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.

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.

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.

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.

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.

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.

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.

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.].

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.

Gluconobacter Oxydans-Based MFC with PEDOT:PSS/Graphene/Nafion Bioanode for Wastewater Treatment.

Microbial fuel cells (MFCs) are a variety of bioelectrocatalytic devices that utilize the metabolism of microorganisms to generate electric energy from organic matter. This study investigates the possibility of using a novel PEDOT:PSS/graphene/Nafion composite in combination with acetic acid bacteria Gluconobacter oxydans to create a pure culture MFC capable of effective municipal wastewater treatment. The developed MFC was shown to maintain its activity for at least three weeks. The level of COD in municipal wastewater treatment was reduced by 32%; the generated power was up to 81 mW/m2 with a Coulomb efficiency of 40%. Combining the MFC with a DC/DC boost converter increased the voltage generated by two series-connected MFCs from 0.55 mV to 3.2 V. A maximum efficiency was achieved on day 8 of MFC operation and was maintained for a week; capacitors of 6800 µF capacity were fully charged in ~7 min. Thus, G. oxydans cells can become an important part of microbial consortia in MFCs used for treatment of wastewaters with reduced pH.

Aluminum Bronze/Udimet 500 Composites Prepared by Electron-Beam Additive Double-Wire-Feed Manufacturing.

Novel composite CuA19Mn2/Udimet-500 alloy walls with different content of the Udimet 500 were built using electron-beam double-wire-feed additive manufacturing. Intermixing both metals within the melted pool resulted in dissolving nickel and forcing out the aluminum from bronze. The resulting phases were NiAl particles and grains, M23C6/NiAl core/shell particles and Cu-Ni-Al solid solution. Precipitation of these phases resulted in the increased hardness and tensile strength as well as reduced ductility of the composite alloys. Such a hardening resulted in improving the wear resistance as compared to that of source aluminum bronze.

The Effect of Heat Input, Annealing, and Deformation Treatment on Structure and Mechanical Properties of Electron Beam Additive Manufactured (EBAM) Silicon Bronze.

Electron beam additive wire-feed manufacturing of Cu-3wt.%S-0.8wt.%Mn bronze thin wall on a stainless steel substrate has been carried out at heat input levels of 0.19, 0.25, and 0.31 kJ/mm. The microstructures of as-deposited metal ranged from low aspect ratio columnar with equiaxed grain layers to zig-zagged and high aspect ratio columnar, as depended on the heat input. Post-deposition annealing at 900 °C for 6 h resulted in recrystallization of the high aspect ratio columnar grains with further grain growth by boundary migration. Pre-deformation by 10% thickness reduction and then annealing at 900 °C for 6 h also allowed obtaining recrystallized grain structures with less fraction of twin boundaries but higher fraction of high-angle ones, as compared to those of only annealed sample. Pre-deformation and ensuing annealing allowed simultaneous increasing of the ultimate tensile strength and strain-to-fracture.

In Situ Intermetallics-Reinforced Composite Prepared Using Multi-Pass Friction Stir Processing of Copper Powder on a Ti6Al4V Alloy.

Multi-pass friction stir processing (FSP) was used to obtain a titanium alloy/copper hybrid composite layer by intermixing copper powder with a Ti6Al4V alloy. A macrostructurally inhomogeneous stir zone was obtained with both its top and middle parts composed of fine dynamically recrystallized α- and ß-Ti grains, as well as coarse intermetallic compounds (IMCs) of Ti2Cu and TiCu2, respectively. Some ß grains experienced ß â†’ α decomposition with the formation of acicular α-Ti microstructures either inside the former ß-Ti grains or at their grain boundaries. Both types of ß â†’ α decomposition were especially clearly manifested in the vicinity of the Ti2Cu grains, i.e., in the copper-lean regions. The middle part of the stir zone additionally contained large dislocation-free ß-Ti grains that resulted from static recrystallization. Spinodal decomposition, as well as solid-state amorphization of copper-rich ß-Ti grains, were discovered. The FSPed stir zone possessed hardness that was enhanced by 25% as compared to that of the base metal, as well as higher strength, ductility, and wear resistance than those obtained using four-pass FSPed Ti6Al4V.

Modification of thermally expanded graphite and its effect on the properties of the amperometric biosensor.

The work considered the properties of a biosensor based on a novel nanomaterial-modified thermally expanded graphite (TEGM). The main focus was on whether the procedure of additional graphite thermal expansion would affect the electrochemical properties of biosensors based on membrane fractions of acetic acid bacteria Gluconobacter oxydans. Raman spectroscopy, scanning electron microscopy and electrochemical analysis were used for the study. Raman spectra showed that the formation of TEGM led to its stratification into smaller particles and a better orderly layered structure with high "graphenization" degree. Modification of TEG led to the formation of additional cavities into which bacterial cells or bacterial membrane fractions could be immobilized and affect the electrical conductivity of the biosensors positively. Calculation of the heterogeneous charge transfer constants showed that processes occurring on the electrodes are quasi-reversible. The limiting stage of these processes is the transfer of an electron from a biological component on the electrode surface, not the diffusion of the analyte from the solution to the active centers of the enzyme. We showed the possibility of developing third-generation mediator-free biosensors for glucose detection based on TEGM, as well as of second-generation mediator biosensors for glucose, ethanol and glycerol detection.

Microstructure and Corrosion Resistance of AA4047/AA7075 Transition Zone Formed Using Electron Beam Wire-Feed Additive Manufacturing.

A gradient transition zone was obtained using electron beam deposition from AA4047 wire on AA7075 substrate and characterized for microstructures, tensile strength and corrosion resistance. The microstructure of the transition zone was composed of aluminum alloy grains, Al/Si eutectics and Fe-rich and Si-rich particles. Such a microstructure provided strength comparable to that of AA7075-T42 substrate but more intense corrosion due to the higher amount of anodic Mg2Si particles. The as-deposited AA4047 zone formed above the transition zone was composed of aluminum alloy dendrites and interdendritic Al/Si eutectics with low mechanical strength and high corrosion potential.