, 1960 = H.perpunctatus Balthasar, 1963 syn. nov.; H.halffteri Balthasar, 1964 = H.dorbignyi Montreuil, 2005 syn. nov.; H.clouei (Harold, 1869) = H.gibbicollis (Fairmaire, 1895) syn. nov. Helictopleurus may have a significantly larger number of synonyms than currently known, indicating potentially inaccurate estimates about its recent extinction.We also publish the newly-established synonyms as nanopublications, which are machine-readable data snippets accessible online. Additionally, we explore the utility of nanopublications in taxonomy and demonstrate their practical use with an example query for data extraction.

Computable species descriptions and nanopublications: applying ontology-based technologies to dung beetles (Coleoptera, Scarabaeinae).

Background: Taxonomy has long struggled with analysing vast amounts of phenotypic data due to computational and accessibility challenges. Ontology-based technologies provide a framework for modelling semantic phenotypes that are understandable by computers and compliant with FAIR principles. In this paper, we explore the use of Phenoscript, an emerging language designed for creating semantic phenotypes, to produce computable species descriptions. Our case study centers on the application of this approach to dung beetles (Coleoptera, Scarabaeinae). New information: We illustrate the effectiveness of Phenoscript for creating semantic phenotypes. We also demonstrate the ability of the Phenospy python package to automatically translate Phenoscript descriptions into natural language (NL), which eliminates the need for writing traditional NL descriptions. We introduce a computational pipeline that streamlines the generation of semantic descriptions and their conversion to NL. To demonstrate the power of the semantic approach, we apply simple semantic queries to the generated phenotypic descriptions. This paper addresses the current challenges in crafting semantic species descriptions and outlines the path towards future improvements. Furthermore, we discuss the promising integration of semantic phenotypes and nanopublications, as emerging methods for sharing scientific information. Overall, our study highlights the pivotal role of ontology-based technologies in modernising taxonomy and aligning it with the evolving landscape of big data analysis and FAIR principles.

Microbial Biofilms: Features of Formation and Potential for Use in Bioelectrochemical Devices.

Microbial biofilms present one of the most widespread forms of life on Earth. The formation of microbial communities on various surfaces presents a major challenge in a variety of fields, including medicine, the food industry, shipping, etc. At the same time, this process can also be used for the benefit of humans-in bioremediation, wastewater treatment, and various biotechnological processes. The main direction of using electroactive microbial biofilms is their incorporation into the composition of biosensor and biofuel cells This review examines the fundamental knowledge acquired about the structure and formation of biofilms, the properties they have when used in bioelectrochemical devices, and the characteristics of the formation of these structures on different surfaces. Special attention is given to the potential of applying the latest advances in genetic engineering in order to improve the performance of microbial biofilm-based devices and to regulate the processes that take place within them. Finally, we highlight possible ways of dealing with the drawbacks of using biofilms in the creation of highly efficient biosensors and biofuel cells.

Effect of "ColdArc" WAAM Regime and Arc Torch Weaving on Microstructure and Properties of As-Built and Subtransus Quenched Ti-6Al-4V.

Defect-free thin-walled samples were built using wire arc additive manufacturing (WAAM) combined with the "coldArc" deposition technique by feeding a Ti-6Al-4V welding wire and using two deposition strategies, namely with and without the welding torch weaving. The microstructures formed in these samples were examined in relation to mechanical characteristics. The arc torch weaving at 1 Hz allowed us to interfere with the epitaxial growth of the ß-Ti columnar grains and, thus, obtain them a lower aspect ratio. Upon cooling, the α/α'+ß structure was formed inside the former ß-Ti grains, and this structure proved to be more uniform as compared to that of the samples built without the weaving. The subtransus quenching of the samples in water did not have any effect on the structure and properties of samples built with the arc torch weaving, whereas a more uniform grain structure was formed in the sample built without weaving. Quenching resulted also in a reduction in the relative elongation by 30% in both cases.

Micron- and Nanosized Alloy Particles Made by Electric Explosion of W/Cu-Zn and W/Cu/Ni-Cr Intertwined Wires for 3D Extrusion Feedstock.

A novel approach to electric explosion of intertwined wires to obtain homogeneous powder mixtures intended for preparing feedstock for extrusion 3D printing has been applied. The powder were composed of spherical micron- and nano-sized W/Cu particles in-situ alloyed by Zn and Ni during electric explosion of intertwined dissimilar metal wires is offered. The mean particle size measured by micron-sized particles was not more than 20 µm. The average number size of these particles was 3 µm and it was dependent on the energy input. The powders contained phases such as α-W, ß-W/W3O as well as FCC α-Cu(Zn) and α-Cu(Ni) solid solutions with the crystalline lattice parameters 3.629 and 3.61 A, respectively.

Evidence of Tribological Adaptation Controlled by Tribosynthesis of FeWO4 on an WC-Reinforced Electron Beam M2 Steel Coating Rubbed against a HSS Disk in a Range of Sliding Speeds.

In the present work, the tribological experiments on sliding the electron beam composite M2+WC coating have been carried out with characterization of the sample microstructures and phases both before and after the testing using metallography, SEM, EDS, and XRD. The sliding in the speed range 0.8-3.6 m/s resulted in simultaneous reduction in both wear rate and coefficient of friction with the sliding speed. Investigations showed that such a tribological adaptation was due to the tribochemical generation of lubricative FeWO4 and Fe2WO6 mixed oxides and the generation of a mechanically mixed composite layer on the worn surfaces that consisted of carbide fragments, an oxidized metal matrix, and was lubricated by in-situ formed mixed iron-tungsten oxides.

In-Situ Al-Mg Alloy Base Composite Reinforced by Oxides and Intermetallic Compounds Resulted from Decomposition of ZrW2O8 during Multipass Friction Stir Processing.

In the presented work, the effect of friction stir processing admixing the zirconium tungstate ZrW2O8 powder on the microstructure, mechanical and tribological properties of the AA5056 Al-Mg alloy stir zone has been studied. The FSP resulted in obtaining dense composite stir zones where α-ZrW2O8 underwent the following changes: (i) high-temperature transformation into metastable ß'-ZrW2O8 and (ii) decomposition into WO3 and ZrO2 oxides followed by the formation of intermetallic compounds WAl12 and ZrAl3. These precipitates served as reinforcing phases to improve mechanical and tribological characteristics of the obtained fine-grained composites. The reduced values of wear rate and friction coefficient are due to the combined action the Hall-Petch mechanism and reinforcement by the decomposition products, including Al2O3, ZrO2, ß'-ZrW2O8 and intermetallic compounds such as WAl12 and ZrAl3. Potential applications of the above-discussed composites maybe related to their improved tribological characteristics, for example in aerospace and vehicle-building industries.

Amplicon metagenomics of dung beetles (Coleoptera, Scarabaeidae, Scarabaeinae) as a proxy for lemur (Primates, Lemuroidea) studies in Madagascar.

Dung beetles (Scarabaeidae, Scarabaeinae) are among the most cost-effective and informative biodiversity indicator groups, conveying rich information about the status of habitats and faunas of an area. Yet their use for monitoring the mammal species, that are the main providers of the food for the dung beetles, has only recently been recognized. In the present work, we studied the diet of four endemic Madagascan dung beetles (Helictopleurusfissicollis (Fairmaire), H.giganteus (Harold), Nanosagaboides (Boucomont), and Epilissussplendidus Fairmaire) using high-throughput sequencing and amplicon metagenomics. For all beetle species, the ⅔-¾ of reads belonged to humans, suggesting that human feces are the main source of food for the beetles in the examined areas. The second most abundant were the reads of the cattle (Bostaurus Linnaeus). We also found lower but significant number of reads of six lemur species belonging to three genera. Our sampling localities agree well with the known ranges of these lemur species. The amplicon metagenomics method proved a promising tool for the lemur inventories in Madagascar.

Conductive Polymers and Their Nanocomposites: Application Features in Biosensors and Biofuel Cells.

Conductive polymers and their composites are excellent materials for coupling biological materials and electrodes in bioelectrochemical systems. It is assumed that their relevance and introduction to the field of bioelectrochemical devices will only grow due to their tunable conductivity, easy modification, and biocompatibility. This review analyzes the main trends and trends in the development of the methodology for the application of conductive polymers and their use in biosensors and biofuel elements, as well as describes their future prospects. Approaches to the synthesis of such materials and the peculiarities of obtaining their nanocomposites are presented. Special emphasis is placed on the features of the interfaces of such materials with biological objects.

Macro- and Microstructure of In Situ Composites Prepared by Friction Stir Processing of AA5056 Admixed with Copper Powders.

This paper is devoted to using multi-pass friction stir processing (FSP) for admixing 1.5 to 30 vol.% copper powders into an AA5056 matrix for the in situ fabrication of a composite alloy reinforced by Al-Cu intermetallic compounds (IMC). Macrostructurally inhomogeneous stir zones have been obtained after the first FSP passes, the homogeneity of which was improved with the following FSP passes. As a result of stirring the plasticized AA5056, the initial copper particle agglomerates were compacted into large copper particles, which were then simultaneously saturated by aluminum. Microstructural investigations showed that various phases such as α-Al(Cu), α-Cu(Al) solid solutions, Cu3Al and CuAl IMCs, as well as both S and S'-Al2CuMg precipitates have been detected in the AA5056/Cu stir zone, depending upon the concentration of copper and the number of FSP passes. The number of IMCs increased with the number of FSP passes, enhancing microhardness by 50-55%. The effect of multipass FSP on tensile strength, yield stress and strain-to-fracture was analyzed.

Microstructures and Phases in Electron Beam Additively Manufactured Ti-Al-Mo-Zr-V/CuAl9Mn2 Alloy.

Electron beam additive manufacturing from dissimilar metal wires was used to intermix 5, 10 and 15 vol.% of Ti-Al-Mo-Z-V titanium alloy with CuAl9Mn2 bronze on a stainless steel substrate. The resulting alloys were subjected to investigations into their microstructural, phase and mechanical characteristics. It was shown that different microstructures were formed in an alloy containing 5 vol.% titanium alloy, as well as others containing 10 and 15 vol.%. The first was characterized by structural components such as solid solution, eutectic intermetallic compound TiCu2Al and coarse grains of γ1-Al4Cu9. It had enhanced strength and demonstrated steady oxidation wear in sliding tests. The other two alloys also contained large flower-like Ti(Cu,Al)2 dendrites that appeared due to the thermal decomposition of γ1-Al4Cu9. This structural transformation resulted in catastrophic embrittlement of the composite and changing of wear mechanism from oxidative to abrasive.