Bairong Shen

Bairong Shen
West China Hospital · Institutes for Systems Genetics

About

367
Publications
59,054
Reads
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6,487
Citations
Additional affiliations
July 2008 - present
Soochow University (PRC)
Position
  • Professor, Director
December 2005 - June 2009
Tongji University
Position
  • Professor (Full)
June 2000 - June 2008
Tampere University
Position
  • Pos-doc, assitant professor

Publications

Publications (367)
Preprint
BACKGROUND Background: The integration of large language models (LLMs) into medical education has demonstrated tremendous potential, with significant implications for learning and assessment. OBJECTIVE Objective: This study aims to present MedExamLLM, a comprehensive platform designed to systematically evaluate the performance of LLMs across a div...
Article
Menopause is an age-related change that persists for around one-third of a woman's life. Menopause increases the risk of metabolic illnesses such as diabetes, osteoporosis (OP), and nonalcoholic fatty liver disease (NAFLD). Immune mediators (pro-inflammatory cytokines), such as interleukin-1 (IL-1), IL-6, IL-17, transforming growth factor (TGF), an...
Article
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Triple negative breast cancer (TNBC) is most aggressive type of breast cancer with multiple invasive sub-types and leading cause of women’s death worldwide. Lack of estrogen receptor (ER), progesterone receptor (PR), and human epidermal growth factor receptor 2 (HER-2) causes it to spread rapidly making its treatment challenging due to unresponsive...
Article
As the world recovers from the COVID-19 pandemic, a resurgence in MPXV cases is causing serious concern. The early clinical similarity of MPXV to common ailments like the flu and cold, coupled with the resemblances of its progressing rash to other infections, underscores the importance of prompt and accurate diagnosis. Among the infections, smallpo...
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Background Academic paper writing holds significant importance in the education of medical students, and poses a clear challenge for those whose first language is not English. This study aims to investigate the effectiveness of employing large language models, particularly ChatGPT, in improving the English academic writing skills of these students....
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Introduction The global distribution and trends in the attributable burden of cataract risk have rarely been systematically explored. To guide the development of targeted and accurate cataract screening and treatment strategies, we analyzed the burden of cataract disease attributable to known risk factors. Method This study utilized detailed catar...
Article
As a prospective payment method, diagnosis-related groups (DRGs)’s implementation has varying effects on different regions and adopt different case classification systems. Our goal is to build a structured public online knowledgebase describing the worldwide practice of DRGs, which includes systematic indicators for DRGs’ performance assessment. Th...
Article
Background Warfarin is a common oral anticoagulant, and its effects vary widely among individuals. Numerous dose-prediction algorithms have been reported based on cross-sectional data generated via multiple linear regression or machine learning. This study aimed to construct an information fusion perturbation theory and machine learning prediction...
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Childhood obesity is a chronic inflammatory epidemic that affects children worldwide. Obesity affects approximately 1 in 5 children worldwide. Obesity in children can worsen weight gain and raise the risk of obesity-related comorbidities like diabetes and non-alcoholic fatty liver disease (NAFLD). It can also negatively impact the quality of life f...
Article
Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer (PCa), large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. A formal representation of PCa-associated knowledge will be e...
Article
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Background Robot-assisted radical prostatectomy (RARP) has emerged as a pivotal surgical intervention for the treatment of prostate cancer. However, the complexity of clinical cases, heterogeneity of prostate cancer, and limitations in physician expertise pose challenges to rational decision-making in RARP. To address these challenges, we aimed to...
Article
Background Punica granatum L. is well-known for its multifaceted therapeutic potential, including anti-inflammatory and immunomodulatory activities. Aim This study aimed to characterize an immunomodulatory compound isolated from Punica granatum L. using a bioactivity-guided approach. Methods Chromatographic techniques were adopted for isolation a...
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Background Large language models like ChatGPT have revolutionized the field of natural language processing with their capability to comprehend and generate textual content, showing great potential to play a role in medical education. This study aimed to quantitatively evaluate and comprehensively analysis the performance of ChatGPT on three types o...
Article
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The common loci represent a distinct set of the human genome sites that harbor genetic variants found in at least 1% of the population. Small somatic mutations occur at the common loci and non-common loci, i.e. csmVariants and ncsmVariants, are presumed with similar probabilities. However, our work revealed that within the coding region, common loc...
Preprint
BACKGROUND Infertility is a significant negative factor affecting societal population growth and economic stability, with male infertility being a major cause of infertility. In recent years, with the development and advancement of next-generation sequencing technologies and high-resolution mass spectrometry, the volume of male infertility-related...
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Prostate cancer is the most common cancer in men worldwide and has a high mortality rate. The complex and heterogeneous development of prostate cancer has become a core obstacle in the treatment of prostate cancer. Simultaneously, the issues of overtreatment in early-stage diagnosis, oligometastasis and dormant tumor recognition, as well as persona...
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The rapidly evolving landscape of biomarkers for colorectal cancer (CRC) necessitates an integrative, updated repository. In response, we constructed the Colorectal Cancer Biomarker Database (CBD), which collected and displayed the curated biomedicine information for 870 CRC biomarkers in the previous study. Building on CBD, we have now developed C...
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Myocardial infarction (MI) is a prevalent cardiovascular disease characterized by myocardial necrosis resulting from coronary artery ischemia and hypoxia, which can lead to severe complications such as arrhythmia, cardiac rupture, heart failure, and sudden death. Despite being a research hotspot, the etiological mechanism of MI remains unclear. The...
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Background Nipah virus (Genus Henipavirus) was first detected in 1999, during the Malaysia-Singapore outbreak, and is an emerging bat-borne pathogen. It causes rare but fatal disease, with a 40-75% fatality rate, and clinically ranging from asymptomatic infection to fatal encephalitis. Methods Publicly available literature, including preclinical a...
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Cancer is a leading cause of mortality worldwide, and conventional cancer therapies such as chemotherapy and radiotherapy often result in undesirable and adverse effects. Natural products have emerged as a promising alternative for cancer treatment, with comparatively fewer side effects reported. Opuntia ficus-indica (L.) Mill., a member of the Cac...
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Captive pandas are suffering from intestinal infection due to intestinal microbiota characterized by a high abundance of Enterobacteriaceae induced by long-term captivity. Probiotic supplements showed improvement in intestinal barrier function and inflammation. However, the effects of panda-derived probiotics on the intestinal epithelium and inflam...
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Background Deep learning methods are increasingly applied in the medical field; however, their lack of interpretability remains a challenge. Captum is a tool that can be used to interpret neural network models by computing feature importance weights. Although Captum is an interpretable model, it is rarely used to study medical problems, and there i...
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Background and objectives: Due to the high individual variability of anticoagulant warfarin, this study aimed to investigate the effects of vitamin K concentration and gut microbiota on individual variability of warfarin in 246 cardiac surgery patients. Methods: The pharmacokinetics and pharmacodynamics (PKPD) model predicted INR and warfarin co...
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Background: Large language models like ChatGPT have revolutionized the field of natural language processing with their capability to comprehend and generate textual content, showing great potential to play a role in medical education. Objective: This study aimed to quantitatively evaluate the performance of ChatGPT on three types of national medica...
Preprint
BACKGROUND Bisphenol A, S and F (BPA,BPS and BPF) are endocrine disruptors. These bisphenols will cause metabolic disorders and impact on body composition. Therefore, to determine the effect of bisphenols on body composition, we aimed to assess it. OBJECTIVE Our study included and analyzed data from seven NHANES survey cycles (200-2016). Finally,...
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With the rapid development of human intestinal microbiology and diverse microbiome-related studies and investigations, a large amount of data have been generated and accumulated. Meanwhile, different computational and bioinformatics models have been developed for pattern recognition and knowledge discovery using these data. Given the heterogeneity...
Article
The number of preclinical and clinical studies evaluating natural products-based management of dementia has gradually increased, with an exponential rise in 2020 and 2021. Keeping this in mind, we examined current trends from 2016 to 2021 in order to assess the growth potential of natural products in the treatment of dementia. Publicly available li...
Chapter
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Despite targeted therapies, such as an arsenal of antibiotics, sepsis therapy remains a global concern. Besides their ineptness in addressing sepsis-related inflammation in patients, antibiotic overuse promotes the rise of multidrug-resistant microbes. The herbal formulations that contain bioactive are all-important in the traditional system of med...
Article
Background: Myocardial infarction (MI) is a major contributor to global mortality, and microRNAs (miRNAs) are important in its pathogenesis. Identifying blood miRNAs with clinical application potential for the early detection and treatment of MI is crucial. Methods: We obtained MI-related miRNA and miRNA microarray datasets from MI Knowledge Bas...
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Adipose tissue develops lipids, aberrant adipokines, chemokines, and pro-inflammatory cytokines as a consequence of the low-grade systemic inflammation that characterizes obesity. This low-grade systemic inflammation can lead to insulin resistance (IR) and metabolic complications, such as type 2 diabetes (T2D) and nonalcoholic fatty liver disease (...
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Background and aims Surgical site infection is a common complication after surgery. Periprocedural antibiotics are necessary to prescribe for preventing or treating infections. The present study aimed to explore the effect of intravenous antibiotics on gut microbiota and menaquinone biosynthesis in patients, especially in elderly patients undergoin...
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Non-small cell lung cancer (NSCLC) is the most common type of lung cancer and the leading cause of cancer-related deaths worldwide. Identification of gene biomarkers and their regulatory factors and signaling pathways is very essential to reveal the molecular mechanisms of NSCLC initiation and progression. Thus, the goal of this study is to identif...
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Trikatu Churna (TC) comprising Zingiber officinale rhizome, Piper longum, and Piper nigrum fruit, is effective in treating liver diseases and has high nutraceutical values. However, the efficacy of TC in treating alcoholic liver disease (ALD) and its mechanism remain largely unknown. This study evaluated the hepatoprotective effects of different do...
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Ovarian cancer, and particularly its most frequent type, epithelial ovarian carcinoma, constitutes one of the most dangerous malignant tumors among females. Substantial evidence has described the potential of phytochemicals against ovarian cancer. The effect of natural compounds on endoplasmic reticulum (ER) stress is of great relevance in this reg...
Article
Background Endometrial carcinoma is the sixth most common cancer in women worldwide. Importantly, endometrial cancer is among the few types of cancers with patient mortality that is still increasing, which indicates that the improvement in its diagnosis and treatment is still urgent. Moreover, biomarker discovery is essential for precise classifica...
Article
Cancer therapy resistance and recurrence (CTRR) are the dominant causes of death in cancer patients. Recent studies have indicated that non-coding RNAs (ncRNAs) can not only reverse the resistance to cancer therapy but also are crucial biomarkers for the evaluation and prediction of CTRR. Herein, we developed CTRR-ncRNA, a knowledgebase of CTRR-ass...
Chapter
Crateva adansonii has a wide range of medicinal properties and is an important part of traditional folk medicine. The leaves and bark are used to treat joint discomfort, ear and toothaches, eye infection, asthma, rheumatoid arthritis, and epilepsy. Other important uses of this plant have also been investigated by folklore medicine. Inflammation, ut...
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Background: Bergenin, 4-O-methyl gallic acid glucoside, is a bioactive compound found in the cortex of Mallotus japonicus (L.f.) Müll.Arg. along with many other natural resources including that from Bergenia species. The present study delineates the neuroprotective potential of bergenin through the modulation of PPAR-γ receptors. Method: Dementia w...
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Background: Crowdsourcing is a low-cost, adaptable, and innovative method to collect ideas from numerous contributors with diverse backgrounds. Crowdsourcing from social media like Twitter can be used for generating ideas in a noticeably brief time based on contributions from globally distributed users. The world has been challenged by the COVID-19...
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Background The easy accessibility of smartphones and internet connections enables people to stay virtually connected to communities via social media. However, social media is also being explored for health care education and dissemination of health-related information. Twitter (Twitter, Inc., San Francisco, California) is one of the popular social...
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Since 2020, we are witnessing a COVID-19 pandemic that has ruled out all other pandemics ever happened in our history. Countries are still not be able to manage the COVID-19 threat properly, and while we are still dealing with it, here comes another deadlyinfectious disease, monkeypox. Rapid circulation of monkeypox infections worldwide has forced...
Preprint
Full-text available
Cancer therapy resistance and recurrence (CTRR) are the dominant causes of death in cancer patients. Recent studies have indicated that non-coding RNAs (ncRNAs) can not only reverse the resistance to cancer therapy but also are crucial biomarkers for the evaluation and prediction of CTRR. Herein, we developed CTRR-ncRNA, a knowledgebase of CTRR-ass...
Article
Full-text available
While frailty corresponds to a multisystem failure, geriatric assessment can recognize multiple pathophysiological lesions and age changes. Up to now, a few frailty indexes have been introduced, presenting definitions of psychological problems, dysregulations in nutritional intake, behavioral abnormalities, and daily functions, genetic, environment...
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Gastrointestinal cancers (GICs) are high-incidence malignant tumors that seriously threaten human health around the world. Their complexity and heterogeneity make the classic staging system insufficient to guide patient management. Recently, competing endogenous RNA (ceRNA) interactions that closely link the function of protein-coding RNAs with tha...
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Breast cancer (BC) is the most prevalent neoplasm among women. Genetic and environmental factors lead to BC development and on this basis, several preventive – screening and therapeutic interventions have been developed. Hormones, both in the form of endogenous hormonal signaling or hormonal contraceptives, play an important role in BC pathogenesis...
Article
Background CD93 is newly reported to normalize vasculature and attenuate pancreatic cancer therapy response, but its role in bladder cancer (BLCA) is unknown. Method The immunologic role of CD93 is analyzed across TCGA pan-cancers. The correlation between CD93 and BLCA clinical and tumor microenvironment features, predicted immunotherapy pathways,...
Chapter
The host immune system recognizes and responds to the selective antigens or epitopes (immunome) of the intruding pathogen over an entire organism. The immune response so generated is ample to confer the desired immunity and protection to the host. This led to the conception of immunome-derived vaccines that exploit selective genome-derived antigens...
Chapter
Virus infection is a common social health issue. In the past decades, serious virus infectious events have caused great loss in people's life and the economics. The nature of rapid widespread and frequent variation increases the difficulty for precision viral prevention and treatment. In the era of big data and artificial intelligence (AI), advance...
Chapter
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Viral infections have remained a serious public health burden despite significant improvements in medical and pharmaceutical research in recent years. In silico approaches for drug discovery and design are fruitful for the management of a plethora of viral diseases. Virtual screening of libraries is performed using various computational tools to se...
Preprint
BACKGROUND Disease ontologies facilitate the semantic organization and representation of domain-specific knowledge. In the case of prostate cancer, large volumes of research results and clinical data have been accumulated and needed to be standardized for sharing and translational researches. OBJECTIVE A formal representation of prostate cancer (P...
Article
Full-text available
Ethnopharmacological relevance: The genus Alternanthera (Amaranthaceae) comprises 139 species including 14 species used traditionally for the treatment of various ailments such as hypertension, pain, inflammation, diabetes, cancer, microbial and mental disorders. Aim of the review: To search research gaps through critical assessment of pharmacologi...
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Endometrial cancer (EC) is the sixth most prevalent type of cancer among women. Kinases, enzymes mediating the transfer of adenosine triphosphate (ATP) in several signaling pathways, play a significant role in carcinogenesis and cancer cells’ survival and proliferation. Cyclin-dependent kinases (CDKs) are involved in EC pathogenesis; therefore, CDK...
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Background Personal lifestyle is an important cause of prostate cancer (PCa), hence establishing a corresponding knowledge graph (KG) and a chatbot is a convenient way for preventing and assessing risks. The chatbot based on a KG of PCa-associated lifestyles will be helpful to PCa management, then save health care resources in the ageing society....
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We are an international group of biological scientists, conservationists, and environmentalists who have been closely following the plight and conservation of pangolins over a number of years. Pangolins comprise the mammalian Order Pholidota, which contains eight living species found in diverse habitats in Africa (4 species) and Asia (4 species), w...
Article
With the increasing demand for low-cost high-throughput sequencing of large genomes, next-generation sequencing (NGS) technology has developed rapidly. NGS can not only be used in basic scientific research but also in clinical diagnostics and healthcare. Numerous software systems and tools have been developed to analyze NGS data, and various data f...