Effective pruning for XML structural match queries

2010 ◽  
Vol 69 (6) ◽  
pp. 640-659 ◽  
Author(s):  
Yefei Xin ◽  
Zhen He ◽  
Jinli Cao
Keyword(s):  
Structural Match

scholarly journals DIVERSIFIKASI EKSPOR NON MIGAS INDONESIA KE PASAR NON TRADISIONAL

2020 ◽  
Vol 14 (2) ◽  
pp. 215-238
Author(s):  
Hotsawadi Harahap ◽  
Widyastutik
Keyword(s):  
United Arab Emirates ◽  
Oil And Gas ◽  
Random Effect ◽  
Random Effect Model ◽  
Structural Match ◽  
Effect Model ◽  
Panel Data Regression ◽  
Data Regression ◽  
Oil Exports

Abstrak Penelitian ini bertujuan untuk menganalisis diversifikasi ekspor non migas Indonesia ke pasar non tradisional. Metode penelitian yang digunakan adalah analisis statistik deskriptif dengan pendekatan pengelompokan (clustering), Structural Match Index dan Demand Index, serta regresi data panel. Hasil penelitian menunjukkan bahwa negara yang diidentifikasikan sebagai negara non tradisional potensial adalah Brazil, Pantai Gading, Mesir, Georgia, Jamaica, Kazakhstan, Kuwait, Myanmar, Nigeria, Norway, Oman, Pakistan, Russian Federation, Trinidad and Tobago, Turkey, United Arab Emirates, dan Uruguay. Hasil regresi data panel menunjukkan bahwa Random Effect Model merupakan model yang terbaik untuk menjelaskan faktor-faktor yang memengaruhi ekspor non migas Indonesia ke negara non tradisional. Hasil regresi menunjukkan bahwa GDP riil negara tujuan, populasi negara tujuan, nilai tukar riil, FDI dan kualitas pelabuhan Indonesia berpengaruh signifikan secara statistik terhadap ekspor non migas Indonesia ke negara non tradisional potensial tersebut. Beberapa rekomendasi kebijakan yang perlu dilakukan untuk meningkatkan ekspor non migas ke negara tujuan non tradisional diantaranya perlu dilakukan intelejen pasar mengenai kebutuhan dan selera dari masing-masing negara non tradisional atas produk Indonesia, peningkatan kualitas pelabuhan Indonesia dan kebijakan tambahan yang memberikan insentif untuk menarik Foreign Direct Investment ke Indonesia. Kata Kunci: Diversifikasi Ekspor, Demand Index, Non traditional, Random Effect Model, Structural Match Index   Abstract This study aims to analyze the diversification of Indonesia's non-oil and gas exports to non-traditional markets. The research method used is descriptive statistical analysis with a clustering approach, Structural Match Index and demand index, and panel data regression. The results showed that countries identified as potential non-traditional countries were Brazil, Ivory Coast, Egypt, Georgia, Jamaica, Kazakhstan, Kuwait, Myanmar, Nigeria, Norway, Oman, Pakistan, Russian Federation, Trinidad and Tobago, Turkey, United Arab Emirates, and Uruguay. The panel data regression results show that the random effect model is the best model to explain the factors that influence Indonesia's non-oil exports to non-traditional countries. The results show that the real GDP of the destination country, the population of the destination country, the real exchange rate, FDI and the quality of Indonesia's ports have a statistically significant effect on Indonesia's non-oil exports to these potential non-traditional countries. Then, in this study there are several policy recommendations that need to be done to increase non-oil and gas exports to non-traditional destination countries including market intelligence regarding the needs and tastes of each non-traditional country for Indonesian products, improving the quality of Indonesian ports and additional policies that provide incentives to attract Foreign Direct Investment to Indonesia. Keywords:  Export Diversification, Demand Index, Non-traditional, Random Effect Model, Structural Match Index JEL Classifications: F13, F15, F18

scholarly journals Structural Match of Heterogeneously Nucleated Mn(OH)2(s) Nanoparticles on Quartz under Various pH Conditions

Langmuir ◽  
2016 ◽  
Vol 32 (41) ◽  
pp. 10735-10743 ◽  
Author(s):  
Haesung Jung ◽  
Byeongdu Lee ◽  
Young-Shin Jun
Keyword(s):  
Structural Match ◽  
Ph Conditions

scholarly journals On the Difference in Quality between Current Heuristic and Optimal Solutions to the Protein Structure Alignment Problem

2013 ◽  
Vol 2013 ◽  
pp. 1-8 ◽  
Author(s):  
Mauricio Arriagada ◽  
Aleksandar Poleksic
Keyword(s):  
Protein Structure ◽  
Heuristic Algorithms ◽  
Structure Alignment ◽  
Protein Structure Alignment ◽  
Optimal Solutions ◽  
Timely Manner ◽  
Matching Problem ◽  
Structural Match ◽  
Alignment Problem ◽  
The Difference

The importance of pairwise protein structural comparison in biomedical research is fueling the search for algorithms capable of finding more accurate structural match of two input proteins in a timely manner. In recent years, we have witnessed rapid advances in the development of methods for approximate and optimal solutions to the protein structure matching problem. Albeit slow, these methods can be extremely useful in assessing the accuracy of more efficient, heuristic algorithms. We utilize a recently developed approximation algorithm for protein structure matching to demonstrate that a deep search of the protein superposition space leads to increased alignment accuracy with respect to many well-established measures of alignment quality. The results of our study suggest that a large and important part of the protein superposition space remains unexplored by current techniques for protein structure alignment.

scholarly journals Epitaxial Growth and Orientation of GaN on (1 0 0) γ-LiAlO2

1997 ◽  
Vol 2 ◽  
Author(s):  
E. S. Hellman ◽  
Z. Liliental-Weber ◽  
D. N. E. Buchanan
Keyword(s):  
Epitaxial Growth ◽  
Orientation Relationship ◽  
Interface Energy ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structural Match ◽  
Image Position

The (1 0 0) face of γ-LiAlO2 has attracted attention as a possible substrate for GaN epitaxial growth. This is partly because this face has an excellent lattice and structural match to (1 0 0) GaN. This orientation would have a misfit of only −1.4% along the c-direction and −0.1% along the b-direction of LiAlO2. We find that in practice this orientation relationship does not occur; instead, (0 0 0 1) oriented GaN grows with a small tilt (0.6° towards the c-direction) between the film and substrate. Although the misfit along the substrate b direction is large (−6.3%) for this orientation, the tilt perfectly accommodates the −1.4% misfit in the c direction. We present characterization of these films by RHEED, X-ray diffraction, and TEM. We propose that the tilt is driven by a reduction of interface energy which occurs in polar, incoherent interfaces.

scholarly journals BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization

2020 ◽  
Author(s):  
José-Emilio Sánchez-Aparicio ◽  
Laura Tiessler-Sala ◽  
Lorea Velasco-Carneros ◽  
Lorena Roldán-Martín ◽  
Giuseppe Sciortino ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
De Novo ◽  
Conformational Transition ◽  
Protein Backbone ◽  
Metal Binding Sites ◽  
Structural Match ◽  
Geometric Descriptors ◽  
Metal Migration

<div><div><div><p>With a large amount of research dedicated to decoding how metallic species bind to protein, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parametrization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 50 metal-binding X-Ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems which structures (either experimental or theoretical) are not optimal for metal binding sites. We report here its application on three different challenging cases i) the modulation of metal-binding sites during conformational transition in human serum albumin, ii) the identification of possible routes of metal migration in hemocyanins, and iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology, and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding.</p></div></div></div>

scholarly journals Structure of Double-Shelled Rice Dwarf Virus

1998 ◽  
Vol 72 (11) ◽  
pp. 8541-8549 ◽  
Author(s):  
Guangying Lu ◽  
Z. Hong Zhou ◽  
Matthew L. Baker ◽  
Joanita Jakana ◽  
Deyou Cai ◽  
...  
Keyword(s):  
Crop Production ◽  
Rna Virus ◽  
Mass Density ◽  
Three Dimensional ◽  
Outer Shell ◽  
Dwarf Virus ◽  
Dimensional Structure ◽  
Rice Dwarf Virus ◽  
Structural Match ◽  
Economic Threat

ABSTRACT Rice dwarf virus (RDV), a member of the Reoviridaefamily, is a double-stranded RNA virus. Infection of rice plants with RDV reduces crop production significantly and can pose a major economic threat to Southeast Asia. A 25-Å three-dimensional structure of the 700-Å-diameter RDV capsid has been determined by 400-kV electron cryomicroscopy and computer reconstruction. The structure revealed two distinctive icosahedral shells: a T=13l outer icosahedral shell composed of 260 trimeric clusters of P8 (46 kDa) and an inner T=1 icosahedral shell of 60 dimers of P3 (114 kDa). Sequence and structural comparisons were made between the RDV outer shell trimer and the two crystal conformations (REF and HEX) of the VP7 trimer of bluetongue virus, an animal analog of RDV. The low-resolution structural match of the RDV outer shell trimer to the HEX conformation of VP7 trimer has led to the proposal that P8 consists of an upper domain of β-sandwich motif and a lower domain of α helices. The less well fit REF conformation of VP7 to the RDV trimer may be due to the differences between VP7 and P8 in the sequence of the hinge region that connects the two domains. The additional mass density and the absence of a known signaling peptide on the surface of the RDV outer shell trimer may be responsible for the different interactions between plants and animal reoviruses.

STRUCTURAL BASIS OF ANTIFREEZE PROTEIN ACTION

2006 ◽  
Vol 01 (03) ◽  
pp. 259-270
Author(s):  
CHRISTINA S. STROM ◽  
XIANG YANG LIU ◽  
ZONGCHAO JIA
Keyword(s):  
Experimental Observation ◽  
Growth Rates ◽  
Binding Sites ◽  
Structural Basis ◽  
Ice Crystal ◽  
One Dimensional ◽  
Structural Match ◽  
Ice Binding ◽  
Broad Variation ◽  
Ice Surfaces

Antifreeze Proteins (AFPs) modify the growth rates and orientations of ice crystal facets through attainment of the best structural match. The insect-type AFPs have ice binding surfaces (IBS) with regularly spaced binding intervals in two directions that engage the primary ice surfaces and reduce their growth rates preferentially. The primary ice surfaces are kinetically stable and have fixed orientations, since they are strongly bonded in two directions. The fish-type AFPs have one-dimensional helical and irregular globular IBSs that are either linearly extended with regular ice binding intervals, or have ice binding sites lacking spacing regularity. They adjust the orientations of the secondary ice surfaces, that have indeterminate face indices since they are strongly bonded in only one direction. The fish-type AFPs stabilize secondary ice surfaces and adjust their orientations by mimicking strong bonding directions, that are not present in the ice structure. The theory agrees with experimental observation and explains hitherto unexplained phenomena. The observed broad variation in prismatic and, more importantly, pyramidal ice crystallites produced in the presence of fish-type AFPs is explained, since these faces are secondary. The observed crystals triggered by most insect-type AFPs are disk shaped, because they consist of primary ice surfaces. The allegedly exceptional ice pyramids triggered by the insect-type TmAFP are the primary ice pyramid with fixed indices, and entirely different from the pyramids of the fish-type AFPs.

scholarly journals BioMetAll: Identifying Metal-Binding Sites in Proteins from Backbone Preorganization

2020 ◽  
Author(s):  
José-Emilio Sánchez-Aparicio ◽  
Laura Tiessler-Sala ◽  
Lorea Velasco-Carneros ◽  
Lorena Roldán-Martín ◽  
Giuseppe Sciortino ◽  
...  
Keyword(s):  
Metal Binding ◽  
Binding Sites ◽  
De Novo ◽  
Conformational Transition ◽  
Protein Backbone ◽  
Metal Binding Sites ◽  
Structural Match ◽  
Geometric Descriptors ◽  
Metal Migration

<div><div><div><p>With a large amount of research dedicated to decoding how metallic species bind to protein, in silico methods are interesting allies for experimental procedures. To date, computational predictors mostly work by identifying the best possible sequence or structural match of the target protein with metal binding templates. These approaches are fundamentally focused on the first coordination sphere of the metal. Here, we present the BioMetAll predictor that is based on a different postulate: the formation of a potential metal-binding site is related to the geometric organization of the protein backbone. We first report the set of convenient geometric descriptors of the backbone needed for the algorithm and their parametrization from a statistical analysis. Then, the successful benchmark of BioMetAll on a set of more than 50 metal-binding X-Ray structures is presented. Because BioMetAll allows structural predictions regardless of the exact geometry of the side chains, it appears extremely valuable for systems which structures (either experimental or theoretical) are not optimal for metal binding sites. We report here its application on three different challenging cases i) the modulation of metal-binding sites during conformational transition in human serum albumin, ii) the identification of possible routes of metal migration in hemocyanins, and iii) the prediction of mutations to generate convenient metal-binding sites for de novo biocatalysts. This study shows that BioMetAll offers a versatile platform for numerous fields of research at the interface between inorganic chemistry and biology, and allows to highlight the role of the preorganization of the protein backbone as a marker for metal binding.</p></div></div></div>

Enhancement in Electrical Properties of (Ba,Sr)TiO3 Films Using Tailored Oxide Electrodes

1999 ◽  
Vol 574 ◽  
Author(s):  
Duck-Kyun Choi ◽  
Kyung-Woong Park ◽  
Jeong-Hee Park ◽  
Se-Hoon Oh ◽  
Boum-Seock Kim ◽  
...  
Keyword(s):  
Electrical Properties ◽  
Leakage Current ◽  
Dielectric Material ◽  
Rf Magnetron Sputtering ◽  
Lattice Parameter ◽  
Structural Match ◽  
Oxide Electrodes ◽  
Interface Characteristics ◽  
High Dielectric ◽  
Perovskite Type

AbstractSelection of a proper electrode for high dielectric material such as (Ba, Sr)TiO3 is a great concern because the deposition of BST requires a high temperature and an oxidizing atmosphere. In this study, we suggested the perovskite-type electrodes, which provide a structural match with the BST dielectric material, under the recognition that the high leakage current is associated with the structural mismatch between BST and the electrode. We studied the (Ca,Sr)RuO3 electrode of which the lattice parameter can be tuned to fit into BST by changing the Ca/Sr ratio. We also studied (Ba,Sr)RuO3 electrode which is not only structurally identical but also chemically similar to BST. In addition, the effect of doping in the BSR electrode was investigated to minimize the leakage current by proper modulation of the barrier height. The electrodes were directly deposited on an Si substrate and all the films in the experiments were deposited by RF magnetron sputtering technique. Electrical properties were measured from MIM structure. The main focus was to address the effect of Ca/Sr and Ba/Sr ratio variations in the electrodes on the resulting dielectric constant and the leakage current. The interface characteristics between the BST film and the electrode were examined in order to interpret the electrical properties of BST films.

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