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Article ; Online: Swarm chondrosarcoma: a continued resource for chondroblastic-like extracellular matrix and chondrosarcoma biology research.

Stevens, Jeff W

2013 Volume 54, Issue 4-5, Page(s) 252–259

Abstract: Since its first description over four decades ago, the Swarm chondrosarcoma (Swarm rat chondrosarcoma, SRC) remains a valuable tool for studies of chondroblastic-like extracellular matrix (ECM) biology and as an animal model of human chondrosarcoma of ... ...

Abstract	Since its first description over four decades ago, the Swarm chondrosarcoma (Swarm rat chondrosarcoma, SRC) remains a valuable tool for studies of chondroblastic-like extracellular matrix (ECM) biology and as an animal model of human chondrosarcoma of histological grades I-III. Moreover, articular joints and skeletal anomalies such as arthritis as well as cartilage regeneration, skeletal development, tissue engineering, hard tissue tumorigenesis and space flight physiology are advanced through studies in hyaline cartilage-like models. With more than 500 articles published since the first report on the characteristics of mucopolysaccharides (glycosaminoglycans) of the tumor in 1971, several transplantable tumor and cell lines have been developed by multiple laboratories worldwide. This review describes the characterization of SRC tumors and cell lines, including the use of SRC lines as a resource for isolation and characterization of several ECM elements that have become vital for the advancement of our understanding of cartilage biology. Also presented is the importance of pertubation of ECM components and the influence of the tumor microenvironment on disease progression. Therapeutic failure and currently pursued avenues of intervention utilizing the SRC lines in treatment of chondrosarcoma are also discussed.
MeSH term(s)	Animals ; Bone Neoplasms/pathology ; Bone Neoplasms/physiopathology ; Bone Neoplasms/therapy ; Cell Line, Tumor ; Cell Proliferation/drug effects ; Chondrosarcoma/pathology ; Chondrosarcoma/physiopathology ; Chondrosarcoma/therapy ; Extracellular Matrix/metabolism ; Extracellular Matrix Proteins/genetics ; Humans ; Mice ; Neoplasm Transplantation ; Proteoglycans/metabolism ; Rats ; Tumor Cells, Cultured
Chemical Substances	Extracellular Matrix Proteins ; Proteoglycans
Language	English
Publishing date	2013
Publishing country	England
Document type	Journal Article ; Review
ZDB-ID	185551-7
ISSN	1607-8438 ; 0091-1690 ; 0300-8207
ISSN (online)	1607-8438
ISSN	0091-1690 ; 0300-8207
DOI	10.3109/03008207.2013.806913
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Zs.MO 44: Show issues

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Article: High-Risk Pedigree Study Identifies

Cannon-Albright, Lisa A / Stevens, Jeff / Facelli, Julio C / Teerlink, Craig C / Allen-Brady, Kristina / Agarwal, Neeraj

Cancers

2023 Volume 15, Issue 7

Abstract: There is evidence for contribution of inherited factors to prostate cancer, and more specifically to lethal prostate cancer, but few responsible genes/variants have been identified. We examined genetic sequence data for 51 affected cousin pairs who each ... ...

Abstract	There is evidence for contribution of inherited factors to prostate cancer, and more specifically to lethal prostate cancer, but few responsible genes/variants have been identified. We examined genetic sequence data for 51 affected cousin pairs who each died from prostate cancer and who were members of high-risk prostate cancer pedigrees in order to identify rare variants shared by the cousins as candidate predisposition variants. Candidate variants were tested for association with prostate cancer risk in UK Biobank data. Candidate variants were also assayed in 1195 additional sampled Utah prostate cancer cases. We used 3D protein structure prediction methods to analyze structural changes and provide insights into mechanisms of pathogenicity. Almost 4000 rare (<0.005) variants were identified as shared in the 51 affected cousin pairs. One candidate variant was also significantly associated with prostate cancer risk among the 840 variants with data in UK Biobank, in the gene
Language	English
Publishing date	2023-03-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15072085
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Article: A Rare Variant in

Cannon-Albright, Lisa A / Stevens, Jeff / Teerlink, Craig C / Facelli, Julio C / Allen-Brady, Kristina / Welm, Alana L

Cancers

2023 Volume 15, Issue 24

Abstract: A significant fraction of breast cancer recurs, with lethal outcome, but specific genetic variants responsible have yet to be identified. Five cousin pairs with recurrent breast cancer from pedigrees with a statistical excess of recurrent breast cancer ... ...

Abstract	A significant fraction of breast cancer recurs, with lethal outcome, but specific genetic variants responsible have yet to be identified. Five cousin pairs with recurrent breast cancer from pedigrees with a statistical excess of recurrent breast cancer were sequenced to identify rare, shared candidate predisposition variants. The candidates were tested for association with breast cancer risk with UKBiobank data. Additional breast cancer cases were assayed for a subset of candidate variants to test for co-segregation. Three-dimensional protein structure prediction methods were used to investigate how the mutation under consideration is predicted to change structural and electrostatic properties in the mutated protein. One hundred and eighty-one rare candidate predisposition variants were shared in at least one cousin pair from a high-risk pedigree. A rare variant in
Language	English
Publishing date	2023-12-15
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2527080-1
ISSN	2072-6694
ISSN	2072-6694
DOI	10.3390/cancers15245851
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Article: Mutual proximity graphs for improved reachability in music recommendation.

Flexer, Arthur / Stevens, Jeff

Journal of new music research

2017 Volume 47, Issue 1, Page(s) 17–28

Abstract: This paper is concerned with the impact of hubness, a general problem of machine learning in high-dimensional spaces, on a real-world music recommendation system based on visualisation of a k-nearest neighbour (knn) graph. Due to a problem of measuring ... ...

Abstract	This paper is concerned with the impact of hubness, a general problem of machine learning in high-dimensional spaces, on a real-world music recommendation system based on visualisation of a k-nearest neighbour (knn) graph. Due to a problem of measuring distances in high dimensions, hub objects are recommended over and over again while anti-hubs are nonexistent in recommendation lists, resulting in poor reachability of the music catalogue. We present mutual proximity graphs, which are an alternative to knn and mutual knn graphs, and are able to avoid hub vertices having abnormally high connectivity. We show that mutual proximity graphs yield much better graph connectivity resulting in improved reachability compared to knn graphs, mutual knn graphs and mutual knn graphs enhanced with minimum spanning trees, while simultaneously reducing the negative effects of hubness.
Language	English
Publishing date	2017-08-03
Publishing country	England
Document type	Journal Article
ZDB-ID	1501763-1
ISSN	1744-5027 ; 0929-8215
ISSN (online)	1744-5027
ISSN	0929-8215
DOI	10.1080/09298215.2017.1354891
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Article: Effects of Two Activated Milt Residence Times on Landlocked Fall Chinook Salmon Egg Survival to the Eyed Stage of Development

Stevens, Jeff / Voorhees, Jill M. / Huysman, Nathan / Krebs, Eric / Barnes, Michael E.

North American journal of aquaculture. 2021 July, v. 83, no. 3

2021

Abstract: During salmonid spawning, the amount of time required for activated milt to successfully fertilize eggs has not been well defined. This study examined the effects of two different activated milt residence times, 20 and 60 s, during production‐scale ... ...

Abstract	During salmonid spawning, the amount of time required for activated milt to successfully fertilize eggs has not been well defined. This study examined the effects of two different activated milt residence times, 20 and 60 s, during production‐scale artificial spawning of 20 landlocked fall Chinook Salmon Oncorhynchus tshawytscha. Mean (SE) survival to the eyed stage of egg development was 29.2% (5.5) in the eggs that were subjected to the 20‐s milt residence time, which was not significantly different from the 32.3% (5.7) survival rate for eggs with the 60‐s residence time. There was considerable variation in egg survival among the individual female spawns, ranging from near 0% to 76.7%. These production‐scale results indicate that activated milt residence times as low as 20 s can be used during the landlocked fall Chinook Salmon spawning, with no significant effect on egg survival to the eyed stage of development.
Keywords	Oncorhynchus tshawytscha ; aquaculture ; developmental stages ; eggs ; females ; milt ; survival rate
Language	English
Dates of publication	2021-07
Size	p. 203-206.
Publishing place	John Wiley & Sons, Ltd
Document type	Article
Note	JOURNAL ARTICLE
ZDB-ID	1482260-x
ISSN	1548-8454 ; 1522-2055
ISSN (online)	1548-8454
ISSN	1522-2055
DOI	10.1002/naaq.10192
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Article ; Online: Detection of tumor-derived cell-free DNA in cerebrospinal fluid using a clinically validated targeted sequencing panel for pediatric brain tumors.

Ronsley, Rebecca / Karvonen, Kristine A / Cole, Bonnie / Paulson, Vera / Stevens, Jeff / Crotty, Erin E / Hauptman, Jason / Lee, Amy / Stasi, Shannon M / Lockwood, Christina M / Leary, Sarah E S

Journal of neuro-oncology

2024

Abstract: Purpose: Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free ...

Abstract	Purpose: Clinical sequencing of tumor DNA is necessary to render an integrated diagnosis and select therapy for children with primary central nervous system (CNS) tumors, but neurosurgical biopsy is not without risk. In this study, we describe cell-free DNA (cfDNA) in blood and cerebrospinal fluid (CSF) as sources for "liquid biopsy" in pediatric brain tumors. Methods: CSF samples were collected by lumbar puncture, ventriculostomy, or surgery from pediatric patients with CNS tumors. Following extraction, CSF-derived cfDNA was sequenced using UW-OncoPlex™, a clinically validated next-generation sequencing platform. CSF-derived cfDNA results and paired plasma and tumor samples concordance was also evaluated. Results: Seventeen CSF samples were obtained from 15 pediatric patients with primary CNS tumors. Tumor types included medulloblastoma (n = 7), atypical teratoid/rhabdoid tumor (n = 2), diffuse midline glioma with H3 K27 alteration (n = 4), pilocytic astrocytoma (n = 1), and pleomorphic xanthoastrocytoma (n = 1). CSF-derived cfDNA was detected in 9/17 (53%) of samples, and sufficient for sequencing in 8/10 (80%) of extracted samples. All somatic mutations and copy-number variants were also detected in matched tumor tissue, and tumor-derived cfDNA was absent in plasma samples and controls. Tumor-derived cfDNA alterations were detected in the absence of cytological evidence of malignant cells in as little as 200 µl of CSF. Several clinically relevant alterations, including a KIAA1549::BRAF fusion were detected. Conclusions: Clinically relevant genomic alterations are detectable using CSF-derived cfDNA across a range of pediatric brain tumors. Next-generation sequencing platforms are capable of producing a high yield of DNA alterations with 100% concordance rate with tissue analysis.
Language	English
Publishing date	2024-05-16
Publishing country	United States
Document type	Journal Article
ZDB-ID	604875-4
ISSN	1573-7373 ; 0167-594X
ISSN (online)	1573-7373
ISSN	0167-594X
DOI	10.1007/s11060-024-04645-y
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Article ; Online: The HOXB13 p.Gly84Glu variant observed in an extended five generation high-risk prostate cancer pedigree supports risk association for multiple cancer sites.

Cannon-Albright, Lisa A / Stevens, Jeff / Teerlink, Craig C / Agarwal, Neeraj

Cancer epidemiology

2020 Volume 69, Page(s) 101834

Abstract: HOXB13 p.Gly84Glu is recognized as a rare variant associated with increased risk for prostate cancer; risk association for other cancers is uncertain. This HOXB13 variant was originally reported in several 3-generation prostate cancer pedigrees and has ... ...

Abstract	HOXB13 p.Gly84Glu is recognized as a rare variant associated with increased risk for prostate cancer; risk association for other cancers is uncertain. This HOXB13 variant was originally reported in several 3-generation prostate cancer pedigrees and has been reported to be associated with increased risk for bladder and colorectal cancer and leukemia in GWAS. A HOXB13 pGly84Glu variant carrier was identified in a set of Utah individuals born more than 100 years ago who were members of high-risk cancer pedigrees. The proband carrier was diagnosed with colon cancer and is a member of a high-risk prostate cancer pedigree. The HOXB13 pGLY84Glu variant was assayed in other sampled relatives in the pedigree and was observed to segregate in relatives of the proband carrier in the extended pedigree; this pedigree showed significant excess of prostate cancer, cervical cancer, leukemia, colorectal cancer, and gastric cancer among descendants. Multiple additional variant carriers were identified, diagnosed with prostate, bladder, and colon cancers in the 5-generation high-risk cancer pedigree. This study shows the power and efficiency of a biorepository of samples with known genealogy from extended high-risk pedigrees for definition of cancer-associated risks. Association of HOXB13 p.Gly84Glu with risk of colon and bladder cancers in this extended pedigree confirms previous reports for risk association for both cancers.
MeSH term(s)	Genetic Predisposition to Disease ; Homeodomain Proteins/metabolism ; Humans ; Male ; Neoplasms/genetics ; Pedigree ; Prostatic Neoplasms/complications ; Prostatic Neoplasms/genetics ; Risk Factors
Chemical Substances	HOXB13 protein, human ; Homeodomain Proteins
Language	English
Publishing date	2020-10-21
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, Non-P.H.S. ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2508729-0
ISSN	1877-783X ; 1877-7821
ISSN (online)	1877-783X
ISSN	1877-7821
DOI	10.1016/j.canep.2020.101834
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Article ; Online: Engaging Institutional Stakeholders to Develop and Implement Guidelines for Recruiting Participants in Research Studies Using Social Media: Mixed Methods, Multi-Phase Process.

Flood-Grady, Elizabeth / Solberg, Lauren B / Baralt, Claire / Meyer, Meghan / Stevens, Jeff / Krieger, Janice L

Journal of medical Internet research

2021 Volume 23, Issue 10, Page(s) e23312

Abstract: Background: Limited regulatory guidance surrounding the use of social media channels for participant recruitment is an interdisciplinary challenge. Establishing stakeholder-informed procedures is essential for ethical and effective use of social media ... ...

Abstract	Background: Limited regulatory guidance surrounding the use of social media channels for participant recruitment is an interdisciplinary challenge. Establishing stakeholder-informed procedures is essential for ethical and effective use of social media for participant recruitment. Objective: This study aims to provide replicable procedures for developing and implementing guidelines for using social media to recruit participants in research studies. Methods: Social media use cases at the university were used to identify institutional stakeholders for the initiative. After establishing workflow procedures, a scoping review of web-based materials about recruitment and research on the internet and social media from 19 peer institutions and 2 federal agencies was conducted to inform the structure of the policies and procedures. End users (investigators and study coordinators; N=14) also provided feedback on the policies and procedures and implementation. Results: Representatives (n=7) from 5 institutional offices and 15 subject-matter experts from 5 areas were identified as stakeholders in the development of policies and procedures. Peers with web-based materials (n=16) identified in the scoping review revealed 4 themes that served as a basis for developing our policies and procedures. End user feedback further informed the policies and procedures and implementation. A centrally managed social media account for communicating with participants and hosting advertising campaigns on social media was also established and, when combined with the policies and procedures, resulted in 39 advertising campaigns, and 2846 participants were enrolled in health and clinical research studies. Conclusions: Our policies and procedures allow research teams to harness the potential of social media to increase study recruitment and participation; the transparent, stakeholder-informed process can be replicated by institutional administrators to establish policies and procedures that meet the interests and needs of their research community.
MeSH term(s)	Advertising ; Humans ; Interdisciplinary Studies ; Review Literature as Topic ; Social Media
Language	English
Publishing date	2021-10-08
Publishing country	Canada
Document type	Journal Article ; Research Support, N.I.H., Extramural
ZDB-ID	2028830-X
ISSN	1438-8871 ; 1439-4456
ISSN (online)	1438-8871
ISSN	1439-4456
DOI	10.2196/23312
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Article ; Online: An intronic variant in the CELF4 gene is associated with risk for colorectal cancer.

Teerlink, Craig C / Stevens, Jeff / Hernandez, Rolando / Facelli, Julio C / Cannon-Albright, Lisa A

Cancer epidemiology

2021 Volume 72, Page(s) 101941

Abstract: Background: Germline predisposition variants associated with colorectal cancer (CRC) have been identified but all are not yet identified. We sought to identify the responsible predisposition germline variant in an extended high-risk CRC pedigree that ... ...

Abstract	Background: Germline predisposition variants associated with colorectal cancer (CRC) have been identified but all are not yet identified. We sought to identify the responsible predisposition germline variant in an extended high-risk CRC pedigree that exhibited evidence of linkage to the 18q12.2 region (TLOD = +2.81). Methods: DNA from two distantly related carriers of the hypothesized predisposition haplotype on 18q12.2 was sequenced to identify candidate variants. The candidate rare variants shared by the related sequenced subjects were screened in 3,094 CRC cases and 5x population-matched controls from UKBiobank to test for association. Further segregation of the variant was tested via Taqman assay in other sampled individuals in the pedigree. Results: Analysis of whole genome sequence data for the two related hypothesized predisposition haplotype carriers, restricted to the shared haplotype boundaries, identified multiple (n = 6) rare candidate non-coding variants that were tested for association with CRC risk in UKBiobank. A rare intronic variant ofCELF4 gene, rs568643870, was significantly associated with CRC (p = 0.004, OR = 5.0), and segregated with CRC in other members of the linked pedigree. Conclusion: Evidence of segregation in a high-risk pedigree, case-control association in an external dataset, and identification of additional CRC-affected carriers in the linked pedigree support a role for a rareCELF4 intronic variant in CRC risk.
MeSH term(s)	CELF Proteins/genetics ; Case-Control Studies ; Colorectal Neoplasms/genetics ; Genetic Predisposition to Disease ; Germ-Line Mutation ; Humans ; Pedigree
Chemical Substances	CELF Proteins ; CELF4 protein, human
Language	English
Publishing date	2021-04-28
Publishing country	Netherlands
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't ; Research Support, U.S. Gov't, P.H.S.
ZDB-ID	2508729-0
ISSN	1877-783X ; 1877-7821
ISSN (online)	1877-783X
ISSN	1877-7821
DOI	10.1016/j.canep.2021.101941
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Article ; Online: A rare FGF5 candidate variant (rs112475347) for predisposition to nonsquamous, nonsmall-cell lung cancer.

Cannon-Albright, Lisa A / Teerlink, Craig C / Stevens, Jeff / Facelli, Julio C / Carr, Shamus R / Allen-Brady, Kristina / Puri, Sonam / Bailey-Wilson, Joan E / Musolf, Anthony M / Akerley, Wallace

International journal of cancer

2023 Volume 153, Issue 2, Page(s) 364–372

Abstract: A unique approach with rare resources was used to identify candidate variants predisposing to familial nonsquamous nonsmall-cell lung cancers (NSNSCLC). We analyzed sequence data from NSNSCLC-affected cousin pairs belonging to high-risk lung cancer ... ...

Abstract	A unique approach with rare resources was used to identify candidate variants predisposing to familial nonsquamous nonsmall-cell lung cancers (NSNSCLC). We analyzed sequence data from NSNSCLC-affected cousin pairs belonging to high-risk lung cancer pedigrees identified in a genealogy of Utah linked to statewide cancer records to identify rare, shared candidate predisposition variants. Variants were tested for association with lung cancer risk in UK Biobank. Evidence for linkage with lung cancer was also reviewed in families from the Genetic Epidemiology of Lung Cancer Consortium. Protein prediction modeling compared the mutation with reference. We sequenced NSNSCLC-affected cousin pairs from eight high-risk lung cancer pedigrees and identified 66 rare candidate variants shared in the cousin pairs. One variant in the FGF5 gene also showed significant association with lung cancer in UKBiobank. This variant was observed in 3/163 additional sampled Utah lung cancer cases, 2 of whom were related in another independent pedigree. Modeling of the predicted protein predicted a second binding site for SO
MeSH term(s)	Humans ; Genetic Predisposition to Disease ; Genotype ; Carcinoma, Non-Small-Cell Lung/genetics ; Lung Neoplasms/epidemiology ; Lung Neoplasms/genetics ; Mutation ; Pedigree ; Fibroblast Growth Factor 5
Chemical Substances	FGF5 protein, human ; Fibroblast Growth Factor 5 (129653-64-1)
Language	English
Publishing date	2023-04-05
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, U.S. Gov't, P.H.S. ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Intramural
ZDB-ID	218257-9
ISSN	1097-0215 ; 0020-7136
ISSN (online)	1097-0215
ISSN	0020-7136
DOI	10.1002/ijc.34510
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