Article
Multidisciplinary Sciences
Run Jin, Samantha Klasfeld, Yang Zhu, Meilin Fernandez Garcia, Jun Xiao, Soon-Ki Han, Adam Konkol, Doris Wagner
Summary: This study reveals that the plant pioneer transcription factor LFY promotes floral cell fate by locally unlocking chromatin through displacing histone H1 and recruiting SWI/SNF chromatin remodelers, providing biochemical evidence for a pioneer factor in plants and showing similarities with animal pioneer transcription factors.
NATURE COMMUNICATIONS
(2021)
Article
Environmental Sciences
Cheng-Shin Jang
Summary: This study investigated groundwater nitrate-nitrogen pollution in the Pingtung Plain of Taiwan using DRASTIC-LU-based aquifer contamination vulnerability and regression kriging. It was found that orchards and the sand fractions of vadose zones were associated with groundwater nitrate-nitrogen concentrations, with orchard fertilizer identified as the primary source of pollution. The findings highlight the importance of correctly determining groundwater nitrate-nitrogen distributions for environmental resource management and public health prevention.
ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH
(2023)
Article
Environmental Sciences
Cheng-Shin Jang, Shih-Kai Chen, Yuan-Yu Lee
Summary: This study used regression kriging (RK) to determine groundwater pollution zones in the Choushui River alluvial fan in Taiwan by integrating agricultural land uses with groundwater nitrate-N pollution. The results showed that orchard land-use type positively contributed to groundwater nitrate-N, while livestock house and agricultural facility land-use types were negatively related to groundwater nitrate-N. RK estimates characterized the potential pollution source of orchard land-use type and enhanced the accuracy of polluted and unpolluted areas classification by modifying the residuals, making it suitable for establishing groundwater pollution zones.
ENVIRONMENTAL EARTH SCIENCES
(2023)
Article
Multidisciplinary Sciences
Elizabeth D. Larson, Hideyuki Komori, Tyler J. Gibson, Cyrina M. Ostgaard, Danielle C. Hamm, Jack M. Schnell, Cheng-Yu Lee, Melissa M. Harrison
Summary: The pioneer transcription factor Zelda plays a crucial role in reprogramming germ cells during early Drosophila embryo development. Research further demonstrates that Zelda promotes undifferentiated stem-cell fate in the larval brain, and its ability to define cis-regulatory regions is influenced by cell-type-specific chromatin architecture. It is proposed that Zelda regulates essential transitions in neuroblasts and embryos through a shared gene-regulatory network driven by cell-type-specific enhancers.
NATURE COMMUNICATIONS
(2021)
Article
Green & Sustainable Science & Technology
Aliasghar Azma, Esmaeil Narreie, Abouzar Shojaaddini, Nima Kianfar, Ramin Kiyanfar, Seyed Mehdi Seyed Alizadeh, Afshin Davarpanah
Summary: By spatially assessing groundwater potential in a semi-arid region of Iran using GIS-based statistical modeling, this study demonstrated that GIS combined with statistical methods can predict groundwater quality effectively. It identified influential factors affecting groundwater quality, improving water resource management in arid and semi-arid lands.
Article
Biochemistry & Molecular Biology
Liyun Miao, Yin Tang, Ashley R. Bonneau, Shun Hang Chan, Mina L. Kojima, Mark E. Pownall, Charles E. Vejnar, Feng Gao, Smita Krishnaswamy, Caroline E. Hendry, Antonio J. Giraldez
Summary: This study reveals the function of NPS in chromatin reprogramming and genome activation in zebrafish. NPS individually or redundantly open chromatin, regulate histone acetylation, and the position of nucleosomes is influenced by different transcription factors.
Article
Biochemical Research Methods
Jennifer Hammelman, Tulsi Patel, Michael Closser, Hynek Wichterle, David Gifford
Summary: This study compares nine computational methods for identifying reprogramming factors for cell differentiation. The researchers found that methods using chromatin accessibility performed the best, with an average identification rate of 50-60% of reprogramming factors in the top ten candidates. Among the chromatin accessibility methods, DeepAccess and diffTF showed the highest correlation with the ranked significance of transcription factor candidates. AME and diffTF were identified as optimal methods for transcription factor recovery, allowing for systematic prioritization of candidates in the design of new reprogramming protocols.
Article
Biotechnology & Applied Microbiology
Jeffrey L. Hansen, Barak A. Cohen
Summary: This study presents a quantitative in vivo measure of pioneer activity, which captures the relative difference in a transcription factor's ability to bind accessible versus inaccessible DNA. The research findings suggest that the relative binding affinities of transcription factors can serve as reasonable measures of pioneer activity, highlighting the context-dependent nature of pioneer activity for most transcription factors.
Article
Chemistry, Organic
Tianhua Tang, Nathan C. Friede, Shelley D. Minteer, Matthew S. Sigman
Summary: This study investigates the reaction mechanism of different metal complexes and compares the effects of metal/ligand combinations on the reaction. The results show that these complexes follow a unified inner-sphere halogen atom abstraction mechanism, but there are subtle differences imparted by metal/ligand combinations.
EUROPEAN JOURNAL OF ORGANIC CHEMISTRY
(2022)
Article
Agronomy
Alexandra Tomaz, Jose Ferro Palma, Tiago Ramos, Maria Natividade Costa, Elizabete Rosa, Marta Santos, Luis Boteta, Jose Dores, Manuel Patanita
Summary: The study highlights the significant impacts of water regimes and nitrogen fertilizer treatments on wheat yield, grain quality, and water use. While supplemental irrigation may lead to lower grain yields, it maintains a similar water productivity to full irrigation. The use of enhanced efficiency fertilizers can improve wheat protein content and dough rheologic properties.
AGRICULTURAL WATER MANAGEMENT
(2021)
Article
Energy & Fuels
Ferhat Kaya, Gokhan Sahin, Mehmet Hakki Alma
Summary: This study employed multivariate linear regression to investigate the effects of environmental and operating factors on photovoltaic panel efficiency, with solar radiation, maximum power, and short circuit current identified as the three most influential parameters on panel efficiency.
INTERNATIONAL JOURNAL OF ENERGY RESEARCH
(2021)
Article
Immunology
Ehud Dahan, Victoria M. Martin, Moran Yassour
Summary: EasyMap is an interactive online tool that helps researchers compare microbial profiles across different groups of people in microbiome studies. It allows running multiple multivariate linear regression models, visualizing associations between microbial features and clinical metadata, and selecting the optimal model through comparisons.
FRONTIERS IN CELLULAR AND INFECTION MICROBIOLOGY
(2022)
Article
Medicine, Research & Experimental
Chunshen Long, Hanshuang Li, Pengfei Liang, Lemuge Chao, Yan Hong, Junping Zhang, Qilemuge Xi, Yongchun Zuo
Summary: Single-cell studies have revealed that somatic cell reprogramming is a continuous process of cell fate transition. The activation of pluripotency networks and the mesenchymal-epithelial transition are crucial for successful reprogramming. By reconstructing cellular trajectory, we identified key factors and genes driving cell fate bifurcations, and found several drivers for successful reprogramming and alternative fates.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)
Article
Neurosciences
Monika Graumann, Lara A. Wallenwein, Radoslaw M. Cichy
Summary: This study aimed to investigate the influence of spatial attention on object location representations, and identified processing stages in time and space through EEG and fMRI experiments. The results showed that spatial attention modulated location representations during late processing stages ( > 150 ms, in middle and high ventral visual stream areas) independent of background condition. This study clarified the processing stage at which attention modulates object location representations in the ventral visual stream and demonstrated that attentional modulation is a cognitive process separate from recurrent processes related to the processing of objects on cluttered backgrounds.
Article
Cell Biology
Yihao Yang, Nicholas Gomez, Nicole Infarinato, Rene C. Adam, Megan Sribour, Inwha Baek, Melanie Laurin, Elaine Fuchs
Summary: This study reveals the crucial role of SOX9 in diverting embryonic epidermal stem cells into hair follicle stem cells. By re-activating SOX9 in adult epidermal stem cells, the researchers induce fate switching. They show that SOX9 binds and opens hair follicle enhancers in epidermal stem cells, while recruiting epigenetic factors away from epidermal enhancers, leading to their silencing. This sustained expression of SOX9 subsequently activates oncogenic transcriptional regulators and contributes to the development of cancer.
NATURE CELL BIOLOGY
(2023)
Article
Computer Science, Information Systems
Shuai Liu, Shuai Wang, Xinyu Liu, Jianhua Dai, Khan Muhammad, Amir H. H. Gandomi, Weiping Ding, Mohammad Hijji, Victor Hugo C. de Albuquerque
Summary: Computer vision, particularly visual monitoring technology, has shown great potential in the complex monitoring environment. This article proposes a fuzzy inference-based monitoring method that utilizes human inertial thinking characteristics to infer the target's location and applies an alternative selection strategy based on thinking set. Experimental results on multiple datasets demonstrate the effectiveness and robustness of the proposed method in IoT-assisted monitoring.
IEEE INTERNET OF THINGS JOURNAL
(2023)
Article
Biochemistry & Molecular Biology
Lei Zheng, Pengfei Liang, Chunshen Long, Haicheng Li, Hanshuang Li, Yuchao Liang, Xiang He, Qilemuge Xi, Yongqiang Xing, Yongchun Zuo
Summary: The lack of global embryogenesis repository and systematic analysis tools hinders the progress of research in stem cells, human congenital diseases, and assisted reproduction. EmAtlas provides a comprehensive collection of multi-omics data and multi-scale tools to explore the spatiotemporal activation during mammalian embryogenesis.
NUCLEIC ACIDS RESEARCH
(2023)
Article
Biology
Cuihong Wen, Shaowu Liu, Shuai Liu, Ali Asghar Heidari, Mohammad Hijji, Carmen Zarco, Khan Muhammad
Summary: Automated diagnostic techniques based on CT scans of the chest have been proposed to detect COVID-19 cases quickly and accurately. Existing capsule networks face challenges in extracting key slices and fusing features from multiple regions. In this study, an attention capsule sampling network (ACSN) is proposed, which achieves high performance with 96.3% accuracy, 98.8% sensitivity, 93.8% specificity, and 98.3% area under the ROC curve on a dataset of 35,000 slices.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Computer Science, Artificial Intelligence
Shuai Liu, Shichen Huang, Shuai Wang, Khan Muhammad, Paolo Bellavista, Javier Del Ser
Summary: Deep learning has transformed computer vision and is widely used for monitoring in various visual scenes. However, traditional machine-learning methods still have certain advantages in terms of complexity and explainability. Traditional visual tracking approaches, particularly those using correlation filtering, have become popular for understanding complex visual scenes, but they may not fully capture the changing target appearances in dynamic visual scenes, leading to inaccurate target locations.
INFORMATION FUSION
(2023)
Article
Computer Science, Information Systems
Shuai Liu, Peng Gao, Yating Li, Weina Fu, Weiping Ding
Summary: Multimodal emotion recognition, using machine learning to generate multi-modal features from videos, is a research hotspot in the field of artificial intelligence. This paper improves the discrimination between modalities through effective weighting and constructs an attention network to capture the complementary relationship between modalities, resulting in a multi-modal feature with good interaction.
INFORMATION SCIENCES
(2023)
Article
Biochemical Research Methods
Mingzhu Liu, Jian Zhou, Qilemuge Xi, Yuchao Liang, Haicheng Li, Pengfei Liang, Yuting Guo, Ming Liu, Temuqile Temuqile, Lei Yang, Yongchun Zuo
Summary: This study developed a cost-effective framework for predicting chronic diseases using routine blood and biochemical test data. The framework achieved high accuracy and identified important markers for different types of chronic diseases.
BRIEFINGS IN BIOINFORMATICS
(2023)
Article
Biotechnology & Applied Microbiology
Dongqing Su, Haoxin Zhang, Yuqiang Xiong, Haodong Wei, Yao Yu, Honghao Li, Tao Wang, Yongchun Zuo, Lei Yang
Summary: The expression and activity of transcription factors play crucial roles in controlling normal cellular processes, while dysregulated transcription factor activity in cancer leads to abnormal gene expression related to tumorigenesis and development. Targeted therapy can reduce the carcinogenicity of transcription factors. However, most studies on ovarian cancer have focused on individual transcription factors, disregarding the need to evaluate multiple transcription factors simultaneously to assess their effects on drug therapies.
BRIEFINGS IN FUNCTIONAL GENOMICS
(2023)
Article
Computer Science, Artificial Intelligence
Xiangbin Liu, Ying Liu, Weina Fu, Shuai Liu
Summary: The global outbreak of COVID-19 has become an important healthcare research topic since 2019. RT-PCR is the main method for detecting COVID-19, but the long detection time is an issue. Therefore, the use of CT imaging for pathological studies of COVID-19 is crucial. The proposed SCTV-UNet addresses the problems of misidentifying normal pixels and blurry boundaries in CT image segmentation, and shows improved results compared to state-of-the-art networks.
Article
Biochemistry & Molecular Biology
Shanghua Liu, Yuchao Liang, Jinzhao Li, Siqi Yang, Ming Liu, Chengfang Liu, Dezhi Yang, Yongchun Zuo
Summary: A copper ion-bound protein classifier, RPCIBP, was developed in this study by integrating reduced amino acid composition into position-specific scoring matrix. The classifier accurately predicts copper ion-binding proteins, facilitating further structural and functional studies, and aiding mechanism exploration and target drug development.
INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES
(2023)
Review
Computer Science, Hardware & Architecture
Yishu Huang, Changling Peng, Shuai Liu
Summary: The research found that the number of empirical studies on classroom behavior is increasing rapidly, with topics mainly focusing on the influencing factors and characteristics of classroom behavior. The studies mostly used manual data collection and were predominantly quantitative, with a focus on primary and secondary school subjects and incomplete overviews of school divisions and disciplines.
MOBILE NETWORKS & APPLICATIONS
(2023)
Proceedings Paper
Computer Science, Software Engineering
Xia Liu, Baojian Hua, Yang Wang, Zhizhong Pan
Summary: This paper presents a large-scale empirical study of smart contract decompilers, aiming to understand the reliability, limitations, and research challenges of state-of-the-art decompilation tools. The study identifies root causes of decompiler failures, performance issues, and factors affecting decompilation effectiveness. It also proposes a completeness metric and investigates the resilience of decompilers against program transformations. Suggestions are given for decompiler builders and security researchers to improve decompilation tools and make appropriate selections. The findings and suggestions provided in this study can benefit decompiler builders, contract developers, and security researchers.
2023 IEEE INTERNATIONAL CONFERENCE ON SOFTWARE ANALYSIS, EVOLUTION AND REENGINEERING, SANER
(2023)
Article
Multidisciplinary Sciences
Hanshuang Li, Chunshen Long, Yan Hong, Liaofu Luo, Yongchun Zuo
Summary: This study quantitatively evaluated the differentiation potency of stem cells using the Hopfield neural network and found that it can be approximated by Hopfield energy values. The analysis of the energy landscape in embryogenesis and cell reprogramming processes revealed that cell fate decision is a continuous process. The study also deciphered the dynamics of the gene regulatory network involved in driving cell fate transition. These findings propose a new energy indicator for characterizing cellular differentiation potency and provide insights into the potential mechanism of cellular plasticity.
Article
Computer Science, Artificial Intelligence
Shichen Huang, Weina Fu, Zhaoyue Zhang, Shuai Liu
Summary: In the era of adversarial machine learning (AML), developing robust and generalized algorithms has become a key research topic. This study proposes a global similarity matching module and a global-local cognition fusion training mechanism based on relationship adversarial sample generation to improve image-text matching algorithm. Experimental results show significant improvements in accuracy and robustness, performing well in facing security challenges and promoting the fusion of visual and linguistic modalities.
INFORMATION FUSION
(2024)
Article
Engineering, Electrical & Electronic
Shuai Liu, Pengfei Chen, Yudong Zhang
Summary: Synthetic aperture radar (SAR) ship detection is widely used in various applications, but existing lightweight algorithms have problems such as misjudgment of targets mixed with the background and poor detection performance for targets with few samples. To address these issues, this paper proposes a detection network based on a multiscale feature pyramid network (FPN) that enhances target features, suppresses interference from the background, and reduces misjudgment. Experimental results show that the proposed network outperforms existing algorithms on public datasets.
IEEE JOURNAL OF SELECTED TOPICS IN APPLIED EARTH OBSERVATIONS AND REMOTE SENSING
(2023)
Article
Medicine, Research & Experimental
Chunshen Long, Hanshuang Li, Pengfei Liang, Lemuge Chao, Yan Hong, Junping Zhang, Qilemuge Xi, Yongchun Zuo
Summary: Single-cell studies have revealed that somatic cell reprogramming is a continuous process of cell fate transition. The activation of pluripotency networks and the mesenchymal-epithelial transition are crucial for successful reprogramming. By reconstructing cellular trajectory, we identified key factors and genes driving cell fate bifurcations, and found several drivers for successful reprogramming and alternative fates.
MOLECULAR THERAPY-NUCLEIC ACIDS
(2023)