Supplemental File 2. The PRISMA Checklist and Statement v1 (protocols.io.bmqnk5ve)

protocols.io ◽  
2020 ◽  
Author(s):  
carolyn berryman
Keyword(s):  
PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e12363
Author(s):  
Paul M. Harrison

Compositionally-biased (CB) regions in biological sequences are enriched for a subset of sequence residue types. These can be shorter regions with a concentrated bias (i.e., those termed ‘low-complexity’), or longer regions that have a compositional skew. These regions comprise a prominent class of the uncharacterized ‘dark matter’ of the protein universe. Here, I report the latest version of the fLPS package for the annotation of CB regions, which includes added consideration of DNA sequences, to label the eight possible biased regions of DNA. In this version, the user is now able to restrict analysis to a specified subset of residue types, and also to filter for previously annotated domains to enable detection of discontinuous CB regions. A ‘thorough’ option has been added which enables the labelling of subtler biases, typically made from a skew for several residue types. In the output, protein CB regions are now labelled with bias classes reflecting the physico-chemical character of the biasing residues. The fLPS 2.0 package is available from: https://github.com/pmharrison/flps2 or in a Supplemental File of this paper.


2014 ◽  
Author(s):  
Andrew Darling ◽  
Kelin Whipple

Geosphere, August 2015, v. 11, p. 958-976, doi:10.1130/GES01131.1, Supplemental File 1 - All stream slope-area data, plotted and compiled for inspection.


2017 ◽  
Author(s):  
Shitij Bhargava ◽  
Tsung-Ting Kuo ◽  
Ankit Goyal ◽  
Vincent Kuri ◽  
Gordon Lin ◽  
...  

Background. There is huge amount of full-text biomedical literatures available in public repositories like PubMed Central (PMC). However, a substantial number of the papers are in Portable Document Format (PDF) and do not provide plain text format ready for text mining and natural language processing (NLP). Although there exist many PDF-to-text converters, they still suffer from several challenges while processing biomedical PDFs, such as the correct transcription of titles/abstracts, segmenting references/acknowledgements, special characters, jumbling errors (the wrong order of the text), and word boundaries. Methods. In this paper, we present bioPDFX, a novel tool which complements weaknesses with strengths of multiple state-of-the-art methods and then applies machine learning methods to address all issues above Results. The experiment results on publications of Genome Wide Association Studies (GWAS) demonstrated that bioPDFX significantly improved the quality of XML comparing to state-of-the-art PDF-to-XML converter, leading to a biomedical database more suitable for text mining. Discussion. Overall, the whole pipeline developed in this paper makes the published literature in form of PDF files much better suited for text mining tasks, while slightly improving the overall text quality as well. The service is open to access freely at URL: http://textmining.ucsd.edu:9000 . A list of PubMed Central IDs of the 941 articles (see Supplemental File 1) used in this study is available for download at the same URL. The instructions of how to run the service with a PubMed ID are described in Supplemental File 2.


2018 ◽  
Author(s):  
Mohsen Kayal ◽  
Hannah Lewis ◽  
Jane Ballard ◽  
Ehsan Kayal

The 21st century will undeniably represent a major turn in the development of human societies, as Earth’s limiting resources can no longer support the current pace of material consumption (supplemental file S1). In this context, Ripple et al. (2017) identified thirteen critical shifts in our ways of life to reduce humanity’s ecological footprint and achieve sustainable development. While we endorse the pertinence and urgency of this call, we direct attention to critical shortcomings in the proposed solutions, which limit their potential to promote sustainability. Indeed, several prescriptions in Ripple et al. address symptoms rather than root causes, or seem to result from a simplistic consideration of inherently complex processes. We emphasize the importance of accounting for historical patterns and underlying drivers of the global socio-economic system, especially in relation to wealth inequality, human demography, and food production, which need deeper consideration than presently given in the warning and subsequent follow-up articles. Without such considerations, this second warning to humanity can be interpreted as prescriptive suggestions from a narrow, western-biased vision of the global socio-ecosystem, rendering it all but ineffective.


2018 ◽  
Author(s):  
Mohsen Kayal ◽  
Hannah Lewis ◽  
Jane Ballard ◽  
Ehsan Kayal

The 21st century will undeniably represent a major turn in the development of human societies, as Earth’s limiting resources can no longer support the current pace of material consumption (supplemental file S1). In this context, Ripple et al. (2017) identified thirteen critical shifts in our ways of life to reduce humanity’s ecological footprint and achieve sustainable development. While we endorse the pertinence and urgency of this call, we direct attention to critical shortcomings in the proposed solutions, which limit their potential to promote sustainability. Indeed, several prescriptions in Ripple et al. address symptoms rather than root causes, or seem to result from a simplistic consideration of inherently complex processes. We emphasize the importance of accounting for historical patterns and underlying drivers of the global socio-economic system, especially in relation to wealth inequality, human demography, and food production, which need deeper consideration than presently given in the warning and subsequent follow-up articles. Without such considerations, this second warning to humanity can be interpreted as prescriptive suggestions from a narrow, western-biased vision of the global socio-ecosystem, rendering it all but ineffective.


Author(s):  
George Gehrels ◽  
Mark Pecha

Geosphere, February 2014, v. 10, p. 49-65, doi:10.1130/GES00889.1, Supplemental File 2 - CL image file (238 pages). File size is ~23 MB.


2020 ◽  
Author(s):  
R.A. Young ◽  
et al.

An extended discussion relating to the identification of glacial tills at the critical sites in this investigation is provided as a Supplemental File to eliminate any concerns that the exposures might be landslide debris as opposed to primary glacial till. The supplement also speculates as to why the advance in western New York State may not have been obvious in the extensive research published for the St. Lawrence Valley.


2014 ◽  
Author(s):  
Andrew Darling ◽  
Kelin Whipple

Geosphere, August 2015, v. 11, p. 958-976, doi:10.1130/GES01131.1, Supplemental File 1 - All stream slope-area data, plotted and compiled for inspection.


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