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Article ; Online: An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery.

Alam, Shahinur / Eom, Tae-Yeon / Steinberg, Jeffrey / Ackerman, David / Schmitt, J Eric / Akers, Walter J / Zakharenko, Stanislav S / Khairy, Khaled

Frontiers in bioinformatics

2022 Volume 2, Page(s) 865443

Abstract: Segmentation of mouse brain magnetic resonance images (MRI) based on anatomical and/or functional features is an important step towards morphogenetic brain structure characterization of murine models in neurobiological studies. State-of-the-art image ... ...

Abstract	Segmentation of mouse brain magnetic resonance images (MRI) based on anatomical and/or functional features is an important step towards morphogenetic brain structure characterization of murine models in neurobiological studies. State-of-the-art image segmentation methods register image volumes to standard presegmented templates or well-characterized highly detailed image atlases. Performance of these methods depends critically on the quality of skull-stripping, which is the digital removal of tissue signal exterior to the brain. This is, however, tedious to do manually and challenging to automate. Registration-based segmentation, in addition, performs poorly on small structures, low resolution images, weak signals, or faint boundaries, intrinsic to
Language	English
Publishing date	2022-06-08
Publishing country	Switzerland
Document type	Journal Article
ISSN	2673-7647
ISSN (online)	2673-7647
DOI	10.3389/fbinf.2022.865443
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Article ; Online: An End-To-End Pipeline for Fully Automatic Morphological Quantification of Mouse Brain Structures From MRI Imagery

Shahinur Alam / Tae-Yeon Eom / Jeffrey Steinberg / David Ackerman / J. Eric Schmitt / Walter J. Akers / Stanislav S. Zakharenko / Khaled Khairy

Frontiers in Bioinformatics, Vol

2022 Volume 2

Abstract	Segmentation of mouse brain magnetic resonance images (MRI) based on anatomical and/or functional features is an important step towards morphogenetic brain structure characterization of murine models in neurobiological studies. State-of-the-art image segmentation methods register image volumes to standard presegmented templates or well-characterized highly detailed image atlases. Performance of these methods depends critically on the quality of skull-stripping, which is the digital removal of tissue signal exterior to the brain. This is, however, tedious to do manually and challenging to automate. Registration-based segmentation, in addition, performs poorly on small structures, low resolution images, weak signals, or faint boundaries, intrinsic to in vivo MRI scans. To address these issues, we developed an automated end-to-end pipeline called DeepBrainIPP (deep learning-based brain image processing pipeline) for 1) isolating brain volumes by stripping skull and tissue from T2w MRI images using an improved deep learning-based skull-stripping and data augmentation strategy, which enables segmentation of large brain regions by atlas or template registration, and 2) address segmentation of small brain structures, such as the paraflocculus, a small lobule of the cerebellum, for which DeepBrainIPP performs direct segmentation with a dedicated model, producing results superior to the skull-stripping/atlas-registration paradigm. We demonstrate our approach on data from both in vivo and ex vivo samples, using an in-house dataset of 172 images, expanded to 4,040 samples through data augmentation. Our skull stripping model produced an average Dice score of 0.96 and residual volume of 2.18%. This facilitated automatic registration of the skull-stripped brain to an atlas yielding an average cross-correlation of 0.98. For small brain structures, direct segmentation yielded an average Dice score of 0.89 and 5.32% residual volume error, well below the tolerance threshold for phenotype detection. Full pipeline execution is ...
Keywords	MRI ; deep learning ; image segmentation ; image registration ; brain atlas ; data augmentation ; Computer applications to medicine. Medical informatics ; R858-859.7
Subject code	004
Language	English
Publishing date	2022-06-01T00:00:00Z
Publisher	Frontiers Media S.A.
Document type	Article ; Online
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Article ; Online: Improving Stability of Roll-to-Roll (R2R) Gravure-Printed Carbon Nanotube-Based Thin Film Transistors via R2R Plasma-Enhanced Chemical Vapor-Deposited Silicon Nitride

Sagar Shrestha / Sajjan Parajuli / Jinhwa Park / Hao Yang / Tae-Yeon Cho / Ji-Ho Eom / Seong-Keun Cho / Jongsun Lim / Gyoujin Cho / Younsu Jung

Nanomaterials, Vol 13, Iss 559, p

2023 Volume 559

Abstract: Single-walled carbon nanotubes (SWCNTs) have an advantage in printing thin film transistors (TFTs) due to their high carrier mobility, excellent chemical stability, mechanical flexibility, and compatibility with solution-based processing. Thus, the ... ...

Abstract	Single-walled carbon nanotubes (SWCNTs) have an advantage in printing thin film transistors (TFTs) due to their high carrier mobility, excellent chemical stability, mechanical flexibility, and compatibility with solution-based processing. Thus, the printed SWCNT-based TFTs (pSWCNT-TFTs) showed significant technological potential such as integrated circuits, conformable sensors, and display backplanes. However, the long-term environmental stability of the pSWCNT-TFTs hinders their commercialization. Thus, to extend the stability of the pSWCNT-TFTs, such devices should be passivated with low water and oxygen permeability. Herein, we introduced the silicon nitride (SiNx) passivation method on the pSWCNT-TFTs via a combination of roll-to-roll (R2R) gravure and the roll-to-roll plasma-enhanced vapor deposition (R2R-PECVD) process at low temperature (45 °C). We found that SiNx-passivated pSWCNT-TFTs showed ± 0.50 V of threshold voltage change at room temperature for 3 days and ±1.2 V of threshold voltage change for 3 h through a Temperature Humidity Test (85/85 test: Humidity 85%/Temperature 85 °C) for both p-type and n-type pSWCNT-TFTs. In addition, we found that the SiNx-passivated p-type and n-type pSWCNT-TFT-based CMOS-like ring oscillator, or 1-bit code generator, operated well after the 85/85 test for 24 h.
Keywords	roll to roll ; PECVD ; passivation ; threshold voltage ; silicon nitride ; 85/85 test ; Chemistry ; QD1-999
Subject code	600
Language	English
Publishing date	2023-01-01T00:00:00Z
Publisher	MDPI AG
Document type	Article ; Online
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Article ; Online: All lactose-oxidizing enzymes of Pseudomonas taetrolens, a highly efficient lactobionic acid-producing microorganism, are pyrroloquinoline quinone-dependent enzymes.

Lee, Seung Soo / Oh, Yu-Ri / Jang, Young-Ah / Han, So Yeon / Eom, Gyeong Tae

International microbiology : the official journal of the Spanish Society for Microbiology

2024

Abstract: In previous and present studies, four enzymes (GCD1, GCD3, GCD4, and MQO1) have been found to act as lactose-oxidizing enzymes of Pseudomonas taetrolens. To investigate whether the four enzymes were the only lactose-oxidizing enzymes of P. taetrolens, we ...

Abstract	In previous and present studies, four enzymes (GCD1, GCD3, GCD4, and MQO1) have been found to act as lactose-oxidizing enzymes of Pseudomonas taetrolens. To investigate whether the four enzymes were the only lactose-oxidizing enzymes of P. taetrolens, we performed the inactivation of gcd1, gcd3, gcd4, and mqo1 genes in P. taetrolens. Compared to the wild-type strain, the lactobionic acid (LBA)-producing ability of P. taetrolens ∆gcd1 ∆gcd3 ∆gcd4 ∆mqo1 was only slightly decreased, implying that P. taetrolens possesses more lactose-oxidizing enzymes. Interestingly, the four lactose-oxidizing enzymes were all pyrroloquinoline quinone (PQQ)-dependent. To identify other unidentified lactose-oxidizing enzymes of P. taetrolens, we prevented the synthesis of PQQ in P. taetrolens by inactivating the genes related to PQQ synthesis such as pqqC, pqqD, and pqqE. Surprisingly, all three knocked-out strains were unable to convert lactose to LBA, indicating that all lactose-oxidizing enzymes in P. taetrolens were inactivated by eliminating PQQ synthesis. In addition, external PQQ supplementation restored the LBA production ability of P. taetrolens ∆pqqC, comparable to the wild-type strain. These results indicate that all lactose-oxidizing enzymes in P. taetrolens are PQQ-dependent.
Language	English
Publishing date	2024-01-31
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	1454951-7
ISSN	1618-1905 ; 1139-6709
ISSN (online)	1618-1905
ISSN	1139-6709
DOI	10.1007/s10123-023-00477-4
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Zs.A 4964: Show issues

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ab Jg. 2022: Lesesaal (EG)

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Article: Improving Stability of Roll-to-Roll (R2R) Gravure-Printed Carbon Nanotube-Based Thin Film Transistors via R2R Plasma-Enhanced Chemical Vapor-Deposited Silicon Nitride.

Shrestha, Sagar / Parajuli, Sajjan / Park, Jinhwa / Yang, Hao / Cho, Tae-Yeon / Eom, Ji-Ho / Cho, Seong-Keun / Lim, Jongsun / Cho, Gyoujin / Jung, Younsu

Nanomaterials (Basel, Switzerland)

2023 Volume 13, Issue 3

Abstract	Single-walled carbon nanotubes (SWCNTs) have an advantage in printing thin film transistors (TFTs) due to their high carrier mobility, excellent chemical stability, mechanical flexibility, and compatibility with solution-based processing. Thus, the printed SWCNT-based TFTs (pSWCNT-TFTs) showed significant technological potential such as integrated circuits, conformable sensors, and display backplanes. However, the long-term environmental stability of the pSWCNT-TFTs hinders their commercialization. Thus, to extend the stability of the pSWCNT-TFTs, such devices should be passivated with low water and oxygen permeability. Herein, we introduced the silicon nitride (SiNx) passivation method on the pSWCNT-TFTs via a combination of roll-to-roll (R2R) gravure and the roll-to-roll plasma-enhanced vapor deposition (R2R-PECVD) process at low temperature (45 °C). We found that SiNx-passivated pSWCNT-TFTs showed ± 0.50 V of threshold voltage change at room temperature for 3 days and ±1.2 V of threshold voltage change for 3 h through a Temperature Humidity Test (85/85 test: Humidity 85%/Temperature 85 °C) for both p-type and n-type pSWCNT-TFTs. In addition, we found that the SiNx-passivated p-type and n-type pSWCNT-TFT-based CMOS-like ring oscillator, or 1-bit code generator, operated well after the 85/85 test for 24 h.
Language	English
Publishing date	2023-01-30
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2662255-5
ISSN	2079-4991
ISSN	2079-4991
DOI	10.3390/nano13030559
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Article ; Online: Alveoli-Like Multifunctional Scaffolds for Optical and Electrochemical In Situ Monitoring of Cellular Responses from Type II Pneumocytes.

Eom, Seonghyeon / Lee, So Yeon / Park, Jung Tae / Choi, Inhee

Advanced science (Weinheim, Baden-Wurttemberg, Germany)

2023 Volume 10, Issue 23, Page(s) e2301395

Abstract: While breathing, alveoli are exposed to external irritants, which contribute to the pathogenesis of lung disease. Therefore, in situ monitoring of alveolar responses to stimuli of toxicants under in vivo environments is important to understand lung ... ...

Abstract	While breathing, alveoli are exposed to external irritants, which contribute to the pathogenesis of lung disease. Therefore, in situ monitoring of alveolar responses to stimuli of toxicants under in vivo environments is important to understand lung disease. For this purpose, 3D cell cultures are recently employed for examining cellular responses of pulmonary systems exposed to irritants; however, most of them have used ex situ assays requiring cell lysis and fluorescent labeling. Here, an alveoli-like multifunctional scaffold is demonstrated for optical and electrochemical monitoring of cellular responses of pneumocytes. Porous foam with dimensions like the alveoli structure is used as a backbone for the scaffold, wherein electroactive metal-organic framework crystals, optically active gold nanoparticles, and biocompatible hyaluronic acid are integrated. The fabricated multifunctional scaffold allows for label-free detection and real-time monitoring of oxidative stress released in pneumocytes under toxic-conditions via redox-active amperometry and nanospectroscopy. Moreover, cellular behavior can be statistically classified based on fingerprint Raman signals collected from the cells on the scaffold. The developed scaffold is expected to serve as a promising platform to investigate cellular responses and disease pathogenesis, owing to its versatility in monitoring electrical and optical signals from cells in situ in the 3D microenvironments.
MeSH term(s)	Humans ; Alveolar Epithelial Cells ; Gold ; Irritants ; Metal Nanoparticles ; Lung Diseases
Chemical Substances	Gold (7440-57-5) ; Irritants
Language	English
Publishing date	2023-05-28
Publishing country	Germany
Document type	Journal Article
ZDB-ID	2808093-2
ISSN	2198-3844 ; 2198-3844
ISSN (online)	2198-3844
ISSN	2198-3844
DOI	10.1002/advs.202301395
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Article ; Online: National population-based study of constipation in children in Korea, 2002-2013.

Eom, Tae-Hoon / Chae, Kyung-Hee / Kim, Sukil / Kim, Kwang Yeon

Pediatrics international : official journal of the Japan Pediatric Society

2022 Volume 64, Issue 1, Page(s) e15211

Abstract: Background: The purpose of this study is to estimate the overall prevalence and incidence of constipation in Korean children and adolescent based on health insurance claims data.: Methods: This study is a retrospective cohort study using the Korean ... ...

Abstract	Background: The purpose of this study is to estimate the overall prevalence and incidence of constipation in Korean children and adolescent based on health insurance claims data. Methods: This study is a retrospective cohort study using the Korean National Health Insurance Service - National Sample Cohort from 2002 to 2013. Patients age less than 19 years old were selected, and the prevalence and incidence of constipation were estimated. Results: The standardized incidence rate was 10.8 per 1,000 persons in 2004 to 14.3 per 1,000 persons in 2012. The standardized prevalence increased from 12.2 per persons in 2002 to 26.4 per persons in 2013. Females had a higher incidence rate and prevalence rate than males during the study period. The overall recurrence rates were 13.2%. The recurrence rates were 12.9% in males and 13.5% in females. The overall average constipation duration was 229 days. The duration was 222 days in males and 236 days in females. Conclusions: This is the first study to conduct a population-based study of all children in Korea with constipation. These data reveal the increasing burden and impact of constipation on children and could enable effective public and clinical health strategies to be planned.
MeSH term(s)	Adolescent ; Adult ; Child ; Constipation/epidemiology ; Female ; Humans ; Incidence ; Male ; Prevalence ; Republic of Korea/epidemiology ; Retrospective Studies ; Young Adult
Language	English
Publishing date	2022-08-08
Publishing country	Australia
Document type	Journal Article
ZDB-ID	1470376-2
ISSN	1442-200X ; 1328-8067
ISSN (online)	1442-200X
ISSN	1328-8067
DOI	10.1111/ped.15211
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Zs.A 848: Show issues

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Jg. 1995 - 2021: Lesesall (1.OG)
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Article ; Online: Innate frequency-discrimination hyperacuity in Williams-Beuren syndrome mice.

Davenport, Christopher M / Teubner, Brett J W / Han, Seung Baek / Patton, Mary H / Eom, Tae-Yeon / Garic, Dusan / Lansdell, Benjamin J / Shirinifard, Abbas / Chang, Ti-Cheng / Klein, Jonathon / Pruett-Miller, Shondra M / Blundon, Jay A / Zakharenko, Stanislav S

Cell

2022 Volume 185, Issue 21, Page(s) 3877–3895.e21

Abstract: Williams-Beuren syndrome (WBS) is a rare disorder caused by hemizygous microdeletion of ∼27 contiguous genes. Despite neurodevelopmental and cognitive deficits, individuals with WBS have spared or enhanced musical and auditory abilities, potentially ... ...

Abstract	Williams-Beuren syndrome (WBS) is a rare disorder caused by hemizygous microdeletion of ∼27 contiguous genes. Despite neurodevelopmental and cognitive deficits, individuals with WBS have spared or enhanced musical and auditory abilities, potentially offering an insight into the genetic basis of auditory perception. Here, we report that the mouse models of WBS have innately enhanced frequency-discrimination acuity and improved frequency coding in the auditory cortex (ACx). Chemogenetic rescue showed frequency-discrimination hyperacuity is caused by hyperexcitable interneurons in the ACx. Haploinsufficiency of one WBS gene, Gtf2ird1, replicated WBS phenotypes by downregulating the neuropeptide receptor VIPR1. VIPR1 is reduced in the ACx of individuals with WBS and in the cerebral organoids derived from human induced pluripotent stem cells with the WBS microdeletion. Vipr1 deletion or overexpression in ACx interneurons mimicked or reversed, respectively, the cellular and behavioral phenotypes of WBS mice. Thus, the Gtf2ird1-Vipr1 mechanism in ACx interneurons may underlie the superior auditory acuity in WBS.
MeSH term(s)	Animals ; Auditory Cortex/cytology ; Auditory Cortex/physiology ; Disease Models, Animal ; Humans ; Induced Pluripotent Stem Cells ; Interneurons/cytology ; Interneurons/physiology ; Mice ; Phenotype ; Trans-Activators/genetics ; Williams Syndrome/genetics ; Williams Syndrome/physiopathology
Chemical Substances	Gtf2ird1 protein, mouse ; Trans-Activators
Language	English
Publishing date	2022-09-23
Publishing country	United States
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	187009-9
ISSN	1097-4172 ; 0092-8674
ISSN (online)	1097-4172
ISSN	0092-8674
DOI	10.1016/j.cell.2022.08.022
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Zs.A 1167: 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)
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Article ; Online: Schizophrenia-Related Microdeletion Impairs Emotional Memory through MicroRNA-Dependent Disruption of Thalamic Inputs to the Amygdala

Tae-Yeon Eom / Ildar T. Bayazitov / Kara Anderson / Jing Yu / Stanislav S. Zakharenko

Cell Reports, Vol 19, Iss 8, Pp 1532-

2017 Volume 1544

Abstract: Individuals with 22q11.2 deletion syndrome (22q11DS) are at high risk of developing psychiatric diseases such as schizophrenia. Individuals with 22q11DS and schizophrenia are impaired in emotional memory, anticipating, recalling, and assigning a correct ... ...

Abstract	Individuals with 22q11.2 deletion syndrome (22q11DS) are at high risk of developing psychiatric diseases such as schizophrenia. Individuals with 22q11DS and schizophrenia are impaired in emotional memory, anticipating, recalling, and assigning a correct context to emotions. The neuronal circuits responsible for these emotional memory deficits are unknown. Here, we show that 22q11DS mouse models have disrupted synaptic transmission at thalamic inputs to the lateral amygdala (thalamo-LA projections). This synaptic deficit is caused by haploinsufficiency of the 22q11DS gene Dgcr8, which is involved in microRNA processing, and is mediated by the increased dopamine receptor Drd2 levels in the thalamus and by reduced probability of glutamate release from thalamic inputs. This deficit in thalamo-LA synaptic transmission is sufficient to cause fear memory deficits. Our results suggest that dysregulation of the Dgcr8–Drd2 mechanism at thalamic inputs to the amygdala underlies emotional memory deficits in 22q11DS.
Keywords	22q11.2 deletion ; schizophrenia ; thalamus ; fear conditioning ; active avoidance ; dopamine receptors ; microRNA processing ; Dgcr8 ; emotional memory ; Biology (General) ; QH301-705.5
Subject code	150
Language	English
Publishing date	2017-05-01T00:00:00Z
Publisher	Elsevier
Document type	Article ; Online
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Article ; Online: Schizophrenia-Related Microdeletion Impairs Emotional Memory through MicroRNA-Dependent Disruption of Thalamic Inputs to the Amygdala.

Eom, Tae-Yeon / Bayazitov, Ildar T / Anderson, Kara / Yu, Jing / Zakharenko, Stanislav S

Cell reports

2017 Volume 19, Issue 8, Page(s) 1532–1544

Abstract	Individuals with 22q11.2 deletion syndrome (22q11DS) are at high risk of developing psychiatric diseases such as schizophrenia. Individuals with 22q11DS and schizophrenia are impaired in emotional memory, anticipating, recalling, and assigning a correct context to emotions. The neuronal circuits responsible for these emotional memory deficits are unknown. Here, we show that 22q11DS mouse models have disrupted synaptic transmission at thalamic inputs to the lateral amygdala (thalamo-LA projections). This synaptic deficit is caused by haploinsufficiency of the 22q11DS gene Dgcr8, which is involved in microRNA processing, and is mediated by the increased dopamine receptor Drd2 levels in the thalamus and by reduced probability of glutamate release from thalamic inputs. This deficit in thalamo-LA synaptic transmission is sufficient to cause fear memory deficits. Our results suggest that dysregulation of the Dgcr8-Drd2 mechanism at thalamic inputs to the amygdala underlies emotional memory deficits in 22q11DS.
Language	English
Publishing date	2017-05-23
Publishing country	United States
Document type	Journal Article
ZDB-ID	2649101-1
ISSN	2211-1247 ; 2211-1247
ISSN (online)	2211-1247
ISSN	2211-1247
DOI	10.1016/j.celrep.2017.05.002
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