Forcing reversibility in the no strand-bias substitution model allows for the theoretical and practical identifiability of its 5 parameters from pairwise DNA sequence comparisons

Because of the base pairing rules in DNA, some mutations experienced by a portion of DNA during its evolution result in the same substitution, as we can only observe differences in coupled nucleotides. Then, in the absence of a bias between the two DNA strands, a model with at most 6 different parameters instead of 12 is sufficient to study the evolutionary relationship between homologous sequences derived from a common ancestor. On the other hand the same symmetry reduces the number of independent observations which can be made. Such a reduction can in some cases invalidate the calculation of the parameters. A compromise between biologically acceptable hypotheses and tractability is introduced and a five parameter reversible no-strand-bias condition (RNSB) is presented. The identifiability of the parameters under this model is shown by examples.Comment: 12 pages, 4 figures, corrected typo

A high quality draft consensus sequence of the genome of a heterozygous grapevine variety

Background. Worldwide, grapes and their derived products have a large market. The cultivated grape species Vitis vinifera has potential to become a model for fruit trees genetics. Like many plant species, it is highly heterozygous, which is an additional challenge to modern whole genome shotgun sequencing. In this paper a high quality draft genome sequence of a cultivated clone of V. vinifera Pinot Noir is presented. Principal Findings. We estimate the genome size of V. vinifera to be 504.6 Mb. Genomic sequences corresponding to 477.1 Mb were assembled in 2,093 metacontigs and 435.1 Mb were anchored to the 19 linkage groups (LGs). The number of predicted genes is 29,585, of which 96.1% were assigned to LGs. This assembly of the grape genome provides candidate genes implicated in traits relevant to grapevine cultivation, such as those influencing wine quality, via secondary metabolites, and those connected with the extreme susceptibility of grape to pathogens. Single nucleotide polymorphism (SNP) distribution was consistent with a diffuse haplotype structure across the genome. Of around 2,000,000 SNPs, 1,751,176 were mapped to chromosomes and one or more of them were identified in 86.7% of anchored genes. The relative age of grape duplicated genes was estimated and this made possible to reveal a relatively recent Vitisspecific large scale duplication event concerning at least 10 chromosomes (duplication not reported before). Conclusions. Sanger shotgun sequencing and highly efficient sequencing by synthesis (SBS), together with dedicated assembly programs, resolved a complex heterozygous genome. A consensus sequence of the genome and a set of mapped marker loci were generated. Homologous chromosomes of Pinot Noir differ by 11.2% of their DNA (hemizygous DNA plus chromosomal gaps). SNP markers are offered as a tool with the potential of introducing a new era in the molecular breeding of grape

Data incongruence and the problem of avian louse phylogeny

Recent studies based on different types of data (i.e. morphological and molecular) have supported conflicting phylogenies for the genera of avian feather lice (Ischnocera: Phthiraptera). We analyse new and published data from morphology and from mitochondrial (12S rRNA and COI) and nuclear (EF1-) genes to explore the sources of this incongruence and explain these conflicts. Character convergence, multiple substitutions at high divergences, and ancient radiation over a short period of time have contributed to the problem of resolving louse phylogeny with the data currently available. We show that apparent incongruence between the molecular datasets is largely attributable to rate variation and nonstationarity of base composition. In contrast, highly significant character incongruence leads to topological incongruence between the molecular and morphological data. We consider ways in which biases in the sequence data could be misleading, using several maximum likelihood models and LogDet corrections. The hierarchical structure of the data is explored using likelihood mapping and SplitsTree methods. Ultimately, we concede there is strong discordance between the molecular and morphological data and apply the conditional combination approach in this case. We conclude that higher level phylogenetic relationships within avian Ischnocera remain extremely problematic. However, consensus between datasets is beginning to converge on a stable phylogeny for avian lice, at and below the familial rank

THE HERMENEUTIC STUDY OF THE MUSICAL AND POETIC TEXTS IN THE VOCAL MUSIC BY E. CHAUSSON

This study proposes an exploration of the symbolism within the works of Ernest Chausson’s of the vocal music, as an example we choose cycle “Poem of Love and the Sea”, (words by Maurice Bouchor) the application of hermeneutic methodology and analysis of the work’s intonational dramaturgy. The uniqueness of the composer’s conception, combined with the multi-layered structure of the poetic text, drives researchers to interpret the hidden symbolic levels inherent in this vocal cycle. As a result of the analysis, it is concluded that the meaning of “Poème” is grounded in core principles: the duality of the real and the otherworldly, expressed through the embodiment of hidden meanings via symbols; Romanticism and Symbolism, manifested in the observed unity between nature and human, as well as in the mystical visions of the lyrical protagonist. An analysis of the poetic text reveals Bouchor’s clear inclination toward phonetic play, the understanding of which helps unveil the symbolic essence of the entire work. The interaction of the idealistic with the realistic, the pictorial exterior with the concealed interior, is likewise evident in musical text and is revealed through the dominance of two overarching intonational graphemes. The musical and poetic levels of the vocal cycle are combined thanks to a common symbolic basis, particularly through the use of symbolism of pictorial origin. This symbolism is decoded in the musical text through principles of the painter Gustave Moreau. The fusion of poetic and musical symbolism results in mutual amplification, thereby enriching the symbolic content of the vocal cycle as a synthesis of the arts

USING GRAPHIC MODELING TO DETERMINE THE ANGLE BETWEEN THE ROLL AXES OFVEHICLES AT THE MOMENT OF COLLISION

An algorithm is proposed for determining the angle of relative position of vehicles at the moment of collision, using a graphic modeling method that involves building a damage model

Comparative analysis of vertebrate EIF2AK2 (PKR) genes and assignment of the equine gene to ECA15q24-q25 and the bovine gene to BTA11q12-q15

The structures of the canine, rabbit, bovine and equine EIF2AK2 genes were determined. Each of these genes has a 5\u27 non-coding exon as well as 15 coding exons. All of the canine, bovine and equine EIF2AK2 introns have consensus donor and acceptor splice sites. In the equine EIF2AK2 gene, a unique single nucleotide polymorphism that encoded a Tyr329Cys substitution was detected. Regulatory elements predicted in the promoter region were conserved in ungulates, primates, rodents, Afrotheria (elephant) and Insectifora (shrew). Western clawed frog and fugu EIF2AK2 gene sequences were detected in the USCS Genome Browser and compared to those of other vertebrate EIF2AK2 genes. A comparison of EIF2AK2 protein domains in vertebrates indicates that the kinase catalytic domains were evolutionarily more conserved than the nucleic acid-binding motifs. Nucleotide substitution rates were uniform among the vertebrate sequences with the exception of the zebrafish and goldfish EIF2AK2 genes, which showed substitution rates about 20% higher than those of other vertebrates. FISH was used to physically assign the horse and cattle genes to chromosome locations, ECA15q24-q25 and BTA11q12-15, respectively. Comparative mapping data confirmed conservation of synteny between ungulates, humans and rodents

ЧАСТНЫЕ СЛУЧАИ ОПРЕДЕЛЕНИЯ ПОЛОЖЕНИЯ ТРАНСПОРТНОГО СРЕДСТВА ПЕРЕД НАЧАЛОМ МАНЕВРА

The paper presents an algorithm for determining the position of the vehicle prior to maneuver using the two-axle vehicle standard steering mode and taking into account the structurally determined minimum turning radius. В статье представлен алгоритм определения положения транспортного средства до начала маневра по известной схеме классического поворота двухосного автомобиля и по заложенному конструкцией минимальному радиусу поворота.

Time-frequency analysis and laser Doppler spectrum decomposition to reveal new feature space for diagnosis of diabetes mellitus vascular complications

AbstractEarly diagnostics of microcirculation complications is an important area for biomedical photonics application. The blood perfusion measurements are capable of identification of particular markers for diagnostics of many pathological conditions of blood microcirculation in the skin. In this work, we apply the laser Doppler flowmetry method with the ability to record and process the power spectra of registered photocurrent. This approach provides the estimation of signal amplitude distribution along with the frequencies of Doppler-broadened laser radiation and blood perfusion distribution. In this work, we investigate the blood ow in the skin by the time- frequency analysis of the recorded laser Doppler spectra. The conducted studies allowed us to propose new diagnostic criteria for the diagnosis of diabetes mellitus type 2 complications. The diagnostic parameters have been tested together with binary classifiers based on the linear discriminant analysis and demonstrated to be able to successfully distinguish the groups of volunteers of different age and patients with microvascular complications.Abstract Early diagnostics of microcirculation complications is an important area for biomedical photonics application. The blood perfusion measurements are capable of identification of particular markers for diagnostics of many pathological conditions of blood microcirculation in the skin. In this work, we apply the laser Doppler flowmetry method with the ability to record and process the power spectra of registered photocurrent. This approach provides the estimation of signal amplitude distribution along with the frequencies of Doppler-broadened laser radiation and blood perfusion distribution. In this work, we investigate the blood ow in the skin by the time- frequency analysis of the recorded laser Doppler spectra. The conducted studies allowed us to propose new diagnostic criteria for the diagnosis of diabetes mellitus type 2 complications. The diagnostic parameters have been tested together with binary classifiers based on the linear discriminant analysis and demonstrated to be able to successfully distinguish the groups of volunteers of different age and patients with microvascular complications

In vivo fluorescence measurements of biological tissue viability

Abstract Modern preclinical and clinical studies show that the use of diagnostic methods based on the registration of fluorescent radiation can improve the early diagnosis of cancer and other destructive processes of various organs. Currently, many studies are being conducted aimed at studying the processes of oxidative metabolism using methods that register the fluorescence of various fluorophores. New instrument designs and analytical tools for the analysis of diagnostic information are being intensively developed. This chapter provides an overview of the main problems of fluorescence detection methods, experimental studies aimed at studying the effect of the main absorbing tissue chromophores on the fluorescence intensity, examples of applications in various fields of medicine and test objects for device calibration and measurement verification. This chapter does not seek to review all the existing problems of the method and present all possible areas of application, but only focuses on a number of important aspects.Abstract Modern preclinical and clinical studies show that the use of diagnostic methods based on the registration of fluorescent radiation can improve the early diagnosis of cancer and other destructive processes of various organs. Currently, many studies are being conducted aimed at studying the processes of oxidative metabolism using methods that register the fluorescence of various fluorophores. New instrument designs and analytical tools for the analysis of diagnostic information are being intensively developed. This chapter provides an overview of the main problems of fluorescence detection methods, experimental studies aimed at studying the effect of the main absorbing tissue chromophores on the fluorescence intensity, examples of applications in various fields of medicine and test objects for device calibration and measurement verification. This chapter does not seek to review all the existing problems of the method and present all possible areas of application, but only focuses on a number of important aspects