Article
Immunology
Sloan A. Lewis, Suhas Sureshchandra, Brianna Doratt, Vanessa A. Jimenez, Cara Stull, Kathleen A. Grant, Ilhem Messaoudi
Summary: Chronic heavy drinking can alter classical monocyte subset composition, leading to a hyper-inflammatory response to LPS but a compromised response to pathogens. This dysregulated inflammatory response may increase susceptibility to infections and impair wound healing.
FRONTIERS IN IMMUNOLOGY
(2021)
Article
Obstetrics & Gynecology
Sule Yildiz, Meric Kinali, Jian Jun Wei, Magdy Milad, Ping Yin, Mazhar Adli, Serdar E. Bulun
Summary: This study used single-cell RNA sequencing to assess the cellular and molecular landscape of adenomyosis. The results revealed that adenomyosis exhibits gene expression patterns similar to the endometrium and that the WNT signaling pathway plays a key role in the pathophysiology of this disease.
FERTILITY AND STERILITY
(2023)
Article
Biology
Yusuf Baran, Berat Dogan
Summary: Single-cell RNA sequencing (scRNA-seq) is a powerful tool for studying gene expression at the single-cell level. However, it lacks spatial information. Spatial transcriptomics is a new method that combines gene expression measurement with spatial information. This study proposes scMAGS, a method for marker gene selection from scRNA-seq data for spatial transcriptomics. scMAGS is scalable, fast, and accurate, even for large datasets. It is freely available for download at https://github.com/doganlab/scmags.
COMPUTERS IN BIOLOGY AND MEDICINE
(2023)
Article
Oncology
Yang-Yang Wang, En-Qiang Chang, Rui-Lou Zhu, Xiao-Zhuan Liu, Guang-Zhi Wang, Ning-Tao Li, Wei Zhang, Jun Zhou, Xiang-Dong Wang, Ming-Yang Sun, Jia-Qiang Zhang
Summary: This study aimed to investigate the impact of general anesthesia on the patient's immune system at a single-cell level. Results showed changes in CD56(+) NK cells and monocytes at different time points after anesthesia, as well as differences in immune cell communication between females and males. Additionally, the severity of surgery and type of anesthesia were found to affect communication between immune cells.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biochemical Research Methods
Hantao Shu, Fan Ding, Jingtian Zhou, Yexiang Xue, Dan Zhao, Jianyang Zeng, Jianzhu Ma
Summary: In this study, a weakly supervised learning framework based on the axial transformer was constructed to infer cell-type-specific gene regulatory networks (GRNs) from both single-cell RNA sequencing data and a generic GRN derived from bulk cells. The assumption that bulk-cell transcriptomic data can improve the prediction of single-cell GRNs was verified through extensive experiments, and the proposed GRN-transformer achieved state-of-the-art prediction accuracy.
BRIEFINGS IN BIOINFORMATICS
(2022)
Article
Biochemistry & Molecular Biology
Changbin Sun, Hailun Wang, Qiwang Ma, Chao Chen, Jianhui Yue, Bo Li, Xi Zhang
Summary: This study utilized single-cell RNA-seq to investigate the transcriptional heterogeneity and expression changes of limbal stem cells derived from human embryonic stem cells. The results revealed candidate developmental trajectories and new markers for LSCs during in vitro differentiation, providing insights into the identity and developmental origin of human LSCs.
CELL AND BIOSCIENCE
(2021)
Article
Developmental Biology
Abdull J. Massri, Laura Greenstreet, Anton Afanassiev, Alejandro Berrio, Gregory A. Wray, Geoffrey Schiebinger, David R. McClay
Summary: By using scRNA-seq and computational methods, researchers studied the transcriptional changes in cell states of sea urchin embryos from development to larval stage. They found that skeletogenic and primordial germ cell trajectories diverged early, and ectodermal progenitors were distinct from other lineages by the 6th cleavage. Endomesoderm cells originated at the 6th cleavage and diverged into endoderm and mesoderm fates asynchronously.
Article
Biochemistry & Molecular Biology
Lingyu Qiu, Chen Liang, Yidong Zheng, Huayu Kang, Aiyue Chen, Chunlin Chen, Xinlong Wang, Jielin Yang, Qiongfang Fang, Xinjie Hui, Yueming Hu, Zewei Chen, Ou Sha, Wei-Guo Zhu, Yejun Wang
Summary: This research systematically investigates stable expressed genes (SEGs) in humans at the single-cell level and observes their specificity in development, tissue, and cell types. The study identifies a list of 408 spatial-temporal SEGs and finds development-specific SEGs as well as tissue-specific SEGs with immune and RNA splicing functions. The research also explores the application of SEGs in cell decomposition and accurately predicts the proportions of major immune cells in peripheral blood samples.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Oncology
Dongsheng Chen, Wei Wang, Linlin Wu, Langchao Liang, Shiyou Wang, Yunfeng Cheng, Tongda Zhang, Chaochao Chai, Qiuhong Luo, Chengcheng Sun, Wandong Zhao, Zhiyuan Lv, Ya Gao, Xiaoxia Wu, Ning Sun, Yiwei Zhang, Jing Zhang, Yixuan Chen, Jianing Tong, Xiangdong Wang, Yong Bai, Chaoyang Sun, Xin Jin, Jianmin Niu
Summary: This study constructed a single-cell atlas of peripheral blood mononuclear cells (PBMCs) in pregnant women and identified immune cell reconfiguration during pregnancy. The researchers also developed a model to predict gestational age of normal pregnancy using transcriptomic data.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Article
Biochemistry & Molecular Biology
Shaoqiang Zhang, Linjuan Xie, Yaxuan Cui, Benjamin R. Carone, Yong Chen
Summary: DEGman, a new method proposed in this study, utilizes multiple diverse distributions combined with Bhattacharyya distance to detect differentially expressed genes. DEGman shows overall improvement in the balance of sensitivity and precision compared to other popular DEG analysis tools, and demonstrates better performance in real data applications.
Review
Cardiac & Cardiovascular Systems
Jenifer Vallejo, Clement Cochain, Alma Zernecke, Klaus Ley
Summary: Single-cell RNA sequencing has been instrumental in studying immune cells in atherosclerosis, identifying new immune cell subsets and significantly upregulated genes, providing a new perspective on the pathogenesis of atherosclerosis.
CARDIOVASCULAR RESEARCH
(2021)
Article
Oncology
Yan Mei, Weiwei Xiao, Hao Hu, Guanming Lu, Lingdan Chen, Zhun Sun, Mengdie Lu, Wenhui Ma, Ting Jiang, YuanHong Gao, LiRen Li, Gong Chen, Zifeng Wang, Hanjie Li, Duojiao Wu, Pinghong Zhou, Qibin Leng, Guangshuai Jia
Summary: This study comprehensively characterized the transcriptomes of single cells from 12 treatment-naive colorectal cancer patients, identifying differences in cell clusters and their association with therapeutic responses. Novel immune cell subtypes associated with colorectal cancer were also discovered, providing a rich resource for further research. Additionally, expanded T-cell clusters linked to high tumor mutational burden status were identified, enhancing understanding of the tumor microenvironment.
CLINICAL AND TRANSLATIONAL MEDICINE
(2021)
Article
Oncology
Yun Hua Lee, Samuel Chuah, Phuong H. D. Nguyen, Chun Jye Lim, Hannah L. H. Lai, Martin Wasser, Camillus Chua, Tony K. H. Lim, Wei Qiang Leow, Tracy Jiezhen Loh, Wei Keat Wan, Yin Huei Pang, Gwyneth Soon, Peng Chung Cheow, Juinn Huar Kam, Shridhar Iyer, Alfred Kow, Glenn K. Bonney, Chung Yip Chan, Alexander Chung, Brian K. P. Goh, Weiwei Zhai, Pierce K. H. Chow, Salvatore Albani, Haiyan Liu, Valerie Chew
Summary: In this study, IL-17-producing CD8 (Tc17) T cells were found to have distinct immunological phenotypes and regulatory circuits in hepatocellular carcinoma (HCC). The IFN gamma(-) Tc17 subset demonstrated pro-tumoral characteristics and higher expression of CCL20, which was associated with increased tumor infiltration of T regulatory cells (Treg) and poorer prognosis in HCC patients.
Article
Multidisciplinary Sciences
Siying Wei, Chenchen Li, Xuemei Luo, Lanzexin Yang, Long Yu, Qintao Wang, Zhuo-Xian Meng, Tao Wang, Yan Chen
Summary: This study explored the effectiveness of intermittent protein restriction (IPR) in diabetes control and found that it can significantly reduce hyperglycemia and improve the number and function of pancreatic islet β cells. Furthermore, IPR can reduce glucose production in the liver and enhance insulin signaling in skeletal muscle.
Article
Immunology
Moein Yaqubi, Adam M. R. Groh, Marie-France Dorion, Elia Afanasiev, Julia Xiao Xuan Luo, Hadi Hashemi, Sarthak Sinha, Nicholas W. Kieran, Manon Blain, Qiao-Ling Cui, Jeff Biernaskie, Myriam Srour, Roy Dudley, Jeffery A. Hall, Joshua A. Sonnen, Nathalie Arbour, Alexandre Prat, Jo Anne Stratton, Jack Antel, Luke M. Healy
Summary: This study aimed to characterize the transcriptional landscape of ex vivo human microglia at different developmental ages. The results showed that pre-natal microglia have a distinct transcriptional signature and an upregulation of phagocytic pathways. Adult microglia exhibit a more pro-inflammatory signature and are more immune responsive. The study also indicated that the transcriptional signatures of microglia are in response to a changing brain microenvironment and not predetermined developmental states.
JOURNAL OF NEUROINFLAMMATION
(2023)
Article
Biochemistry & Molecular Biology
Budd A. Tucker, Erin R. Burnight, Cathryn M. Cranston, Mallory J. Ulferts, Meagan A. Luse, Trudi Westfall, C. Anthony Scott, Autumn Marsden, Katherine Gibson-Corley, Luke A. Wiley, Ian C. Han, Diane C. Slusarski, Robert F. Mullins, Edwin M. Stone
Summary: A study identified a genetic mutation in the MAK gene leading to retinitis pigmentosa, and explored the feasibility of using a viral gene augmentation strategy for treatment.
Article
Oncology
Kelly Mulfaul, Nathaniel K. Mullin, Joseph C. Giacalone, Andrew P. Voigt, Melette DeVore, Edwin M. Stone, Budd A. Tucker, Robert F. Mullins
Summary: Activation of the alternative complement pathway is a crucial event in the development of age-related macular degeneration (AMD). Uncontrolled complement activation leads to the formation of the membrane attack complex (MAC). This study demonstrates that reduced levels of complement factor H (FH) in the choroid can contribute to MAC deposition on choroidal endothelial cells (CECs), while overexpression of FH can protect against MAC deposition. These findings highlight the importance of local FH production in preventing MAC deposition in AMD.
JOURNAL OF PATHOLOGY
(2022)
Article
Endocrinology & Metabolism
Benjamin A. Palmer, Karissa Soltys, M. Bridget Zimmerman, Andrew W. Norris, Eva Tsalikian, Michael J. Tansey, Catherina T. Pinnaro
Summary: This study investigated the proportion of caregivers of youth with type 1 diabetes who perform retrospective review of glucose data and make retroactive insulin adjustments. The results showed that caregivers who performed retrospective review were usually younger in age (12.2 years) and had a higher usage of continuous glucose monitoring (92%), but this behavior was not associated with significant improvement in glycemic control. It was also found that the fear of hypoglycemia was associated with the performance of retrospective review.
JOURNAL OF DIABETES SCIENCE AND TECHNOLOGY
(2023)
Article
Zoology
Shuo Qi, Zhi-Tong Lyu, Wei-Liang Xie, Shao-Ping Wan, Wei Zhang, Jun Liu, Yun-Ming Mo, Ying-Yong Wang
Summary: Two specimens of the genus Sphenomorphus were collected in Shiwandashan Nature Reserve, Guangxi, China. They were identified as Sphenomorphus cryptotis, a new herpetological record for China and the first found outside of Vietnam. Morphological descriptions of the specimens were provided, and molecular data of this poorly known species were presented for the first time.
RUSSIAN JOURNAL OF HERPETOLOGY
(2022)
Article
Ophthalmology
Lola P. Lozano, Budd A. Tucker, Connie J. Hinz, H. Culver Boldt, Elaine M. Binkley
Summary: Von Hippel-Lindau (VHL) disease is a rare inherited cancer syndrome that leads to the development of tumors in multiple systems. This case report highlights the importance of being aware that rare diagnoses can co-exist, as seen in a patient with both retinopathy of prematurity (ROP) and VHL.
CASE REPORTS IN OPHTHALMOLOGY
(2022)
Article
Computer Science, Information Systems
Xiao Li, Mingshuo Wei, Weiliang Xie
Summary: This paper investigates technical solutions for carrying 5G voice services in shared network infrastructure, and provides a comparison of voice bearer solutions in different stages. The results can serve as a reference for countries around the world.
Article
Biochemistry & Molecular Biology
Ian C. Han, Luke A. Wiley, Dalyz Ochoa, Mallory J. Lang, Brynnon E. Harman, Katie M. Sheehan, Robert F. Mullins, Edwin M. Stone, Budd A. Tucker
Summary: In this study, a novel Pde6b-deficient rat model was generated using CRISPR-Cas9 genome editing. The model exhibited rapid photoreceptor degeneration and adeno-associated viral vectors were successfully manufactured to drive human PDE6B expression. Subretinal gene therapy using these vectors was able to delay photoreceptor loss in the rat model.
Article
Cell Biology
Guillermo L. Lehmann, Michael Ginsberg, Daniel J. Nolan, Cristina Rodriguez, Jose Martinez-Gonzalez, Shemin Zeng, Andrew P. Voigt, Robert F. Mullins, Shahin Rafii, Enrique Rodriguez-Boulan, Ignacio Benedicto
Summary: A2M, a protease inhibitor, is found to be expressed in endothelial cells of the human eye choroid. The expression of A2M is induced by retinal pigment epithelium (RPE)-conditioned medium, with VEGF-A playing a key role. Furthermore, the inhibition of A2M leads to the restoration of gelatinase activity in culture supernatants. This study provides important insights into the alterations in choroidal ECM and visual function due to dysfunctional RPE or choroidal blood vessels.
Article
Chemistry, Multidisciplinary
Mingshuo Wei, Xiao Li, Weiliang Xie, Chunlei Hu
Summary: The 5G network is rapidly developing, but due to spectrum resource limitation, it is necessary to implement dynamic spectrum-sharing (DSS) technology to enable coexistence of 4G and 5G networks in the same band. However, this DSS technology can introduce intra-frequency interference, affecting network performance. To address this issue, two interference mitigation schemes, buffer setting and rate matching, were proposed and their practical performance was verified. These schemes effectively mitigate the interference introduced by DSS, improving network rate and user experience in the DSS architecture.
APPLIED SCIENCES-BASEL
(2023)
Article
Biotechnology & Applied Microbiology
Luke A. Wiley, Timothy M. Boyce, Emily E. Meyering, Dalyz Ochoa, Katie M. Sheehan, Edwin M. Stone, Robert F. Mullins, Budd A. Tucker, Ian C. Han
Summary: Adeno-associated virus (AAV)-mediated gene therapy has the potential to treat retinal degenerative diseases, but recent evidence of AAV-associated inflammation has raised concerns. This study characterizes the severity and distribution of AAV-induced inflammation in rats, testing five different AAV vectors and three different routes of ocular delivery. The results show that AAV2 and AAV6 induce the most inflammation, with AAV6 causing the highest levels when delivered suprachoroidally. AAV8 and AAV9 induce minimal inflammation. These findings highlight the importance of considering ocular inflammation when developing gene therapy strategies.
HUMAN GENE THERAPY
(2023)
Review
Endocrinology & Metabolism
Cameron Mitsch, Eirene Alexandrou, Andrew W. Norris, Catherina T. Pinnaro
Summary: Turner syndrome (TS) is a common chromosomal disorder resulting from the absence of the second sex chromosome. TS is frequently associated with hyperglycemia, which is linked to increased mortality. Despite being reported 60 years ago, the reasons for high prevalence of hyperglycemia in TS remain poorly understood. This review explores the physiological and genetic mechanisms underlying TS hyperglycemia and highlights the challenges in studying glucose metabolism and diagnosing hyperglycemia in TS population.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Medicine, Research & Experimental
Nathaniel K. Mullin, Andrew P. Voigt, Miles J. Flamme-Wiese, Xiuying Liu, Megan J. Riker, Katayoun Varzavand, Edwin M. Stone, Budd A. Tucker, Robert F. Mullins
Summary: Variants in the high copy number mitochondrial genome can disrupt organelle function and lead to severe multisystem disease. Heteroplasmy, the uneven distribution of abnormal mtDNA molecules in different cells and tissues, contributes to the wide range of manifestations observed in patients with mitochondrial disease. This study reveals the nonrandom nature of mitochondrial variant distribution in human mitochondrial disease, highlighting its importance for understanding pathogenesis and developing treatments.
Article
Computer Science, Information Systems
Yuetian Zhou, Fei Qi, Weiliang Xie
Summary: This paper proposes an evaluation method for predicting the spectrum needs of HIBS and predicts the capacity demand and spectral efficiency of HIBS in 2025. The results show that this method can effectively predict the spectrum needs of HIBS in various deployment scenarios.
Proceedings Paper
Computer Science, Information Systems
Xiao Li, Weiliang Xie, Chunlei Hu
Summary: This paper introduces the evolution of URLLC standard, analyzes key technologies for achieving URLLC, describes the integration of URLLC with TSN, and provides experimental verification in 5G applications.
2022 3RD INFORMATION COMMUNICATION TECHNOLOGIES CONFERENCE (ICTC 2022)
(2022)
Proceedings Paper
Computer Science, Information Systems
Pingping Lin, Chunlei Hu, Weiliang Xie, Jinyang Yu
Summary: This paper introduces the problem of insufficient uplink coverage in 5G and its solutions, including traditional uplink coverage enhancement techniques and super uplink techniques. Through the analysis of various schemes, it provides references for network construction.
2022 3RD INFORMATION COMMUNICATION TECHNOLOGIES CONFERENCE (ICTC 2022)
(2022)