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A Computational Approach to Historical Ontologies [article]

Mat Kelly
2020 arXiv   pre-print
This paper presents a use case exploring the application of the Archival Resource Key (ARK) persistent identifier for promoting and maintaining ontologies. In particular, we look at improving computation with an in-house ontology server in the context of temporally aligned vocabularies. This effort demonstrates the utility of ARKs in preparing historical ontologies for computational archival science.
arXiv:2011.13114v1 fatcat:7rdimds2bfc2hgfhkxr2kw2hf4

An evaluation of mattresses and mats in two dairy units

S.J Chaplin, G Tierney, C Stockwell, D.N Logue, M Kelly
2000 Applied Animal Behaviour Science  
Chaplin et al.r Applied Animal BehaÕiour Science 66 2000 263-272 264 advantages in terms of production or performance, cows were slightly cleaner on mats but behavioural indices suggest that cow comfort  ...  A small study on faecal contamination run in conjunction with the main trial showed that there was no Ž difference in the coliform count of sawdust collected from mats and mattresses Kelly et . al., 1999  ...  Ž were housed on either mats Cow Comfort ''Maxi-bed'' or mattresses Pasture B.V. . Ž. ''Pasture Mat'' .  ... 
doi:10.1016/s0168-1591(99)00100-8 pmid:10700626 fatcat:4ad3q3rcuzcxnjowvnogzv7ujq

Multiple cyanotoxin congeners produced by sub-dominant cyanobacterial taxa in riverine cyanobacterial and algal mats [article]

Laura T. Kelly, Keith Bouma-Gregson, Jonathan Puddick, Rich Fadness, Ken G. Ryan, Timothy W. Davis, Susanna A. Wood
2019 bioRxiv   pre-print
Mats dominated by the green alga C. glomerata contained both anatoxins and nodularin-R at concentrations similar to those of cyanobacteria-dominated mats.  ...  This highlights that even when cyanobacteria are not the dominant taxa in periphyton, these mats may still pose a serious health risk and indicates that more widespread monitoring of all mats in a river  ...  Colours represent the dominant taxa in mats collected from each site. dw = dry weight. Note log scale on the 277 y-axes.  ... 
doi:10.1101/705848 fatcat:r3h2zb2qnvalhmgkahetamb46u

On the Change in Archivability of Websites Over Time [article]

Mat Kelly, Justin F. Brunelle, Michele C. Weigle, Michael L. Nelson
2013 arXiv   pre-print
As web technologies evolve, web archivists work to keep up so that our digital history is preserved. Recent advances in web technologies have introduced client-side executed scripts that load data without a referential identifier or that require user interaction (e.g., content loading when the page has scrolled). These advances have made automating methods for capturing web pages more difficult. Because of the evolving schemes of publishing web pages along with the progressive capability of web
more » ... preservation tools, the archivability of pages on the web has varied over time. In this paper we show that the archivability of a web page can be deduced from the type of page being archived, which aligns with that page's accessibility in respect to dynamic content. We show concrete examples of when these technologies were introduced by referencing mementos of pages that have persisted through a long evolution of available technologies. Identifying these reasons for the inability of these web pages to be archived in the past in respect to accessibility serves as a guide for ensuring that content that has longevity is published using good practice methods that make it available for preservation.
arXiv:1307.8067v1 fatcat:642udrwtjnd4vb7yofxgd6xha4

Development and Application of a Quantitative PCR Assay to Assess Genotype Dynamics and Anatoxin Content in Microcoleus autumnalis-Dominated Mats

Laura Kelly, Susanna Wood, Tara McAllister, Ken Ryan
2018 Toxins  
Some species form thick, cohesive mats over large areas of the benthos in rivers and lakes.  ...  The anatoxin content in mats had a significant relationship with the percentage of toxic cells (R2 = 0.38, p < 0.001), indicating that changes in anatoxin content in M. autumnalis-dominated mats are primarily  ...  to the entire cyanobacterial community within the mat.  ... 
doi:10.3390/toxins10110431 fatcat:cmr4mshqajgvnoa5i2sgmmy4dm

Impact of URI Canonicalization on Memento Count [article]

Mat Kelly, Lulwah M. Alkwai, Michael L. Nelson, Michele C. Weigle, and Herbert Van de Sompel
2017 arXiv   pre-print
Quantifying the captures of a URI over time is useful for researchers to identify the extent to which a Web page has been archived. Memento TimeMaps provide a format to list mementos (URI-Ms) for captures along with brief metadata, like Memento-Datetime, for each URI-M. However, when some URI-Ms are dereferenced, they simply provide a redirect to a different URI-M (instead of a unique representation at the datetime), often also present in the TimeMap. This infers that confidently obtaining an
more » ... curate count quantifying the number of non-forwarding captures for a URI-R is not possible using a TimeMap alone and that the magnitude of a TimeMap is not equivalent to the number of representations it identifies. In this work we discuss this particular phenomena in depth. We also perform a breakdown of the dynamics of counting mementos for a particular URI-R (google.com) and quantify the prevalence of the various canonicalization patterns that exacerbate attempts at counting using only a TimeMap. For google.com we found that 84.9% of the URI-Ms result in an HTTP redirect when dereferenced. We expand on and apply this metric to TimeMaps for seven other URI-Rs of large Web sites and thirteen academic institutions. Using a ratio metric DI for the number of URI-Ms without redirects to those requiring a redirect when dereferenced, five of the eight large web sites' and two of the thirteen academic institutions' TimeMaps had a ratio of ratio less than one, indicating that more than half of the URI-Ms in these TimeMaps result in redirects when dereferenced.
arXiv:1703.03302v1 fatcat:pol23hlnz5hpbjmsobkucib5k4

WARCreate

Mat Kelly, Michele C. Weigle
2012 Proceedings of the 12th ACM/IEEE-CS joint conference on Digital Libraries - JCDL '12  
The Internet Archive's Wayback Machine is the most common way that typical users interact with web archives. The Internet Archive uses the Heritrix web crawler to transform pages on the publicly available web into Web ARChive (WARC) files, which can then be accessed using the Wayback Machine. Because Heritrix can only access the publicly available web, many personal pages (e.g., passwordprotected pages, social media pages) cannot be easily archived into the standard WARC format. We have created
more » ... a Google Chrome extension, WARCreate, that allows a user to create a WARC file from any webpage. Using this tool, content that might have been otherwise lost in time can be archived in a standard format by any user. This tool provides a way for casual users to easily create archives of personal online content. This is one of the first steps in resolving issues of "long term storage, maintenance, and access of personal digital assets that have emotional, intellectual, and historical value to individuals" [3] .
doi:10.1145/2232817.2232930 dblp:conf/jcdl/KellyW12 fatcat:usni2vwnhbbevkm662tamfonbi

Multiple cyanotoxin congeners produced by sub-dominant cyanobacterial taxa in riverine cyanobacterial and algal mats

Laura T. Kelly, Keith Bouma-Gregson, Jonathan Puddick, Rich Fadness, Ken G. Ryan, Timothy W. Davis, Susanna A. Wood, Jean-François Humbert
2019 PLoS ONE  
Mats dominated by the green alga C. glomerata contained both anatoxins and nodularin-R at concentrations similar to those of cyanobacteria-dominated mats.  ...  This highlights that even when cyanobacteria are not the dominant taxa in periphyton, these mats may still pose a serious health risk and indicates that more widespread monitoring of all mats in a river  ...  Anatoxin quota were calculated as the summed anatoxins mass per mg dw (from the LC-MS/MS) divided by the anaC copy number per mg dw from the ddPCR as described by Kelly et al. [20] .  ... 
doi:10.1371/journal.pone.0220422 pmid:31841562 pmcid:PMC6913960 fatcat:2zpj4j6o5ve3rolc5gjzwswyje

Visualizing Webpage Changes Over Time [article]

Abigail Mabe and Dhruv Patel and Maheedhar Gunnam and Surbhi Shankar and Mat Kelly and Sawood Alam and Michael L. Nelson and Michele C. Weigle
2020 arXiv   pre-print
For any URI-R Abigail Mabe, Dhruv Patel, Maheedhar Gunnam, Surbhi Shankar, Mat Kelly, Sawood Alam, Michael L. Nelson, and Michele C.  ...  The initial implementation of the base summarization algorithm was developed by Kelly [11].  ... 
arXiv:2006.02487v1 fatcat:xbzuknslg5dodjdack7uajw23u

The impact of JavaScript on archivability

Justin F. Brunelle, Mat Kelly, Michele C. Weigle, Michael L. Nelson
2015 International Journal on Digital Libraries  
As web technologies evolve, web archivists work to adapt so that digital history is preserved. Recent advances in web technologies have introduced client-side executed scripts (Ajax) that, for example, load data without a change in top level Universal Resource Identifier (URI) or require user interaction (e.g., content loading via Ajax when the page has scrolled). These advances have made automating methods for capturing web pages more difficult. In an effort to understand why mementos
more » ... versions of live resources) in today's archives vary in completeness and sometimes pull content from the live web, we present a study of web resources and archival tools. We used a collection of URIs shared over Twitter and a collection of URIs curated by Archive-It in our investigation. We created local archived versions of the URIs from the Twitter and Archive-It sets using WebCite, wget, and the Heritrix crawler. We found that only 4.2 % of the Twitter collection is perfectly archived by all of these tools, while 34.2 % of the Archive-It collection is perfectly archived. After studying the quality of these mementos, we identified the practice of loading resources via JavaScript (Ajax) as the source of archival difficulty. Further, we show that resources are increasing their use of JavaScript to load embedded resources. By 2012, over half (54.5 %) of pages use JavaScript to load embedded resources. The number of embedded resources loaded via JavaScript has increased by 12.0 % from 2005 to 2012. We also show that JavaScript is responsible for 33.2 % more missing resources in 2012 than in 2005. This shows that JavaScript is responsible for an increasing proportion of the embedded resources unsuccessfully loaded by mementos. JavaScript is also responsible for 52.7 % of all missing embedded resources in our study.
doi:10.1007/s00799-015-0140-8 fatcat:qjadggzfoze3lnknsxz4inmbde

InterPlanetary Wayback: Peer-To-Peer Permanence of Web Archives [chapter]

Mat Kelly, Sawood Alam, Michael L. Nelson, Michele C. Weigle
2016 Lecture Notes in Computer Science  
We have integrated Web ARChive (WARC) files with the peerto-peer content addressable InterPlanetary File System (IPFS) to allow the payload content of web archives to be easily propagated. We also provide an archival replay system extended from pywb to fetch the WARC content from IPFS and re-assemble the originally archived HTTP responses for replay. From a 1.0 GB sample Archive-It collection of WARCs containing 21,994 mementos, we show that extracting and indexing the HTTP response content of
more » ... ARCs containing IPFS lookup hashes takes 66.6 minutes inclusive of dissemination into IPFS.
doi:10.1007/978-3-319-43997-6_35 fatcat:me7ktxtxtnczbnaik4fslih7ae

On the Change in Archivability of Websites Over Time [chapter]

Mat Kelly, Justin F. Brunelle, Michele C. Weigle, Michael L. Nelson
2013 Lecture Notes in Computer Science  
As web technologies evolve, web archivists work to keep up so that our digital history is preserved. Recent advances in web technologies have introduced client-side executed scripts that load data without a referential identifier or that require user interaction (e.g., content loading when the page has scrolled). These advances have made automating methods for capturing web pages more difficult. Because of the evolving schemes of publishing web pages along with the progressive capability of web
more » ... preservation tools, the archivability of pages on the web has varied over time. In this paper we show that the archivability of a web page can be deduced from the type of page being archived, which aligns with that page's accessibility in respect to dynamic content. We show concrete examples of when these technologies were introduced by referencing mementos of pages that have persisted through a long evolution of available technologies. Identifying these reasons for the inability of these web pages to be archived in the past in respect to accessibility serves as a guide for ensuring that content that has longevity is published using good practice methods that make it available for preservation.
doi:10.1007/978-3-642-40501-3_5 fatcat:42abgkkybjd2bm7s7koxfln4um

Platelet association with leukocytes in active eosinophilic esophagitis

Kelly A Bartig, Kristine E Lee, Deane F Mosher, Sameer K Mathur, Mats W Johansson
2021 PLoS ONE  
We previously demonstrated that the percentage of blood eosinophils that are associated with platelets and thus positive for CD41 (integrin αIIb-subunit) correlates with and predicts peak eosinophil count (PEC) in biopsies of eosinophilic esophagitis (EoE) patients after treatment. Thus, flow cytometric determination of CD41+ eosinophils is a potential measure of EoE disease activity. Determinants of association of platelets with eosinophils and other leukocytes in EoE are largely unknown. The
more » ... bjectives of this study were to test the hypotheses that platelets associate with blood leukocytes other than eosinophils in EoE and that such associations also predict EoE activity. Whole blood flow cytometry was performed on samples from 25 subjects before and after two months of standard of care EoE treatment. CD41 positivity of cells within gates for eosinophils, neutrophils, monocytes, lymphocytes, and natural killer cells was compared. We found that percent CD41+ neutrophils, monocytes, and eosinophils correlated with one another such that principal component analysis of the five cell types identified "myeloid" and "lymphoid" factors. Percent CD41+ neutrophils or monocytes, or the myeloid factor, like CD41+ eosinophils, correlated with PEC after treatment, and CD41+ neutrophils or the myeloid factor predicted PEC < 6/high power field after treatment, albeit with lower area under the curve than for CD41+ eosinophils. We conclude that the processes driving platelets to associate with eosinophils in EoE also drive association of platelets with neutrophils and monocytes and that association of platelets with all three cell types is related to disease activity. Clinicaltrials.gov identifier: NCT02775045.
doi:10.1371/journal.pone.0250521 pmid:33891621 pmcid:PMC8064567 fatcat:tz5wz35yc5d5hokv7uh3naeckq

A Method for Identifying Personalized Representations in the Archives

Mat Kelly, Justin F. Brunelle, Michele C. Weigle, Michael L. Nelson
2013 D-Lib Magazine  
Copyright © 2013 Mat Kelly, Justin F. Brunelle, Michele C. Weigle and Michael L. Nelson  ... 
doi:10.1045/november2013-kelly fatcat:iubv6sd3tzcsldxdytqrdx3spu

A Retasking Framework for Wireless Sensor Networks

Michael Ruffing, Yangyang He, Mat Kelly, Jason O. Hallstrom, Stepahn Olariu, Michele C. Weigle
2014 2014 IEEE Military Communications Conference  
Wireless sensor networks have been widely used in scientific research, industrial manufacturing, and environmental monitoring over the past decade. Using pre-existing networks to assist in responding to disaster events can be cost-effective. In this paper, we present Alert, a software framework for retasking wireless sensor networks, enabling these networks to respond rapidly to unexpected events without neglecting their originally assigned tasks. Alert, built upon Deluge [1], is a wireless
more » ... ork code distribution protocol enabling node group management, selective node and group reprogramming, and network state monitoring. We used a testbed of 25 Tmote Sky nodes to evaluate the reprogramming performance and space overhead of Alert under different network sizes and densities.
doi:10.1109/milcom.2014.181 fatcat:spujifzazzgk3dnkwndvmmbwj4
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