QuantumChemistry
LiteratureSearch
search the scientific literature
Calling Sequence Parameters Description
Options References Examples
Calling Sequence
LiteratureSearch(searchterms, options)
Parameters
searchterms
-
string or list of strings; each string contains a term to be included in the literature search
options
(optional) equation(s) of the form option = value where option is one of database, filename, pagesize, prettyprint, resetpage, sortby, sortorder, or source (see section Options for details).
Description
The LiteratureSearch command searches the scientific literature, returning results within Maple.
The parameter searchterms is a string or list of strings where each string contains a term to be included in the literature search. For example, searching for "electron transport" returns articles that contain the exact phrase "electron transport" in any of the searchable fields, i.e. title, author, and abstract. By contrast, searching for ["electron","transport"] discovers articles that have "electron" and "transport" separately but not necessarily together in one of the fields.
LiteratureSearch returns text containing the total number of articles found, the page number, and the article data for each of the page's entries. The article data includes: title, author, abstract, journal, first publication date, and URL. The number of entries per page is controlled by the keyword pagesize whose default value is 10. Upon re-executing LiteratureSearch without changing its input parameters, the command will return the next page. To return to the first page, the user can set the optional boolean keyword resetpage to true. The output can also be duplicated in a file by using the keyword filename to set the path and filename.
The command can search two databases: EuropePMC (default) and arXiv. The searched database can be changed by setting the keyword database to "EuropePMC" or "arXiv" respectively. The EuropePMC database contains more than 40 million science articles and preprints including the complete PubMed and PubMed Central collections. The arXiv database includes physics preprints from quantum physics to chemical physics and biophysics.
The keyword source is a string or list of strings that allows the user to specify the search field for each term in searchterms. The allowed sources are: "ti","au","abs","jr","id", and "all". The "ti", "au", "abs", and "jr" represent title, author, abstract, and journal fields. The "id" is the doi (for EuropePMC) or arXiv id (for arXiv). The "all" (default) indicates that all available fields will be searched. The source list must match the length of the list in searchterms.
The keyword sortby is a string indicating whether the articles should be sorted by relevance, date, or number of citations. For EuropePMC the options are: "relevance" (default), "date", and "cited". For arXiv the options are "date" (default), "relevance", "lastUpdatedDate", and "submittedDate" where "date" is equivalent to "lastUpdatedDate".
The keyword sortorder is a string indicating whether the entries are sorted in descending or ascending order with respect to the criterion set by the keyword sortby. The keyword options are: "descending" (default) or "ascending".
Options
database = string -- a string that selects the database "EuropePMC" (default) or "arXiv".
filename = string -- a string that optionally sets the filename to which the search's output to the screen is duplicated; if relevant, the path should be included as part of the filename. The default is no output to a file.
pagesize = posint -- a positive integer that sets the number of entries returned per page. Default is 10.
prettyprint = truefalse -- when true (default for Worksheet/Document), the output is prettyprinted with the print command; when false (default for Command Line), the output is line printed in a terminal font.
resetpage = true/false -- setting to true resets the output to the first page. Default is false.
sortby = string -- a string indicating whether the articles should be sorted by relevance, date, or number of citations. For EuropePMC the options are: "relevance" (default), "date", and "cited". For arXiv the options are "date" (default), "relevance", "lastUpdatedDate", and "submittedDate" where "date" is equivalent to "lastUpdatedDate".
sortorder = string -- a string indicating whether the entries are sorted in descending or ascending order with respect to the criterion set by the keyword sortby. The keyword options are: "descending" (default) or "ascending".
source = string or list of strings --a string or list of strings that allows the user to specify the search field for each term in searchterms. The allowed sources are: "ti","au","abs","jr","id", and "all". The "ti", "au", "abs", and "jr" represent title, author, abstract, and journal fields. The "id" is the doi (for EuropePMC) or arXiv id (for arXiv). The "all" (default) indicates that all available fields will be searched. The source list must match the length of the list in searchterms.
References
Europe PMC: https://europepmc.org/
Thank you to arXiv for use of its open access interoperability. This product was not reviewed or approved by, nor does it necessarily express or reflect the policies or opinions of, arXiv.
Examples
withQuantumChemistry:
Let's find articles on the methylation of RNA
LiteratureSearchRNA,methylation, pagesize=2;
Total Number of Articles Available = 171858
Page = 1
Title: RNA N6-methyladenosine methylation and skin diseases.
Author: Yu Y, Lu S, Jin H, Zhu H, Wei X, Zhou T, Zhao M.
Abstract: Skin diseases are global health issues caused by multiple pathogenic factors, in which epigenetics plays an invaluable role. Post-transcriptional RNA modifications are important epigenetic mechanism that regulate gene expression at the genome-wide level. N6-methyladenosine (m6A) is the most prevalent modification that occurs in the messenger RNAs (mRNA) of most eukaryotes, which is installed by methyltransferases called "writers", removed by demethylases called "erasers", and recognised by RNA-binding proteins called "readers". To date, m6A is emerging to play essential part in both physiological processes and pathological progression, including skin diseases. However, a systematic summary of m6A in skin disease has not yet been reported. This review starts by illustrating each m6A-related modifier specifically and their roles in RNA processing, and then focus on the existing research advances of m6A in immune homeostasis and skin diseases.
Journal: Autoimmunity 56, 2167983 (2023)
First Publication Date: 2023-12-01
URL: https://doi.org/10.1080/08916934.2023.2167983
Title: The chromatin signatures of enhancers and their dynamic regulation.
Author: Barral A, Déjardin J.
Abstract: Enhancers are <i>cis</i>-regulatory elements that can stimulate gene expression from distance, and drive precise spatiotemporal gene expression profiles during development. Functional enhancers display specific features including an open chromatin conformation, Histone H3 lysine 27 acetylation, Histone H3 lysine 4 mono-methylation enrichment, and enhancer RNAs production. These features are modified upon developmental cues which impacts their activity. In this review, we describe the current state of knowledge about enhancer functions and the diverse chromatin signatures found on enhancers. We also discuss the dynamic changes of enhancer chromatin signatures, and their impact on lineage specific gene expression profiles, during development or cellular differentiation.
Journal: Nucleus 14, 2160551 (2023)
URL: https://doi.org/10.1080/19491034.2022.2160551
By default the pagesize is 10 entries per page. Here we selected 2 entries per page to facilitate the demonstration. Upon executing the command again, QCT automatically gives you the next page of entries. The command can be reset to the first page of entries with the keyword resetpage. Search results can be simultaneously printed to the screen and a file with the filename keyword. We can search by keyword, author, and journal separately or all at once. Next let us search the arXiv for the most recently posted preprints on quantum tunneling in molecules.
LiteratureSearchquantum tunneling,molecules, pagesize=2, database=arXiv;
Total Number of Articles Available = 117
Page = 2
Title: Radical Addition and H Abstraction Reactions in C2H2, C2H4 and C2H6: A Gateway for Ethyl and Vinyl Bearing Molecules in the Interstellar Medium
Author: German Molpeceres and Victor M. Rivilla
Summary: Recent interstellar detections include a significant number of moleculescontaining vinyl (C2H3) and ethyl (C2H5) groups in their structure. For severalof these molecules, there is not a clear experimental or theoretical evidencethat support their formation from simpler precursors. We carried out asystematic search of viable reactions starting from closed shell hydrocarbonscontaining two carbon atoms (ethane, C2H6; ethylene, C2H4; and acetylene, C2H2)with the goal of determining viable chemical routes for the formation of vinyland ethyl molecules on top of interstellar dust grains. Our results show thatboth H and OH radicals are key in converting acetylene and ethylene into morecomplex radicals that are susceptible to continue reacting and forminginterstellar complex organic molecules. The relevant reactions, for example OHadditions, present rate constants above 10$^{1}$ s$^{-1}$ that are likelycompetitive with OH diffusion on grains. Similarly, H atom addition toacetylene and ethylene is a very fast process with rate constants above10$^{4}$ s$^{-1}$ in all cases, and greatly enhanced by quantum tunneling.Hydrogen abstraction reactions are less relevant, but may play a role inspecific cases involving the OH radical. Reactions with other radicals NH2, CH3are likely to have a much lesser impact in the chemistry of ethyl and vinylbearing molecules.
ID: http://arxiv.org/abs/2206.00350v1
Published arXiv: 2022-06-01T09:34:15Z
Updated arXiv: 2022-06-01T09:34:15Z
Journal: A&A 665, A27 (2022)
Title: Quantum tunnelling driven H$_2$ formation on graphene
Author: Erxun Han, Wei Fang, Michail Stamatakis, Jeremy O. Richardson, and Ji Chen
Summary: It is commonly believed that it is unfavourable for adsorbed H atoms oncarbonaceous surfaces to form H$_2$ without the help of incident H atoms. Usingring-polymer instanton theory to describe multidimensional tunnelling effects,combined with ab initio electronic structure calculations, we find that thesequantum-mechanical simulations reveal a qualitatively different picture.Recombination of adsorbed H atoms, which was believed to be irrelevant at lowtemperature due to high barriers, is enabled by deep tunnelling, with reactionrates enhanced by tens of orders of magnitude. Furthermore, we identify a newpath for H recombination that proceeds via multidimensional tunnelling, butwould have been predicted to be unfeasible by a simple one-dimensionaldescription of the reaction. The results suggest that hydrogen moleculeformation at low temperatures are rather fast processes that should not beignored in experimental settings and natural environments with graphene,graphite and other planar carbon segments.
ID: http://arxiv.org/abs/2204.00808v1
Published arXiv: 2022-04-02T08:30:39Z
Updated arXiv: 2022-04-02T08:30:39Z
See Also
Download Help Document