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An Approach for Searching Insertions in Bacterial Genes Leading to the Phase Shift of Triplet Periodicity

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Genomics, Proteomics & Bioinformatics 2011年第4期9卷 158-170页

作者： Maria A. Korotkova nikolay A. Kudryashov Eugene V. Korotkov Centre of Bioengineering Russian Academy of Sciences National University of Nuclear Investigations (MIFI)

The concept of the phase shift of triplet periodicity （TP） was used for searching potential DNA insertions in genes from 17 bacterial genomes. A mathematical algorithm for detection of these insertions has been developed. This approach can detect potential insertions and deletions with lengths that are not multiples of three bases, especially insertions of relatively large DNA fragments （〉 100 bases）. New similarity measure between triplet matrixes was employed to improve the sensitivity for detecting the TP phase shift. Sequences of 17,220 bacterial genes with each consisting of more than 1,200 bases were analyzed, and the presence of a TP phase shift has been shown in -16% of analysed genes （2,809 genes）, which is about 4 times more than that detected in our previous work. We propose that shifts of the TP phase may indicate the shifts of reading frame in genes after insertions of the DNA fragments with lengths that are not multiples of three bases. A relationship between the phase shifts of TP and the frame shifts in genes is discussed.

关键词： triplet periodicity insertion gene sequence reading frame phase shift change-point problem

Two-dimensional control of light with light on metasurfaces

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Light(Science & Applications) 2016年第1期5卷 826-830页

作者： Maria Papaioannou Eric Plum João Valente Edward TF Rogers nikolay I Zheludev Optoelectronics Research Centre and Centre for Photonic Metamaterials University of SouthamptonHighfieldSouthampton SO171BJUK Institute for Life Sciences University of SouthamptonHighfieldSouthampton SO171BJUK The Photonics Institute and Centre for Disruptive Photonic Technologies Nanyang Technological UniversitySingapore 637371Singapore

The ability to control the wavefront of light is fundamental to focusing and redistribution of light,enabling many applications from imaging to *** interaction on highly nonlinear photorefractive materials is essentially the only established technology allowing the dynamic control of the wavefront of a light beam with another beam of light,but it is slow and requires large optical *** we report a proof-of-principle demonstration of a new technology for two-dimensional(2D)control of light with light based on the coherent interaction of optical beams on highly absorbing plasmonic *** illustrate this by performing 2D all-optical logical operations(AND,XOR and OR)and image *** approach offers diffractionlimited resolution,potentially at arbitrarily-low intensity levels and with 100 THz bandwidth,thus promising new applications in space-division multiplexing,adaptive optics,image correction,processing and recognition,2D binary optical data processing and reconfigurable optical devices.

关键词： all-optical data processing all-optical image processing coherent control metasurfaces

Ruthenium-mediated assembly and enhanced stability of heterometallic polystannides[Ru_(2)Sn_(19)]^(4−)and[Ru_(2)Sn_(20)]^(6−)

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Nano Research 2022年第6期15卷 5705-5711页

作者： Wei-Xing Chen nikolay V.Tkachenko Alvaro Muñoz-Castro Alexander I.Boldyrev Zhong-Ming Sun State Key Laboratory of Elemento-Organic Chemistry Tianjin Key Lab of Rare Earth Materials and ApplicationsSchool of Materials Science and EngineeringNankai UniversityTianjin 300350China Department of Chemistry and Biochemistry Utah State University0300 Old Main HillLoganUT 84322-0300USA Grupo de Química Inorgánicay Materiales Moleculares Facultad de IngenieriaUniversidad Autonoma de ChileEl Llano SubercaseauxSantiago 2801Chile

In this work,we report the synthesis and characterization of two novel Ru-containing Zintl clusters:[Sn_(19){Ru(COD)(en)}_(2)]^(4−)and[Sn_(20){Ru(COD)}_(2)]^(6−).The synthesized compounds not only expand the family of Ru-Sn cluster systems but also shed light on the structure of heterometallic complexes in a previously unknown range of tin *** single-crystal X-ray diffraction(XRD)analysis reveals the dimeric nature of the *** different assembly patterns of the formal[Sn(η^(3)-Sn_(9))]monomer were observed:the dimerization through the vertex fusion process and the direct dimerization through the formation of 2c–2e Sn–Snσ*** both clusters,the density functional theory calculations reveal the locallyσ-aromatic nature of the[Sn(η^(3)-Sn_(9))]monomer resulting in two independent magnetic shielding *** believe that our findings will help the community to further explore the fascinating chemistry of polystannide clusters.

关键词： heterometallic clusters aromaticity polystannide ruthenium Zintl anion

Fluctuating fine-scale spatial genetic structure in the common shrews (Eulipotyphla, Mammalia)

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Integrative Zoology 2023年第3期18卷 469-492页

作者： nikolay A.SHCHIPANOV Artem V.ARTAMONOV Sergey V.TITOV Svetlana V.PAVLOVA A.N.Severtsov Institute of Ecology and Evolution Russian Academy of SciencesMoscowRussia Department of Zoology and Ecology Penza State UniversityPenzaRussia

The spatial genetic structure is a topical issue in the studies of various aspects of ecology and *** the multilocus autocorrelation method with hypervariable microsatellite genetic markers,we investigated aﬁne-scale pattern of genetic structure in 5 local populations of the common shrew Sorex araneus separated by distances of 300–1000 m(the Moscow chromosomal race).Spatial genetic autocorrelation analysis based on 5 microsatellite loci(expected heterozygosity>0.79)with 90 alleles revealed a consistent pattern of signiﬁcant positive genetic *** testing the autocorrelation at multiple scales from 25 to 500 m,we found that positive spatial genetic structure is detectable in distance classes of<500 *** weaker spatial genetic structure positively correlated with a higher ratio of nonresident individuals to residents’activity(number of captures).In contrast to nonresident animals,the residents demonstrated prominent genetic *** difference(FST)between the populations was signiﬁcant(0.016–0.051)and comparable with that between populations of different races analyzed previously(0.016–0.038).FST was not associated with geographic *** demographic patterns allowed us to propose a scheme of genetic-structure dynamics involving periodic appearance of more related local groups and renewal of allelic proﬁles fromаcommon pool where the alleles are *** scheme predictsﬂuctuating genetic structure and random similar differences among local populations.

关键词： demographic pattern geneﬂow microsatellite spatial autocorrelation

The determination of white dwarf parameters in dwarf novae by optical spectral modeling

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Research in Astronomy and Astrophysics 2021年第7期21卷 37-40页

作者： Anastasiya Andreevna Dudnik Arina Alekseevna Mitrofanova Vladislav Vladimirovich Shimansky nikolay Vladimirovich Borisov Nail Abdullovich Sakhibullin Kazan(Volga Region)Federal University KazanRepublic of TatarstanRussia Special Astrophysical Observatory Russian Academy of ScienceNizhnii ArkhysKarachai-Cherkessian RepublicRussia

This paper presents the results of a model analysis of optical spectra and determination of the parameters of three individual SU UMa and WZ Sge type dwarf *** moderate resolution spectra of TY Psc,FL Psc and V455 And were obtained at the 6-m BTA of the SAO RAS in the low state of these systems with the determination of white dwarf *** theoretical spectra were calculated using the grid models of hydrogen dwarf atmospheres of white dwarfs by varying the parameters(T_(eff) and log g) to reach the best agreement with the observed *** highlight different effects of the parameters on the shape and intensity of the HI ***,it is possible to unambiguously determine T_(eff) and log g from the analysis of *** fundamental parameters of white dwarfs(M and R) were found by comparing the parameters of atmospheres with theoretical models of the internal *** obtained parameters of the primaries of TY Psc,FL Psc and V455 And are consistent with the average values for SU UMa and WZ Sge *** a result,we demonstrate the efficiency of the method for determining the parameters of such systems based on the analysis of a limited set of observed optical spectra.

关键词： techniques:spectroscopic stars:variables:dwarf novae stars:individual:TY Psc stars:individual:FL Psc stars:individual:V455 And

Computational Cluster with Entangled States

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Journal of Applied Mathematics and Physics 2016年第9期4卷 1777-1786页

作者： nikolay Raychev Varna University of Management Varna Bulgaria

In this article the inherent computational power of the quantum entangled cluster states examined by measurement-based quantum computations is studied. By defining a common framework of rules for measurement of quantum entangled cluster states based on classical computations, the precise and detailed meaning of the computing power of the correlations in the quantum cluster states is made. This study exposes a connection, arousing interest, between the infringement of the realistic models that are local and the computing power of the quantum entangled cluster states.

关键词： Quantum Computing Computational Complexity Cluster States Gates

An optical fiber network oracle for NP-complete problems

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Light(Science & Applications) 2014年第1期3卷 304-308页

作者： Kan Wu Javier Garcia de Abajo Cesare Soci Perry Ping Shum nikolay I Zheludev Centre for Disruptive Photonic Technologies Nanyang Technological UniversitySingapore 637371Singapore Optoelectronics Research Centre University of SouthamptonSouthampton SO171BJUK IQFR-CSIC 28006 MadridSpain

The modern information society is enabled by photonic fiber networks characterized by huge coverage and great complexity and ranging in size from transcontinental submarine telecommunication cables to fiber to the home and local *** world-wide network has yet to match the complexity of the human brain,which contains a hundred billion neurons,each with thousands of synaptic connections on ***,it already exceeds the complexity of brains from primitive organisms,i.e.,the honey bee,which has a brain containing approximately one million *** this study,we present a discussion of the computing potential of optical networks as information *** a simple fiber network,we provide a proof-of-principle demonstration that this network can be treated as an optical oracle for the Hamiltonian path problem,the famous mathematical complexity problem of finding whether a set of towns can be travelled via a path in which each town is visited only *** of a Hamiltonian path is achieved by monitoring the delay of an optical pulse that interrogates the network,and this delay will be equal to the sum of the travel times needed to visit all of the nodes(towns).We argue that the optical oracle could solve this NP-complete problem hundreds of times faster than brute-force ***,we discuss secure communication applications for the optical oracle and propose possible implementation in silicon photonics and plasmonic networks.

关键词： Hamiltonian path problem NP complete optical oracle

A new species of the genus Theloderma Tschudi, 1838 (Amphibia： Anura： Rhacophoridae) from Tay Nguyen Plateau, central Vietnam

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Zoological Research 2018年第3期39卷 158-184页

作者： nikolay A. Poyarkov Ivan I. Kropachev Svetlana S. Gogoleva Nikolai L. Orlov Department of Vertebrate Zoology Biological Faculty Lomonosov Moscow State University Moscow 119234 Russia Joint Russian-Vietnamese Tropical Research and Technological Center Nghia Do Cau Giay Hanoi Vietnam Tula Exotarium Tula 300004 Russia A.N. Severtsov Institute of Ecology and Evolution Russian Academy of Sciences Moscow 119071 Russia Joint Russian-Vietnamese Tropical Research and Technological Center South Branch Ho Chi Minh City Vietnam Zoological Museum of the Lomonosov Moscow State University Moscow 125009 Russia Zoological Institute Russian Academy of Sciences St. Petersburg 199034 Russia

A new species of small tree frog from a primary montane tropical forest of central Vietnam, Tay Nguyen Plateau, is described based on morphological, molecular, and acoustic evidence. The Golden Bug-Eyed Frog, Theloderma auratum sp. nov., is distinguishable from its congeners and other small rhacophorid species based on a combination of the following morphological attributes：（1） bony ridges on head absent; （2） smooth skin completely lacking calcified warts or asperities; （3） pointed elongated tapering snout; （4） vocal opening in males absent; （5） vomerine teeth absent; （6） males of small body size （SVL 21.8-26.4 mm）; （7） head longer than wide; ED/SVL ratio 13%-15%; ESL/SVL ratio 16%-20%; （8） small tympanum （TD/EL ratio 50%-60%） with few tiny tubercles; （9） supratympanic fold absent; （10） ventral surfaces completely smooth; （11 ） webbing between fingers absent; （12） outer and inner metacarpal tubercles present, supernumerary metacarpal tubercle single, medial, oval in shape; （13） toes half-webbed： I 2-21/4 II 11/^-23/~ III 2-31/4 IV 3-11/2 V; （14） inner metatarsal tubercle present, oval; outer metatarsal tubercle absent; （15） iris bicolored; （16） dorsal surfaces golden-yellow with sparse golden-orange speckling or reticulations and few small dark-brown spots; （17） lateral sides of head and body with wide dark reddish-brown to black lateral stripes, clearlyseparated from lighter dorsal coloration by straight contrasting edge; （18） ventral surfaces of body, throat, and chest greyish-blue with indistinct brown confluent blotches; （19） upper eyelids with few （3-5） very small flat reddish superciliary tubercles; （20） limbs dorsally reddish-brown, ventrally brown with small bluish-white speckles. The new species is also distinct from all congeners in 12S rRNA to 16S rRNA mitochondrial DNA fragment sequences （uncorrected genetic distance P〉8.9%）. Advertisement call and tadpole morphology of the new species are described. Our molecular data showed Theloderma auratum sp. nov.

关键词： Theloderma auratum sp. nov. mtDNAphylogeny 12S rRNA 16S rRNA Kon Tum Gia Lai Endemism Taxonomy

A new species of the genus Leptolalax (Anura： Megophryidae) from southern Vietnam

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Zoological Research 2018年第3期39卷 185-201页

作者： Tang Van Duong Dang Trong Do Chung Dac Ngo Truong Quang Nguyen nikolay A. Poyarkov Vietnam National Museum of Nature Vietnam Academy of Science and Technology Hanoi Vietnam Department of Vertebrate Zoology Biological FacultyLomonosov Moscow State University Moscow 119234 Russia Faculty of Natural Sciences Phu Yen University Tuy Hoa Phu Yen Vietnam College of Education Hue University Hue Vietnam Institute of Ecology and Biological Resources Vietnam Academy of Science and Technology Hanoi Vietnam Graduate University of Science and Technology Vietnam Academy of Science and Technology Cau Giay Hanoi Vietnam Joint Russian- Vietnamese Tropical Research and Technological Center Nghia Do Cau Giay Hanoi Vietnam

We describe a new species of megophryid frog from Phu Yen Province in southern Vietnam. Leptolalax macrops sp. nov. is distinguished from its congeners by a combination of the following morphological attributes：（1） body size medium （SVL 28.0-29.3 mm in three adult males, 30.3 mm in single adult female）; （2） supra-axillary glands present, creamy white; ventrolateral glands indistinct; （3） tympanum externally distinct; （4） dorsal skin roughly granular with larger tubercles, dermal ridges on dorsum absent; （5） rudimentary webbing present between fingers I-II and I1-111; rudimentary webbing between all toes; fingers and toes without dermal fringes; （6） in life ventral surface greyish-violet with white speckling; （7） supratympanic fold distinct, dark brown in life; （8） iris bicolored, typically golden in upper half, fading to golden green in lower half; （9） tibia short （TbL/SVL 0.44-0.45 in males）; and （10） eyes large and protuberant （ED/SVL 0.15-0.16 in males） From all congeners for which comparable sequences are available, the new species differs markedly in the 16S rRNA mitochondrial gene sequence （P-distance〉5.7%）. The new species is currently known only from montane evergreen tropical forests of Song Hinh District, Phu Yen Province, and M＇Drak District of Dak Lak Province at elevations of 470-630 m a.s.l.. We suggest the new species should be considered as Data Deficient following the IUCN＇s Red List categories. We also report a previously unknownLeptolalax mtDNA lineage from an evergreen tropica forest in the Hoa Thinh District of Phu Yen Province which may also represent an undescribed species.

关键词： Leptolalax macrops sp. nov. Phu YenProvince Dak Lak Province Southern coastal regionof Vietnam