Types Of Complex Structures Research Articles

Lin_F9: A Linear Empirical Scoring Function for Protein-Ligand Docking.

Molecular docking is one of the most widely used computational tools in structure-based drug design and is critically dependent on accuracy and robustness of the scoring function. In this work, we introduce a new scoring function Lin_F9, which is a linear combination of nine empirical terms, including a unified metal bond term to specifically describe metal-ligand interactions. Parameters in Lin_F9 are obtained with a multistage fitting protocol using explicit water-included structures. For the CASF-2016 benchmark test set, Lin_F9 achieves the top scoring power among all 34 classical scoring functions for both original crystal poses and locally optimized poses with Pearson correlation coefficients (R) of 0.680 and 0.687, respectively. Meanwhile, in comparison with Vina, Lin_F9 achieves consistently better scoring power and ranking power with various types of protein-ligand complex structures that mimic real docking applications, including end-to-end flexible docking for the CASF-2016 benchmark test set using a single or an ensemble of protein receptor structures, as well as for D3R Grand Challenge (GC4) test sets. Lin_F9 has been implemented in a fork of Smina as an optional built-in scoring function that can be used for docking applications as well as for further improvement of scoring functions and docking protocols. Lin_F9 is accessible through https://yzhang.hpc.nyu.edu/Lin_F9/.

Ternary Zinc Antimonides Unlocked Using Hydride Synthesis

Three new sodium zinc antimonides Na11Zn2Sb5, Na4Zn9Sb9, and NaZn3Sb3 were synthesized utilizing sodium hydride NaH as a reactive sodium source. In comparison to the synthesis using sodium metal, salt-like NaH can be ball-milled, leading to the easy and uniform mixing of precursors in the desired stoichiometric ratios. Such comprehensive compositional control enables a fast screening of the Na-Zn-Sb system and identification of new compounds, followed by their preparation in bulk with high purity. Na11Zn2Sb5 crystallizes in the triclinic P1 space group (No. 2, Z = 2, a = 8.8739(6) Å, b = 10.6407(7) Å, c = 11.4282(8) Å, α = 103.453(2)°, β = 96.997(2)°, γ = 107.517(2)°) and features polyanionic [Zn2Sb5]11- clusters with unusual 3-coordinated Zn atoms. Both Na4Zn9Sb9 (Z = 4, a = 28.4794(4) Å, b = 4.47189(5) Å, c = 17.2704(2) Å, β = 98.3363(6)°) and NaZn3Sb3 (Z = 8, a = 32.1790(1) Å, b = 4.51549(1) Å, c = 9.64569(2) Å, β = 98.4618(1)°) crystallize in the monoclinic C2/m space group (No. 12) and have complex new structure types. For both compounds, their frameworks are built from ZnSb4 distorted tetrahedra, which are linked via edge-, vertex-sharing, or both, while Na cations fill in the framework channels. Due to the complex structures, Na4Zn9Sb9 and NaZn3Sb3 compounds exhibit low thermal conductivities (0.97-1.26 W·m-1 K-1) at room temperature, positive Seebeck coefficients (19-32 μV/K) suggestive of holes as charge carriers, and semimetallic electrical resistivities (∼1.0-2.3 × 10-4 Ω·m). Na4Zn9Sb9 and NaZn3Sb3 decompose into the equiatomic NaZnSb above ∼800 K, as determined by in situ synchrotron powder X-ray diffraction. The discovery of multiple ternary compounds highlights the importance of judicious choice of the synthetic method.

ОСОБЛИВОСТІ УРОКУ ІНОЗЕМНОЇ МОВИ

The article considers the main features of a foreign language lesson in view of the goals and content of the lesson, its complex nature, structure and main types. Considerable attention is paid to the complex nature of work in the classroom, as all elements of language material – phonetic, lexical and grammatical – are interdependent in the implementation of foreign language speech activities. The specifics of goal setting are considered taking into account the features of the lesson, its structure and typology. The purpose of the lesson is a definite reflection of the ultimate goal, a specific part of it. Proper understanding of the purpose of the lesson should be based on a combination of two features of the lesson – language learning and complexity. Each foreign language lesson has a practical, educational and upbringing purpose. The structure of the lesson involves closely interrelated and independent activities of teachers and students, in which the learning process is embodied. The article focuses on the initial stage of a foreign language lesson, which prepares students to implement skills and abilities in various types of speech activities, such as speaking, listening, reading and writing. The beginning of the lesson is one of the constant stages of a foreign language lesson. The initial stage consists of various exercises, mostly oral. It can also be implemented in the form of dialogue between students, in the form of students asking a series of questions on a particular topic addressed to the class. The teacher may also suggest starting the lesson with a story based on familiar and understandable learning material. In addition, individual or frontal control can be performed at the beginning of the lesson. Since a foreign language lesson is a lesson in the development of skills, the stages of communication and consolidation of new knowledge are combined with the performance of various exercises. Lessons of different types, combined for a specific purpose, can form a system of thematic series, within which the objectives of the lessons vary in quantitative and qualitative terms. There are three such systems, namely, the system of lessons aimed at: 1) the development of oral skills and abilities; 2) reading and understanding the text; 3) for the development of both groups of skills. An overview of the typology of foreign language lessons developed and proposed by leading experts in the field of methods of teaching foreign languages is presented in order to emphasize the features of a foreign language lesson.

Advances in understanding of the biosynthetic pathway and regulatory mechanism of triterpenoid saponins in plants

Triterpenoid saponins are a type of triterpenoid glycoside. Widely distributed in plants, triterpenoid saponins play a role in resisting pathogenic microorganisms and herbivores, but they also have a variety of pharmacological activities that have been widely adopted in medicine, common chemicals, food, and agriculture, to name a few. In recent years, with the development of science and technology and the deepening of research, the basic framework and regulatory mechanisms of triterpenoid saponin biosynthesis in plants have become better understood. Plant triterpenoid saponins have multiple types of complex structures and, although they share a common precursor synthesis pathway, their post-modification stages are highly specific and diverse. In this paper, the biosynthetic pathway, key enzyme genes, transcriptional regulation, and microbial cell engineering of triterpenoid saponins were reviewed, and the future development direction of triterpenoid saponins, which could provide theoretical reference for related research in the abovementioned fields, was prospected.

Weighted homogeneous surface singularities homeomorphic to Brieskorn complete intersections

For a given topological type of a normal surface singularity, there are various types of complex structures which realize it. We are interested in the following problem: Find the maximum of the geometric genus and a condition for that the maximal ideal cycle coincides with the undamental cycle on the minimal good resolution. In this paper, we study weighted homogeneous surface singularities homeomorphic to Brieskorn complete intersection singularities from the perspective of the problem.

Analysis of Key Points of Radiation Sources in Proton and Carbon Ion Radiotherapy Facilities in Shanghai

Compared with conventional high energy X-ray radiotherapy, proton/carbon ion has obvious advantages because of its Bragg peak dose distribution. However, proton heavy ion facility has complex structure, high energy and various radiation types due to various nuclear reaction processes, the radiation protection safety brought by the operation of facilities has gradually attracted attention. Taking the proton/carbon ion radiotherapy facility of Shanghai Proton and Heavy Ion Center as an example, the author mainly analyzed the operation principle of proton/carbon ion treatment facility, the basis of radiation protection, analysis of key radiation source points, etc., so as to provide theoretical support and experience for radiation protection.

Structural analysis and reaction mechanism of the disproportionating enzyme (D-enzyme) from potato.

Starch produced by plants is a stored form of energy and is an important dietary source of calories for humans and domestic animals. Disproportionating enzyme (D-enzyme) catalyzes intramolecular and intermolecular transglycosylation reactions of α-1, 4-glucan. D-enzyme is essential in starch metabolism in the potato. We present the crystal structures of potato D-enzyme, including two different types of complex structures: a primary Michaelis complex (substrate binding mode) for 26-meric cycloamylose (CA26) and a covalent intermediate for acarbose. Our study revealed that the acarbose and CA26 reactions catalyzed by potato D-enzyme involve the formation of a covalent intermediate with the donor substrate. HPAEC of reaction substrates and products revealed the activity of the potato D-enzyme on acarbose and CA26 as donor substrates. The structural and chromatography analyses provide insight into the mechanism of the coupling reaction of CA and glucose catalyzed by the potato D-enzyme. The enzymatic reaction mechanism does not involve residual hydrolysis. This could be particularly useful in preventing unnecessary starch degradation leading to reduced crop productivity. Optimization of this mechanism would be important for improvements of starch storage and productivity in crops.

Protein interactions studies of the small TbTims chaperons in the mitochondrion of Trypanosoma brucei

Trypanosoma brucei causes a neglected tropical disease known as trypanosomiasis that causes death in population of Sub‐Sahara Africa. T. brucei possesses a single mitochondrion and like other eukaryotes it imports most of its proteins into the mitochondria, however mitochondrial protein import machinery is divergent in this parasite, which makes it a useful target to control this disease. Nucleus‐encoded proteins are imported into T. brucei mitochondrion via two major heteromeric protein complexes in the outer and inner membrane, ATOM and TbTIM, respectively. Besides the membrane integral protein components of these complexes, TbTIM is also peripherally associated with 6 small TbTims (Tim9, 10, 8/13, 11, 12, and 13). At least three of these small TbTims (TbTim8/13, 11, & 12) are unique for T. brucei. Knock‐down of any of these 6 small TbTims destabilized the TbTIM17 complex therefore these proteins are essential in T. brucei. In fungi and human, the small Tims are soluble proteins that form hetero‐hexameric complexes. Each small Tims possesses two pairs of CX3C motifs that are required for proper folding of the monomers by formation of the two intramolecular disulfide bonds. T. brucei small Tims also possess these conserved motifs, except for TbTim12, which has only one pair. However, it is not clear how small TbTims interact with each other and what type of complex structure they form. Thus, our goal for these studies is to find the direct interaction pattern for the small TbTims. To complete this goal, we use yeast two hybrid (Y2H) analysis. Results showed that although all small TbTims can interact with one another, some of these interactions are stronger than others. Overall, we found that TbTim8/13 interacts strongly with TbTim9, TbTim10, and TbTim8/13 while TbTim13 interacts strongly with TbTim13. Based on these results we proposed 3 possible model for small TbTim heterohexameric complexes; 1) random order, and 2) defined order, and 3) modular with different sub‐complexes. We are now testing these models by structure‐modeling and site‐directed mutagenesis studies.Support or Funding InformationThis work is supported by the following NIH grants: 5RO1AI125666, 2SC1GM081146, and R25 GM05994

Cluster computing‐aided model updating for a high‐fidelity finite element model of a long‐span cable‐stayed bridge

SummaryAccurate and high‐fidelity finite element (FE) models are in great demand in the design, performance assessment, and life‐cycle maintenance of long‐span cable‐stayed bridges. The structural system of a long‐span cable‐stayed bridge is often huge in size and complex with many components connected and various materials constituted. Therefore, the FE model of a long‐span cable‐stayed bridge involves a large number of elements and nodes with many uncertainties. The model updating of the FE model to best represent a real bridge is necessary but very challenging. One of the challenging issues is that the numerical computation needed for searching the global optimum of a large set of structural parameters is so extensive that the existing FE (not surrogate) model‐based updating methods cannot fulfill this task. In this study, a cluster computing‐aided FE model updating framework is proposed for the high‐performance FE model updating of large and complex structures. In the framework, several computer software packages, including MSC.Marc, Python, and MATLAB, are interconnected for making use of their respective functions of strength. The shake table test of a scaled physical structure of the Sutong cable‐stayed bridge in China is used to validate the accuracy and efficiency of the proposed framework. The simulated bridge responses based on the updated FE model are in good agreement with the measured ones from the shake table test. The successful application of the proposed framework provides a reference for the model updating of other types of large and complex structures.

Research on the Cognitive Effort of Sight-Interpreting Complex English Sentences into Chinese: Evidence from Eye Tracking

It is widely known that sight-interpreting, one of the typical forms of conference interpreting, requires the interpreters to exert great effort in transforming one language into another. Due to the difference between Chinese and English, some sentence structures such as relative clauses prove to be even more difficult to render. Some experienced interpreters are able to do such strenuous task with ease. Uncovering what is going on during information processing is enlightening in that it would shed light on how human brain uses certain types of mechanism to process information, which is conducive to the artificial intelligence. Eye-tracking experiment is designed, 31 subjects are recruited with an average age of 22 and comparable linguistic competence to participate in a 40-50 min experiment, during which each subject is required to sight-interpret the self-designed, expert-proven sentences which differ only in the role of the relative pronoun in the relative clauses. Data analysis clearly indicates that the cognitive effort of processing complex sentences as evidenced by two types of relative clauses (one is called OR because the relative pronouns function as object in the relative clause, the other SB because the relative pronouns function as subject in the relative clause) are different, the former requiring more cognitive effort than the latter, as shown in several key eye-movement measures such as regression-in, regression-out, first fixation duration, gaze duration, regression duration, and total reading duration. These differences are statistically significant within the AOIs such as the antecedent, relative clause. The finding further substantiates the hypothesis that sight-interpreting is more strenuous and thus requires more cognitive effort than the common readers. Besides, different structure of the relative clauses also plays a role in consuming the cognitive effort of the interpreters. However, it remains unclear whether the length of the relative clause plays a decisive role in influencing the cognition of whole sentence while sight-interpreting. Besides, whether the research results are applicable to other types of complex structure remain unanswered. More data should be collected to incorporate more complex structure in order to uncover the possible cognitive effort during sight-interpreting.

Enclosure Utilization and Enrichment Structure Preferences of Captive Coyotes

Environmental enrichment improves well-being of captive animals using a variety of tools, including adding complexity to the physical environment. Designing enrichment structures requires an understanding of behavioral and biological responses to enrichment efforts. Captive coyotes (Canis latrans) utilize shelter structures to hide, rest, and display vigilant behavior. Because these simple structures are regularly used, new and more complex enrichment structures could enhance enclosure enrichment. This study examined the time captive coyotes spent at discrete, complex enclosure features to determine: (1) how coyotes utilize enclosure space and shelter structures; and (2) if coyotes have a preferred enrichment structure design. Three enrichment structure designs (ramp, closed, and neutral) were installed simultaneously in 0.6-ha enclosures during two breeding seasons (January – March). Additional coyote pairs were monitored in control enclosures with simple structures. GPS-collars and scan sampling were used throughout a 28-day testing period to record space use and behavior. Coyotes spent most of their time at perimeter and open areas, but also exhibited a preference for shelter structures. Coyotes utilized the complex enrichment structures in treatment enclosures more than simple structures in control enclosures. Although there was no statistical preference for one specific type of complex structure, composite evidence from GPS-collars and behavioral data suggested that coyotes were most frequently located at ramp structures. Coyotes utilized ramp structures more during the daytime and demonstrated higher rates of vigilance there. This study advances the knowledge of captive coyote spatial patterns while helping improve environmental enrichment planning for captive facilities through the exploration of adding complexity to animal enclosures.

Stabilization of the pyrochlore phase of Mn2Sb2O7 by double substitution

Polycrystalline samples of (Ce4+Mn2+3)(Ga3+Sb5+3)O14 were synthesized by a high-temperature solid-state reaction. In contrast with the parent Mn2Sb2O7 compound that adopts a rhombohedral or monoclinic structure at T > 600 °C, the pyrochlore structure of CeMn3GaSb3O14 is retained up to at least T = 1070°C. High-resolution synchrotron x-ray diffraction measurements show no sign of a superstructure or distortion from cubic symmetry in the substituted compound. The stabilization of the pyrochlore structure can be attributed to the effect of configurational disorder due to partial substitution of A and B site. Magnetization and heat capacity data suggest a spin-glass transition below T ≈ 2 K. Our results extends the range of available pyrochlore oxides, and demonstrate that entropic stabilization is a viable route to stabilize novel materials with complex structure types.

A review on cubosome: The novel drug delivery system

Cubosomes are nanoparticles in structure which is mainly made of certain amphiphilic lipids in definite proportion, known as bicontinuous cubic phase liquid crystals. Hydrating a surfactant or polar lipid that forms cubic phase and then dispersing a solid like phase into smaller particles usually forms a cubosomes. They perform solid like rheology with unique properties of practical interest. They are thermodynamically stable and they have carvenous (honeycomb) structures which are tightly packed twisted into three dimensional bilayers. This type of complex structure allows them to have greater drug loading ability. Cubosomes have ability to encapsulate the hydrophobic, hydrophilic, amphiphilic substances. Cubosomes can increase the solubility of poorly soluble drug. Cubosome dispersions are bioadhesive and biocompatible. Because of their properties, cubosome are versatile systems, administrable by different ways such as orally, percutaneously and parenterally. Cubosome structure by means of electron microscopy, light scattering, x-ray and NMR, nevertheless few researchers has been studying the potential of cubosome as delivery systems.

Electronic, Optical, and Mechanical Properties of Diamond Nanowires Encapsulated in Carbon Nanotubes: A First-Principles View

In recent years, carbon-based complex nanostructures have been explored due to many of their unique properties and related applications. Here we employ theoretical simulation based on density functional theory to investigate electronic, optical, and mechanical properties of a new type of the carbon-based complex nanostructure, i.e., experimentally fabricated one-dimensional complex material of hydrogenated diamond nanowires encapsulated in carbon nanotubes (CNW@CNT). The complex structure CNW@CNT is found to possess metallicity for the outer CNT and wide band gap nature for the inner CNW simultaneously. Under uniaxial strain a specific insulator-to-metal transition occurs for the inner CNW in the complex structure, with threshold value much smaller than that for the individual insulator. This effect is interpreted as that the strain induces relative shifting of bands of CNW and CNT and even charge transfer between them, making the valence band of CNW become not fully occupied. The inner CNW in the complex structure has optical absorption only in the ultraviolet waveband. The further examinations on the conductive bands reveal existences of nearly free-electron states which entirely dominate the conductive bands of the inner CNW and suggest that the electron–hole separation will happen in the CNW@CNT upon the ultraviolet illumination. The simulation results also reveal higher Young’s modulus of the CNW@CNT and the individual CNW even larger than those of CNT and graphene. We propose a simple parallel spring model to establish the relationship between the Young’s modulus of the complex structure and the one of its component which should be helpful to future predictions for other complex structures. The potential applications of this new type of carbon-based complex structure as a multifunctional integrated nanomaterial in future nanoelectronics, nano-optoelectronics, and nanoelectromechanics are discussed.

Analysis of Structural Types and Mechanical Performance of Steel–Concrete Connections without Cells

AbstractSteel–concrete connections, as key components of hybrid bridges, present a complex structural type and mechanical behavior. On the basis of the steel–concrete connections in the Lichuan Bri...

Key geological issues and main controls on accumulation and enrichment of Chinese shale gas

Abstract By analyzing geological characteristics of shale gas in Southern China and the United States, main factors controlling the accumulation and key issues in the exploration and development of shale gas in China have been examined. The geological characteristics of shale gas in China include multi-stage tectonic evolution, complex structure types, abundant faults, small continuous distribution area of shale formations, and no corresponding relationship between current thermal evolution degree and current burial depth of two main sets of shale formations (the Cambrian and Silurian). According to the analysis of the factors affecting shale gas enrichment such as fracture, tectonic type, shale gas migration, and gas content etc, the enrichment mechanisms of shale gas in China are: “sedimentary facies and preservation condition” are the main reservoir-controlling factors affecting the accumulation of shale gas, and “structure types and tectonism” are the main factors controlling the enrichment of shale gas in China; The former factors define shale gas plays, and the latter ones determine the position of sweet spots. The future research directions of shale gas in China are: firstly, contrary to the shale gas development in the United States, shale gas exploration and development in China should extend from the overpressure to normal pressure, and even low pressure areas; secondly, shale gas exploration in the Sichuan basin should extend from middle-deep to deep formations, studies should be done on the shale gas enrichment mechanism and accumulation models in formations deeper than 4 000 m, and horizontal well fracturing technology for these formations; thirdly, the development of transitional facies and continental facies shale gas should be brought along by drawing on exploration and development experience of marine shale gas.

Advantages of complex SQL types in storing XML documents

This contribution looks at and evaluates new ways to map XML documents to relational database systems preserving their hierarchical structure. In particular we take advantage of the advanced features available following the SQL:2003 standard, which defines complex structure and collection types. Starting out with a survey of existing methods, basic questions concerning appropriate and efficient forms of mapping XML documents to SQL-compliant data types are addressed. This leads to a reversible conversion method, which is subsequently implemented in a prototype application. The design of the mapping is geared towards existing, mature relational database management systems (DBMS). It turns out that among the products considered, IBM Informix seems to offer the best support for complex structure and collection types in the context of our application. To better assess the performance of the mapping process, the observed running time and the required in-memory and database storage of the implementation are measured and evaluated.

Clause linking in L2 English

The development of clause linkage in a second language has been studied extensively in the fields of applied linguistics and second language research. Several studies have focused on the development of specific types of complex structures, essentially based on the development of different classes of subordinate clauses distinguished by traditional grammar. The present contribution uses as a theoretical framework Role and Reference Grammar. RRG’s model of clause linkage proposes a different array of possible relations between combined clauses, adding the concept of cosubordination to the traditional dichotomy coordination/subordination, and pays attention to both predicate-based complexification within the clause and full clause combinations. RRG bases its classification of linkage types on the Interclausal Relations Hierarchy (Van Valin & LaPolla 1997), which unites syntactic and semantic aspects of clause complexification. The present article focuses on the syntax-semantics interface as realized within the Interclausal Relations Hierarchy, and on its impact on the acquisition of clause linkage structures by adolescent L2 learners of English. The corpus consists of oral narrative English interlanguage data elicited from 12- to 18-year-old Dutch-speaking secondary school pupils in Flanders (Belgium). Results show that RRG’s main principles of clause linkage are easily applicable to second language acquisition. The syntactic and semantic strength of a given juncture were found to often coincide in the data, as predicted, and any syntactic encoding of a semantic juncture which matches its semantic strength is likely to be acquired more easily and/or earlier than non-matching realizations. Although not all predictions made by RRG concerning structural variation were confirmed by our L2 English data, we conclude that RRG provides a fruitful, coherent and powerful framework for studying clause linkage and sentence complexification in spoken L2 learner discourse.

Convergence Properties of a Sequential Regression Multiple Imputation Algorithm

A sequential regression or chained equations imputation approach uses a Gibbs sampling-type iterative algorithm that imputes the missing values using a sequence of conditional regression models. It is a flexible approach for handling different types of variables and complex data structures. Many simulation studies have shown that the multiple imputation inferences based on this procedure have desirable repeated sampling properties. However, a theoretical weakness of this approach is that the specification of a set of conditional regression models may not be compatible with a joint distribution of the variables being imputed. Hence, the convergence properties of the iterative algorithm are not well understood. This article develops conditions for convergence and assesses the properties of inferences from both compatible and incompatible sequence of regression models. The results are established for the missing data pattern where each subject may be missing a value on at most one variable. The sequence of regression models are assumed to be empirically good fit for the data chosen by the imputer based on appropriate model diagnostics. The results are used to develop criteria for the choice of regression models. Supplementary materials for this article are available online.

Finding optimal interaction interface alignments between biological complexes.

Motivation: Biological molecules perform their functions through interactions with other molecules. Structure alignment of interaction interfaces between biological complexes is an indispensable step in detecting their structural similarities, which are keys to understanding their evolutionary histories and functions. Although various structure alignment methods have been developed to successfully access the similarities of protein structures or certain types of interaction interfaces, existing alignment tools cannot directly align arbitrary types of interfaces formed by protein, DNA or RNA molecules. Specifically, they require a ‘blackbox preprocessing’ to standardize interface types and chain identifiers. Yet their performance is limited and sometimes unsatisfactory.Results: Here we introduce a novel method, PROSTA-inter, that automatically determines and aligns interaction interfaces between two arbitrary types of complex structures. Our method uses sequentially remote fragments to search for the optimal superimposition. The optimal residue matching problem is then formulated as a maximum weighted bipartite matching problem to detect the optimal sequence order-independent alignment. Benchmark evaluation on all non-redundant protein–DNA complexes in PDB shows significant performance improvement of our method over TM-align and iAlign (with the ‘blackbox preprocessing’). Two case studies where our method discovers, for the first time, structural similarities between two pairs of functionally related protein–DNA complexes are presented. We further demonstrate the power of our method on detecting structural similarities between a protein–protein complex and a protein–RNA complex, which is biologically known as a protein–RNA mimicry case.Availability and implementation: The PROSTA-inter web-server is publicly available at http://www.cbrc.kaust.edu.sa/prosta/.Contact: xin.gao@kaust.edu.sa