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Article: De novo

Chang, Joanna C / Perich, Matthew G / Miller, Lee E / Gallego, Juan A / Clopath, Claudia

bioRxiv : the preprint server for biology

2023

Abstract: Animals can quickly adapt learned movements in response to external perturbations. Motor adaptation is likely influenced by an animal's existing movement repertoire, but the nature of this influence is unclear. Long-term learning causes lasting changes ... ...

Abstract	Animals can quickly adapt learned movements in response to external perturbations. Motor adaptation is likely influenced by an animal's existing movement repertoire, but the nature of this influence is unclear. Long-term learning causes lasting changes in neural connectivity which determine the activity patterns that can be produced. Here, we sought to understand how a neural population's activity repertoire, acquired through long-term learning, affects short-term adaptation by modeling motor cortical neural population dynamics during
Language	English
Publishing date	2023-05-24
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.05.23.541925
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Article: De novo

Roy, Anindya / Shi, Lei / Chang, Ashley / Dong, Xianchi / Fernandez, Andres / Kraft, John C / Li, Jing / Le, Viet Q / Winegar, Rebecca Viazzo / Cherf, Gerald Maxwell / Slocum, Dean / Daniel Poulson, P / Casper, Garrett E / Vallecillo-Zúniga, Mary L / Valdoz, Jonard Corpuz / Miranda, Marcos C / Bai, Hua / Kipnis, Yakov / Olshefsky, Audrey /

bioRxiv : the preprint server for biology

2023

Abstract: The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between the two closely related integrin proteins and other RGD integrins, ... ...

Abstract	The RGD (Arg-Gly-Asp)-binding integrins αvβ6 and αvβ8 are clinically validated cancer and fibrosis targets of considerable therapeutic importance. Compounds that can discriminate between the two closely related integrin proteins and other RGD integrins, stabilize specific conformational states, and have sufficient stability enabling tissue restricted administration could have considerable therapeutic utility. Existing small molecules and antibody inhibitors do not have all of these properties, and hence there is a need for new approaches. Here we describe a method for computationally designing hyperstable RGD-containing miniproteins that are highly selective for a single RGD integrin heterodimer and conformational state, and use this strategy to design inhibitors of αvβ6 and αvβ8 with high selectivity. The αvβ6 and αvβ8 inhibitors have picomolar affinities for their targets, and >1000-fold selectivity over other RGD integrins. CryoEM structures are within 0.6-0.7Å root-mean-square deviation (RMSD) to the computational design models; the designed αvβ6 inhibitor and native ligand stabilize the open conformation in contrast to the therapeutic anti-αvβ6 antibody BG00011 that stabilizes the bent-closed conformation and caused on-target toxicity in patients with lung fibrosis, and the αvβ8 inhibitor maintains the constitutively fixed extended-closed αvβ8 conformation. In a mouse model of bleomycin-induced lung fibrosis, the αvβ6 inhibitor potently reduced fibrotic burden and improved overall lung mechanics when delivered via oropharyngeal administration mimicking inhalation, demonstrating the therapeutic potential of
Language	English
Publishing date	2023-06-12
Publishing country	United States
Document type	Preprint
DOI	10.1101/2023.06.12.544624
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Article ; Online: De novo

Hu, Chaojie / Chang, E / Yu, Rucui / Wu, Zhiwei / Li, Qing / Xie, Qiang / Wang, Hua / Yin, Shi

Genes & diseases

2022 Volume 9, Issue 5, Page(s) 1163–1165

Language	English
Publishing date	2022-01-10
Publishing country	China
Document type	Journal Article
ZDB-ID	2821806-1
ISSN	2352-3042 ; 2352-3042
ISSN (online)	2352-3042
ISSN	2352-3042
DOI	10.1016/j.gendis.2021.12.008
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: De novo

Kang, Sang-Ho / Lee, Woo-Haeng / Sim, Joon-Soo / Thaku, Niha / Chang, Saemin / Hong, Jong-Pil / Oh, Tae-Jin

Frontiers in plant science

2022 Volume 12, Page(s) 773553

Abstract: ... Senna ... ...

Abstract	Senna occidentalis
Language	English
Publishing date	2022-01-03
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2021.773553
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Article ; Online: De Novo

Yang, Heyu / Chen, Haimei / Ni, Yang / Li, Jingling / Cai, Yisha / Ma, Binxin / Yu, Jing / Wang, Jiehua / Liu, Chang

International journal of molecular sciences

2022 Volume 23, Issue 22

Abstract: ... Salvia ... ...

Abstract	Salvia miltiorrhiza
MeSH term(s)	Genome, Mitochondrial ; DNA, Mitochondrial/genetics ; Salvia miltiorrhiza/genetics ; Salvia ; Phylogeny ; Microsatellite Repeats/genetics ; Lamiales ; Chromosomes
Chemical Substances	DNA, Mitochondrial
Language	English
Publishing date	2022-11-17
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2019364-6
ISSN	1422-0067 ; 1422-0067 ; 1661-6596
ISSN (online)	1422-0067
ISSN	1422-0067 ; 1661-6596
DOI	10.3390/ijms232214267
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Article: De Novo

Tan, Hong Chang / Hsu, Jean W / Tai, E Shyong / Chacko, Shaji / Wu, Vieon / Lee, Chun Fan / Kovalik, Jean-Paul / Jahoor, Farook

Frontiers in endocrinology

2022 Volume 13, Page(s) 900343

Abstract: Background: Glycine is a dietary non-essential amino acid that is low in obesity and increases following bariatric surgery. However, the exact mechanism responsible remains unclear and it is unknown whether hypoglycinemia is a cause or consequence of ... ...

Abstract	Background: Glycine is a dietary non-essential amino acid that is low in obesity and increases following bariatric surgery. However, the exact mechanism responsible remains unclear and it is unknown whether hypoglycinemia is a cause or consequence of insulin resistance. Objective: Using multiple isotopically labeled tracers, we aimed to determine the underlying kinetic changes responsible for hypoglycinemia in obesity by: 1) Comparing glycine kinetics between participants with morbid obesity (BMI ≥ 32.5 kg/m Methods: [1,2- Results: Compared to controls, participants with morbid obesity had significantly lower plasma glycine concentrations at 163 (153-171) vs. 201 (172-227) µmol/L and significantly reduced Conclusion: Hypoglycinemia in participants with morbid obesity was associated with impaired Clinical trial registration: [https://tinyurl.com/6wfj7yss], identifier [NCT04660513].
MeSH term(s)	Adult ; Amino Acids ; Bariatric Surgery ; Glycine ; Humans ; Insulin Resistance ; Obesity, Morbid/surgery
Chemical Substances	Amino Acids ; Glycine (TE7660XO1C)
Language	English
Publishing date	2022-06-09
Publishing country	Switzerland
Document type	Clinical Study ; Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2592084-4
ISSN	1664-2392
ISSN	1664-2392
DOI	10.3389/fendo.2022.900343
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Article: De novo

Yin, Liangyu / Song, Chunhua / Cui, Jiuwei / Lin, Xin / Li, Na / Fan, Yang / Zhang, Ling / Liu, Jie / Chong, Feifei / Wang, Chang / Liang, Tingting / Liu, Xiangliang / Deng, Li / Yang, Mei / Yu, Jiami / Wang, Xiaojie / Liu, Xing / Yang, Shoumei / Zuo, Zheng /

Yuan, Kaitao / Yu, Miao / Cong, Minghua / Li, Zengning / Weng, Min / Yao, Qinghua / Jia, Pingping / Li, Suyi / Guo, Zengqing / Li, Wei / Shi, Hanping / Xu, Hongxia

Frontiers in nutrition

2022 Volume 9, Page(s) 860285

Abstract: Background and aims: Malnutrition is highly prevalent and is related to multiple impaired clinical outcomes in cancer patients. This study aimed to : Methods: We performed a multicenter cohort study including 14,134 cancer patients. The prognostic ... ...

Abstract	Background and aims: Malnutrition is highly prevalent and is related to multiple impaired clinical outcomes in cancer patients. This study aimed to Methods: We performed a multicenter cohort study including 14,134 cancer patients. The prognostic impact for each baseline characteristic was estimated by calculating Harrell's C-index. The optimal parameters reflecting the nutritional and inflammatory impact on patients' overall survival were selected to develop the fat-age-inflammation (FAIN) index. The associations of the FAIN with the nutritional status, physical performance, quality of life, short-term outcomes and mortality of patients were comprehensively evaluated. Independent external validation was performed to further assess the prognostic value of the FAIN. Results: The study enrolled 7,468 men and 6,666 women with a median age of 57 years and a median follow-up of 42 months. The FAIN index was defined as: (triceps skinfold thickness + albumin) / [age + 5 × (neutrophil count/lymphocyte count)]. There were significant associations of the FAIN with the nutritional status, physical performance, quality of life and short-term outcomes. The FAIN also showed better discrimination performance than the Nutritional Risk Index, the Prognostic Nutritional Index and the Controlling Nutritional Status index (all Conclusions: This study created and assessed the prognostic FAIN index, which might act as a feasible option to monitor the nutritional status and help develop intervention strategies to optimize the survival outcomes of cancer patients.
Language	English
Publishing date	2022-04-13
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2776676-7
ISSN	2296-861X
ISSN	2296-861X
DOI	10.3389/fnut.2022.860285
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Article ; Online: De novo design of modular peptide-binding proteins by superhelical matching.

Nature

2023 Volume 616, Issue 7957, Page(s) 581–589

Abstract: General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in ... ...

Abstract	General approaches for designing sequence-specific peptide-binding proteins would have wide utility in proteomics and synthetic biology. However, designing peptide-binding proteins is challenging, as most peptides do not have defined structures in isolation, and hydrogen bonds must be made to the buried polar groups in the peptide backbone
MeSH term(s)	Amino Acid Sequence ; Models, Molecular ; Peptides/chemistry ; Peptides/metabolism ; Proteins/chemistry ; Proteins/metabolism ; Protein Engineering/methods ; Hydrogen Bonding ; Protein Binding ; Protein Folding ; Protein Conformation
Chemical Substances	Peptides ; Proteins
Language	English
Publishing date	2023-04-05
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-05909-9
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Book ; Online: De-END

Fang, Han / Jia, Zhaoyang / Qiu, Yupeng / Zhang, Jiyi / Zhang, Weiming / Chang, Ee-Chien

Decoder-driven Watermarking Network

2022

Abstract: ... creatively design a decoder-driven watermarking network dubbed De-END which greatly outperforms the existing ... END-based methods. The motivation for designing De-END originated from the potential drawback ... that such limitations are caused by unsatisfactory coupling between the encoder and decoder in END. De-END addresses ...

Abstract	With recent advances in machine learning, researchers are now able to solve traditional problems with new solutions. In the area of digital watermarking, deep-learning-based watermarking technique is being extensively studied. Most existing approaches adopt a similar encoder-driven scheme which we name END (Encoder-NoiseLayer-Decoder) architecture. In this paper, we revamp the architecture and creatively design a decoder-driven watermarking network dubbed De-END which greatly outperforms the existing END-based methods. The motivation for designing De-END originated from the potential drawback we discovered in END architecture: The encoder may embed redundant features that are not necessary for decoding, limiting the performance of the whole network. We conducted a detailed analysis and found that such limitations are caused by unsatisfactory coupling between the encoder and decoder in END. De-END addresses such drawbacks by adopting a Decoder-Encoder-Noiselayer-Decoder architecture. In De-END, the host image is firstly processed by the decoder to generate a latent feature map instead of being directly fed into the encoder. This latent feature map is concatenated to the original watermark message and then processed by the encoder. This change in design is crucial as it makes the feature of encoder and decoder directly shared thus the encoder and decoder are better coupled. We conducted extensive experiments and the results show that this framework outperforms the existing state-of-the-art (SOTA) END-based deep learning watermarking both in visual quality and robustness. On the premise of the same decoder structure, the visual quality (measured by PSNR) of De-END improves by 1.6dB (45.16dB to 46.84dB), and extraction accuracy after JPEG compression (QF=50) distortion outperforms more than 4% (94.9% to 99.1%).
Keywords	Computer Science - Multimedia
Subject code	006
Publishing date	2022-06-26
Publishing country	us
Document type	Book ; Online
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Article ; Online: A De-Identification Model for Korean Clinical Notes: Using Deep Learning Models.

Chang, Junhyuk / Park, Jimyung / Kim, Chungsoo / Park, Rae Woong

Studies in health technology and informatics

2024 Volume 310, Page(s) 1456–1457

Abstract: ... information PHI in the records pre-processing of de-identification is required. Therefore we aimed to identify ... PHI list and fine-tune the deep learning BERT model for developing de-identification model. The result ... for the development of a de-identification model. ...

Abstract	To extract information from free-text in clinical records due to the patient's protected health information PHI in the records pre-processing of de-identification is required. Therefore we aimed to identify PHI list and fine-tune the deep learning BERT model for developing de-identification model. The result of fine-tuning the model is strict F1 score of 0.924. Due to the convinced score the model can be used for the development of a de-identification model.
MeSH term(s)	Humans ; Data Anonymization ; Deep Learning ; Republic of Korea
Language	English
Publishing date	2024-01-24
Publishing country	Netherlands
Document type	Journal Article
ISSN	1879-8365
ISSN (online)	1879-8365
DOI	10.3233/SHTI231242
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