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Article ; Online: Connecting to the Living History of Radiation Exposure.

Hamblin, Jacob / Richards, Linda M

2021 Volume 54, Issue 1, Page(s) 1–6

MeSH term(s)	History, 20th Century ; History, 21st Century ; Humans ; Radiation Exposure/history
Language	English
Publishing date	2021-04-20
Publishing country	Germany
Document type	Editorial ; Historical Article ; Introductory Journal Article
ZDB-ID	6925-5
ISSN	1573-0387 ; 0022-5010
ISSN (online)	1573-0387
ISSN	0022-5010
DOI	10.1007/s10739-021-09634-9
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Article: A High-Quality Genome Assembly for

Searight, Jacob / Famoso, Adam N / Zhou, Xin-Gen / Doyle, Vinson P / Richards, Jonathan K

Molecular plant-microbe interactions : MPMI

2023 Volume 36, Issue 10, Page(s) 666–669

Abstract: Cercospora ... ...

Abstract	Cercospora janseana
MeSH term(s)	Oryza/genetics ; Genome ; Molecular Sequence Annotation ; Ascomycota/genetics
Language	English
Publishing date	2023-10-20
Publishing country	United States
Document type	Journal Article
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-10-22-0222-A
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Article ; Online: Excitability mediates allocation of pre-configured ensembles to a hippocampal engram supporting contextual conditioned threat in mice.

Mocle, Andrew J / Ramsaran, Adam I / Jacob, Alexander D / Rashid, Asim J / Luchetti, Alessandro / Tran, Lina M / Richards, Blake A / Frankland, Paul W / Josselyn, Sheena A

Neuron

2024

Abstract: Little is understood about how engrams, sparse groups of neurons that store memories, are formed endogenously. Here, we combined calcium imaging, activity tagging, and optogenetics to examine the role of neuronal excitability and pre-existing functional ... ...

Abstract	Little is understood about how engrams, sparse groups of neurons that store memories, are formed endogenously. Here, we combined calcium imaging, activity tagging, and optogenetics to examine the role of neuronal excitability and pre-existing functional connectivity on the allocation of mouse cornu ammonis area 1 (CA1) hippocampal neurons to an engram ensemble supporting a contextual threat memory. Engram neurons (high activity during recall or TRAP2-tagged during training) were more active than non-engram neurons 3 h (but not 24 h to 5 days) before training. Consistent with this, optogenetically inhibiting scFLARE2-tagged neurons active in homecage 3 h, but not 24 h, before conditioning disrupted memory retrieval, indicating that neurons with higher pre-training excitability were allocated to the engram. We also observed stable pre-configured functionally connected sub-ensembles of neurons whose activity cycled over days. Sub-ensembles that were more active before training were allocated to the engram, and their functional connectivity increased at training. Therefore, both neuronal excitability and pre-configured functional connectivity mediate allocation to an engram ensemble.
Language	English
Publishing date	2024-02-27
Publishing country	United States
Document type	Journal Article
ZDB-ID	808167-0
ISSN	1097-4199 ; 0896-6273
ISSN (online)	1097-4199
ISSN	0896-6273
DOI	10.1016/j.neuron.2024.02.007
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Article: Effects of acute exercise on directed forgetting.

Loprinzi, Paul D / Harper, Jacob / Olinyk, Tatjana / Richards, Jessica

Health promotion perspectives

2020 Volume 10, Issue 4, Page(s) 418–421

Abstract: Background: ...

Abstract	Background:
Language	English
Publishing date	2020-11-07
Publishing country	Iran
Document type	Journal Article
ZDB-ID	2691688-5
ISSN	2228-6497
ISSN	2228-6497
DOI	10.34172/hpp.2020.61
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Article: Development and comparative selection of surrogate models using artificial neural network for an integrated regenerative transcritical cycle

Zhang, Yili / Bryan, Jacob / Richards, Geordie / Wang, Hailei

Applied energy. 2022 Apr. 14,

2022

Abstract: Surrogate models are becoming increasingly important in replacing the computationally-expensive physics-based simulation models in many applications, such as system optimization, sensitivity analysis and design space exploration. As one of the fastest- ... ...

Abstract	Surrogate models are becoming increasingly important in replacing the computationally-expensive physics-based simulation models in many applications, such as system optimization, sensitivity analysis and design space exploration. As one of the fastest-growing field, machine-learning, specifically artificial neural networks (ANN) have been adapted to model various energy systems. In the present study, five ANN-based surrogate models are developed in replacing the physics-based model of a novel regenerative transcritical power cycle using methanol as the working fluid that is integrated with a small modular reactor. The input layer of the surrogate models consists of the seven design parameters of the cycle, and the output layer returns the 1st-law efficiency, levelized cost of energy and penalty. The evaluation results show that all five candidate surrogate models have demonstrated high R2 score, low relative absolute errors (RAE) and low L1 losses, with the separate multi-layer feed-forward (MLF) neural network model outperforming the others. Once coupled with global optimization, the surrogate model is expected to find the optimal design parameters in order to minimize levelized cost of energy (LCOE) and penalty value in the system.
Keywords	artificial intelligence ; energy ; methanol ; neural networks ; system optimization
Language	English
Dates of publication	2022-0414
Publishing place	Elsevier Ltd
Document type	Article
Note	Pre-press version
ZDB-ID	2000772-3
ISSN	0306-2619
ISSN	0306-2619
DOI	10.1016/j.apenergy.2022.119146
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: A High-Quality Genome Assembly for Cercospora janseana, Causal Agent of Narrow Brown Leaf Spot of Rice

Searight, Jacob / Famoso, Adam N. / Zhou, Xin-Gen / Doyle, Vinson P. / Richards, Jonathan K.

Molecular Plant-Microbe Interactions. 2023 Oct., v. 36, no. 10 p.666-669

2023

Abstract: Cercospora janseana causes narrow brown leaf spot of rice. A nearly complete telomere-to-telomere reference genome was assembled with a combination of Oxford Nanopore and Illumina sequences. The genome assembly has a total length of 39,075,509 bp and ... ...

Abstract	Cercospora janseana causes narrow brown leaf spot of rice. A nearly complete telomere-to-telomere reference genome was assembled with a combination of Oxford Nanopore and Illumina sequences. The genome assembly has a total length of 39,075,509 bp and consists of 15 chromosomes, 14 of which have telomeric repeats at both ends. The assembly N₅₀ is 2.97 Mb and the L₅₀ is five contigs. RNA-seq-mediated gene annotation identified 10,850 genes, including 955 predicted secreted proteins and 361 predicted effector proteins. This highly contiguous and almost complete C. janseana reference genome will be a vital resource for further investigation of host-pathogen interactions and genome evolution within this pathosystem. Copyright © 2023 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.
Keywords	Cercospora ; evolution ; genes ; genome assembly ; leaf spot ; nanopores ; rice ; telomeres ; host-pathogen interactions ; narrow brown leaf spot
Language	English
Dates of publication	2023-10
Size	p. 666-669.
Publishing place	The American Phytopathological Society
Document type	Article ; Online
ZDB-ID	743331-1
ISSN	1943-7706 ; 0894-0282
ISSN (online)	1943-7706
ISSN	0894-0282
DOI	10.1094/MPMI-10-22-0222-A
Database	NAL-Catalogue (AGRICOLA)

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Article ; Online: Multi-objective design optimization of an integrated regenerative transcritical cycle considering sensitivity in Pareto-optimal solutions

Bryan, Jacob A. / Zhang, Yili / Wang, Hailei / Richards, Geordie

Energy Conversion and Management: X. 2023 Apr., v. 18 p.100364-

2023

Abstract: Small modular nuclear reactors (SMRs) are an emerging technology with many potential benefits to cost, manufacturing, and safety over more traditional reactor designs. The NuScale Power Module (NPM) is a pressurized water SMR that uses natural convection ...

Abstract	Small modular nuclear reactors (SMRs) are an emerging technology with many potential benefits to cost, manufacturing, and safety over more traditional reactor designs. The NuScale Power Module (NPM) is a pressurized water SMR that uses natural convection to circulate its coolant. Variations of steam Rankine cycles have been the predominant design for power cycles in the nuclear energy space for decades, but ongoing research has suggested promising alternatives to be used in future designs. Previous works have suggested that a transcritical Rankine cycle with an organic working fluid like ethanol or methanol could have superior thermal efficiency compared to comparable steam Rankine cycles for mid-temperature applications. This study presents a design optimization and sensitivity analysis of an organic transcritical Rankine cycle (ORTC) with methanol as a working fluid, with a model of the NPM used as the primary cycle. Multi-objective optimization is used to analyze the trade-off between thermal efficiency and levelized cost of energy (LCOE) for this cycle design. All of the optimal designs identified in the multi-objective optimization show improvements in LCOE compared to the benchmark regenerative steam Rankine cycle at comparable thermal efficiencies, with LCOE being reduced by as much as 19.1% by using the ORTC. In the Pareto front, higher efficiency solutions use regenerative cycle designs, while lower LCOE solutions do not utilize regenerators. A sensitivity analysis of the optimal design points reveals that regenerative design points have greater sensitivity in both LCOE and thermal efficiency to the variation in the design parameters.
Keywords	administrative management ; convection ; energy conversion ; ethanol ; methanol ; models ; nuclear power ; steam ; Multi-objective optimization ; Sensitivity analysis ; Organic transcritical Rankine cycle ; Small modular reactor
Language	English
Dates of publication	2023-04
Publishing place	Elsevier Ltd
Document type	Article ; Online
Note	Use and reproduction
ISSN	2590-1745
DOI	10.1016/j.ecmx.2023.100364
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Article ; Online: Impact of a trauma recovery center on emergency department utilization for victims of violence.

Pyles, Olivia / Richards, Rebekah / Galligher, Arianna / Du, Joanne / Brooks, Jacob / Southerland, Lauren T

The American journal of emergency medicine

2022 Volume 65, Page(s) 125–129

Abstract: Background: Victims of violence are at high risk for unmet mental and physical health care needs which can translate into increased Emergency Department (ED) visits. We investigated the effectiveness of participation in a psychosocial, case management- ... ...

Abstract	Background: Victims of violence are at high risk for unmet mental and physical health care needs which can translate into increased Emergency Department (ED) visits. We investigated the effectiveness of participation in a psychosocial, case management-based trauma recovery program on ED utilization. Methods: A retrospective cohort study of ED utilization before and after referral to a Trauma Recovery Center (TRC). Charts of TRC participants from 6/2017-5/2019 who consented in clinic to their medical records being used for research were reviewed. The primary outcome was the change in ED utilization 6 months pre- and post-referral to a TRC. The secondary outcomes were factors associated with ED visits after TRC referral, including victimization or mental health issues. Results: The study group contained 143 patients, of which 82% identified as female and 62% identified as white. Many (39%, n = 56) were part of one or more vulnerable populations and type of victimization varied extensively. Intervention uptake was high as almost all (92%, n = 132) had at least one TRC encounter [median of 6 encounters (IQR 2-13)] and an average of 2.7 services used. Most participants (67.1%, n = 96) had no change in ED use. Forty (28.0%) had at least 1 ED visit 6 months before, 38 (26.8%) had at least 1 ED visit 6 months afterwards, and 81 (56.6%) had no ED visits during either timeframe. ED visits per person in the 6 months prior to referral were not different from visits per person in the 6 months after referral (0.52 vs 0.49, p = 0.76, paired t-test). Negative binomial regression indicated number of ED visits before referral (IRR 1.5, 95% confidence interval [1.27-1.79]) and pre-existing mental health conditions (IRR 2.2, 95% confidence interval [0.98-5.02]) were most associated with an increase in the incidence rate ratio of ED visits in the 6 months after referral. Conclusion: Despite high engagement, a multidisciplinary Trauma Recovery Center did not reduce ED utilization. ED utilization prior to TRC was the most predictive factor of ED utilization afterwards.
MeSH term(s)	Humans ; Female ; Retrospective Studies ; Violence ; Emergency Service, Hospital ; Trauma Centers ; Crime Victims
Language	English
Publishing date	2022-12-22
Publishing country	United States
Document type	Journal Article
ZDB-ID	605890-5
ISSN	1532-8171 ; 0735-6757
ISSN (online)	1532-8171
ISSN	0735-6757
DOI	10.1016/j.ajem.2022.12.024
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Article ; Online: DeepDOF-SE: affordable deep-learning microscopy platform for slide-free histology.

Jin, Lingbo / Tang, Yubo / Coole, Jackson B / Tan, Melody T / Zhao, Xuan / Badaoui, Hawraa / Robinson, Jacob T / Williams, Michelle D / Vigneswaran, Nadarajah / Gillenwater, Ann M / Richards-Kortum, Rebecca R / Veeraraghavan, Ashok

Nature communications

2024 Volume 15, Issue 1, Page(s) 2935

Abstract: Histopathology plays a critical role in the diagnosis and surgical management of cancer. However, access to histopathology services, especially frozen section pathology during surgery, is limited in resource-constrained settings because preparing slides ... ...

Abstract	Histopathology plays a critical role in the diagnosis and surgical management of cancer. However, access to histopathology services, especially frozen section pathology during surgery, is limited in resource-constrained settings because preparing slides from resected tissue is time-consuming, labor-intensive, and requires expensive infrastructure. Here, we report a deep-learning-enabled microscope, named DeepDOF-SE, to rapidly scan intact tissue at cellular resolution without the need for physical sectioning. Three key features jointly make DeepDOF-SE practical. First, tissue specimens are stained directly with inexpensive vital fluorescent dyes and optically sectioned with ultra-violet excitation that localizes fluorescent emission to a thin surface layer. Second, a deep-learning algorithm extends the depth-of-field, allowing rapid acquisition of in-focus images from large areas of tissue even when the tissue surface is highly irregular. Finally, a semi-supervised generative adversarial network virtually stains DeepDOF-SE fluorescence images with hematoxylin-and-eosin appearance, facilitating image interpretation by pathologists without significant additional training. We developed the DeepDOF-SE platform using a data-driven approach and validated its performance by imaging surgical resections of suspected oral tumors. Our results show that DeepDOF-SE provides histological information of diagnostic importance, offering a rapid and affordable slide-free histology platform for intraoperative tumor margin assessment and in low-resource settings.
MeSH term(s)	Microscopy ; Deep Learning ; Fluorescent Dyes ; Hematoxylin ; Eosine Yellowish-(YS)
Chemical Substances	Fluorescent Dyes ; Hematoxylin (YKM8PY2Z55) ; Eosine Yellowish-(YS) (TDQ283MPCW)
Language	English
Publishing date	2024-04-05
Publishing country	England
Document type	Journal Article
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-024-47065-2
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Article: Investigating the relationship between DNA methylation, genetic variation, and suicide attempt in bipolar disorder.

Alrfooh, Aysheh / Casten, Lucas G / Richards, Jenny Gringer / Wemmie, John A / Magnotta, Vincent A / Fiedorowicz, Jess G / Michaelson, Jacob / Williams, Aislinn J / Gaine, Marie E

medRxiv : the preprint server for health sciences

2024

Abstract: Individuals with bipolar disorder are at increased risk for suicide, and this can be influenced by a range of biological, clinical, and environmental risk factors. Biological components associated with suicide include DNA modifications that lead to ... ...

Abstract	Individuals with bipolar disorder are at increased risk for suicide, and this can be influenced by a range of biological, clinical, and environmental risk factors. Biological components associated with suicide include DNA modifications that lead to changes in gene expression. Common genetic variation and DNA methylation changes are some of the most frequent types of DNA findings associated with an increased risk for suicidal behavior. Importantly, the interplay between genetic predisposition and DNA methylation patterns is becoming more prevalent in genetic studies. We hypothesized that DNA methylation patterns in specific loci already genetically associated with suicide would be altered in individuals with bipolar disorder and a history of suicide attempt. To test this hypothesis, we searched the literature to identify common genetic variants (N=34) previously associated with suicidal thoughts and behaviors in individuals with bipolar disorder. We then created a customized sequencing panel that covered our chosen genomic loci. We profiled DNA methylation patterns from blood samples collected from bipolar disorder participants with suicidal behavior (N=55) and without suicidal behavior (N=51). We identified seven differentially methylated CpG sites and five differentially methylated regions between the two groups. Additionally, we found that DNA methylation changes in
Language	English
Publishing date	2024-04-03
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.04.03.24305263
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