PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public repository for information on chemical substances and their biological activities, launched in 2004 as a component of the Molecular Libraries Roadmap Initiatives of the US National Institutes of Health (NIH). For the past 11 years, PubChem has grown to a sizable system, serving as a chemical information resource for the scientific research community. PubChem consists of three inter-linked databases, Substance, Compound and BioAssay. The Substance database contains chemical information deposited by individual data contributors to PubChem, and the Compound database stores unique chemical structures extracted from the Substance database. Biological activity data of chemical substances tested in assay experiments are contained in the BioAssay database. This paper provides an overview of the PubChem Substance and Compound databases, including data sources and contents, data organization, data submission using PubChem Upload, chemical structure standardization, web-based interfaces for textual and non-textual searches, and programmatic access. It also gives a brief description of PubChem3D, a resource derived from theoretical three-dimensional structures of compounds in PubChem, as well as PubChemRDF, Resource Description Framework (RDF)-formatted PubChem data for data sharing, analysis and integration with information contained in other databases.
We propose a new EIT image reconstruction algorithm using multiple boundary voltage data from a planar array of voltage-sensing electrodes. The current injection electrodes are placed so that the induced internal currents approximately flow in the direction parallel to the surface of the voltage-sensing probe. The proposed algorithm uses the interrelationship between the measured voltage differences and the computed current, which allows us to derive a PDE-based Ohms law. Based on the derived voltage-current relation, we produce images of conductivity changes within a local region underneath the voltage-sensing probe. We describe the new image reconstruction algorithm and its numerical simulation results.
This is the dataset used in the publication of "Resource Description Framework (RDF) Modeling of Named Entity Co-occurrences in Biomedical Literature and Its Integration with PubChemRDF"
PubChem (https://pubchem.ncbi.nlm.nih.gov) is a public chemical database at the U.S. National Institutes of Health. Visited by millions of users every month, it plays a role as a key chemical information resource for biomedical research communities. Data in PubChem is from hundreds of contributors and organized into multiple collections by record type. Among these are the Protein, Gene, Pathway, and Taxonomy data collections. Records in these collections contain information on chemicals related to a given biological target (i.e., protein, gene, pathway, or taxon), helping users to analyze and interpret the biological activity data of molecules. In addition, annotations about the biological targets are collected from authoritative or curated data sources and integrated into the four collections. The content can be programmatically accessed through PubChem's web service interfaces (including PUG View). A machine-readable representation of this content is also provided within PubChemRDF.
Purpose - The purpose of this study was to investigate the effects of 4th Industrial Revolution technologies adopted by Korean firms on their exports in the global market Design/methodology/approach - This study collected 106,175 observations of 6,976 firms from the MDIS (Micro Data Integrated Service) by the Department of Statistics, specifically on the Survey of Corporate Activities together with the survey and financial data from 2006 till 2017. Using fixed effects panel models and PSM methods, this study introduces a revised gravity model on exports and OFDI. Findings - First, the technologies in the Fourth Industrial Revolution adopted by firms as a whole have a negative effect on their exports. Second, while the effect of width and level of applied technologies separately have a positive effect gradually changing from negative effect in their initial stage on their exports. Third, corporate outward direct investments, both overseas and domestic, have a negative effect on exports. Research implications or Originality - The findings reject many of those in prior studies by incorporating various gravity factors in the empirical models, such as the distance to the host country, its average tariff rate, foreign exchange rate, population, etc. pertaining to corporate OFDI decisions in addition to many corporate characteristic factors like firm size, ROA, shareholdings, etc, which is unique.
The B3LYP/DZP++ level of theory has been employed to investigate the structures and energetics of the deprotonated adenine-uracil base pairs, (AU-H)-. Formation of the lowest-energy structure, [A(N9)-U]- (which corresponds to deprotonation at the N9 atom of adenine), through electron attachment to the corresponding neutral is accompanied by proton transfer from the uracil N3 atom to the adenine N1 atom. The driving force for this proton transfer is a significant stabilization from the base pairing in the proton transferred form. Such proton transfer upon electron attachment is also observed for the [A(N6b)-U]- and [A(C2)-U]- anions. Electron attachment to the A-U(N3) radical causes strong lone pair repulsion between the adenine N1 and the uracil N3 atoms, driving the two bases apart. Similarly, lone pair repulsion in the anion A(N6a)-U causes the loss of coplanarity of the two base units. The computed adiabatic electron attachment energies for nine AU-H radicals range from 1.86 to 3.75 eV, implying that the corresponding (AU-H)- anions are strongly bound. Because of the large AEAs of the (AU-H) radicals, the C-H and N-H bond dissociation in the AU- base pair anions requires less energy than the neutral AU base pair. The computed C-H and N-H bond dissociation energies for the AU- anion (i.e., the AU base pair plus one electron) are in the range 1.0-3.2 eV, while those for neutral AU are 4.08 eV or higher.
Abstract Background To improve the utility of PubChem, a public repository containing biological activities of small molecules, the PubChem3D project adds computationally-derived three-dimensional (3-D) descriptions to the small-molecule records contained in the PubChem Compound database and provides various search and analysis tools that exploit 3-D molecular similarity. Therefore, the efficient use of PubChem3D resources requires an understanding of the statistical and biological meaning of computed 3-D molecular similarity scores between molecules. Results The present study investigated effects of employing multiple conformers per compound upon the 3-D similarity scores between ten thousand randomly selected biologically-tested compounds (10-K set) and between non-inactive compounds in a given biological assay (156-K set). When the “best-conformer-pair” approach, in which a 3-D similarity score between two compounds is represented by the greatest similarity score among all possible conformer pairs arising from a compound pair, was employed with ten diverse conformers per compound, the average 3-D similarity scores for the 10-K set increased by 0.11, 0.09, 0.15, 0.16, 0.07, and 0.18 for ST ST-opt , CT ST-opt , ComboT ST-opt , ST CT-opt , CT CT-opt , and ComboT CT-opt , respectively, relative to the corresponding averages computed using a single conformer per compound. Interestingly, the best-conformer-pair approach also increased the average 3-D similarity scores for the non-inactive–non-inactive (NN) pairs for a given assay, by comparable amounts to those for the random compound pairs, although some assays showed a pronounced increase in the per-assay NN-pair 3-D similarity scores, compared to the average increase for the random compound pairs. Conclusion These results suggest that the use of ten diverse conformers per compound in PubChem bioassay data analysis using 3-D molecular similarity is not expected to increase the separation of non-inactive from random and inactive spaces “on average”, although some assays show a noticeable separation between the non-inactive and random spaces when multiple conformers are used for each compound. The present study is a critical next step to understand effects of conformational diversity of the molecules upon the 3-D molecular similarity and its application to biological activity data analysis in PubChem. The results of this study may be helpful to build search and analysis tools that exploit 3-D molecular similarity between compounds archived in PubChem and other molecular libraries in a more efficient way.
The effects of hydration on the lowest triplet states of the DNA/RNA pyrimidines have been studied by including one and two water molecules explicitly. Three configurations for the singly hydrated cytosine moiety were located, and six for the doubly hydrated system. For thymine and uracil, four singly and eight doubly hydrated structures were found. The singlet-triplet energy gaps of all three pyrimidines (cytosine, thymine, and uracil) fall in the low-energy range of ultraviolet radiation (UVA). Energetic excited states can be a step leading to lesions in DNA, such as a mismatched base pairs. Although the adiabatic and vertical electronic excitation energies for all three pyrimidines slightly increase upon inclusion of additional water molecules, this effect upon the excitation energies is much smaller than hydration effects upon the electron affinities and ionization energies of the three nucleobases. Because both the ground state and the triplet state are neutral, the hydration energy difference between the two states is not significant (compared to those between the neutral and charged species), making the excitation energy less sensitive to hydration.
We report unprecedentedly high output powers measured from large area two-dimensional square-lattice photonic-crystal band-edge lasers (BELs), patterned by holographic lithography. In order to ensure mechanical rigidity, the BELs were fabricated in an InP-based epilayer bonded onto a fused silica substrate beforehand. The BEL devices, employing the surface-emitting Γ-point monopole band-edge mode, provide a fiber-coupled single mode output power as high as 2.6 mW and an external differential quantum efficiency of ~4%. The results of a three-dimensional finite-difference time-domain simulation agree with the experimental observation that the large BELs are beneficial for achieving both high power output and high differential quantum efficiency.
Magnetic resonance electrical impedance tomography (MREIT) attempts to provide conductivity images of an electrically conducting object with a high spatial resolution. When we inject current into the object, it produces internal distributions of current density J and magnetic flux density B =( Bx , By , Bz ). By using a magnetic resonance imaging (MRI) scanner, we can measure Bz data where z is the direction of the main magnetic field of the scanner. Conductivity images are reconstructed based on the relation between the injection current and Bz data. The harmonic Bz algorithm was the first constructive MREIT imaging method and it has been quite successful in previous numerical and experimental studies. Its performance is, however, degraded when the imaging object contains low-conductivity regions such as bones and lungs. To overcome this difficulty, we carefully analyzed the structure of a current density distribution near such problematic regions and proposed a new technique, called the local harmonic Bz algorithm. We first reconstruct conductivity values in local regions with a low conductivity contrast, separated from those problematic regions. Then, the method of characteristics is employed to find conductivity values in the problematic regions. One of the most interesting observations of the new algorithm is that it can provide a scaled conductivity image in a local region without knowing conductivity values outside the region. We present the performance of the new algorithm by using computer simulation methods.
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