The locality dilemma of Sankoff-like RNA alignments

Motivation Elucidating the functions of non-coding RNAs by homology has been strongly limited due to fundamental computational and modeling issues. While existing simultaneous alignment and folding (SA&F) algorithms successfully align homologous RNAs with precisely known boundaries (global SA&F), the more pressing problem of identifying new classes of homologous RNAs in the genome (local SA&F) is intrinsically more difficult and much less understood. Typically, the length of local alignments is strongly overestimated and alignment boundaries are dramatically mispredicted. We hypothesize that local SA&F approaches are compromised this way due to a score bias, which is caused by the contribution of RNA structure similarity to their overall alignment score. Results In the light of this hypothesis, we study pairwise local SA&F for the first time systematically—based on a novel local RNA alignment benchmark set and quality measure. First, we vary the relative influence of structure similarity compared to sequence similarity. Putting more emphasis on the structure component leads to overestimating the length of local alignments. This clearly shows the bias of current scores and strongly hints at the structure component as its origin. Second, we study the interplay of several important scoring parameters by learning parameters for local and global SA&F. The divergence of these optimized parameter sets underlines the fundamental obstacles for local SA&F. Third, by introducing a position-wise correction term in local SA&F, we constructively solve its principal issues. Availability and implementation The benchmark data, detailed results and scripts are available at https://github.com/BackofenLab/local_alignment. The RNA alignment tool LocARNA, including the modifications proposed in this work, is available at https://github.com/s-will/LocARNA/releases/tag/v2.0.0RC6. Supplementary information Supplementary data are available at Bioinformatics online.

Regularity of Dynamics of Academic Adaptation of First Year Students

Academic adaptation serves as a foundation for further professional development of a sudject. The paper considers the dynamics of first year students who entered university in 2011-2019 to identify the nature of correlation of social and socio-psychological adaptations. A systemic approach has been used to examine the data. The results obtained helped to identify correlations and structure of academic adaptation of first year students. Intercorrelations of the components have been examined; functional regularity has been identified using the average for each structure component; basic attribute of the structures and their systemic entities have been found. The structure was studied using divergence, coherence, and structure orderliness indices. The macrodynamics of academic adaptation has been revealed.

SPECIALLY PROTECTED NATURAL AND TECHNOGENIC TERRITORIES OF THE KIROV REGION

The article presents comprehensive data on one of the nature monuments of the Kirov region under the name “Zhukovlyansky sandstone spherical concretions”. The status of a specially protected natural area of local importance was granted to it in 2017 due to the presence of clusters of spherical geological bodies of human size, which give the area a very scenic view. They were discovered during the quarrying of gravel and sand materials in the early 80-s of the last century and soon became a reason to put forward various hypotheses regarding the time and methods of their formation. The latter was the motivation for this publication, which is based on field and laboratory geological and soil-geochemical studies carried out by the authors in 2014-18. The results below give an idea of the peculiarities of the spatial structure, component composition and properties of local geosystems, the time of formation of their lithogenic basis, scientific and cognitive, tourist-recreational importance and problems of preservation of the original natural heritage of the region under consideration. From the genetic point of view, the spherical sandstone concretions located within the paleolacial province of the Vyatka Territory are treated by the authors as native Permian formations, not affected or slightly affected by fluvioglacial processes at the Pleistocene stage of geological development. They serve as a basis for the designation of a special category of protected areas on Vyatka land - natural and man-made monuments - as an example of spontaneous creation of nature and man.

Sikap Warga Desa Ekowisata Pancoh terhadap Partisipasi Perempuan Pemilik Usaha Pariwisata Berdasarkan Pengukuran Women Owned Operated Tourism Businesses (WOOTB)

This research aimed to understand resident’s attitudes toward women participation in tourism businesses especially understanding potential impacts-based Women Owned and Operated Tourism Businesses (WOOTB) measurement. This research is being held in Pancoh Ecotourism Village, Turi, Sleman, Yogyakarta Special Region, Indonesia. WOOTB measurement created by Beedle (2011) through quantitative method. WOOTB is measured by six components. The components are tourism impact, tourism enhancement, economic enhancement, capacity building, community structure, and tourist contact. This measurement will seek for total score of each items from six components of WOOTB interpreted by scale that have been done by Umar (2001). By collecting the data from 100 residents from 15 – 64 years old, both who are involved and non-involved in tourism activities in Pancoh Ecotourism Village, the result shows that there are di erent attitudes from the residents. The di erence shown from the average of total score in tourism impact component, economic enhancement component, and community structure component. Other than that, there is a similarity from the component of capacity building and tourism enhancement that revealed both high average to the statement by involved and non-involved residents. Meanwhile, in the component of tourism contact about “Women owned businesses in Pancoh would result in too much contact between local women and foreign tourists” revealed a low average to the statement both from involved and non-involved residents in Pancoh Ecotourism Village.

Good congruences on abundant semigroups with quasi-ideal adequate transversals

The aim of this paper is to study the congruences on abundant semigroups with quasi-ideal adequate transversals. The good congruences on an abundant semigroup with a quasi-ideal adequate transversal S° are described by the equivalence triple abstractly which consists of equivalences on the structure component parts I, S° and Λ. Also, it is shown that the set of all good congruences on this kind of semigroup forms a complete lattice.

The maximum oxygen consumption and body structure component of women at the first period of mature age with a different somatotypes

Purpose: the identification of features of the maximum oxygen consumption of women in the first period of mature age and connection with body structure component. Material: 22-35 years old women (n=210) have participated in a research. Results. It was determined that women with endomorphic and mesomorphic somatotype prevail according to the absolute measure VO2 max. They have large body weight and higher percentage content of the muscular component. The women with low body weight and low values of fat component prevail according to a relative measure VO2 max. Large body weight in women of endomorphic, endomorphic and mesomorphic somatotype stipulates low values of a relative measure VO2 max. It is indicated by the high degree of the return correlation between a relative measure VO2 max and body weight. Conclusions. The relative measure VO2 max is considered more informative as its dependence on body weight is leveled. The obtained data indicate the advantage according to a relative measure VO2 max of women with low body weight somatotype (ectomorphic and balanced). Such feature is explained by authentically low percentage content of the fat component in women.

Influence Factors Analysis of RC Beams under Falling Weight Impact Based on HJC Model

Impact loads may cause serious or even fatal damage to the structure (component), in most existing specifications in China, and there are no special terms that take impact load into consideration. So, the response analysis of the structure (component) under impact loads is very important. In this paper, the sensitivity analysis was conducted for the 22 parameters of the Holmquist–Johnson concrete (HJC) constitutive model of concrete, and the sensitive parameters of the HJC model are identified with A, B, G, Pl, μl, and fc respectively. LS-DYNA nonlinear transient finite element analysis code was used for this paper. Based on the validation of finite element modeling and choosing midspan deflection of RC beams and impact loads as response indices, some influencing factors on RC beams under falling weight impact were investigated, such as the mass and speed of falling weight, impact position, the strength of concrete and rebar, longitudinal reinforcement ratio, and the span of the beam.