18 Works

Using BART to Perform Pareto Optimization and Quantify its Uncertainties

Akira Horiguchi, Thomas J. Santner, Ying Sun & Matthew T. Pratola
Techniques to reduce the energy burden of an industrial ecosystem often require solving a multiobjective optimization problem. However, collecting experimental data can often be either expensive or time-consuming. In such cases, statistical methods can be helpful. This article proposes Pareto Front (PF) and Pareto Set (PS) estimation methods using Bayesian Additive Regression Trees (BART), which is a nonparametric model whose assumptions are typically less restrictive than popular alternatives, such as Gaussian Processes (GPs). These less...

Comprehensive analysis of PPPCs family reveals the clinical significance of PPP1CA and PPP4C in breast cancer

Wenjun Xie, Ying Sun, Yu Zeng, Linfei Hu, Jingtai Zhi, Hang Ling, Xiangqian Zheng, Xianhui Ruan & Ming Gao
The phosphoprotein phosphatase catalytic subunit (PPPCs) family has been shown to play an important role in the development and progression of various malignancies, but its expression patterns and biological functions in breast cancer (BC) remain unclear. Therefore, we aimed to investigate the clinical significance and biological functions of the PPPCs family to understand its possible significance in the diagnosis, prognosis and treatment of breast cancer. We comprehensively investigated the expression levels, diagnostic accuracy, prognostic outcomes,...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

Additional file 1 of Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Weichen Song, Wei Qian, Weidi Wang, Shunying Yu & Guan Ning Lin
Additional file 1. Summary statistics for all instrument variables after data harmonization.

Additional file 3 of Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Weichen Song, Wei Qian, Weidi Wang, Shunying Yu & Guan Ning Lin
Additional file 3. Full results for ROI-Disease association analysis.

Additional file 2 of Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Weichen Song, Wei Qian, Weidi Wang, Shunying Yu & Guan Ning Lin
Additional file 2. Full results for DTI-Disease association analysis.

Identification of fibronectin 1 (FN1) and complement component 3 (C3) as immune infiltration-related biomarkers for diabetic nephropathy using integrated bioinformatic analysis

Yuejun Wang, Mingming Zhao & Yu Zhang
Immune cell infiltration (ICI) plays a pivotal role in the development of diabetic nephropathy (DN). Evidence suggests that immune-related genes play an important role in the initiation of inflammation and the recruitment of immune cells. However, the underlying mechanisms and immune-related biomarkers in DN have not been elucidated. Therefore, this study aimed to explore immune-related biomarkers in DN and the underlying mechanisms using bioinformatic approaches. In this study, four DN glomerular datasets were downloaded, merged,...

Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p

Hongyan Wang, Xin Di, Yingjie Bi, Shidong Sun & Tao Wang
Although long non-coding RNA (LncRNA) LINC00649 is reported to be closely associated with acute myeloid leukemia (AML), prostate cancer and colorectal cancer, its role in regulating other types of cancer, such as gastric cancer (GC), has not been studied. This study analyzed the expression status of LINC00649 in GC tissues and cells by performing Real-Time qPCR analysis, and we found that LINC00649 tended to be enriched in cancerous tissues and cells but not in their...

Comprehensive analysis of PPPCs family reveals the clinical significance of PPP1CA and PPP4C in breast cancer

Wenjun Xie, Ying Sun, Yu Zeng, Linfei Hu, Jingtai Zhi, Hang Ling, Xiangqian Zheng, Xianhui Ruan & Ming Gao
The phosphoprotein phosphatase catalytic subunit (PPPCs) family has been shown to play an important role in the development and progression of various malignancies, but its expression patterns and biological functions in breast cancer (BC) remain unclear. Therefore, we aimed to investigate the clinical significance and biological functions of the PPPCs family to understand its possible significance in the diagnosis, prognosis and treatment of breast cancer. We comprehensively investigated the expression levels, diagnostic accuracy, prognostic outcomes,...

Quasispecies of SARS-CoV-2 revealed by single nucleotide polymorphisms (SNPs) analysis

Rongsui Gao, Wenhong Zu, Yang Liu, Junhua Li, Zeyao Li, Yanling Wen, Haiyan Wang, Jing Yuan, Lin Cheng, Shengyuan Zhang, Yu Zhang, Shuye Zhang, Weilong Liu, Xun Lan, Lei Liu, Feng Li & Zheng Zhang
New SARS-CoV-2 mutants have been continuously indentified with enhanced transmission ever since its outbreak in early 2020. As an RNA virus, SARS-CoV-2 has a high mutation rate due to the low fidelity of RNA polymerase. To study the single nucleotide polymorphisms (SNPs) dynamics of SARS-CoV-2, 158 SNPs with high confidence were identified by deep meta-transcriptomic sequencing, and the most common SNP type was C > T. Analyses of intra-host population diversity revealed that intra-host quasispecies’...

Long non-coding RNA LINC00649 regulates YES-associated protein 1 (YAP1)/Hippo pathway to accelerate gastric cancer (GC) progression via sequestering miR-16-5p

Hongyan Wang, Xin Di, Yingjie Bi, Shidong Sun & Tao Wang
Although long non-coding RNA (LncRNA) LINC00649 is reported to be closely associated with acute myeloid leukemia (AML), prostate cancer and colorectal cancer, its role in regulating other types of cancer, such as gastric cancer (GC), has not been studied. This study analyzed the expression status of LINC00649 in GC tissues and cells by performing Real-Time qPCR analysis, and we found that LINC00649 tended to be enriched in cancerous tissues and cells but not in their...

Additional file 1 of Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Weichen Song, Wei Qian, Weidi Wang, Shunying Yu & Guan Ning Lin
Additional file 1. Summary statistics for all instrument variables after data harmonization.

Additional file 3 of Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Weichen Song, Wei Qian, Weidi Wang, Shunying Yu & Guan Ning Lin
Additional file 3. Full results for ROI-Disease association analysis.

Additional file 2 of Mendelian randomization studies of brain MRI yield insights into the pathogenesis of neuropsychiatric disorders

Weichen Song, Wei Qian, Weidi Wang, Shunying Yu & Guan Ning Lin
Additional file 2. Full results for DTI-Disease association analysis.

Identification of fibronectin 1 (FN1) and complement component 3 (C3) as immune infiltration-related biomarkers for diabetic nephropathy using integrated bioinformatic analysis

Yuejun Wang, Mingming Zhao & Yu Zhang
Immune cell infiltration (ICI) plays a pivotal role in the development of diabetic nephropathy (DN). Evidence suggests that immune-related genes play an important role in the initiation of inflammation and the recruitment of immune cells. However, the underlying mechanisms and immune-related biomarkers in DN have not been elucidated. Therefore, this study aimed to explore immune-related biomarkers in DN and the underlying mechanisms using bioinformatic approaches. In this study, four DN glomerular datasets were downloaded, merged,...

S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in Fusarium graminearum

Dongya Shi, Yu Zhang, Jin Wang, Weichao Ren, Jie Zhang, Jane Ifunanya Mbadianya, Yuanye Zhu, Changjun Chen & Hongyu Ma
The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence,...

S-adenosyl-L-homocysteine hydrolase FgSah1 is required for fungal development and virulence in Fusarium graminearum

Dongya Shi, Yu Zhang, Jin Wang, Weichao Ren, Jie Zhang, Jane Ifunanya Mbadianya, Yuanye Zhu, Changjun Chen & Hongyu Ma
The S-adenosyl-L-homocysteine hydrolase (Sah1) plays a crucial role in methylation and lipid metabolism in yeast and mammals, yet its function remains elusive in filamentous fungi. In this study, we characterized Sah1 in the phytopathogenic fungus F. graminearum by generating knockout and knockout-complemented strains of FgSAH1. We found that the FgSah1-GFP fusion protein was localized to the cytoplasm, and that deletion of FgSAH1 resulted in defects in vegetative growth, asexual and sexual reproduction, stress responses, virulence,...

Using BART to Perform Pareto Optimization and Quantify its Uncertainties

Akira Horiguchi, Thomas J. Santner, Ying Sun & Matthew T. Pratola
Techniques to reduce the energy burden of an industrial ecosystem often require solving a multiobjective optimization problem. However, collecting experimental data can often be either expensive or time-consuming. In such cases, statistical methods can be helpful. This article proposes Pareto Front (PF) and Pareto Set (PS) estimation methods using Bayesian Additive Regression Trees (BART), which is a nonparametric model whose assumptions are typically less restrictive than popular alternatives, such as Gaussian Processes (GPs). These less...

Registration Year

  • 2021
    18

Resource Types

  • Dataset
    18

Affiliations

  • Shanghai Mental Health Center
    18
  • Shanghai Jiao Tong University
    13
  • Nanjing Medical University
    12
  • Sun Yat-sen University
    10
  • West China Hospital of Sichuan University
    10
  • Fudan University
    9
  • Capital Medical University
    9
  • Huazhong University of Science and Technology
    8
  • Shandong University
    8
  • First Affiliated Hospital of Zhengzhou University
    8