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Article ; Online: A Controlled Vocabulary and Metadata Schema for Materials Science Data Discovery

Andrea Medina-Smith / Chandler A. Becker / Raymond L. Plante / Laura M. Bartolo / Alden Dima / James A. Warren / Robert J. Hanisch

Data Science Journal, Vol 20, Iss

2021 Volume 1

Abstract: The International Materials Resource Registries (IMRR) working group of the Research Data Alliance (RDA) was created to spur initial development of a federated registry system to allow for easier discovery and access to materials data. As part of this ... ...

Abstract	The International Materials Resource Registries (IMRR) working group of the Research Data Alliance (RDA) was created to spur initial development of a federated registry system to allow for easier discovery and access to materials data. As part of this effort, a controlled vocabulary and metadata schema were developed with contributions from members of the working group and other experts. Here we describe the process, the resulting vocabulary and XML schema, and lessons learned in the development and use of the schema.
Keywords	controlled vocabulary ; metadata schema ; materials science ; rda ; federated registry system ; Science (General) ; Q1-390
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Ubiquity Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Implementing a Registry Federation for Materials Science Data Discovery.

Plante, Raymond L / Becker, Chandler A / Medina-Smith, Andrea / Brady, Kevin / Dima, Alden / Long, Benjamin / Bartolo, Laura M / Warren, James A / Hanisch, Robert J

Data science journal

2021 Volume 20

Abstract: As a result of a number of national initiatives, we are seeing rapid growth in the data important to materials science that are available over the web. Consequently, it is becoming increasingly difficult for researchers to learn what data are available ... ...

Abstract	As a result of a number of national initiatives, we are seeing rapid growth in the data important to materials science that are available over the web. Consequently, it is becoming increasingly difficult for researchers to learn what data are available and how to access them. To address this problem, the Research Data Alliance (RDA) Working Group for International Materials Science Registries (IMRR) was established to bring together materials science and information technology experts to develop an international federation of registries that can be used for global discovery of data resources for materials science. A resource registry collects high-level metadata descriptions of resources such as data repositories, archives, websites, and services that are useful for data-driven research. By making the collection searchable, it aids scientists in industry, universities, and government laboratories to discover data relevant to their research and work interests. We present the results of our successful piloting of a registry federation for materials science data discovery. In particular, we out a blueprint for creating such a federation that is capable of amassing a global view of all available materials science data, and we enumerate the requirements for the standards that make the registries interoperable within the federation. These standards include a protocol for exchanging resource descriptions and a standard metadata schema for encoding those descriptions. We summarize how we leveraged an existing standard (OAI-PMH) for metadata exchange. Finally, we review the registry software developed to realize the federation and describe the user experience.
Language	English
Publishing date	2021-11-18
Publishing country	England
Document type	Journal Article
ZDB-ID	2128236-5
ISSN	1683-1470 ; 1683-1470
ISSN (online)	1683-1470
ISSN	1683-1470
DOI	10.5334/dsj-2021-015
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Librarians and Scientists Partner to Address Data Management: Taking Collaboration to the Next Level.

Medina-Smith, Andrea / Tryka, Kimberly A / Silcox, Barbara P / Hanisch, Robert J

Digital library perspectives

2016 Volume 32, Issue 3, Page(s) 142–152

Abstract: Purpose: This study looks at the changing way in which the Information Services Office (ISO) at the National Institute of Standards and Technology (NIST) provides services to NIST scientific and technical staff throughout their research and publishing ... ...

Abstract	Purpose: This study looks at the changing way in which the Information Services Office (ISO) at the National Institute of Standards and Technology (NIST) provides services to NIST scientific and technical staff throughout their research and publishing cycles. These services include the more traditional services of a research library as well as publishing NIST technical reports and Design/methodology/approach: This paper discusses the relationship ISO has developed with the Office of Data and Informatics (ODI), how this relationship was forged, and how this collaboration will serve as a model for working with the other labs and programs at NIST. It will also discuss the risks and opportunities of this new collaborative service model, how ISO positioned itself to become an equal partner with ODI in the exploration of solutions to data management issues, and the benefits of the relationship from ODI's perspective. Findings: A pattern of strategic changes to the services and activities offered by the Lab Liaison program has put ISO in the position to collaborate as peers with researchers at NIST. Originality/value: This study provides an overview of how ISO made strategic decisions to incorporate non-traditional services to support data management at NIST.
Language	English
Publishing date	2016-11-16
Publishing country	England
Document type	Journal Article
ZDB-ID	2862498-1
ISSN	2059-5824 ; 2059-5816
ISSN (online)	2059-5824
ISSN	2059-5816
DOI	10.1108/DLP-08-2015-0010
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Article ; Online: Implementing a Registry Federation for Materials Science Data Discovery

Raymond L. Plante / Chandler A. Becker / Andrea Medina-Smith / Kevin Brady / Alden Dima / Benjamin Long / Laura M. Bartolo / James A. Warren / Robert J. Hanisch

Data Science Journal, Vol 20, Iss

2021 Volume 1

Abstract	As a result of a number of national initiatives, we are seeing rapid growth in the data important to materials science that are available over the web. Consequently, it is becoming increasingly difficult for researchers to learn what data are available and how to access them. To address this problem, the Research Data Alliance (RDA) Working Group for International Materials Science Registries (IMRR) was established to bring together materials science and information technology experts to develop an international federation of registries that can be used for global discovery of data resources for materials science. A resource registry collects high-level metadata descriptions of resources such as data repositories, archives, websites, and services that are useful for data-driven research. By making the collection searchable, it aids scientists in industry, universities, and government laboratories to discover data relevant to their research and work interests. We present the results of our successful piloting of a registry federation for materials science data discovery. In particular, we out a blueprint for creating such a federation that is capable of amassing a global view of all available materials science data, and we enumerate the requirements for the standards that make the registries interoperable within the federation. These standards include a protocol for exchanging resource descriptions and a standard metadata schema for encoding those descriptions. We summarize how we leveraged an existing standard (OAI-PMH) for metadata exchange. Finally, we review the registry software developed to realize the federation and describe the user experience.
Keywords	registry ; informatics ; data discovery ; metadata ; oai-pmh ; Science (General) ; Q1-390
Subject code	028 ; 302
Language	English
Publishing date	2021-04-01T00:00:00Z
Publisher	Ubiquity Press
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Utility of Banff Human Organ Transplant Gene Panel in Human Kidney Transplant Biopsies.

Smith, Rex N / Rosales, Ivy A / Tomaszewski, Kristen T / Mahowald, Grace T / Araujo-Medina, Milagros / Acheampong, Ellen / Bruce, Amy / Rios, Andrea / Otsuka, Takuya / Tsuji, Takahiro / Hotta, Kiyohiko / Colvin, Robert

Transplantation

2023 Volume 107, Issue 5, Page(s) 1188–1199

Abstract: Background: Microarray transcript analysis of human renal transplantation biopsies has successfully identified the many patterns of graft rejection. To evaluate an alternative, this report tests whether gene expression from the Banff Human Organ ... ...

Abstract	Background: Microarray transcript analysis of human renal transplantation biopsies has successfully identified the many patterns of graft rejection. To evaluate an alternative, this report tests whether gene expression from the Banff Human Organ Transplant (B-HOT) probe set panel, derived from validated microarrays, can identify the relevant allograft diagnoses directly from archival human renal transplant formalin-fixed paraffin-embedded biopsies. To test this hypothesis, principal components (PCs) of gene expressions were used to identify allograft diagnoses, to classify diagnoses, and to determine whether the PC data were rich enough to identify diagnostic subtypes by clustering, which are all needed if the B-HOT panel can substitute for microarrays. Methods: RNA was isolated from routine, archival formalin-fixed paraffin-embedded tissue renal biopsy cores with both rejection and nonrejection diagnoses. The B-HOT panel expression of 770 genes was analyzed by PCs, which were then tested to determine their ability to identify diagnoses. Results: PCs of microarray gene sets identified the Banff categories of renal allograft diagnoses, modeled well the aggregate diagnoses, showing a similar correspondence with the pathologic diagnoses as microarrays. Clustering of the PCs identified diagnostic subtypes including non-chronic antibody-mediated rejection with high endothelial expression. PCs of cell types and pathways identified new mechanistic patterns including differential expression of B and plasma cells. Conclusions: Using PCs of gene expression from the B-Hot panel confirms the utility of the B-HOT panel to identify allograft diagnoses and is similar to microarrays. The B-HOT panel will accelerate and expand transcript analysis and will be useful for longitudinal and outcome studies.
MeSH term(s)	Humans ; Kidney Transplantation/adverse effects ; Kidney/pathology ; Transplantation, Homologous ; Biopsy ; Formaldehyde ; Graft Rejection/diagnosis ; Graft Rejection/genetics ; Graft Rejection/pathology
Chemical Substances	Formaldehyde (1HG84L3525)
Language	English
Publishing date	2023-04-22
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	208424-7
ISSN	1534-6080 ; 0041-1337
ISSN (online)	1534-6080
ISSN	0041-1337
DOI	10.1097/TP.0000000000004389
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Article ; Online: Lianas and Trees From a Seasonally Dry and a Wet Tropical Forest Did Not Differ in Embolism Resistance but Did Differ in Xylem Anatomical Traits in the Dry Forest

Chris M. Smith-Martin / Steven Jansen / Timothy J. Brodribb / José A. Medina-Vega / Christopher Lucani / Andrea Huppenberger / Jennifer S. Powers

Frontiers in Forests and Global Change, Vol

2022 Volume 5

Abstract: One of the most prominent changes in neotropical forests has been the increase in abundance and size of lianas. Studies suggest that lianas have more acquisitive strategies than trees, which could allow them to take advantage of water more effectively ... ...

Abstract	One of the most prominent changes in neotropical forests has been the increase in abundance and size of lianas. Studies suggest that lianas have more acquisitive strategies than trees, which could allow them to take advantage of water more effectively when it is available in water-limited forests, but few studies compared across growth form (i.e., lianas vs. trees) and forest type (i.e., wet vs. seasonally dry). We measured hydraulic and anatomical traits of co-occurring lianas and trees that convey drought resistance (xylem embolism resistance and intervessel pit membranes) and water transport capacity (xylem vessel diameter and density) in a seasonally dry and a wet evergreen tropical forest to address: (1) Are there differences between vulnerability to embolisms (P50—water potential at 50% loss of hydraulic conductivity) and hydraulic safety margins (HSM) across growth form and forest type? (2) How do vessel diameter and density vary across growth form and forest type? (3) Are there differences in xylem intervessel pit membrane thickness across growth form and forest type and does it predict xylem embolism vulnerability in trees and lianas? We examined hydraulic and xylem anatomical traits of 32 species—eight lianas and eight trees in each forest type. We found no difference in P50 and HSMs between lianas and trees and between the wetter and drier forest. Dry forest lianas had 81% greater maximum vessel diameter and 125% greater range in vessel diameter sizes than dry forest trees but, there was no significant difference between life forms in the wet forest. Dry forest species had 50% greater vessel density and 30% greater maximum pit membrane thickness than wet forest ones. Maximum pit membrane thickness was correlated to P50 and HSMs. The main difference between lianas and trees occurred in the dry forest, where lianas had larger maximum xylem vessel size than trees, implying that they have proportionally greater hydraulic conductive capacity than the trees in seasonal forests.
Keywords	canopy crane ; Isthmus of Panama ; plant functional traits ; plant hydraulic strategies ; P50 optical vulnerability technique ; rainfall gradient ; Forestry ; SD1-669.5 ; Environmental sciences ; GE1-350
Subject code	580 ; 333
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Treatment with Ad5-Porcine Interferon-α Attenuates Ebolavirus Disease in Pigs.

Senthilkumaran, Chandrika / Kroeker, Andrea L / Smith, Gregory / Embury-Hyatt, Carissa / Collignon, Brad / Ramirez-Medina, Elizabeth / Azzinaro, Paul A / Pickering, Bradley S / Diaz-San Segundo, Fayna / Weingartl, Hana M / de Los Santos, Teresa

Pathogens (Basel, Switzerland)

2022 Volume 11, Issue 4

Abstract: Under experimental conditions, pigs infected with Ebola Virus (EBOV) develop disease and can readily transmit the virus to non-human primates or pigs. In the event of accidental or intentional EBOV infection of domestic pigs, complex and time-consuming ... ...

Abstract	Under experimental conditions, pigs infected with Ebola Virus (EBOV) develop disease and can readily transmit the virus to non-human primates or pigs. In the event of accidental or intentional EBOV infection of domestic pigs, complex and time-consuming safe depopulation and carcass disposal are expected. Delaying or preventing transmission through a reduction in viral shedding is an absolute necessity to limit the spread of the virus. In this study, we tested whether porcine interferon-α or λ3 (porIFNα or porIFNλ3) delivered by a replication-defective human type 5 adenovirus vector (Ad5-porIFNα or Ad5-porIFNλ3) could limit EBOV replication and shedding in domestic pigs. Our results show that pigs pre-treated with Ad5-porIFNα did not develop measurable clinical signs, did not shed virus RNA, and displayed strongly reduced viral RNA load in tissues. A microarray analysis of peripheral blood mononuclear cells indicated that Ad5-porIFNα treatment led to clear upregulation in immune and inflammatory responses probably involved in protection against disease. Our results indicate that administration of Ad5-porIFNα can potentially be used to limit the spread of EBOV in pigs.
Language	English
Publishing date	2022-04-08
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2695572-6
ISSN	2076-0817
ISSN	2076-0817
DOI	10.3390/pathogens11040449
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Article ; Online: Lianas and Trees From a Seasonally Dry and a Wet Tropical Forest Did Not Differ in Embolism Resistance but Did Differ in Xylem Anatomical Traits in the Dry Forest

Smith-Martin, Chris M. / Jansen, Steven / Brodribb, Timothy J. / Medina-Vega, José A. / Lucani, Christopher / Huppenberger, Andrea / Powers, Jennifer S.

Frontiers in Forests and Global Change

2022 Volume 5

Abstract	One of the most prominent changes in neotropical forests has been the increase in abundance and size of lianas. Studies suggest that lianas have more acquisitive strategies than trees, which could allow them to take advantage of water more effectively when it is available in water-limited forests, but few studies compared across growth form (i.e., lianas vs. trees) and forest type (i.e., wet vs. seasonally dry). We measured hydraulic and anatomical traits of co-occurring lianas and trees that convey drought resistance (xylem embolism resistance and intervessel pit membranes) and water transport capacity (xylem vessel diameter and density) in a seasonally dry and a wet evergreen tropical forest to address: (1) Are there differences between vulnerability to embolisms (P50—water potential at 50% loss of hydraulic conductivity) and hydraulic safety margins (HSM) across growth form and forest type? (2) How do vessel diameter and density vary across growth form and forest type? (3) Are there differences in xylem intervessel pit membrane thickness across growth form and forest type and does it predict xylem embolism vulnerability in trees and lianas? We examined hydraulic and xylem anatomical traits of 32 species—eight lianas and eight trees in each forest type. We found no difference in P50 and HSMs between lianas and trees and between the wetter and drier forest. Dry forest lianas had 81% greater maximum vessel diameter and 125% greater range in vessel diameter sizes than dry forest trees but, there was no significant difference between life forms in the wet forest. Dry forest species had 50% greater vessel density and 30% greater maximum pit membrane thickness than wet forest ones. Maximum pit membrane thickness was correlated to P50 and HSMs. The main difference between lianas and trees occurred in the dry forest, where lianas had larger maximum xylem vessel size than trees, implying that they have proportionally greater hydraulic conductive capacity than the trees in seasonal forests.
Keywords	Isthmus of Panama ; P optical vulnerability technique ; canopy crane ; plant functional traits ; plant hydraulic strategies ; rainfall gradient ; woody plant growth forms ; xylem intervessel pit membranes
Subject code	580
Language	English
Publishing country	nl
Document type	Article ; Online
ISSN	2624-893X
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Treatment with Ad5-Porcine Interferon-α Attenuates Ebolavirus Disease in Pigs

Chandrika Senthilkumaran / Andrea L. Kroeker / Gregory Smith / Carissa Embury-Hyatt / Brad Collignon / Elizabeth Ramirez-Medina / Paul A. Azzinaro / Bradley S. Pickering / Fayna Diaz-San Segundo / Hana M. Weingartl / Teresa de los Santos

Pathogens, Vol 11, Iss 449, p

2022 Volume 449

Abstract	Under experimental conditions, pigs infected with Ebola Virus (EBOV) develop disease and can readily transmit the virus to non-human primates or pigs. In the event of accidental or intentional EBOV infection of domestic pigs, complex and time-consuming safe depopulation and carcass disposal are expected. Delaying or preventing transmission through a reduction in viral shedding is an absolute necessity to limit the spread of the virus. In this study, we tested whether porcine interferon-α or λ3 (porIFNα or porIFNλ3) delivered by a replication-defective human type 5 adenovirus vector (Ad5-porIFNα or Ad5-porIFNλ3) could limit EBOV replication and shedding in domestic pigs. Our results show that pigs pre-treated with Ad5-porIFNα did not develop measurable clinical signs, did not shed virus RNA, and displayed strongly reduced viral RNA load in tissues. A microarray analysis of peripheral blood mononuclear cells indicated that Ad5-porIFNα treatment led to clear upregulation in immune and inflammatory responses probably involved in protection against disease. Our results indicate that administration of Ad5-porIFNα can potentially be used to limit the spread of EBOV in pigs.
Keywords	ebola virus ; swine ; adenovirus ; interferon alpha ; interferon lambda ; IFN ; Medicine ; R
Subject code	630
Language	English
Publishing date	2022-04-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Banff Human Organ Transplant Transcripts Correlate with Renal Allograft Pathology and Outcome: Importance of Capillaritis and Subpathologic Rejection.

Journal of the American Society of Nephrology : JASN

2022 Volume 33, Issue 12, Page(s) 2306–2319

Abstract: Background: To seek insights into the pathogenesis of chronic active antibody-mediated rejection (CAMR), we performed mRNA analysis and correlated transcripts with pathologic component scores and graft outcomes.: Methods: We utilized the NanoString ... ...

Abstract	Background: To seek insights into the pathogenesis of chronic active antibody-mediated rejection (CAMR), we performed mRNA analysis and correlated transcripts with pathologic component scores and graft outcomes. Methods: We utilized the NanoString nCounter platform and the Banff Human Organ Transplant gene panel to quantify transcripts on 326 archived renal allograft biopsy samples. This system allowed correlation of transcripts with Banff pathology scores from the same tissue block and correlation with long-term outcomes. Results: The only pathology score that correlated with AMR pathways in CAMR was peritubular capillaritis (ptc). C4d, cg, g, v, i, t, or ci scores did not correlate. DSA-negative CAMR had lower AMR pathway scores than DSA-positive CAMR. Transcript analysis in non-CAMR biopsies yielded evidence of increased risk of later CAMR. Among 108 patients without histologic CAMR, 23 developed overt biopsy-documented CAMR within 5 years and as a group had higher AMR pathway scores ( Conclusions: Peritubular capillary inflammation and DSA are the primary drivers of AMR transcript elevation. Transcripts revealed subpathological evidence of AMR, which often preceded histologic CAMR and subpathological evidence of TCMR that predicted graft loss in CAMR.
MeSH term(s)	Humans ; Kidney Transplantation/adverse effects ; Organ Transplantation ; Transplantation, Homologous ; Vascular Diseases ; Antibodies ; Allografts
Chemical Substances	Antibodies
Language	English
Publishing date	2022-08-31
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	1085942-1
ISSN	1533-3450 ; 1046-6673
ISSN (online)	1533-3450
ISSN	1046-6673
DOI	10.1681/ASN.2022040444
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