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Article: Impact of genome build on RNA-seq interpretation and diagnostics.

Ungar, Rachel A / Goddard, Pagé C / Jensen, Tanner D / Degalez, Fabien / Smith, Kevin S / Jin, Christopher A / Bonner, Devon E / Bernstein, Jonathan A / Wheeler, Matthew T / Montgomery, Stephen B

medRxiv : the preprint server for health sciences

2024

Abstract: Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To ... ...

Abstract	Transcriptomics is a powerful tool for unraveling the molecular effects of genetic variants and disease diagnosis. Prior studies have demonstrated that choice of genome build impacts variant interpretation and diagnostic yield for genomic analyses. To identify the extent genome build also impacts transcriptomics analyses, we studied the effect of the hg19, hg38, and CHM13 genome builds on expression quantification and outlier detection in 386 rare disease and familial control samples from both the Undiagnosed Diseases Network (UDN) and Genomics Research to Elucidate the Genetics of Rare Disease (GREGoR) Consortium. We identified 2,800 genes with build-dependent quantification across six routinely-collected biospecimens, including 1,391 protein-coding genes and 341 known rare disease genes. We further observed multiple genes that only have detectable expression in a subset of genome builds. Finally, we characterized how genome build impacts the detection of outlier transcriptomic events. Combined, we provide a database of genes impacted by build choice, and recommend that transcriptomics-guided analyses and diagnoses are cross-referenced with these data for robustness.
Language	English
Publishing date	2024-01-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.01.11.24301165
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Article ; Online: Surface-Functionalized Boron Nanoparticles with Reduced Oxide Content by Nonthermal Plasma Processing for Nanoenergetic Applications.

Agarwal, Prawal P K / Jensen, Devon / Chen, Chien-Hua / Rioux, Robert M / Matsoukas, Themis

ACS applied materials & interfaces

2021 Volume 13, Issue 5, Page(s) 6844–6853

Abstract: The development of an in situ nonthermal plasma technology improved the oxidation and energy release of boron nanoparticles. We reduced the native oxide layer on the surface of boron nanoparticles (70 nm) by treatment in a nonthermal hydrogen plasma, ... ...

Abstract	The development of an in situ nonthermal plasma technology improved the oxidation and energy release of boron nanoparticles. We reduced the native oxide layer on the surface of boron nanoparticles (70 nm) by treatment in a nonthermal hydrogen plasma, followed by the formation of a passivation barrier by argon plasma-enhanced chemical vapor deposition (PECVD) using perfluorodecalin (C
Language	English
Publishing date	2021-01-29
Publishing country	United States
Document type	Journal Article
ISSN	1944-8252
ISSN (online)	1944-8252
DOI	10.1021/acsami.0c20825
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Integration of transcriptomics and long-read genomics prioritizes structural variants in rare disease.

Jensen, Tanner D / Ni, Bohan / Reuter, Chloe M / Gorzynski, John E / Fazal, Sarah / Bonner, Devon / Ungar, Rachel A / Goddard, Pagé C / Raja, Archana / Ashley, Euan A / Bernstein, Jonathan A / Zuchner, Stephan / Greicius, Michael D / Montgomery, Stephen B / Schatz, Michael C / Wheeler, Matthew T / Battle, Alexis

medRxiv : the preprint server for health sciences

2024

Abstract: Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals ... ...

Abstract	Rare structural variants (SVs) - insertions, deletions, and complex rearrangements - can cause Mendelian disease, yet they remain difficult to accurately detect and interpret. We sequenced and analyzed Oxford Nanopore long-read genomes of 68 individuals from the Undiagnosed Disease Network (UDN) with no previously identified diagnostic mutations from short-read sequencing. Using our optimized SV detection pipelines and 571 control long-read genomes, we detected 716 long-read rare (MAF < 0.01) SV alleles per genome on average, achieving a 2.4x increase from short-reads. To characterize the functional effects of rare SVs, we assessed their relationship with gene expression from blood or fibroblasts from the same individuals, and found that rare SVs overlapping enhancers were enriched (LOR = 0.46) near expression outliers. We also evaluated tandem repeat expansions (TREs) and found 14 rare TREs per genome; notably these TREs were also enriched near overexpression outliers. To prioritize candidate functional SVs, we developed Watershed-SV, a probabilistic model that integrates expression data with SV-specific genomic annotations, which significantly outperforms baseline models that don't incorporate expression data. Watershed-SV identified a median of eight high-confidence functional SVs per UDN genome. Notably, this included compound heterozygous deletions in
Language	English
Publishing date	2024-03-26
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.22.24304565
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Article: Sleep and Pain in Veterans with Chronic Pain: Effects of Psychological Pain Treatment and Temporal Associations.

Wilson, Marian / Skeiky, Lillian / Muck, Rachael A / Miller, Megan A / Hansen, Devon A / Williams, Rhonda M / Jensen, Mark P / Van Dongen, Hans P A

Nature and science of sleep

2023 Volume 15, Page(s) 1061–1077

Abstract: Introduction: Chronic pain is highly prevalent in US military Veterans. Non-opioid and non-pharmacologic treatments are recommended when clinically appropriate, but research on the mechanisms underlying benefits of these treatments is lacking. Here, we ... ...

Abstract	Introduction: Chronic pain is highly prevalent in US military Veterans. Non-opioid and non-pharmacologic treatments are recommended when clinically appropriate, but research on the mechanisms underlying benefits of these treatments is lacking. Here, we examined the role of sleep in the effects of three non-pharmacologic pain treatments in Veterans. Specifically, we investigated whether treatment effects on sleep predicted treatment effects on pain occurring later, or vice versa. Methods: Veterans enrolled in a randomized controlled trial were invited to participate in this supplementary sleep study. A total of 174 Veterans were randomized to one of three 8-session, in-person, group-based pain treatments: hypnosis, mindfulness meditation, or education control. Measurements included self-reported sleep disturbance, pain intensity, and pain catastrophizing; sleep duration was assessed with actigraphy. Sleep and pain measurements were obtained at baseline, posttreatment, and 3-month posttreatment follow-up. Results: At baseline, average pain intensity was moderate (mean ± SD: 5.7 ± 1.7 on the 0-10 Numeric Rating Scale), pain catastrophizing was just below the clinically relevant threshold (mean ± SD: 28.6 ± 12.2 on the Pain Catastrophizing Scale), and subjective sleep disturbance exceeded the US population average (mean ± SD: 58.5 ± 8.1 on the Patient Reported Outcomes Measurement Information System Sleep Disturbance - Short Form). By contrast, objective sleep duration was consistent with the recommended daily sleep amount of 7-8 h for adults (mean ± SD: 8.3 ± 1.4 h). Across treatment conditions, pain intensity, pain catastrophizing, and subjective sleep disturbance were significantly less at posttreatment and 3-month follow-up than at baseline (p < 0.001). Actigraphic sleep duration did not differ significantly as a function of time. There was a high degree of covariation among the measures of pain intensity, pain catastrophizing, and sleep disturbance (p < 0.05). However, self-reported sleep disturbance was not significantly correlated with actigraphic sleep duration (\|r\| <= 0.13, p > 0.05). Sleep and pain variables observed at prior assessments predicted these same variables at subsequent assessments. There was no significant evidence that changes in pain preceded changes in sleep or that changes in sleep preceded changes in pain (all p > 0.05). Discussion: For this study's Veterans, treatment-related changes in sleep and pain appeared to occur in parallel. The concomitant changes in sleep and pain suggest that therapies improving pain in Veterans may yield attendant benefits for the treatment of sleep, and possibly vice versa.
Language	English
Publishing date	2023-12-19
Publishing country	New Zealand
Document type	Journal Article
ZDB-ID	2587468-8
ISSN	1179-1608
ISSN	1179-1608
DOI	10.2147/NSS.S418532
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Article ; Online: Metaphors as a Bridge to Understanding Educational and Social Contexts

Devon Jensen

International Journal of Qualitative Methods, Vol

2006 Volume 5

Abstract: Educational researchers and practitioners are frequently asking questions about how better to understand educational theory and practice. Through the years, they have employed a variety of both quantitative and qualitative methods to elucidate the world ... ...

Abstract	Educational researchers and practitioners are frequently asking questions about how better to understand educational theory and practice. Through the years, they have employed a variety of both quantitative and qualitative methods to elucidate the world of education. In this article, the author explores the epistemological legitimacy of metaphor analysis as a viable means for qualitative educational inquiry. In so doing, he explores the concepts of the theory of abduction, educational research and social constructivism, categories of metaphors, and metaphorical analysis in educational research. In addition, a review of the literature on educational research that uses metaphor analysis as the primary methodology revealed five major themes.
Keywords	Social sciences (General) ; H1-99
Language	English
Publishing date	2006-03-01T00:00:00Z
Publisher	SAGE Publishing
Document type	Article ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Hypnotic Enhancement of Virtual Reality Distraction Analgesia during Thermal Pain:

Patterson, David R / Hoffman, Hunter G / Chambers, Gloria / Bennetts, Devon / Hunner, Harley H / Wiechman, Shelley A / Garcia-Palacios, Azucena / Jensen, Mark P

The International journal of clinical and experimental hypnosis

2021 Volume 69, Issue 2, Page(s) 225–245

Abstract: Excessive pain during medical procedures is a pervasive health challenge. This study tested the (additive) analgesic efficacy of combining hypnotic analgesia and virtual reality (VR) pain distraction. A single blind, randomized, and controlled trial was ... ...

Abstract	Excessive pain during medical procedures is a pervasive health challenge. This study tested the (additive) analgesic efficacy of combining hypnotic analgesia and virtual reality (VR) pain distraction. A single blind, randomized, and controlled trial was used to study 205 undergraduate volunteers aged 18 to 20. The individual and combined effects of hypnotic analgesia (H) and VR distraction on experimentally induced acute thermal pain were examined using a 2 X 2, between-groups parallel design (4 groups total). Participants in groups that received hypnosis remained hypnotized during the test phase pain stimulus. The main outcome measure was "worst pain" ratings. Hypnosis reduced acute pain even for people who scored low on hypnotizability. As predicted, H+ VR was significantly more effective than VR distraction alone. However, H+ VR was not significantly more effective than hypnotic analgesia alone. Being hypnotized during thermal pain enhanced VR distraction analgesia.
MeSH term(s)	Analgesia ; Humans ; Hypnosis ; Hypnotics and Sedatives ; Pain ; Pain Measurement ; Single-Blind Method ; Virtual Reality
Chemical Substances	Hypnotics and Sedatives
Language	English
Publishing date	2021-03-16
Publishing country	England
Document type	Journal Article ; Randomized Controlled Trial ; Research Support, N.I.H., Extramural
ZDB-ID	218267-1
ISSN	1744-5183 ; 0020-7144
ISSN (online)	1744-5183
ISSN	0020-7144
DOI	10.1080/00207144.2021.1882259
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Book ; Online: Revisiting Submicron-Gap Thermionic Power Generation Based on Comprehensive Charge and Thermal Transport Modeling

Jensen, Devon / Ghashami, Mohammad / Park, Keunhan

2019

Abstract: Over the past years, thermionic energy conversion (TEC) with a reduced inter-electrode vacuum gap has been studied as an effective way to mitigate a large potential barrier due to space charge accumulation. However, existing theoretical models do not ... ...

Abstract	Over the past years, thermionic energy conversion (TEC) with a reduced inter-electrode vacuum gap has been studied as an effective way to mitigate a large potential barrier due to space charge accumulation. However, existing theoretical models do not fully consider the fundamental aspects of thermionic emission when the inter-electrode gap shrinks to the nanoscale, which results in underestimation of thermionic power generation for such small gaps. The present work addresses this challenge by comprehensively modeling charge and thermal transport processes with specific consideration of nanoscale gap effects, such as image charge perturbation, electron tunneling, and near-field thermal radiation. Carefully conducted energy balance analysis reveals that if optimized, submicron-gap TEC can excel the micron-gap counterpart with $\sim$4 times the power output and ~5-10 % higher energy conversion efficiency. Moreover, the high-temperature collector of the submicron-gap TEC, which is due to thermionic and near-field radiative heat transfer, allows the addition of a bottom-cycle heat engine to further enhance the power and efficiency when combined. Electric field concentration due to engineered surface roughness is also examined as a potential approach to produce an additional increase in power generation. We believe that the present work provides a theoretical framework for submicron-gap thermionic power generation as a promising energy recycling scheme for high-quality heat sources. Comment: 24 pages; 7 figures
Keywords	Physics - Applied Physics ; Condensed Matter - Mesoscale and Nanoscale Physics
Subject code	621
Publishing date	2019-07-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: COPII-mediated vesicle formation at a glance.

Jensen, Devon / Schekman, Randy

Journal of cell science

2011 Volume 124, Issue Pt 1, Page(s) 1–4

MeSH term(s)	Animals ; COP-Coated Vesicles/genetics ; COP-Coated Vesicles/metabolism ; Humans ; Protein Transport ; Vesicular Transport Proteins/genetics ; Vesicular Transport Proteins/metabolism
Chemical Substances	Vesicular Transport Proteins
Language	English
Publishing date	2011-01-01
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2993-2
ISSN	1477-9137 ; 0021-9533
ISSN (online)	1477-9137
ISSN	0021-9533
DOI	10.1242/jcs.069773
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Zs.A 1200: Show issues			Location: Je nach Verfügbarkeit (siehe Angabe bei Bestand) bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular Jg. 1995 - 2021: Lesesall (1.OG) ab Jg. 2022: Lesesaal (EG)
Zs.MG 14: Show issues

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Article ; Online: The glucagon-like peptide 1 (GLP-1) receptor agonist exendin-4 reduces cocaine self-administration in mice.

Sørensen, Gunnar / Reddy, India A / Weikop, Pia / Graham, Devon L / Stanwood, Gregg D / Wortwein, Gitta / Galli, Aurelio / Fink-Jensen, Anders

Physiology & behavior

2015 Volume 149, Page(s) 262–268

Abstract: Glucagon-like peptide 1 (GLP-1) analogues are used for the treatment of type 2 diabetes. The ability of the GLP-1 system to decrease food intake in rodents has been well described and parallels results from clinical trials. GLP-1 receptors are expressed ... ...

Abstract	Glucagon-like peptide 1 (GLP-1) analogues are used for the treatment of type 2 diabetes. The ability of the GLP-1 system to decrease food intake in rodents has been well described and parallels results from clinical trials. GLP-1 receptors are expressed in the brain, including within the ventral tegmental area (VTA) and the nucleus accumbens (NAc). Dopaminergic neurons in the VTA project to the NAc, and these neurons play a pivotal role in the rewarding effects of drugs of abuse. Based on the anatomical distribution of GLP-1 receptors in the brain and the well-established effects of GLP-1 on food reward, we decided to investigate the effect of the GLP-1 analogue exendin-4 on cocaine- and dopamine D1-receptor agonist-induced hyperlocomotion, on acute and chronic cocaine self-administration, on cocaine-induced striatal dopamine release in mice and on cocaine-induced c-fos activation. Here, we report that GLP-1 receptor stimulation reduces acute and chronic cocaine self-administration and attenuates cocaine-induced hyperlocomotion. In addition, we show that peripheral administration of exendin-4 reduces cocaine-induced elevation of striatal dopamine levels and striatal c-fos expression implicating central GLP-1 receptors in these responses. The present results demonstrate that the GLP-1 system modulates cocaine's effects on behavior and dopamine homeostasis, indicating that the GLP-1 receptor may be a novel target for the pharmacological treatment of drug addiction.
MeSH term(s)	Analysis of Variance ; Animals ; Benzazepines/toxicity ; Cocaine/administration & dosage ; Corpus Striatum/drug effects ; Corpus Striatum/metabolism ; Dopamine/metabolism ; Dopamine Agonists/toxicity ; Dopamine Uptake Inhibitors/administration & dosage ; Dose-Response Relationship, Drug ; Exploratory Behavior/drug effects ; Gene Expression Regulation/drug effects ; Hyperkinesis/chemically induced ; Hypoglycemic Agents/pharmacology ; Male ; Mice ; Microdialysis ; Motor Activity/drug effects ; Peptides/pharmacology ; Proto-Oncogene Proteins c-fos/genetics ; Proto-Oncogene Proteins c-fos/metabolism ; Self Administration ; Time Factors ; Venoms/pharmacology
Chemical Substances	Benzazepines ; Dopamine Agonists ; Dopamine Uptake Inhibitors ; Hypoglycemic Agents ; Peptides ; Proto-Oncogene Proteins c-fos ; Venoms ; SK&F 82958 (80751-65-1) ; exenatide (9P1872D4OL) ; Cocaine (I5Y540LHVR) ; Dopamine (VTD58H1Z2X)
Language	English
Publishing date	2015-10-01
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	3907-x
ISSN	1873-507X ; 0031-9384
ISSN (online)	1873-507X
ISSN	0031-9384
DOI	10.1016/j.physbeh.2015.06.013
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Zs.A 747: Show issues

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Article ; Online: Endoplasmic Reticulum Stress-Activated Transcription Factor ATF6α Requires the Disulfide Isomerase PDIA5 To Modulate Chemoresistance

Higa, Arisa / Taouji, Said / Lhomond, Stéphanie / Jensen, Devon / Fernandez-Zapico, Martin E. / Simpson, Jeremy C. / Pasquet, Jean-Max / Schekman, Randy / Chevet, Eric

Molecular and Cellular Biology. 2014 May 1, v. 34, no. 10 p.1839-1849

2014

Abstract: ATF6α, a membrane-anchored transcription factor from the endoplasmic reticulum (ER) that modulates the cellular response to stress as an effector of the unfolded-protein response (UPR), is a key player in the development of tumors of different origin. ... ...

Abstract	ATF6α, a membrane-anchored transcription factor from the endoplasmic reticulum (ER) that modulates the cellular response to stress as an effector of the unfolded-protein response (UPR), is a key player in the development of tumors of different origin. ATF6α activation has been linked to oncogenic transformation and tumor maintenance; however, the mechanism(s) underlying this phenomenon remains elusive. Here, using a phenotypic small interfering RNA (siRNA) screening, we identified a novel role for ATF6α in chemoresistance and defined the protein disulfide isomerase A5 (PDIA5) as necessary for ATF6α activation upon ER stress. PDIA5 contributed to disulfide bond rearrangement in ATF6α under stress conditions, thereby leading to ATF6α export from the ER and activation of its target genes. Further analysis of the mechanism demonstrated that PDIA5 promotes ATF6α packaging into coat protein complex II (COPII) vesicles and that the PDIA5/ATF6α activation loop is essential to confer chemoresistance on cancer cells. Genetic and pharmacological inhibition of the PDIA5/ATF6α axis restored sensitivity to the drug treatment. This work defines the mechanisms underlying the role of ATF6α activation in carcinogenesis and chemoresistance; furthermore, it identifies PDIA5 as a key regulator ATF6α-mediated cellular functions in cancer.
Keywords	RNA ; carcinogenesis ; coat proteins ; disulfide bonds ; disulfides ; drug therapy ; endoplasmic reticulum ; neoplasms ; phenotype ; protein disulfide-isomerase ; stress response ; transcription factors
Language	English
Dates of publication	2014-0501
Size	p. 1839-1849.
Publishing place	Taylor & Francis
Document type	Article ; Online
ZDB-ID	779397-2
ISSN	1098-5549 ; 0270-7306
ISSN (online)	1098-5549
ISSN	0270-7306
DOI	10.1128/MCB.01484-13
Database	NAL-Catalogue (AGRICOLA)

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