SNAD: sequence name annotation-based designer

<p>Abstract</p> <p>Background</p> <p>A growing diversity of biological data is tagged with unique identifiers (UIDs) associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions.</p> <p>Results</p> <p>Here we introduce SNAD (Sequence Name Annotation-based Designer) that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list) into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology.</p> <p>Conclusion</p> <p>A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.</p

The occurrence of ideal plastic state in CP titanium processed by twist extrusion

This paper deals with the analysis of strength and plastic characteristics of commercially pure (CP) titanium as a function of equivalent plastic strain accumulated during Twist Extrusion (TE) process. It is shown experimentally that multipass TE leads to the saturation of the following characteristics of the material: yield stress, reduction in area, elongation to failure, and uniform elongation. This fact indicates the occurrence of an ideal plastic state in the processed material. The threshold value of accumulated plastic strain for ideal plastic behavior of CP titanium during TE is defined. The strain state and mechanical properties of CP titanium billets processed by TE are studied. An explanation for the hardening on the axis of a billet during TE is offered. The analysis of deformation modes on the billet axis during TE and High Pressure Torsion is carried out. It is shown that the differences in strain state on the axis are caused by the difference in symmetry of these processes

Cellular effects of terahertz waves

Significance: An increasing interest in the area of biological effects at exposure of tissues and cells to the terahertz (THz) radiation is driven by a rapid progress in THz biophotonics, observed during the past decades. Despite the attractiveness of THz technology for medical diagnosis and therapy, there is still quite limited knowledge about safe limits of THz exposure. Different modes of THz exposure of tissues and cells, including continuous-wave versus pulsed radiation, various powers, and number and duration of exposure cycles, ought to be systematically studied. Aim: We provide an overview of recent research results in the area of biological effects at exposure of tissues and cells to THz waves. Approach: We start with a brief overview of general features of the THz-wave–tissue interactions, as well as modern THz emitters, with an emphasis on those that are reliable for studying the biological effects of THz waves. Then, we consider three levels of biological system organization, at which the exposure effects are considered: (i) solutions of biological molecules;(ii) cultures of cells, individual cells, and cell structures; and (iii) entire organs or organisms; special attention is devoted to the cellular level. We distinguish thermal and nonthermal mechanisms of THz-wave–cell interactions and discuss a problem of adequate estimation of the THz biological effects’ specificity. The problem of experimental data reproducibility, caused by rareness of the THz experimental setups and an absence of unitary protocols, is also considered. Results: The summarized data demonstrate the current stage of the research activity and knowledge about the THz exposure on living objects. Conclusions: This review helps the biomedical optics community to summarize up-to-date knowledge in the area of cell exposure to THz radiation, and paves the ways for the development of THz safety standards and THz therapeutic applications

Multi-level ray tracing algorithm

We propose new approaches to ray tracing that greatly reduce the required number of operations while strictly preserving the geometrical correctness of the solution. A hierarchical “beam” structure serves as a proxy for a collection of rays. It is tested against a kd-tree representing the overall scene in order to discard from consideration the sub-set of the kd-tree (and hence the scene) that is guaranteed not to intersect with any possible ray inside the beam. This allows for all the rays inside the beam to start traversing the tree from some node deep inside thus eliminating unnecessary operations. The original beam can be further sub-divided, and we can either continue looking for new optimal entry points for the sub-beams, or we can decompose the beam into individual rays. This is a hierarchical process that can be adapted to the geometrical complexity of a particular view direction allowing for efficient geometric anti-aliasing. By amortizing the cost of partially traversing the tree for all the rays in a beam, up to an order of magnitude performance improvement can be achieved enabling interactivity for complex scenes on ordinary desktop machines

Acquisition of invasive traits in ant, Crematogaster subdentata mayr (Hymenoptera: Formicidae) in urban environments

The native (primary) range of Crematogaster subdentata Mayr lies in Central Asia. Within the secondary range in Ukraine and Russia, it is invasive. The 1st objective of this work was to study the evolution of the biological and ecological features (habitats, queen number, colony structure, behavior, worker’s activity on foraging trails) of C. subdentata in the urban environments (Tashkent) and secondary ranges (Crimea, Rostov-On-Don region). Whilst, the 2nd objective was to compared these parameters in the natural habitats in the native (Uzbekistan) range. Result showed that in the territory of the primary range in Kyzylkum, colonies of C. subdentata are strictly monogynous; in Zarafshan’s oasis (riparian forests) they were polygynous (5.0±1.2 queens), but in cities of Uzbekistan C. subdentata forms supercolonies with hundreds of nests, and in total with hundreds of queens (on average 17.7±4.4 queens per one nest in supercolony). In the secondary range, C. subdentata forms even larger supercolonies with thousands of nests, containing 53.0±8.7 queens per nest. C. subdentata avoids contacts with another invasive ant species, Lasius neglectus, in the foraging territories both in the primary and secondary ranges, but other ant species avoid C. subdentata. Workers of C. subdentata are aggressive toward conspecific ones from other nests in the natural habitats, but are tolerance to those in both the secondary range and in the cities in the primary range. In conclusion, our results show that some ants may acquire invasive species traits in the urban habitats in the primary range

Experimental Biointegration of a Titanium Implant in Delayed Mandibular Reconstruction

Background: Mandibular reconstruction, after extensive resection of the mandible for the treatment of oral cancer, is a well-known procedure, however, relatively little is known about bone integration into the titanium implant after reconstruction with a temporary plastic implant. The main goal of this experimental study was to study the process of osseous integration into the titanium implant in an in vivo experiment following prior mandibular reconstruction with a temporary plastic implant. Materials and Methods: Four ewes initially underwent a partial one-sided resection of the mandible, with the formation of an approximately 3 &times; 1 cm defect. All of the subjects received reconstruction with an implantation of a plastic plate (3 cm). The plastic plate was removed and replaced by a titanium implant at 1, 3, 6, and 12 months, accordingly. Both plastic and titanium implants were made via 3D-printing technology and personalized modeling. A total of 6 months after titanium implantation, a histological evaluation of biointegration was performed. Results: All surgeries were uncomplicated. The integration of osseous tissue into the titanium implant was seen in all cases. Histologically, each case showed variable integration of dense fibrotic tissue with fibroblasts and non-mature bone tissue with a definitive layer of bone matrix with many osteoblasts on the periphery. The prior implantation of the plastic plate did not interfere with bone integration into the titanium implant. Conclusion: Preliminary results demonstrated that a temporary plastic implant for mandibular reconstruction does not interfere with the consequent osseous biointegration of a permanent titanium implant. This shows that temporary reconstruction is a safe solution when delayed mandibular reconstruction is required due to disease severity