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The archaeal ancestor of eukaryotes apparently belonged to the phylum Asgardarchaeota, but the ecology and evolution of Asgard archaea are poorly understood. The optimal GDP-binding temperature of a translation elongation factor (EF-1A or EF-Tu) has been previously shown to correlate with the optimal growth temperature of diverse prokaryotes. Here, we reconstruct ancestral EF-1A sequences and experimentally measure the optimal GDP-binding temperature of EF-1A from ancient and extant Asgard archaea, to infer the evolution of optimal growth temperatures in Asgardarchaeota. Our results suggest that the Asgard ancestor of eukaryotes was a moderate thermophile, with an optimal growth temperature around 53 °C. The origin of eukaryotes appears to coincide with a transition from thermophilic to mesophilic lifestyle during the evolution of Asgard archaea. The archaeal ancestor of eukaryotes belonged to the phylum Asgardarchaeota, or Asgard archaea. Here, the authors use ancestral sequence reconstruction and experimentally determine the optimal GDP-binding temperature of a translation elongation factor from ancient and extant Asgard archaea, to infer optimal growth temperatures for eukaryotes' ancestors. [ABSTRACT FROM AUTHOR]

We investigate the relation between two different mathematical problems: the construction of bounds on sphere packing density using Cohn–Elkies functions and the construction of Gabor frames for signal analysis. In particular, we present a general construction of Cohn–Elkies functions in arbitrary dimension, obtained from an approximate Wexel–Raz dual for Gabor frames with Gaussian window. [ABSTRACT FROM AUTHOR]

The paper is devoted to studying the Fredholmness of operators from the Banach algebra B of singular integral operators with complex conjugation and slowly oscillating coefficients on the Lebesgue spaces L p (Γ) with p ∈ (1 , ∞) over star-like curves Γ with cusps. Applying reductions to a Banach algebra of Wiener–Hopf operators with slowly oscillating coefficients on weighted Lebesgue spaces over the half-line R + and a Banach algebra of convolution type operators with piecewise slowly oscillating coefficients on weighted Lebesgue spaces over the real line R , we construct a Fredholm symbol calculus for the Banach algebra B and establish a Fredholm criterion for the operators in B . [ABSTRACT FROM AUTHOR]

We report a theoretical study of the localized spatial magnetization configuration, which is a confined spin configuration of the target skyrmion/hopfion type in an antiferromagnet with perpendicular magnetic anisotropy, and then we solve the particular problem of self-oscillations of such a topological spin texture. Using the energy approach, a self-consistent account of inhomogeneity of the characteristics of the topological magnetic spin texture was carried out. On this basis, the equation of free oscillations of the confined spin configuration magnetization was derived and its quasi-classical solution was found. For a thin ring spin texture, the frequency, period of oscillations and relative amplitude of the main tone of oscillations are found. For the first time, we determined the topological mass, inertial mass and total energy of the main tone of oscillations of such spatial spin texture. The self-oscillatory process of a spatial spin texture is interpreted as a magnetic nano-oscillator. [ABSTRACT FROM AUTHOR]

Several groups of bacteria have complex life cycles involving cellular differentiation and multicellular structures. For example, actinobacteria of the genus Streptomyces form multicellular vegetative hyphae, aerial hyphae, and spores. However, similar life cycles have not yet been described for archaea. Here, we show that several haloarchaea of the family Halobacteriaceae display a life cycle resembling that of Streptomyces bacteria. Strain YIM 93972 (isolated from a salt marsh) undergoes cellular differentiation into mycelia and spores. Other closely related strains are also able to form mycelia, and comparative genomic analyses point to gene signatures (apparent gain or loss of certain genes) that are shared by members of this clade within the Halobacteriaceae. Genomic, transcriptomic and proteomic analyses of non-differentiating mutants suggest that a Cdc48-family ATPase might be involved in cellular differentiation in strain YIM 93972. Additionally, a gene encoding a putative oligopeptide transporter from YIM 93972 can restore the ability to form hyphae in a Streptomyces coelicolor mutant that carries a deletion in a homologous gene cluster (bldKA-bldKE), suggesting functional equivalence. We propose strain YIM 93972 as representative of a new species in a new genus within the family Halobacteriaceae, for which the name Actinoarchaeum halophilum gen. nov., sp. nov. is herewith proposed. Our demonstration of a complex life cycle in a group of haloarchaea adds a new dimension to our understanding of the biological diversity and environmental adaptation of archaea. Bacteria of the genus Streptomyces have complex life cycles involving cellular differentiation and multicellular structures that have never been observed in archaea. Here, the authors show that several halophilic archaea display a life cycle resembling that of Streptomyces bacteria, undergoing cellular differentiation into mycelia and spores. [ABSTRACT FROM AUTHOR]

Applying recent results on Mellin pseudodifferential operators with quasicontinuous symbols and decreasing the smoothness of data, we construct the Fredholm theory for the Haseman boundary value problem Φ + ∘ α = G Φ - + g on a star-like curve Γ composed by N rays Γ k in the setting of Lebesgue spaces, where Φ ± are angular boundary values of an unknown analytic function Φ on Γ , G and g are given functions, and α is an orientation-preserving homeomorphism of Γ onto itself. Provided that the coefficient G and the shift derivative α ′ are quasicontinuous functions on each ray Γ k , a Fredholm criterion and an index formula are established for the equivalent singular integral operator with shift T = V α P + + G P - on the space L p (Γ) , where the operators P ± = 2 - 1 (I ± S Γ) are related to the Cauchy singular integral operator S Γ , and the shift operator V α is given by V α f = f ∘ α . [ABSTRACT FROM AUTHOR]

For p ∈ (1 , ∞) , we establish several criteria of one-sided invertibility on spaces l p = l p (Z) for discrete band-dominated operators being either absolutely convergent series ∑ k ∈ Z a k V k or uniform limits of band operators of the form A = ∑ k ∈ F a k V k , where F is a finite subset of Z , a k ∈ l ∞ , and the isometric operator V is given on functions f ∈ l p by (V f) (n) = f (n + 1) for all n ∈ Z . We also obtain sufficient conditions of one-sided invertibility on spaces l p with p ∈ (1 , ∞) for the so-called E-modulated and slant-dominated discrete Wiener-type operators. [ABSTRACT FROM AUTHOR]

In Figuer 4, the image for control BT474 cells, after pulsed field, was inadvertently duplicated from the control BT474 cells, no field, condition. In addition, for Supplementary Figure S12, the images for MCF10A cells, field only; MDA-MB-231 cells, MNP only; and MDA-MB-231 cells, MNP and field treatment, are incorrect. The cells exposed to hydrogen peroxide exhibit loss of punctate red fluorescence while negative controls and cells treated with SMNPs do not. [Extracted from the article]

Asgard is a recently discovered superphylum of archaea that appears to include the closest archaeal relatives of eukaryotes1–5. Debate continues as to whether the archaeal ancestor of eukaryotes belongs within the Asgard superphylum or whether this ancestor is a sister group to all other archaea (that is, a two-domain versus a three-domain tree of life)6–8. Here we present a comparative analysis of 162 complete or nearly complete genomes of Asgard archaea, including 75 metagenome-assembled genomes that—to our knowledge—have not previously been reported. Our results substantially expand the phylogenetic diversity of Asgard and lead us to propose six additional phyla that include a deep branch that we have provisionally named Wukongarchaeota. Our phylogenomic analysis does not resolve unequivocally the evolutionary relationship between eukaryotes and Asgard archaea, but instead—depending on the choice of species and conserved genes used to build the phylogeny—supports either the origin of eukaryotes from within Asgard (as a sister group to the expanded Heimdallarchaeota–Wukongarchaeota branch) or a deeper branch for the eukaryote ancestor within archaea. Our comprehensive protein domain analysis using the 162 Asgard genomes results in a major expansion of the set of eukaryotic signature proteins. The Asgard eukaryotic signature proteins show variable phyletic distributions and domain architectures, which is suggestive of dynamic evolution through horizontal gene transfer, gene loss, gene duplication and domain shuffling. The phylogenomics of the Asgard archaea points to the accumulation of the components of the mobile archaeal ‘eukaryome’ in the archaeal ancestor of eukaryotes (within or outside Asgard) through extensive horizontal gene transfer.Comparative analysis of 162 genomes of Asgard archaea results in six newly proposed phyla, including a deep branch that is provisionally named Wukongarchaeota, and sheds light on the evolutionary history of this clade. [ABSTRACT FROM AUTHOR]

Background: The morphometric analysis of the individual bones of the human skeleton can be used to estimate the sex of unidentified corpses. Our aims were as follows: to test whether thyroid cartilage can be used for forensic purposes as a predictor of biological sex; to establish the level of sexual dimorphism of the thyroid cartilage in a sample of adult subjects from a population of European Russia; and to test the accuracy of the morphometric parameters obtained from the thyroid cartilage. Results: The thyroid cartilage from 100 adults of known age (50 males and 50 females) was obtained during forensic examination; morphometric tests were conducted using Vernier Digital ROKTOOLS ABS DIN 862 0-200/6 inch with measurement accuracy ± 0.01 mm. The measured parameters were N = 31 for each subject. Intra- and inter-observer reproducibility was tested. Multivariate statistical analysis was applied to the measurements. To check the data set for normal distribution, the Kolmogorov-Smirnov test was used. Finally, to estimate the sex of the observed individuals, a stepwise discriminant analysis was conducted, using the Wilks' lambda selection method. The most significant parameters were the outer distance between bases of inferior horn; the inner distance between distal ends of inferior horns; distance between distal ends of left superior and inferior horns; left superior horn length (distance between left superior horn distal end and base); distance between superior and inferior notches; thyroid angle; left lamina height (vertical line along left lamina middle); horizontal distance between anterior intermedium line and the right lamina posterior edge; distance between inferior thyroid notch and line connecting left and right thyroid laminae; and left superior horn thickness at mid-line. The stepwise discriminant analysis resulted in an equation with ten parameters. Conclusions: The results of the current study indicated that in the European Russian population, the equation obtained in the stepwise discriminant analysis makes it possible to predict sex with a probability of 100% on the validation set. On the test set, the resultant accuracy was 100% for females and 100% for males. Our findings confirm the scientific evidence that the thyroid cartilage has a pronounced sexual dimorphism. [ABSTRACT FROM AUTHOR]

CrAssphage is the most abundant human-associated virus and the founding member of a large group of bacteriophages, discovered in animal-associated and environmental metagenomes, that infect bacteria of the phylum Bacteroidetes. We analyze 4907 Circular Metagenome Assembled Genomes (cMAGs) of putative viruses from human gut microbiomes and identify nearly 600 genomes of crAss-like phages that account for nearly 87% of the DNA reads mapped to these cMAGs. Phylogenetic analysis of conserved genes demonstrates the monophyly of crAss-like phages, a putative virus order, and of 5 branches, potential families within that order, two of which have not been identified previously. The phage genomes in one of these families are almost twofold larger than the crAssphage genome (145-192 kilobases), with high density of self-splicing introns and inteins. Many crAss-like phages encode suppressor tRNAs that enable read-through of UGA or UAG stop-codons, mostly, in late phage genes. A distinct feature of the crAss-like phages is the recurrent switch of the phage DNA polymerase type between A and B families. Thus, comparative genomic analysis of the expanded assemblage of crAss-like phages reveals aspects of genome architecture and expression as well as phage biology that were not apparent from the previous work on phage genomics. Here, the authors analyze 4907 Circular Metagenome Assembled Genomes from human microbiomes and identify and characterize nearly 600 diverse genomes of crAss-like phages, finding two putative families with unusual genomic features, including high density of self-splicing introns and inteins. [ABSTRACT FROM AUTHOR]

We present results of magnetization and magnetic susceptibility dependence investigations performed for undecane-based ferrofluids with dominant of Brownian relaxation for particles. A robust and effective method of fine particle size characterization is presented. It is based on the core–shell model and the analysis of the dependence of saturation magnetization on particle concentration. A novel advantage method has been used as a straightforward way to determine the concentration dependence of the effective field related to particle interaction that was calculated from the experimentally obtained concentration dependence of low field susceptibility. The computed relationship is compared with the concentration dependences of effective fields derived from several well-known theoretical models. We present some peculiarities of the real part of dynamic magnetic susceptibility on temperature. Investigated features are defined both by the magnetic state of fine particles and by crystallization of carrier at the liquid to a solid phase transition. For the first time, the dependence of the magnetization relaxation time on the colloidal particle concentration and the magnitude of bias DC magnetic field was investigated experimentally. Results are in good agreement with theoretical predictions for moderate concentration and significantly differs for concentration greater 7 vol%. It is concluded that this effect can be related either to the enhanced particle interaction or to the transition of some particles from superparamagnetic to a ferromagnetic state. These predictions are verified through the calculation in terms of Cole–Cole diagrams methods. [ABSTRACT FROM AUTHOR]

The effect of the natural saponin glycyrrhizic acid (GA) and polysaccharide arabinogalactan (AG) on the transmembrane potential of rat thymocytes was investigated using the potential-sensitive fluorescent probe 4-(p-dimethylaminostyryl)-1-methylpyridinium (DSM). Incubation of cells with GA in micellar form resulted in a decrease of the amplitude of observed fluorescence kinetics that points out to a decrease of the transmembrane potential. The proposed mechanism is an increase of membrane ion permeability (passive ion transport) of the plasma cell membrane due to GA incorporation. The incorporation of GA molecules into the cell membrane is extremely sensitive to the degree of GA dissociation. The neutral form of glycyrrhizic acid enters the lipid bilayer in contrast to the deprotonated anionic form. The incubation of rat thymocytes with anionic form of GA, namely with its disodium salt, has no effect on the fluorescence kinetics. The possible reasons of this phenomenon are discussed in the light of the nuclear magnetic resonance (NMR) and molecular dynamics (MD) data. The treatment of thymocytes with AG affects only the initial rate of the probe incorporation. The proposed mechanism is that AG covers the surface of the cell membrane and forms a barrier for the probe. Additionally, our experiments demonstrated that both polysaccharide AG and GA in the neutral form (but not Na2GA) effectively capture the cationic probe in an aqueous solution and then deliver it to the cell membrane. [ABSTRACT FROM AUTHOR]

The CRISPR-Cas are adaptive bacterial and archaeal immunity systems that have been harnessed for the development of powerful genome editing and engineering tools. In the incessant host-parasite arms race, viruses evolved multiple anti-defense mechanisms including diverse anti-CRISPR proteins (Acrs) that specifically inhibit CRISPR-Cas and therefore have enormous potential for application as modulators of genome editing tools. Most Acrs are small and highly variable proteins which makes their bioinformatic prediction a formidable task. We present a machine-learning approach for comprehensive Acr prediction. The model shows high predictive power when tested against an unseen test set and was employed to predict 2,500 candidate Acr families. Experimental validation of top candidates revealed two unknown Acrs (AcrIC9, IC10) and three other top candidates were coincidentally identified and found to possess anti-CRISPR activity. These results substantially expand the repertoire of predicted Acrs and provide a resource for experimental Acr discovery. CRISPR-Cas is a host adaptive immunity system and viruses harbor diverse anti-CRISPR proteins (Acrs). Here, the authors develop a random forest machine-learning approach to predict Acrs, identifying 2500 candidate Acr families, which expand the current repertoire of predicted Acrs by two orders of magnitude. [ABSTRACT FROM AUTHOR]

CRISPR arrays contain spacers, some of which are homologous to genome segments of viruses and other parasitic genetic elements and are employed as portion of guide RNAs to recognize and specifically inactivate the target genomes. However, the fraction of the spacers in sequenced CRISPR arrays that reliably match protospacer sequences in genomic databases is small, leaving the question of the origin(s) open for the great majority of the spacers. Here, we extend the spacer analysis by examining the distribution of partial matches (matching k-mers) between spacers and genomes of viruses infecting the given host as well as the host genomes themselves. The results indicate that most of the spacers originate from the host-specific viromes, whereas self-targeting is strongly selected against. However, we present evidence that the vast majority of the viruses comprising the viromes currently remain unknown although they are likely to be related to identified viruses. Sergey A. Shmakov et al. investigate the origin of the CRISPR spacers. They examine the distribution of partial matches between the spacers, viral genomes, and the host genomes and report that most of the spacers originate from host specific viromes. They demonstrate that most of the viruses are unknown although are likely related to known viruses. [ABSTRACT FROM AUTHOR]

Remote nano-magneto-mechanical actuation of magnetic nanoparticles (MNPs) by non-heating extremely low frequency magnetic field (ELF MF) is explored as a tool for non-invasive modification of bionanomaterials in pharmaceutical and medical applications. Here we study the effects of ELF MF (30–160 Hz, 8–120 kA/m) on the activity and release of a model enzyme, superoxide dismutase 1 (SOD1) immobilized by polyion coupling on dispersed MNPs aggregates coated with poly(L-lysine)-block-poly(ethylene glycol) block copolymer (s-MNPs). Such fields do not cause any considerable heating of MNPs but promote their rotating-oscillating mechanical motion that produces mechanical forces and deformations in adjacent materials. We observed the changes in the catalytic activity of immobilized SOD1 as well as its release from the s-MNPs/SOD1 polyion complex upon application of the ELF MF for 5 to 15 min. At longer exposures (25 min) the s-MNPs/SOD1 dispersion destabilizes. The bell-shaped effect of the field frequency with maximum at f = 50 Hz and saturation effect of field strength (between 30 kA/m and 120 kA/m at f = 50 Hz) are reported and explained. The findings are significant as one early indication of the nano-magneto-mechanical disruption by ELF MF of cooperative polyion complexes that are widely used for design of current functional healthcare bionanomaterials. [ABSTRACT FROM AUTHOR]

Driver mutations and chromosomal aneuploidy are major determinants of tumorigenesis that exhibit complex relationships. Here, we identify associations between driver mutations and chromosomal aberrations that define two tumor clusters, with distinct regimes of tumor evolution underpinned by unique sets of mutations in different components of DNA damage response. Gastrointestinal and endometrial tumors comprise a separate cluster for which chromosomal-arm aneuploidy and driver mutations are mutually exclusive. The landscape of driver mutations in these tumors is dominated by mutations in DNA repair genes that are further linked to microsatellite instability. The rest of the cancer types show a positive association between driver mutations and aneuploidy, and a characteristic set of mutations that involves primarily genes for components of the apoptotic machinery. The distinct sets of mutated genes derived here show substantial prognostic power and suggest specific vulnerabilities of different cancers that might have therapeutic potential. The interplay between driver mutations and aneuploidy during tumorigenesis is largely unexplored. Here, the authors show two types of associations, leading to different therapeutic vulnerabilities and prognoses. [ABSTRACT FROM AUTHOR]

Recently, it was found that there is a remarkable intuitive similarity between studies in theoretical computer science dealing with large data sets on the one hand, and categorical methods of topology and geometry in pure mathematics, on the other. In this article, we treat the key notion of persistency from computer science in the algebraic geometric context involving Nori motivic constructions and related methods. We also discuss model structures for persistent topology. [ABSTRACT FROM AUTHOR]

Atopic dermatitis (AD), the leading cause of skin-related burden of disease worldwide, is increasing in prevalence in developing countries of Asia, Africa, Latin America, and the Middle East. Although AD presents similarly across racial and ethnic groups as chronic and relapsing pruritic eczematous lesions, some features of the disease may be more or less prominent in patients with darker skin. Despite a similar presentation, consistent diagnostic criteria and consistent treatment guidelines are lacking. Because of these and other challenges, adherence to treatment guidelines is difficult or impossible. Previous studies have stated that many patients with AD receive ineffective or inappropriate care, such as oral antihistamines, oral corticosteroids, or traditional medicines, if they are treated at all; one study showed that approximately one-third of patients received medical care for their dermatologic condition; of those, almost three-quarters received inappropriate or ineffective treatment. In addition, other challenges endemic to developing countries include cost, access to care, and lack of specialists in AD. Furthermore, most of the available diagnostic criteria and treatment guidelines are based on European and North American populations and few clinical trials report the racial or ethnic makeup of the study population. Drug pharmacokinetics in varying ethnicities and adverse effects in different skin physiologies are areas yet to be explored. The objective of this review is to describe the diagnosis, treatment, and management of AD in developing countries in Asia, Africa, Latin America, and the Middle East; to discuss the differences among the countries; and to establish the unmet needs of patients with AD in them. The unmet medical need for treatment of AD in developing countries can be addressed by continuing to train medical specialists, improve access to and affordability of care, and develop new and effective treatments. Funding Pfizer Inc. [ABSTRACT FROM AUTHOR]

Bacterial and archaeal evolution involve extensive gene gain and loss. Thus, phylogenetic trees of prokaryotes can be constructed both by traditional sequence-based methods (gene trees) and by comparison of gene compositions (genome trees). Comparing the branch lengths in gene and genome trees with identical topologies for 34 clusters of closely related bacterial and archaeal genomes, we show here that terminal branches of gene trees are systematically compressed compared to those of genome trees. Thus, sequence evolution is delayed compared to genome evolution by gene gain and loss. The extent of this delay differs widely among bacteria and archaea. Mathematical modeling shows that the divergence delay can result from sequence homogenization by homologous recombination. The model explains how homologous recombination maintains the cohesiveness of the core genome of a species while allowing extensive gene gain and loss within the accessory genome. Once evolving genomes become isolated by barriers impeding homologous recombination, gene and genome evolution processes settle into parallel trajectories, and genomes diverge, resulting in speciation. [ABSTRACT FROM AUTHOR]

In this paper, the sorption of the heavy metal ions (Sr2+, Ba2+, and Cs+) on the hybrid CNF/TiO2 and CNF/Fe2O3 materials is considered. The colloid–chemical properties of the TiO2 and Fe2O3 nanoparticles and carbon nanofibers in the dispersions were studied, and interaction between nanoparticles and nanofibers in accordance with the hetero-coagulation principle was estimated. The carbon nanofibers used were prepared by catalytic chemical vapor deposition of a propane–butane mixture over the nickel–copper catalyst and then functionalized by boiling in a mixture of concentrated hydrochloric and nitric acids. The TiO2 and Fe2O3 nanoparticles were synthesized via a sol–gel technique. The sol was mixed with carbon nanofibers. After drying, the hybrid materials with a uniform distribution of the oxide NPs along the nanofiber's surface were obtained. The CNF-to-metal oxide ratios were 10:1 and 1:1. The samples were characterized by a set of physicochemical methods. The hybrid CNF/TiO2 system was found to have a synergetic effect toward the sorption of the metal ions from their aqueous solutions. Highlights: Hybrid materials CNF/Fe2O3 and CNF/TiO2 were synthesized by ex situ method. The colloid–chemical properties of metal oxide NPs and CNFs in the dispersions were studied. Metal oxide NPs are coaxially coated and uniformly distributed on the CNF surface. Sorption of Sr2+, Ba2+, and Cs+ on the hybrid materials is considered. The hybrid CNF/TiO2 was found to have a synergetic effect toward the sorption of Sr2+ and Cs+. [ABSTRACT FROM AUTHOR]

We have investigated the structural, optical, and magnetic properties of D03 Fe3Al alloys along with the electronic structure calculations. X-ray diffraction patterns confirm the single-phase cubic structure with a symmetry for the arc-melted samples. In the field dependence of magnetic data, ferromagnetic behavior is witnessed down to 2 K from room temperature. The electronic structure calculation corroborates the experimental observation of ferromagnetism in this alloy. Further, optical conductivity data in excellent agreement with the electronic structure calculations confirmed that electronic transitions are predominant by the 3d states of Fe. [ABSTRACT FROM AUTHOR]

A Correction to this paper has been published: https://doi.org/10.1007/s00010-020-00773-8 [ABSTRACT FROM AUTHOR]

For any simply connected domain U⊂C with a piecewise Dini-smooth boundary ∂U which admits Dini-smooth corners of openings lying in (0,2π], the C∗-algebra BU=alg{aI,BU,B~U:a∈PC(L)} generated by the operators of multiplication by piecewise continuous functions with discontinuities on a finite union L⊂U of piecewise Dini-smooth curves that have one-sided tangents at every point, do not form cusps and are not tangent to ∂U at the points of L∩∂U, and by the Bergman projection BU and anti-Bergman projection B~U acting on the Lebesgue space L2(U) is studied. A Fredholm symbol calculus for the C∗-algebra BU is constructed and a Fredholm criterion for the operators A∈BU in terms of their symbols is established. Results essentially depend on openings of corners and angles between curves of discontinuity of coefficients at the points z∈∂U∩L. [ABSTRACT FROM AUTHOR]

Encoding, transmission and decoding of information are ubiquitous in biology and human history: from DNA transcription to spoken/written languages and languages of sciences. During the last decades, the study of neural networks in brain performing their multiple tasks was providing more and more detailed pictures of (fragments of) this activity. Mathematical models of this multifaceted process led to some fascinating problems about "good codes" in mathematics, engineering, and now biology as well. The notion of "good" or "optimal" codes depends on the technological progress and criteria defining optimality of codes of various types: error-correcting ones, cryptographic ones, noise-resistant ones etc. In this note, I discuss recent suggestions that activity of some neural networks in brain, in particular those responsible for space navigation, can be well approximated by the assumption that these networks produce and use good error-correcting codes. I give mathematical arguments supporting the conjecture that search for optimal codes is built into neural activity and is observable. [ABSTRACT FROM AUTHOR]

In a previous paper, I have defined non-commutative generalised Dedekind symbols for classical $$PSL(2,\mathbf {Z})$$ -cusp forms using iterated period polynomials. Here I generalise this construction to forms of real weights using their iterated period functions introduced and studied in a recent article by R. Bruggeman and Y. Choie. [ABSTRACT FROM AUTHOR]

Intriguing, yet uncultured ‘ARMAN’-like archaea are metabolically dependent on other members of the microbial community. It remains uncertain though which hosts they rely upon, and, because of the lack of complete genomes, to what extent. Here, we report the co-culturing of ARMAN-2-related organism, Mia14, with Cuniculiplasma divulgatum PM4 during the isolation of this strain from acidic streamer in Parys Mountain (Isle of Anglesey, UK). Mia14 is highly enriched in the binary culture (ca. 10% genomic reads) and its ungapped 0.95 Mbp genome points at severe voids in central metabolic pathways, indicating dependence on the host, C. divulgatum PM4. Analysis of C. divulgatum isolates from different sites and shotgun sequence data of Parys Mountain samples suggests an extensive genetic exchange between Mia14 and hosts in situ. Within the subset of organisms with high-quality genomic assemblies representing the ‘DPANN’ superphylum, the Mia14 lineage has had the largest gene flux, with dozens of genes gained that are implicated in the host interaction. [ABSTRACT FROM AUTHOR]

Viruses hold solutions to a lot of problems, so let's fund and reward cataloguing, urge Jens H. Kuhn and colleagues. Viruses hold solutions to a lot of problems, so let's fund and reward cataloguing, urge Jens H. Kuhn and colleagues. [ABSTRACT FROM AUTHOR]

The evolution of CRISPR-cas loci, which encode adaptive immune systems in archaea and bacteria, involves rapid changes, in particular numerous rearrangements of the locus architecture and horizontal transfer of complete loci or individual modules. These dynamics complicate straightforward phylogenetic classification, but here we present an approach combining the analysis of signature protein families and features of the architecture of cas loci that unambiguously partitions most CRISPR-cas loci into distinct classes, types and subtypes. The new classification retains the overall structure of the previous version but is expanded to now encompass two classes, five types and 16 subtypes. The relative stability of the classification suggests that the most prevalent variants of CRISPR-Cas systems are already known. However, the existence of rare, currently unclassifiable variants implies that additional types and subtypes remain to be characterized. [ABSTRACT FROM AUTHOR]