NobleBlocks

Southern Medical University

UniversityGuangzhou, China

Research output, citation impact, and the most-cited recent papers from Southern Medical University (China). Aggregated across the NobleBlocks index of 300M+ scholarly works.

Total works
88.1K
Citations
6.3M
h-index
496
i10-index
126.8K
Also known as
First Military Medical UniversitySouthern Medical University南方医科大学

Top-cited papers from Southern Medical University

clusterProfiler 4.0: A universal enrichment tool for interpreting omics data
Tianzhi Wu, Erqiang Hu, Shuangbin Xu, Meijun Chen +4 more
2021· The Innovation12.9Kdoi:10.1016/j.xinn.2021.100141

Functional enrichment analysis is pivotal for interpreting high-throughput omics data in life science. It is crucial for this type of tool to use the latest annotation databases for as many organisms as possible. To meet these requirements, we present here an updated version of our popular Bioconductor package, clusterProfiler 4.0. This package has been enhanced considerably compared with its original version published 9 years ago. The new version provides a universal interface for functional enrichment analysis in thousands of organisms based on internally supported ontologies and pathways as well as annotation data provided by users or derived from online databases. It also extends the dplyr and ggplot2 packages to offer tidy interfaces for data operation and visualization. Other new features include gene set enrichment analysis and comparison of enrichment results from multiple gene lists. We anticipate that clusterProfiler 4.0 will be applied to a wide range of scenarios across diverse organisms.

Minimal information for studies of extracellular vesicles 2018 (MISEV2018): a position statement of the International Society for Extracellular Vesicles and update of the MISEV2014 guidelines
Clotilde Théry, Kenneth W. Witwer, Elena Aïkawa, María José Alcaraz +4 more
2018· Journal of Extracellular Vesicles11.3Kdoi:10.1080/20013078.2018.1535750

The last decade has seen a sharp increase in the number of scientific publications describing physiological and pathological functions of extracellular vesicles (EVs), a collective term covering various subtypes of cell-released, membranous structures, called exosomes, microvesicles, microparticles, ectosomes, oncosomes, apoptotic bodies, and many other names. However, specific issues arise when working with these entities, whose size and amount often make them difficult to obtain as relatively pure preparations, and to characterize properly. The International Society for Extracellular Vesicles (ISEV) proposed Minimal Information for Studies of Extracellular Vesicles ("MISEV") guidelines for the field in 2014. We now update these "MISEV2014" guidelines based on evolution of the collective knowledge in the last four years. An important point to consider is that ascribing a specific function to EVs in general, or to subtypes of EVs, requires reporting of specific information beyond mere description of function in a crude, potentially contaminated, and heterogeneous preparation. For example, claims that exosomes are endowed with exquisite and specific activities remain difficult to support experimentally, given our still limited knowledge of their specific molecular machineries of biogenesis and release, as compared with other biophysically similar EVs. The MISEV2018 guidelines include tables and outlines of suggested protocols and steps to follow to document specific EV-associated functional activities. Finally, a checklist is provided with summaries of key points.

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)
Daniel J. Klionsky, Kotb Abdelmohsen, Akihisa Abe, Md. Joynal Abedin +4 more
2016· Autophagy6.0Kdoi:10.1080/15548627.2015.1100356

In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. For example, a key point that needs to be emphasized is thatthere is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process versus those that measure flux through the autophagy pathway (i.e., the completeprocess including the amount and rate of cargo sequestered and degraded). In particular, a block in macroautophagy that results in autophagosome accumulation must be differentiated from stimuli that increase autophagic activity, defined as increasedautophagy induction coupled with increased delivery to, and degradation within, lysosomes (inmost higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in manycases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. It is worth emphasizing here that lysosomal digestion is a stage of autophagy and evaluating its competence is a crucial part of the evaluation of autophagic flux, or complete autophagy. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as forreviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multipleassays to monitor autophagy. Along these lines, because of the potential for pleiotropic effects due to blocking autophagy through genetic manipulation, it is imperative to target by gene knockout or RNA interference more than one autophagyrelated protein. In addition, some individual Atg proteins, or groups of proteins, are involved in other cellular pathways implying that not all Atg proteins can be used as a specific marker for an autophagic process. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular assays, we hope to encourage technical innovation in the field.

Dapagliflozin in Patients with Chronic Kidney Disease
Hiddo J.L. Heerspink, Bergur V. Stefánsson, Ricardo Correa‐Rotter, Glenn M. Chertow +4 more
2020· New England Journal of Medicine5.3Kdoi:10.1056/nejmoa2024816

BACKGROUND: Patients with chronic kidney disease have a high risk of adverse kidney and cardiovascular outcomes. The effect of dapagliflozin in patients with chronic kidney disease, with or without type 2 diabetes, is not known. METHODS: of body-surface area and a urinary albumin-to-creatinine ratio (with albumin measured in milligrams and creatinine measured in grams) of 200 to 5000 to receive dapagliflozin (10 mg once daily) or placebo. The primary outcome was a composite of a sustained decline in the estimated GFR of at least 50%, end-stage kidney disease, or death from renal or cardiovascular causes. RESULTS: The independent data monitoring committee recommended stopping the trial because of efficacy. Over a median of 2.4 years, a primary outcome event occurred in 197 of 2152 participants (9.2%) in the dapagliflozin group and 312 of 2152 participants (14.5%) in the placebo group (hazard ratio, 0.61; 95% confidence interval [CI], 0.51 to 0.72; P<0.001; number needed to treat to prevent one primary outcome event, 19 [95% CI, 15 to 27]). The hazard ratio for the composite of a sustained decline in the estimated GFR of at least 50%, end-stage kidney disease, or death from renal causes was 0.56 (95% CI, 0.45 to 0.68; P<0.001), and the hazard ratio for the composite of death from cardiovascular causes or hospitalization for heart failure was 0.71 (95% CI, 0.55 to 0.92; P = 0.009). Death occurred in 101 participants (4.7%) in the dapagliflozin group and 146 participants (6.8%) in the placebo group (hazard ratio, 0.69; 95% CI, 0.53 to 0.88; P = 0.004). The effects of dapagliflozin were similar in participants with type 2 diabetes and in those without type 2 diabetes. The known safety profile of dapagliflozin was confirmed. CONCLUSIONS: Among patients with chronic kidney disease, regardless of the presence or absence of diabetes, the risk of a composite of a sustained decline in the estimated GFR of at least 50%, end-stage kidney disease, or death from renal or cardiovascular causes was significantly lower with dapagliflozin than with placebo. (Funded by AstraZeneca; DAPA-CKD ClinicalTrials.gov number, NCT03036150.).

The antimicrobial activity of nanoparticles: present situation and prospects for the future
Linlin Wang, Hu Chen, Longquan Shao
2017· International Journal of Nanomedicine4.0Kdoi:10.2147/ijn.s121956

Nanoparticles (NPs) are increasingly used to target bacteria as an alternative to antibiotics. Nanotechnology may be particularly advantageous in treating bacterial infections. Examples include the utilization of NPs in antibacterial coatings for implantable devices and medicinal materials to prevent infection and promote wound healing, in antibiotic delivery systems to treat disease, in bacterial detection systems to generate microbial diagnostics, and in antibacterial vaccines to control bacterial infections. The antibacterial mechanisms of NPs are poorly understood, but the currently accepted mechanisms include oxidative stress induction, metal ion release, and non-oxidative mechanisms. The multiple simultaneous mechanisms of action against microbes would require multiple simultaneous gene mutations in the same bacterial cell for antibacterial resistance to develop; therefore, it is difficult for bacterial cells to become resistant to NPs. In this review, we discuss the antibacterial mechanisms of NPs against bacteria and the factors that are involved. The limitations of current research are also discussed.

Minimal information for studies of extracellular vesicles (MISEV2023): From basic to advanced approaches
Joshua A Welsh, Deborah C. I. Goberdhan, Lorraine O’Driscoll, Edit I. Buzás +4 more
2024· Journal of Extracellular Vesicles3.8Kdoi:10.1002/jev2.12404

Extracellular vesicles (EVs), through their complex cargo, can reflect the state of their cell of origin and change the functions and phenotypes of other cells. These features indicate strong biomarker and therapeutic potential and have generated broad interest, as evidenced by the steady year-on-year increase in the numbers of scientific publications about EVs. Important advances have been made in EV metrology and in understanding and applying EV biology. However, hurdles remain to realising the potential of EVs in domains ranging from basic biology to clinical applications due to challenges in EV nomenclature, separation from non-vesicular extracellular particles, characterisation and functional studies. To address the challenges and opportunities in this rapidly evolving field, the International Society for Extracellular Vesicles (ISEV) updates its 'Minimal Information for Studies of Extracellular Vesicles', which was first published in 2014 and then in 2018 as MISEV2014 and MISEV2018, respectively. The goal of the current document, MISEV2023, is to provide researchers with an updated snapshot of available approaches and their advantages and limitations for production, separation and characterisation of EVs from multiple sources, including cell culture, body fluids and solid tissues. In addition to presenting the latest state of the art in basic principles of EV research, this document also covers advanced techniques and approaches that are currently expanding the boundaries of the field. MISEV2023 also includes new sections on EV release and uptake and a brief discussion of in vivo approaches to study EVs. Compiling feedback from ISEV expert task forces and more than 1000 researchers, this document conveys the current state of EV research to facilitate robust scientific discoveries and move the field forward even more rapidly.

Comorbidity and its impact on 1590 patients with COVID-19 in China: a nationwide analysis
Wei-Jie Guan, Wenhua Liang, Yi Zhao, Heng-rui Liang +4 more
2020· European Respiratory Journal3.8Kdoi:10.1183/13993003.00547-2020

BACKGROUND: The coronavirus disease 2019 (COVID-19) outbreak is evolving rapidly worldwide. OBJECTIVE: To evaluate the risk of serious adverse outcomes in patients with COVID-19 by stratifying the comorbidity status. METHODS: We analysed data from 1590 laboratory confirmed hospitalised patients from 575 hospitals in 31 provinces/autonomous regions/provincial municipalities across mainland China between 11 December 2019 and 31 January 2020. We analysed the composite end-points, which consisted of admission to an intensive care unit, invasive ventilation or death. The risk of reaching the composite end-points was compared according to the presence and number of comorbidities. RESULTS: The mean age was 48.9 years and 686 (42.7%) patients were female. Severe cases accounted for 16.0% of the study population. 131 (8.2%) patients reached the composite end-points. 399 (25.1%) reported having at least one comorbidity. The most prevalent comorbidity was hypertension (16.9%), followed by diabetes (8.2%). 130 (8.2%) patients reported having two or more comorbidities. After adjusting for age and smoking status, COPD (HR (95% CI) 2.681 (1.424-5.048)), diabetes (1.59 (1.03-2.45)), hypertension (1.58 (1.07-2.32)) and malignancy (3.50 (1.60-7.64)) were risk factors of reaching the composite end-points. The hazard ratio (95% CI) was 1.79 (1.16-2.77) among patients with at least one comorbidity and 2.59 (1.61-4.17) among patients with two or more comorbidities. CONCLUSION: Among laboratory confirmed cases of COVID-19, patients with any comorbidity yielded poorer clinical outcomes than those without. A greater number of comorbidities also correlated with poorer clinical outcomes.

Guidelines for the use and interpretation of assays for monitoring autophagy (4th edition)<sup>1</sup>
Daniel J. Klionsky, Amal Kamal Abdel‐Aziz, Sara Abdelfatah, Mahmoud Abdellatif +4 more
2021· Autophagy2.7Kdoi:10.1080/15548627.2020.1797280

autophagic responses. Here, we critically discuss current methods of assessing autophagy and the information they can, or cannot, provide. Our ultimate goal is to encourage intellectual and technical innovation in the field.

Expanded encyclopaedias of DNA elements in the human and mouse genomes
Federico Abascal, Reyes Acosta, Nicholas J. Addleman, Jessika Adrian +4 more
2020· Nature2.6Kdoi:10.1038/s41586-020-2493-4

Abstract The human and mouse genomes contain instructions that specify RNAs and proteins and govern the timing, magnitude, and cellular context of their production. To better delineate these elements, phase III of the Encyclopedia of DNA Elements (ENCODE) Project has expanded analysis of the cell and tissue repertoires of RNA transcription, chromatin structure and modification, DNA methylation, chromatin looping, and occupancy by transcription factors and RNA-binding proteins. Here we summarize these efforts, which have produced 5,992 new experimental datasets, including systematic determinations across mouse fetal development. All data are available through the ENCODE data portal ( https://www.encodeproject.org ), including phase II ENCODE 1 and Roadmap Epigenomics 2 data. We have developed a registry of 926,535 human and 339,815 mouse candidate cis -regulatory elements, covering 7.9 and 3.4% of their respective genomes, by integrating selected datatypes associated with gene regulation, and constructed a web-based server (SCREEN; http://screen.encodeproject.org ) to provide flexible, user-defined access to this resource. Collectively, the ENCODE data and registry provide an expansive resource for the scientific community to build a better understanding of the organization and function of the human and mouse genomes.

Treatment Strategies for Acute Ischemic Stroke Caused by Carotid Artery Occlusion
Wei Li, Qin Yin, Gelin Xu, Xinfeng Liu
2016· Interventional Neurology2.3Kdoi:10.1159/000445304

Acute ischemic stroke caused by internal carotid artery (ICA) occlusion usually has a poor prognosis, especially the T occlusion cases without functional collaterals. The efficacy of intravenous (IV) or intra-arterial (IA) thrombolysis with recombinant tissue plasminogen activator (rt-PA) remains ambiguous in these patients. Eendovascular recanalization of the occluded carotid has been attempted in recent years as a potential strategy. However, the different etiologies of ICA occlusion pose a significant challenge to neurointerventionists. Recently, several endovascular evolvements have been reported in treating carotid occlusion-related stroke. This review summarizes the current status of treatment for acute ICA occlusion.

Coronavirus infections and immune responses
Geng Li, Yaohua Fan, Yanni Lai, Tiantian Han +4 more
2020· Journal of Medical Virology2.0Kdoi:10.1002/jmv.25685

Coronaviruses (CoVs) are by far the largest group of known positive-sense RNA viruses having an extensive range of natural hosts. In the past few decades, newly evolved Coronaviruses have posed a global threat to public health. The immune response is essential to control and eliminate CoV infections, however, maladjusted immune responses may result in immunopathology and impaired pulmonary gas exchange. Gaining a deeper understanding of the interaction between Coronaviruses and the innate immune systems of the hosts may shed light on the development and persistence of inflammation in the lungs and hopefully can reduce the risk of lung inflammation caused by CoVs. In this review, we provide an update on CoV infections and relevant diseases, particularly the host defense against CoV-induced inflammation of lung tissue, as well as the role of the innate immune system in the pathogenesis and clinical treatment.

Development and Validation of a Radiomics Nomogram for Preoperative Prediction of Lymph Node Metastasis in Colorectal Cancer
Yanqi Huang, Changhong Liang, Lan He, Jie Tian +4 more
2016· Journal of Clinical Oncology1.9Kdoi:10.1200/jco.2015.65.9128

PURPOSE: To develop and validate a radiomics nomogram for preoperative prediction of lymph node (LN) metastasis in patients with colorectal cancer (CRC). PATIENTS AND METHODS: The prediction model was developed in a primary cohort that consisted of 326 patients with clinicopathologically confirmed CRC, and data was gathered from January 2007 to April 2010. Radiomic features were extracted from portal venous-phase computed tomography (CT) of CRC. Lasso regression model was used for data dimension reduction, feature selection, and radiomics signature building. Multivariable logistic regression analysis was used to develop the predicting model, we incorporated the radiomics signature, CT-reported LN status, and independent clinicopathologic risk factors, and this was presented with a radiomics nomogram. The performance of the nomogram was assessed with respect to its calibration, discrimination, and clinical usefulness. Internal validation was assessed. An independent validation cohort contained 200 consecutive patients from May 2010 to December 2011. RESULTS: The radiomics signature, which consisted of 24 selected features, was significantly associated with LN status (P < .001 for both primary and validation cohorts). Predictors contained in the individualized prediction nomogram included the radiomics signature, CT-reported LN status, and carcinoembryonic antigen level. Addition of histologic grade to the nomogram failed to show incremental prognostic value. The model showed good discrimination, with a C-index of 0.736 (C-index, 0.759 and 0.766 through internal validation), and good calibration. Application of the nomogram in the validation cohort still gave good discrimination (C-index, 0.778 [95% CI, 0.769 to 0.787]) and good calibration. Decision curve analysis demonstrated that the radiomics nomogram was clinically useful. CONCLUSION: This study presents a radiomics nomogram that incorporates the radiomics signature, CT-reported LN status, and clinical risk factors, which can be conveniently used to facilitate the preoperative individualized prediction of LN metastasis in patients with CRC.

Using ggtree to Visualize Data on Tree‐Like Structures
Guangchuang Yu
2020· Current Protocols in Bioinformatics1.6Kdoi:10.1002/cpbi.96

Ggtree is an R/Bioconductor package for visualizing tree-like structures and associated data. After 5 years of continual development, ggtree has been evolved as a package suite that contains treeio for tree data input and output, tidytree for tree data manipulation, and ggtree for tree data visualization. Ggtree was originally designed to work with phylogenetic trees, and has been expanded to support other tree-like structures, which extends the application of ggtree to present tree data in other disciplines. This article contains five basic protocols describing how to visualize trees using the grammar of graphics syntax, how to visualize hierarchical clustering results with associated data, how to estimate bootstrap values and visualize the values on the tree, how to estimate continuous and discrete ancestral traits and visualize ancestral states on the tree, and how to visualize a multiple sequence alignment with a phylogenetic tree. The ggtree package is freely available at https://www.bioconductor.org/packages/ggtree. © 2020 by John Wiley & Sons, Inc. Basic Protocol 1: Using grammar of graphics for visualizing trees Basic Protocol 2: Visualizing hierarchical clustering using ggtree Basic Protocol 3: Visualizing bootstrap values as symbolic points Basic Protocol 4: Visualizing ancestral status Basic Protocol 5: Visualizing a multiple sequence alignment with a phylogenetic tree.

Clinical characteristics of 2019 novel coronavirus infection in China
Wei‐jie Guan, Zhengyi Ni, Yu Hu, Wenhua Liang +4 more
2020· medRxiv1.5Kdoi:10.1101/2020.02.06.20020974

Abstract Background Since December 2019, acute respiratory disease (ARD) due to 2019 novel coronavirus (2019-nCoV) emerged in Wuhan city and rapidly spread throughout China. We sought to delineate the clinical characteristics of these cases. Methods We extracted the data on 1,099 patients with laboratory-confirmed 2019-nCoV ARD from 552 hospitals in 31 provinces/provincial municipalities through January 29 th , 2020. Results The median age was 47.0 years, and 41.90% were females. Only 1.18% of patients had a direct contact with wildlife, whereas 31.30% had been to Wuhan and 71.80% had contacted with people from Wuhan. Fever (87.9%) and cough (67.7%) were the most common symptoms. Diarrhea is uncommon. The median incubation period was 3.0 days (range, 0 to 24.0 days). On admission, ground-glass opacity was the typical radiological finding on chest computed tomography (50.00%). Significantly more severe cases were diagnosed by symptoms plus reverse-transcriptase polymerase-chain-reaction without abnormal radiological findings than non-severe cases (23.87% vs. 5.20%, P &lt;0.001). Lymphopenia was observed in 82.1% of patients. 55 patients (5.00%) were admitted to intensive care unit and 15 (1.36%) succumbed. Severe pneumonia was independently associated with either the admission to intensive care unit, mechanical ventilation, or death in multivariate competing-risk model (sub-distribution hazards ratio, 9.80; 95% confidence interval, 4.06 to 23.67). Conclusions The 2019-nCoV epidemic spreads rapidly by human-to-human transmission. Normal radiologic findings are present among some patients with 2019-nCoV infection. The disease severity (including oxygen saturation, respiratory rate, blood leukocyte/lymphocyte count and chest X-ray/CT manifestations) predict poor clinical outcomes.

Inhibition of SARS-CoV-2 (previously 2019-nCoV) infection by a highly potent pan-coronavirus fusion inhibitor targeting its spike protein that harbors a high capacity to mediate membrane fusion
Shuai Xia, Meiqin Liu, Chao Wang, Wei Xu +4 more
2020· Cell Research1.4Kdoi:10.1038/s41422-020-0305-x

The recent outbreak of coronavirus disease (COVID-19) caused by SARS-CoV-2 infection in Wuhan, China has posed a serious threat to global public health. To develop specific anti-coronavirus therapeutics and prophylactics, the molecular mechanism that underlies viral infection must first be defined. Therefore, we herein established a SARS-CoV-2 spike (S) protein-mediated cell-cell fusion assay and found that SARS-CoV-2 showed a superior plasma membrane fusion capacity compared to that of SARS-CoV. We solved the X-ray crystal structure of six-helical bundle (6-HB) core of the HR1 and HR2 domains in the SARS-CoV-2 S protein S2 subunit, revealing that several mutated amino acid residues in the HR1 domain may be associated with enhanced interactions with the HR2 domain. We previously developed a pan-coronavirus fusion inhibitor, EK1, which targeted the HR1 domain and could inhibit infection by divergent human coronaviruses tested, including SARS-CoV and MERS-CoV. Here we generated a series of lipopeptides derived from EK1 and found that EK1C4 was the most potent fusion inhibitor against SARS-CoV-2 S protein-mediated membrane fusion and pseudovirus infection with IC50s of 1.3 and 15.8 nM, about 241- and 149-fold more potent than the original EK1 peptide, respectively. EK1C4 was also highly effective against membrane fusion and infection of other human coronavirus pseudoviruses tested, including SARS-CoV and MERS-CoV, as well as SARSr-CoVs, and potently inhibited the replication of 5 live human coronaviruses examined, including SARS-CoV-2. Intranasal application of EK1C4 before or after challenge with HCoV-OC43 protected mice from infection, suggesting that EK1C4 could be used for prevention and treatment of infection by the currently circulating SARS-CoV-2 and other emerging SARSr-CoVs.

A Prospective Randomized Trial Comparing Percutaneous Local Ablative Therapy and Partial Hepatectomy for Small Hepatocellular Carcinoma
Min-Shan Chen, Jin-Qing Li, Yun Zheng, Rong Guo +4 more
2006· Annals of Surgery1.4Kdoi:10.1097/01.sla.0000201480.65519.b8

In Brief Objective: To compare the results of percutaneous local ablative therapy (PLAT) with surgical resection in the treatment of solitary and small hepatocellular carcinoma (HCC). Summary Background Data: PLAT is effective in small HCC. Whether it is as effective as surgical resection in the long-term survivals remains unknown. Methods: We conducted a prospective randomized trial on 180 patients with a solitary HCC ≦5 cm to receive either PLAT or surgical resection. The patients were regularly followed up after treatment with physical examination, blood, and radiologic tests. Results: Of the 90 patients who were randomized to PLAT, only 71 received PLAT because 19 withdrew their consent. Of the 90 patients who were randomized to surgical resection, a single Couinaud liver segment resection was carried out in 69 patients, 2 segments in 16 patients, and 3 or more segments in 3 patients. Ethanol injection was given during open surgery in 2 patients. Only 1 patient died after surgical resection within the same hospital admission. Posttreatment complications were more often and severe after surgery than PLAT. The 1-, 2-, 3-, and 4-year overall survival rates after PLAT and surgery were 95.8%, 82.1%, 71.4%, 67.9% and 93.3%, 82.3%, 73.4%, 64.0%, respectively. The corresponding disease-free survival rates were 85.9%, 69.3%, 64.1%, 46.4% and 86.6%, 76.8%, 69%, 51.6%, respectively. Statistically, there was no difference between these 2 treatments. Conclusion: PLAT was as effective as surgical resection in the treatment of solitary and small HCC. PLAT had the advantage over surgical resection in being less invasive. A prospective randomized trial on 180 patients with a solitary hepatocellular carcinoma ≦ 5 cm showed there was no significant difference in the long-term overall and disease-free survivals between treatment with percutaneous local ablative therapy or partial hepatectomy. Percutaneous local ablative therapy has the advantage over surgery in being less invasive.

ceRNA in cancer: possible functions and clinical implications
Xiaolong Qi, Dahong Zhang, Nan Wu, Junhua Xiao +2 more
2015· Journal of Medical Genetics1.4Kdoi:10.1136/jmedgenet-2015-103334

Competing endogenous RNAs (ceRNAs) are transcripts that can regulate each other at post-transcription level by competing for shared miRNAs. CeRNA networks link the function of protein-coding mRNAs with that of non-coding RNAs such as microRNA, long non-coding RNA, pseudogenic RNA and circular RNA. Given that any transcripts harbouring miRNA response element can theoretically function as ceRNAs, they may represent a widespread form of post-transcriptional regulation of gene expression in both physiology and pathology. CeRNA activity is influenced by multiple factors such as the abundance and subcellular localisation of ceRNA components, binding affinity of miRNAs to their sponges, RNA editing, RNA secondary structures and RNA-binding proteins. Aberrations in these factors may deregulate ceRNA networks and thus lead to human diseases including cancer. In this review, we introduce the mechanisms and molecular bases of ceRNA networks, discuss their roles in the pathogenesis of cancer as well as methods of predicting and validating ceRNA interplay. At last, we discuss the limitations of current ceRNA theory, propose possible directions and envision the possibilities of ceRNAs as diagnostic biomarkers or therapeutic targets.

IOBR: Multi-Omics Immuno-Oncology Biological Research to Decode Tumor Microenvironment and Signatures
Dongqiang Zeng, Zilan Ye, Rongfang Shen, Guangchuang Yu +4 more
2021· Frontiers in Immunology1.3Kdoi:10.3389/fimmu.2021.687975

Recent advances in next-generation sequencing (NGS) technologies have triggered the rapid accumulation of publicly available multi-omics datasets. The application of integrated omics to explore robust signatures for clinical translation is increasingly emphasized, and this is attributed to the clinical success of immune checkpoint blockades in diverse malignancies. However, effective tools for comprehensively interpreting multi-omics data are still warranted to provide increased granularity into the intrinsic mechanism of oncogenesis and immunotherapeutic sensitivity. Therefore, we developed a computational tool for effective Immuno-Oncology Biological Research (IOBR), providing a comprehensive investigation of the estimation of reported or user-built signatures, TME deconvolution, and signature construction based on multi-omics data. Notably, IOBR offers batch analyses of these signatures and their correlations with clinical phenotypes, long non-coding RNA (lncRNA) profiling, genomic characteristics, and signatures generated from single-cell RNA sequencing (scRNA-seq) data in different cancer settings. Additionally, IOBR integrates multiple existing microenvironmental deconvolution methodologies and signature construction tools for convenient comparison and selection. Collectively, IOBR is a user-friendly tool for leveraging multi-omics data to facilitate immuno-oncology exploration and to unveil tumor-immune interactions and accelerating precision immunotherapy.

Hepatogastroenterology
Yidong Cai, Haoxuan Zheng, Wei Gong, Yufang Che +1 more
2011· Hepatogastroenterology1.3Kdoi:10.5754/hge11155

BACKGROUND/AIMS: In this study, we explored the role of the Hedgehog signaling pathway in liver regeneration. METHODOLOGY: Retrorsine, partial hepatectomy and combined were utilized in mature Fisher344 rats. Specific assays, such as RT-PCR, real-time PCR and immunohistochemistry were used to detect the constituents of the Hedgehog signaling pathway during liver regeneration. RESULTS: mRNA expression of Ihh, Ptc, Smo, Gli1, Gli2 and Gli3 were all shown in liver tissue homogenates in control/normal, retrorsine, partial hepatectomy and retrorsine/partial hepatectomy groups while no Shh expression was found. Real-time PCR analysis indicated that there were significant differences in Hedgehog signaling pathway-related constituents (Ihh, Ptc, Gli1 and Gli3) among the different treatment groups and at distinct time points in the same treatment group during liver regeneration. The data also suggested an interaction effect between different treatment and time to the variation of Ihh, Ptc, Gli1 and Gli3. The protein expression of Ptc and Gli1 in liver regeneration was confirmed by immunohistochemistry, which differed in the duration among different groups. Nevertheless, the protein expression of Ptc and Gli1 were not detected successfully by western blot. CONCLUSIONS: It appears that the Hedgehog signaling pathway may be involved in liver regeneration.

Progression of Mental Health Services during the COVID-19 Outbreak in China
Wen Li, Yuan Yang, Zihan Liu, Yan-Jie Zhao +4 more
2020· International Journal of Biological Sciences1.2Kdoi:10.7150/ijbs.45120

The novel coronavirus disease (COVID-19) has been rapidly transmitted in China, Macau, Hong Kong, and other Asian and European counterparts. This COVID-19 epidemic has aroused increasing attention nationwide. Patients, health professionals, and the general public are under insurmountable psychological pressure which may lead to various psychological problems, such as anxiety, fear, depression, and insomnia. Psychological crisis intervention plays a pivotal role in the overall deployment of the disease control. The National Health Commission of China has summoned a call for emergency psychological crisis intervention and thus, various mental health associations and organizations have established expert teams to compile guidelines and public health educational articles/videos for mental health professionals and the general public alongside with online mental health services. In addition, mental health professionals and expert groups are stationed in designated isolation hospitals to provide on-site services. Experts have reached a consensus on the admission of patients with severe mental illness during the COVID-19 outbreak in mental health institutions. Nevertheless, the rapid transmission of the COVID-19 has emerged to mount a serious challenge to the mental health service in China.