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Article: Pediatric mandibular chronic nonbacterial osteomyelitis: A case report with 12 years of radiologic follow-up.

Choi, Sehyun / Kim, Min-Ji / Kang, Sang-Hoon / Park, In-Woo

2024 Volume 54, Issue 1, Page(s) 93–104

Abstract: Chronic nonbacterial osteomyelitis (CNO) is histologically characterized by nonspecific osteitis. This inflammatory disorder, which lacks an infectious origin, typically presents with chronic pain and swelling at the affected site that can persist for ... ...

Abstract	Chronic nonbacterial osteomyelitis (CNO) is histologically characterized by nonspecific osteitis. This inflammatory disorder, which lacks an infectious origin, typically presents with chronic pain and swelling at the affected site that can persist for months or even years. However, it is rare for CNO to affect the mandible. A 10-year-old girl presented with a primary complaint of pain in her left mandible. She had no significant medical or dental history. On examination, swelling was visible on the left buccal side, and imaging revealed radiolucent bone deterioration within the left mandible. This case report presents the radiological changes observed over a 12-year follow-up period. Variations in radiopacity, radiolucency, and periosteal reactions were noted periodically. This case highlights the radiological characteristics and findings that are crucial for the diagnosis of CNO, a condition for which no clear diagnostic criteria are currently available.
Language	English
Publishing date	2024-02-06
Publishing country	Korea (South)
Document type	Case Reports
ZDB-ID	2631801-5
ISSN	2233-7830 ; 2233-7822
ISSN (online)	2233-7830
ISSN	2233-7822
DOI	10.5624/isd.20230189
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Book ; Online: KCTS

Choi, Sehyun / Fang, Tianqing / Wang, Zhaowei / Song, Yangqiu

Knowledge-Constrained Tree Search Decoding with Token-Level Hallucination Detection

2023

Abstract: Large Language Models (LLMs) have demonstrated remarkable human-level natural language generation capabilities. However, their potential to generate misinformation, often called the hallucination problem, poses a significant risk to their deployment. A ... ...

Abstract	Large Language Models (LLMs) have demonstrated remarkable human-level natural language generation capabilities. However, their potential to generate misinformation, often called the hallucination problem, poses a significant risk to their deployment. A common approach to address this issue is to retrieve relevant knowledge and fine-tune the LLM with the knowledge in its input. Unfortunately, this method incurs high training costs and may cause catastrophic forgetting for multi-tasking models. To overcome these limitations, we propose a knowledge-constrained decoding method called KCTS (Knowledge-Constrained Tree Search), which guides a frozen LM to generate text aligned with the reference knowledge at each decoding step using a knowledge classifier score and MCTS (Monte-Carlo Tree Search). To adapt the sequence-level knowledge classifier to token-level guidance, we also propose a novel token-level hallucination detection method called RIPA (Reward Inflection Point Approximation). Our empirical results on knowledge-grounded dialogue and abstractive summarization demonstrate the strength of KCTS as a plug-and-play, model-agnostic decoding method that can effectively reduce hallucinations in natural language generation. Comment: Accepted at EMNLP 2023 Main Conference
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence ; Computer Science - Machine Learning
Subject code	004
Publishing date	2023-10-13
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Digitalizing breeding in plants: A new trend of next-generation breeding based on genomic prediction.

Jeon, Donghyun / Kang, Yuna / Lee, Solji / Choi, Sehyun / Sung, Yeonjun / Lee, Tae-Ho / Kim, Changsoo

Frontiers in plant science

2023 Volume 14, Page(s) 1092584

Abstract: As the world's population grows and food needs diversification, the demand for cereals and horticultural crops with beneficial traits increases. In order to meet a variety of demands, suitable cultivars and innovative breeding methods need to be ... ...

Abstract	As the world's population grows and food needs diversification, the demand for cereals and horticultural crops with beneficial traits increases. In order to meet a variety of demands, suitable cultivars and innovative breeding methods need to be developed. Breeding methods have changed over time following the advance of genetics. With the advent of new sequencing technology in the early 21st century, predictive breeding, such as genomic selection (GS), emerged when large-scale genomic information became available. GS shows good predictive ability for the selection of individuals with traits of interest even for quantitative traits by using various types of the whole genome-scanning markers, breaking away from the limitations of marker-assisted selection (MAS). In the current review, we briefly describe the history of breeding techniques, each breeding method, various statistical models applied to GS and methods to increase the GS efficiency. Consequently, we intend to propose and define the term digital breeding through this review article. Digital breeding is to develop a predictive breeding methods such as GS at a higher level, aiming to minimize human intervention by automatically proceeding breeding design, propagating breeding populations, and to make selections in consideration of various environments, climates, and topography during the breeding process. We also classified the phases of digital breeding based on the technologies and methods applied to each phase. This review paper will provide an understanding and a direction for the final evolution of plant breeding in the future.
Language	English
Publishing date	2023-01-19
Publishing country	Switzerland
Document type	Journal Article ; Review
ZDB-ID	2613694-6
ISSN	1664-462X
ISSN	1664-462X
DOI	10.3389/fpls.2023.1092584
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Book ; Online: CKBP v2

Fang, Tianqing / Do, Quyet V. / Choi, Sehyun / Wang, Weiqi / Song, Yangqiu

An Expert-Annotated Evaluation Set for Commonsense Knowledge Base Population

2023

Abstract: Populating Commonsense Knowledge Bases (CSKB) is an important yet hard task in NLP, as it tackles knowledge from external sources with unseen events and entities. Fang et al. (2021a) proposed a CSKB Population benchmark with an evaluation set CKBP v1. ... ...

Abstract	Populating Commonsense Knowledge Bases (CSKB) is an important yet hard task in NLP, as it tackles knowledge from external sources with unseen events and entities. Fang et al. (2021a) proposed a CSKB Population benchmark with an evaluation set CKBP v1. However, CKBP v1 adopts crowdsourced annotations that suffer from a substantial fraction of incorrect answers, and the evaluation set is not well-aligned with the external knowledge source as a result of random sampling. In this paper, we introduce CKBP v2, a new high-quality CSKB Population benchmark, which addresses the two mentioned problems by using experts instead of crowd-sourced annotation and by adding diversified adversarial samples to make the evaluation set more representative. We conduct extensive experiments comparing state-of-the-art methods for CSKB Population on the new evaluation set for future research comparisons. Empirical results show that the population task is still challenging, even for large language models (LLM) such as ChatGPT. Codes and data are available at https://github.com/HKUST-KnowComp/CSKB-Population.
Keywords	Computer Science - Computation and Language
Subject code	400
Publishing date	2023-04-20
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article ; Online: Physio-chemical and co-expression network analysis associated with salt stress in sorghum.

Choi, Sehyun / Kang, Yuna / Lee, Solji / Jeon, Dong-Hyun / Seo, Sumin / Lee, Tae-Ho / Kim, Changsoo

Frontiers in bioscience (Landmark edition)

2022 Volume 27, Issue 2, Page(s) 55

Abstract: Background: Abiotic stress can damage crops and reduce productivity. Among them, salt stress is related to water stress such as osmosis and ions, and like other abiotic stresses, it can affect the growth of plants by changing gene expressions. ... ...

Abstract	Background: Abiotic stress can damage crops and reduce productivity. Among them, salt stress is related to water stress such as osmosis and ions, and like other abiotic stresses, it can affect the growth of plants by changing gene expressions. Investigating the profiles of gene expression under salt stress may help us understand molecular mechanisms of plants to cope with unfavorable conditions. Results: To study salt tolerance in sorghum, physiological and comparative transcriptomic studies were performed using a Korean sorghum cultivar 'Sodamchal' which is considered sensitive to soil salinity. In this study, the samples were treated with two concentrations of NaCl [0 (control) and 150 mM], and the leaves and roots were harvested at 0, 3, and 9 days after the treatment. For the physiological study, the levels of anthocyanin, proline, reducing sugar, and chlorophyll were evaluated in the control and the treatment group at each sampling point. The results show that the cultivar 'Sodamchal' has salt-susceptible profiles. We also analyzed the transcription profile in the presence of 0 and 150 mM NaCl to confirm the candidate genes under the saline stress condition. Between the control and salt treatment, we found a total of 1506 and 1510 differentially expressed genes (DEGs) in the leaves and roots, respectively. We also built a gene co-expression network to determine the association of the candidate genes in terms of biological pathways. Conclusions: Through the co-expression network, genes related to salt stress such as AP2/ERF and Dehydrin were identified. This study provides the physiological and genic markers that could be used during intense salt stress in sorghum. These markers could be used to lay the foundation for the distribution of high-quality seeds that are tolerant to salt in the future.
MeSH term(s)	Gene Expression Regulation, Plant ; Salinity ; Salt Stress/genetics ; Salt Tolerance/genetics ; Sodium Chloride/pharmacology ; Sorghum/genetics ; Stress, Physiological/genetics
Chemical Substances	Sodium Chloride (451W47IQ8X)
Language	English
Publishing date	2022-02-28
Publishing country	Singapore
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	2704569-9
ISSN	2768-6698 ; 2768-6698
ISSN (online)	2768-6698
ISSN	2768-6698
DOI	10.31083/j.fbl2702055
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Expression Profile of Sorghum Genes and

Lee, Solji / Jeon, Donghyun / Choi, Sehyun / Kang, Yuna / Seo, Sumin / Kwon, Soonjae / Lyu, Jaeil / Ahn, Joonwoo / Seo, Jisu / Kim, Changsoo

Plants (Basel, Switzerland)

2022 Volume 11, Issue 7

Abstract: Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum ( ...

Abstract	Salinity stress is one of the most important abiotic stresses that causes great losses in crop production worldwide. Identifying the molecular mechanisms of salt resistance in sorghum will help develop salt-tolerant crops with high yields. Sorghum (
Language	English
Publishing date	2022-03-24
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2704341-1
ISSN	2223-7747
ISSN	2223-7747
DOI	10.3390/plants11070869
Database	MEDical Literature Analysis and Retrieval System OnLINE

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Article: Evolutionary impact of whole genome duplication in Poaceae family

Lee, Solji / Choi, Sehyun / Jeon, Donghyun / Kang, Yuna / Kim, Changsoo

Journal of crop science and biotechnology. 2020 Dec., v. 23, no. 5

2020

Abstract: Whole genome duplication (WGD) is a common phenomenon in plants, inducing species diversity, promoting speciation, and playing an important role in providing new genetic material in plant evolution. So far, numerous new gene functions such as ... ...

Abstract	Whole genome duplication (WGD) is a common phenomenon in plants, inducing species diversity, promoting speciation, and playing an important role in providing new genetic material in plant evolution. So far, numerous new gene functions such as pseudogenization, neofunctionalization, and subfunctionalization have evolved through WGD. WGD has occurred several times during the evolution of angiosperms over the past 200 million years. Poaceae, one of the largest plant families in the angiosperms, is considered one of the most economically important and ecologically successful plants, with approximately 600 genera and 10,000 species. Many genetic studies have been conducted on these plants. However, study of the most active phylogeny in the Poaceae family study has not yet been completed. Through comparative studies of major Poaceae groups, this review focuses on the effects of genome duplication in the Poaceae family on its evolutionary history and the changes in chromosome numbers.
Keywords	Poaceae ; biotechnology ; chromosomes ; genes ; phylogeny ; species diversity
Language	English
Dates of publication	2020-12
Size	p. 413-425.
Publishing place	Springer Singapore
Document type	Article
Note	NAL-AP-2-clean ; Review
ZDB-ID	2300030-2
ISSN	2005-8276 ; 1975-9479
ISSN (online)	2005-8276
ISSN	1975-9479
DOI	10.1007/s12892-020-00049-2
Database	NAL-Catalogue (AGRICOLA)

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Book ; Online: AbsPyramid

Wang, Zhaowei / Shi, Haochen / Wang, Weiqi / Fang, Tianqing / Zhang, Hongming / Choi, Sehyun / Liu, Xin / Song, Yangqiu

Benchmarking the Abstraction Ability of Language Models with a Unified Entailment Graph

2023

Abstract: Cognitive research indicates that abstraction ability is essential in human intelligence, which remains under-explored in language models. In this paper, we present AbsPyramid, a unified entailment graph of 221K textual descriptions of abstraction ... ...

Abstract	Cognitive research indicates that abstraction ability is essential in human intelligence, which remains under-explored in language models. In this paper, we present AbsPyramid, a unified entailment graph of 221K textual descriptions of abstraction knowledge. While existing resources only touch nouns or verbs within simplified events or specific domains, AbsPyramid collects abstract knowledge for three components of diverse events to comprehensively evaluate the abstraction ability of language models in the open domain. Experimental results demonstrate that current LLMs face challenges comprehending abstraction knowledge in zero-shot and few-shot settings. By training on our rich abstraction knowledge, we find LLMs can acquire basic abstraction abilities and generalize to unseen events. In the meantime, we empirically show that our benchmark is comprehensive to enhance LLMs across two previous abstraction tasks. Comment: Work in progress
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
Subject code	004
Publishing date	2023-11-15
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Book ; Online: Benchmarking Commonsense Knowledge Base Population with an Effective Evaluation Dataset

Fang, Tianqing / Wang, Weiqi / Choi, Sehyun / Hao, Shibo / Zhang, Hongming / Song, Yangqiu / He, Bin

2021

Abstract: Reasoning over commonsense knowledge bases (CSKB) whose elements are in the form of free-text is an important yet hard task in NLP. While CSKB completion only fills the missing links within the domain of the CSKB, CSKB population is alternatively ... ...

Abstract	Reasoning over commonsense knowledge bases (CSKB) whose elements are in the form of free-text is an important yet hard task in NLP. While CSKB completion only fills the missing links within the domain of the CSKB, CSKB population is alternatively proposed with the goal of reasoning unseen assertions from external resources. In this task, CSKBs are grounded to a large-scale eventuality (activity, state, and event) graph to discriminate whether novel triples from the eventuality graph are plausible or not. However, existing evaluations on the population task are either not accurate (automatic evaluation with randomly sampled negative examples) or of small scale (human annotation). In this paper, we benchmark the CSKB population task with a new large-scale dataset by first aligning four popular CSKBs, and then presenting a high-quality human-annotated evaluation set to probe neural models' commonsense reasoning ability. We also propose a novel inductive commonsense reasoning model that reasons over graphs. Experimental results show that generalizing commonsense reasoning on unseen assertions is inherently a hard task. Models achieving high accuracy during training perform poorly on the evaluation set, with a large gap between human performance. We will make the data publicly available for future contributions. Codes and data are available at https://github.com/HKUST-KnowComp/CSKB-Population. Comment: EMNLP 2021 Main Conference
Keywords	Computer Science - Computation and Language ; Computer Science - Artificial Intelligence
Subject code	006
Publishing date	2021-09-15
Publishing country	us
Document type	Book ; Online
Database	BASE - Bielefeld Academic Search Engine (life sciences selection)

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Article: Quantitative Trait Loci (QTLs) Associated with Microspore Culture in <i>Raphanus sativus</i> L. (Radish)

Kim, Kyeongmin / Kang, Yuna / Lee, Sol-Ji / Choi, Se-Hyun / Jeon, Dong-Hyun / Park, Min-Young / Park, Suhyoung / Lim, Yong Pyo / Kim, Changsoo

Genes. 2020 Mar. 21, v. 11, no. 3

2020

Abstract: The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly ... ...

Abstract	The radish is a highly self-incompatible plant, and consequently it is difficult to produce homozygous lines. Bud pollination in cross-fertilization plants should be done by opening immature pollen and attaching pollen to mature flowers. It accordingly takes a lot of time and effort to develop lines with fixed alleles. In the current study, a haploid breeding method has been applied to obtain homozygous plants in a short period of time by doubling chromosomes through the induction of a plant body in the haploid cells, in order to shorten the time to breed inbred lines. We constructed genetic maps with an F1 population derived by crossing parents that show a superior and inferior ability to regenerate microspores, respectively. Genetic maps were constructed from the maternal and parental maps, separately, using the two-way pseudo-testcross model. The phenotype of the regeneration rate was examined by microspore cultures and a quantitative trait loci (QTL) analysis was performed based on the regeneration rate. From the results of the culture of microspores in the F1 population, more than half of the group did not regenerate, and only a few showed a high regeneration rate. A total of five significant QTLs were detected in the F1 population, and five candidate genes were found based on the results. These candidate genes are divided into two classes, and appear to be related to either PRC2 subunits or auxin synthesis.
Keywords	Raphanus sativus ; alleles ; auxins ; chromosomes ; crossing ; flowers ; haploidy ; homozygosity ; inbred lines ; microspores ; models ; parents ; phenotype ; pollen ; pollination ; quantitative trait loci ; radishes
Language	English
Dates of publication	2020-0321
Publishing place	Multidisciplinary Digital Publishing Institute
Document type	Article
ZDB-ID	2527218-4
ISSN	2073-4425
ISSN	2073-4425
DOI	10.3390/genes11030337
Database	NAL-Catalogue (AGRICOLA)

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