bolognese 2.3.7 → 2.3.9

data/spec/fixtures/funding_reference.xml

@@ -1,53 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://datacite.org/schema/kernel-4" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">
-  <identifier identifierType="DOI">10.7907/G31J-CH52</identifier>
-  <creators>
-    <creator>
-      <creatorName>Singhal,Vipul</creatorName>
-    </creator>
-  </creators>
-  <titles>
-    <title>Modeling, Computation, and Characterization to Accelerate the Development of Synthetic Gene Circuits in Cell-Free Extracts</title>
-  </titles>
-  <publisher>California Institute of Technology</publisher>
-  <publicationYear>2019</publicationYear>
-  <resourceType resourceTypeGeneral="Text">Dissertation</resourceType>
-  <alternateIdentifiers>
-    <alternateIdentifier alternateIdentifierType="Eprint_ID">11161</alternateIdentifier>
-  </alternateIdentifiers>
-  <subjects>
-    <subject>Synthetic Biology</subject>
-    <subject>System Identification</subject>
-    <subject>Control Theory</subject>
-    <subject>Mathematical Modeling</subject>
-    <subject>Chemical Reaction Networks</subject>
-    <subject>Transcription</subject>
-    <subject>Translation</subject>
-    <subject>Gene Regulatory Networks</subject>
-    <subject>Calibration</subject>
-    <subject>Computation and Neural Systems</subject>
-  </subjects>
-  <fundingReferences>
-    <fundingReference/>
-    <fundingReference/>
-    <fundingReference>
-      <funderName>Agency for Science, Technology and Research (Singapore)</funderName>
-    </fundingReference>
-    <fundingReference/>
-  </fundingReferences>
-  <dates>
-    <date dateType="Issued">2019</date>
-  </dates>
-  <version>Final</version>
-  <descriptions>
-    <description descriptionType="Abstract">Synthetic biology may be defined as an attempt at using engineering principles to design and build novel biological functionalities. An important class of such functionalities involves the bottom up design of genetic networks (or 'circuits') to control cellular behavior. Performing design iterations on these circuits in vivo is often a time consuming process. One approach that has been developed to address these long design times is to use E. coli cell extracts as simplified circuit prototyping environments. The analogy with similar approaches in engineering, such as prototyping using wind tunnels and breadboards, may be extended by developing accompanying computer aided design tools. In this thesis, we discuss the development of computational and mathematical tools to accelerate circuit prototyping in the TX-TL cell free prototyping platform, and demonstrate some applications of these tools.
-
-We start by discussing the problem of reducing circuit behavior variability between different batches of TX-TL cell extracts. To this end, we demonstrate a model-based methodology for calibrating extract batches, and for using the calibrations to 'correct' the behavior of genetic circuits between batches. We also look at the interaction of this methodology with the phenomenon of parameter non-identifiability, which occurs when the parameter identification inverse problem has multiple solutions. In particular, we derive conditions under which parameter non-identifiability does not hinder our modeling objectives, and subsequently demonstrate the use of such non-identifiable models in performing data variability reduction. 
-
-Next, we describe txtlsim, a MATLAB Simbiology based toolbox for automatically generating models of genetic circuits in TX-TL, and for using these models for part characterization and circuit behavior prediction. Large genetic circuits can have non-negligible resource usage needs, leading to unintended interactions between circuit nodes arising due to the loading of cellular machinery, transcription factors or other regulatory elements. The usage of consumable resources like nucleotides and amino acids can also have non-trivial effects on complex genetic circuits. These types of effects are handled by the modeling framework of txtlsim in a natural way.
-
-We also highlight mcmc-simbio, a smaller toolbox within txtlsim for performing concurrent Bayesian parameter inference on Simbiology models. Concurrent inference here means that a common set of parameters can be identified using data from an ensemble of different circuits and experiments, with each experiment informing a subset of the parameters. The combination of the concurrence feature with the fact that Markov chain Monte Carlo based Bayesian inference methods allow for the direct visualization of parameter non-identifiability enables the design of ensembles of experiments that reduce such non-identifiability.
-
-Finally, we end with a method for performing model order reduction on transcription and translation elongation models while maintaining the ability of these models to track resource consumption. We show that due to their network topology, our models cannot be brought into the two-timescale form of singular perturbation theory when written in species concentration coordinates. We identify a coordinate system in which singular perturbation theory may be applied to chemical reaction networks more naturally, and use this to achieve the desired model reduction.</description>
-  </descriptions>
-</resource>

data/spec/fixtures/gtex.xml

@@ -1,71 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-
-<resource xmlns="http://datacite.org/schema/kernel-4" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd">  
-  <identifier identifierType="DOI">10.25491/9HX8-KE93</identifier>  
-  <creators> 
-    <creator> 
-      <creatorName nameType="Organizational">The GTEx Consortium</creatorName> 
-    </creator> 
-  </creators>  
-  <titles> 
-    <title>DroNc-seq data</title> 
-  </titles>  
-  <publisher>GTEx</publisher>  
-  <publicationYear>2017</publicationYear>  
-  <subjects> 
-    <subject>gtex</subject>  
-    <subject>annotation</subject>  
-    <subject>phenotype</subject>  
-    <subject>gene regulation</subject>  
-    <subject>transcriptomics</subject> 
-  </subjects>  
-  <fundingReferences> 
-    <fundingReference> 
-      <funderName>Common Fund of the Office of the Director of the NIH</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000052</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Cancer Institute (NCI)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000054</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Human Genome Research Institute (NHGRI)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000051</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Heart, Lung, and Blood Institute (NHLBI)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000050</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Institute on Drug Abuse (NIDA)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000026</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Institute of Mental Health (NIMH)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000025</funderIdentifier> 
-    </fundingReference>  
-    <fundingReference> 
-      <funderName>National Institute of Neurological Disorders and Stroke (NINDS)</funderName>  
-      <funderIdentifier funderIdentifierType="Crossref Funder ID">http://doi.org/10.13039/100000065</funderIdentifier> 
-    </fundingReference> 
-  </fundingReferences>  
-  <resourceType resourceTypeGeneral="Dataset">DroNc-seq data</resourceType>  
-  <dates> 
-    <date dateType="Issued">2017</date> 
-  </dates>  
-  <relatedIdentifiers> 
-    <relatedIdentifier relationType="Documents" relatedIdentifierType="URL">http://identifiers.org/dbgap:phs000424.v7.p2</relatedIdentifier>  
-    <relatedIdentifier relationType="IsDocumentedBy" relatedIdentifierType="DOI">https://doi.org/10.1038/nature24277</relatedIdentifier>  
-    <relatedIdentifier relationType="IsSupplementTo" relatedIdentifierType="DOI">https://doi.org/10.1038/nmeth.4407</relatedIdentifier> 
-    <relatedIdentifier relationType="IsPartOf" relatedIdentifierType="URL">https://www.ebi.ac.uk/miriam/main/datatypes/MIR:00000663</relatedIdentifier> 
-  </relatedIdentifiers> 
-  <formats> 
-    <format>application/tar</format> 
-  </formats> 
-  <sizes> 
-    <size>15.7M</size> 
-  </sizes>
-  <descriptions> 
-    <description descriptionType="SeriesInformation">GTEx</description> 
-  </descriptions> 
-</resource>

data/spec/fixtures/maremma/codemeta.json

@@ -1,36 +0,0 @@
-{
-	"@context": "https://raw.githubusercontent.com/codemeta/codemeta/master/codemeta.jsonld",
-	"@type": "SoftwareSourceCode",
-	"@id": "https://doi.org/10.5438/QEG0-3GM3",
-	"authors": {
-		"@id": "http://orcid.org/0000-0003-0077-4738",
-		"@type": "person",
-		"name": "Martin Fenner",
-		"affiliation": "DataCite",
-		"mustBeCited": true,
-		"isMaintainer": true,
-		"isRightsHolder": true
-	},
-	"identifier": "https://doi.org/10.5438/QEG0-3GM3",
-	"codeRepository": "https://github.com/datacite/maremma",
-	"controlledTem": "software",
-	"dateCreated": "2015-11-28",
-	"datePublished": "2017-02-24",
-	"dateModified": "2017-02-24",
-	"description": "Simplifies network calls, including json/xml parsing and error handling. Based on Faraday.",
-	"isAutomatedBuild": true,
-	"licenseId": "MIT",
-	"publisher": "DataCite",
-	"tags": [
-		"faraday",
-		"excon",
-		"net/http"
-	],
-	"title": "Maremma: a Ruby library for simplified network calls",
-	"programmingLanguage": {
-		"name": "Ruby",
-		"version": "≥ 2.3.3",
-		"URL": "https://www.ruby-lang.org"
-	},
-	"readme": "https://github.com/datacite/maremma/blob/master/README.md"
-}

data/spec/fixtures/nist.xml

@@ -1,35 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<resource xmlns="http://datacite.org/schema/kernel-3" 
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://datacite.org/schema/kernel-3 http://schema.datacite.org/meta/kernel-3/metadata.xsd">
-  <identifier identifierType="DOI">https://doi.org/10.5072/M32163</identifier>
-  <creators>
-    <creator>
-      <creatorName nameType="personal">William Turner</creatorName>
-      <givenName>William</givenName>
-      <familyName>Turner</familyName>
-      <affiliation>National Institute of Standards and Technology</affiliation>
-    </creator>
-  </creators>
-  <titles>
-    <title>Peter Auto Dataset 501</title>
-  </titles>
-  <publisher>National Institute of Standards and Technology</publisher>
-  <publicationYear>2018</publicationYear>
-  <subjects>
-    <subject>Einstein</subject>
-  </subjects>
-  <dates>
-    <date dateType="Updated">2018-10-30</date>
-  </dates>
-  <language>en</language>
-  <resourceType resourceTypeGeneral="Dataset">Dataset</resourceType>
-  <rightsList>
-    <rights rightsURI="https://www.nist.gov/director/licensing">NIST Licensing</rights>
-  </rightsList>
-  <descriptions>
-    <description descriptionType="Abstract">This is to overturn Einstein's Relativity Theory.</description>
-  </descriptions>
-  <alternateIdentifiers alternateIdentifierType="text">
-    <alternateIdentifier>7CE9D6400C0A30C9E053B357068182C92163</alternateIdentifier>
-  </alternateIdentifiers>
-</resource>

data/spec/fixtures/ns0.xml

@@ -1,2 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<ns0:resource xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns:ns0="http://datacite.org/schema/kernel-2.2" xsi:schemaLocation="http://datacite.org/schema/kernel-2.2 http://schema.datacite.org/meta/kernel-2.2/metadata.xsd"><ns0:identifier identifierType="DOI">10.4231/D38G8FK8B</ns0:identifier><ns0:creators><ns0:creator>	<ns0:creatorName>Patiño, Carlos</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Alzate-Vargas, Lorena</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Li, Chunyu</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Haley, Benjamin</ns0:creatorName></ns0:creator><ns0:creator>	<ns0:creatorName>Strachan, Alejandro</ns0:creatorName></ns0:creator></ns0:creators><ns0:titles>	<ns0:title>LAMMPS Data-File Generator</ns0:title></ns0:titles><ns0:publisher>nanoHUB</ns0:publisher><ns0:publicationYear>2018</ns0:publicationYear><ns0:dates>	<ns0:date dateType="Valid">2018-07-18</ns0:date>	<ns0:date dateType="Accepted">2018-07-18</ns0:date></ns0:dates><ns0:language>en</ns0:language><ns0:resourceType resourceTypeGeneral="Software">Simulation Tool</ns0:resourceType><ns0:version>1.5.2</ns0:version><ns0:descriptions>	<ns0:description descriptionType="Other">This tool generates all necessary input files for LAMMPS simulations of molecular systems starting with an atomistic structure.</ns0:description></ns0:descriptions></ns0:resource>

data/spec/fixtures/pure.bib

@@ -1,14 +0,0 @@
-@phdthesis{dbbe66e459a446a0b6fddf42d3401ccb,
-  title     = "A multiscale analysis of the urban heat island effect: from city averaged temperatures to the energy demand of individual buildings",
-  abstract  = "Designing the climates of cities",
-  author    = "Y. Toparlar",
-  note      = "Proefschrift",
-  year      = "2018",
-  month     = "4",
-  day       = "25",
-  language  = "English",
-  isbn      = "978-90-386-4503-2",
-  series    = "Bouwstenen",
-  publisher = "Technische Universiteit Eindhoven",
-  school    = "Department of Built Environment",
-}

data/spec/fixtures/pure.ris

@@ -1,15 +0,0 @@
-TY  - THES
-T1  - A multiscale analysis of the urban heat island effect
-T2  - from city averaged temperatures to the energy demand of individual buildings
-AU  - Toparlar,Y.
-N1  - Proefschrift
-PY  - 2018/4/25
-Y1  - 2018/4/25
-N2  - Designing the climates of cities
-AB  - Designing the climates of cities
-M3  - Phd Thesis 1 (Research TU/e / Graduation TU/e)
-SN  - 978-90-386-4503-2
-T3  - Bouwstenen
-PB  - Technische Universiteit Eindhoven
-CY  - Eindhoven
-ER  - 

data/spec/fixtures/pure.xml

@@ -1,188 +0,0 @@
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-<resource xsi:schemaLocation="http://datacite.org/schema/kernel-4 http://schema.datacite.org/meta/kernel-4/metadata.xsd" 
-  xmlns="http://datacite.org/schema/kernel-4" 
-  xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance">
-  <identifier identifierType="DOI">10.17630/bb43e6a3-72e0-464c-9fdd-fbe5d3e56a09</identifier>
-  <creators>
-    <creator>
-      <creatorName>Haywood, Raphaelle Dawn</creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Raphaelle Dawn</givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Haywood</familyName>
-      <affiliation xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">School of Physics and Astronomy</affiliation>
-    </creator>
-    <creator>
-      <creatorName>Cameron, Andrew Collier</creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Andrew Collier</givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Cameron</familyName>
-      <affiliation xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">School of Physics and Astronomy</affiliation>
-    </creator>
-    <creator>
-      <creatorName>Unruh, Y. C. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Y. C. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Unruh</familyName>
-    </creator>
-    <creator>
-      <creatorName>Lovis, C. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">C. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Lovis</familyName>
-    </creator>
-    <creator>
-      <creatorName>Lanza, A.F. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">A.F. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Lanza</familyName>
-    </creator>
-    <creator>
-      <creatorName>Llama, Joseph</creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Joseph</givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Llama</familyName>
-      <affiliation xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">School of Physics and Astronomy</affiliation>
-    </creator>
-    <creator>
-      <creatorName>Deleuil, M. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">M. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Deleuil</familyName>
-    </creator>
-    <creator>
-      <creatorName>Fares, Rim</creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Rim</givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Fares</familyName>
-    </creator>
-    <creator>
-      <creatorName>Gillon, M. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">M. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Gillon</familyName>
-    </creator>
-    <creator>
-      <creatorName>Moutou, C. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">C. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Moutou</familyName>
-    </creator>
-    <creator>
-      <creatorName>Pepe, F. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">F. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Pepe</familyName>
-    </creator>
-    <creator>
-      <creatorName>Pollacco, D. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">D. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Pollacco</familyName>
-    </creator>
-    <creator>
-      <creatorName>Queloz, D. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">D. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Queloz</familyName>
-    </creator>
-    <creator>
-      <creatorName>Ségransan, D. </creatorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">D. </givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Ségransan</familyName>
-    </creator>
-  </creators>
-  <titles>
-    <title xml:lang="en">Data underpinning - The Sun as a planet-host star: Proxies from SDO images for HARPS radial-velocity variations</title>
-  </titles>
-  <publisher>University of St Andrews</publisher>
-  <publicationYear>2016</publicationYear>
-  <resourceType resourceTypeGeneral="Audiovisual">Dataset</resourceType>
-  <contributors>
-    <contributor contributorType="ContactPerson">
-      <contributorName>Haywood, Raphaelle Dawn</contributorName>
-      <givenName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Raphaelle Dawn</givenName>
-      <familyName xsi:type="xs:string" 
-        xmlns:xs="http://www.w3.org/2001/XMLSchema">Haywood</familyName>
-    </contributor>
-  </contributors>
-  <dates>
-    <date dateType="Available">2016-01-20</date>
-  </dates>
-  <sizes>
-    <size>1KB</size>
-    <size>6KB</size>
-    <size>25KB</size>
-    <size>4KB</size>
-    <size>11KB</size>
-    <size>7MB</size>
-  </sizes>
-  <formats>
-    <format>application/octet-stream</format>
-    <format>application/x-rtf</format>
-    <format>text/plain</format>
-    <format>text/plain</format>
-    <format>application/octet-stream</format>
-    <format>application/x-gzip</format>
-  </formats>
-  <rightsList>
-    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/">CC BY</rights>
-    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/">CC BY</rights>
-    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/">CC BY</rights>
-    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/">CC BY</rights>
-    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/">CC BY</rights>
-    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/">CC BY</rights>
-  </rightsList>
-  <descriptions>
-    <description descriptionType="Abstract" xml:lang="en"></description>
-  </descriptions>
-  <fundingReferences>
-    <fundingReference>
-      <funderName>Science &amp; Technology Facilities Council</funderName>
-      <awardNumber>ST/M001296/1</awardNumber>
-      <awardTitle>Astronomy at St Andrews 2015-2018</awardTitle>
-    </fundingReference>
-    <fundingReference>
-      <funderName>European Commission</funderName>
-      <awardTitle>ETAEARTH</awardTitle>
-    </fundingReference>
-    <fundingReference>
-      <funderName>Science &amp; Technology Facilities Council</funderName>
-      <awardNumber>ST/I000666/1</awardNumber>
-      <awardTitle>St Andrrews Astronomy PATT linked Travel and subsistence</awardTitle>
-    </fundingReference>
-    <fundingReference>
-      <funderName>Science &amp; Technology Facilities Council</funderName>
-      <awardNumber>ST/J001651/1</awardNumber>
-      <awardTitle>Astrophysics at St Andrews: 2012 - 2014</awardTitle>
-    </fundingReference>
-    <fundingReference>
-      <funderName>PPARC - Now STFC</funderName>
-      <awardNumber>PP/D000890/1</awardNumber>
-      <awardTitle>Astrophysics at St.Andrews</awardTitle>
-    </fundingReference>
-    <fundingReference>
-      <funderName>Science &amp; Technology Facilities Council</funderName>
-      <awardNumber>ST/G001006/1</awardNumber>
-      <awardTitle>Patt Linked Travel &amp; Subsistence</awardTitle>
-    </fundingReference>
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data/spec/fixtures/ris_bug.ris

@@ -1,9 +0,0 @@
-TY -  BOOK
-T1  - Validation of an Image-based Subject-Specific Dynamic Model of the Ankle Joint Complex and its Applications to the Study of the Effect of Articular Surface Morphology on Ankle Joint Mechanics
-AU  - Balakrishnan, Vishnuvardhan
-DO  - 10.17918/ERNK-6431
-UR  - https://idea.library.drexel.edu/islandora/object/idea:8247
-AB  - 3D image based subject specific models of the ankle complex can be extremely significant in a wide variety of clinical and biomechanical applications such as evaluating the effect of ligament ruptures, diagnosing and comparing surgical procedures. However, there are very few computational models that can accurately capture the full 3D biomechanical properties of the ankle complex. One such computational model was introduced by our group in 2004 [1], and this model was partially validated with a very limited set of parameters for comparison. In the current study, we have developed an improvised version of this model and validated it on a subject to subject basis for a number of specimens. This is achieved by comparing a wide range of biomechanical parameters between the experiments and the simulation. Once, the model is validated, it can be used for a wide variety of clinical and surgical applications .Some applications include comparing the effects of surface morphology on the kinematics of the ankle joint, diagnosing and evaluation of ankle disorders like ligament tears and reconstruction surgeries. Previous experimental studies conducted to understand and validate the effect of morphological variations to kinematics involved invasive surgical procedures and hence could only be conducted in cadaveric foot. Hence a need for a dynamic model which could predict and recreate the kinematics of an ankle using only CT and, or MRI data was realized. Such a model could help in development and non-invasive testing of subject specific TAR. This thesis focusses on the subject specific validation of rigid body models of four specimens and an one-to-one validation based on Load-displacement curves, Range of Motion, Surface-to-surface interaction and Ligament straining patterns. Post validation of the MBS model in MSC ADAMS, the model is used to investigate the effect of axial loads, total ankle arthrodesis and the effect of varying surface morphologies on the behavior of the ankle joint complex. An in-depth comparative analysis on the use of a numerical model for the development and performance evaluation of an implant derived from the morphological parameters of the ankle joint is also presented.
-PY  - 2018
-PB  - Drexel University
-ER  -

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-      <affiliation>UC Merced</affiliation>
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-    <creator>
-      <creatorName>Meadows, Matt</creatorName>
-      <affiliation>UC Merced</affiliation>
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-      <creatorName>Stacy, Erin</creatorName>
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-      <affiliation>UC Merced</affiliation>
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-      <creatorName>Conklin, Martha</creatorName>
-      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0002-9627-2427</nameIdentifier>
-      <affiliation>UC Merced</affiliation>
-    </creator>
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-      <creatorName>Meng, Xiande</creatorName>
-      <affiliation>UC Merced</affiliation>
-    </creator>
-    <creator>
-      <creatorName>Southern Sierra Critical Zone Observatory, SSCZO</creatorName>
-      <affiliation>NSF</affiliation>
-    </creator>
-  </creators>
-  <titles>
-    <title>
-      Southern Sierra Critical Zone Observatory (SSCZO), Providence Creek
-      meteorological data, soil moisture and temperature, snow depth and air
-      temperature
-    </title>
-  </titles>
-  <publisher>UC Merced</publisher>
-  <publicationYear>2013</publicationYear>
-  <subjects>
-    <subject>Earth sciences</subject>
-    <subject>soil moisture</subject>
-    <subject>soil temperature</subject>
-    <subject>snow depth</subject>
-    <subject>air temperature</subject>
-    <subject>water balance</subject>
-    <subject>Nevada, Sierra (mountain range)</subject>
-  </subjects>
-  <fundingReferences>
-    <fundingReference>
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-        National Science Foundation, Division of Earth Sciences, Critical Zone
-        Observatories
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-      <awardNumber>1331939, 0725097</awardNumber>
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-      <affiliation>University of California, Merced</affiliation>
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-      <affiliation>University of California, Merced</affiliation>
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-      <affiliation>University of California, Merced</affiliation>
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-      <contributorName>Southern Sierra Critical Zone Observatory</contributorName>
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-  <dates>
-    <date dateType="Updated">2014-10-17</date>
-    <date dateType="Available">2016-03-14T17:02:02Z</date>
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-      Snow depth, soil moisture and soil temperature are measured at lower
-      Providence South facing (LowMetS) and North facing (LowMetN), Upper
-      Providence South facing (UpMetS), North facing (UpMetN) and Flat aspect
-      (UpMetF), and Subcatchment basin P301 (P301) with a wireless sensor
-      network, using a Campbell Scientific logger to control peripheral devices.
-      Snow depth is measured in the open, at the drip edge and under canopies.
-      Soil moisture and temperature are measured at 10, 30, 60 and 90 cm depths
-      coincident with the snow depth nodes. 10 watt solar panels provides power
-      for monitoring at 10 minute intervals. Raw data have been processed to
-      level 1 (QA/QC) and level 2 (gap-filled, derived) data. Time period: water
-      year 2008 through water year 2012 (version 1), 2013 to 2016 (version 2).
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-    <description descriptionType="Methods">
-      Soil volumetric water content (VWC) and soil temperature measured using
-      Decagon Devices ECHO-TM at depths of 10, 30, 60, an 90 cm below the
-      mineral soil surface. Sensor now equivalent to 5TM
-      (http://www.decagon.com/soil-moisture-sensors/). Distance to snow/soil
-      surface and air temperature measured with Judd Communications ultrasonic
-      depth sensor, using analog control ( http://www.juddcom.com/ ). Data
-      control and storage on Campbell Scientific CR1000 datalogger, using
-      AM16/32B multiplexer ( http://www.campbellsci.com ). Program for data
-      acquisition are located on UC Merced-SNRI digital library (
-      https://eng.ucmerced.edu/snsjho/files/MHWG/Field/Southern...)
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-      under canopy
-    </description>
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-      <geoLocationPlace>Providence Creek (Lower, Upper and P301)</geoLocationPlace>
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