BACKGROUND Gastrointestinal stromal tumors(GISTs) are the most common mesenchymal tumor type in the gastrointestinal system. Presently, various classification systems to prognosticate GISTs have been proposed.AIM To e...BACKGROUND Gastrointestinal stromal tumors(GISTs) are the most common mesenchymal tumor type in the gastrointestinal system. Presently, various classification systems to prognosticate GISTs have been proposed.AIM To evaluate the application value of four different risk stratification systems for GISTs.METHODS Patients who were diagnosed with GISTs and underwent surgical resection at four hospitals from 1998 to 2015 were identified from a database. Risk of recurrence was stratified by the modified National Institute of Health(NIH)criteria, the Armed Forces Institute of Pathology(AFIP) criteria, the Memorial Sloan Kettering Cancer Center(MSKCC) prognostic nomogram, and the contour maps. Receiver operating characteristic(ROC) curves were established to compare the four abovementioned risk stratification systems based on the area under the curve(AUC).RESULTS A total of 1303 patients were included in the study. The mean age of the patients was 55.77 ± 13.70 yr; 52.3% of the patients were male. The mean follow-up period was 64.91 ± 35.79 mo. Approximately 67.0% the tumors were located in the stomach, and 59.5% were smaller than 5 cm; 67.3% of the patients had a mitotic count ≤ 5/50 high-power fields(HPFs). Thirty-four tumors ruptured before and during surgery. Univariate analysis demonstrated that tumor size > 5 cm(P <0.05), mitotic count > 5/50 HPFs(P < 0.05), non-gastric location(P < 0.05), and tumor rupture(P < 0.05) were significantly associated with increased recurrence rates. According to the ROC curve, the AFIP criteria showed the largest AUC(0.754).CONCLUSION According to our data, the AFIP criteria were associated with a larger AUC than the NIH modified criteria, the MSKCC nomogram, and the contour maps, which might indicate that the AFIP criteria have better accuracy to support therapeutic decision-making for patients with GISTs.展开更多
Dear Editor,Dioscorea alata L.(2n=2x=40,3x=60,and 4x=80)is a perennial,tangled,herbaceous vine in the Dioscoreaceae family that migrated from Asia to Africa and America via the Indian Ocean and the Caribbean(Sharif et...Dear Editor,Dioscorea alata L.(2n=2x=40,3x=60,and 4x=80)is a perennial,tangled,herbaceous vine in the Dioscoreaceae family that migrated from Asia to Africa and America via the Indian Ocean and the Caribbean(Sharif et al.,2020).The rich starch and crude protein in its inflated tuber(commonly known as the greater yam)make this plant an essential crop in the tropical and subtropical regions of Southeast Asia,Africa,and Latin America(Sharif et al.,2020).Moreover,D.alata,D.cayenensis and D.rotundata represent the three major food crops among 11 cultivated yam species,whereas the other eight are often referred to as"minor yams"(Lebot et al.,2023).The global production of yam tubers reached 75 million tons in 2021(Food and Agriculture Organization Statistical Database,2022),indicating their importance in the food supply.A high-quality reference genome serves as an essential resource for the molecular breeding of crops to improve their quality and resistance to pathogens.With the recent publication of a chromosome-level genome,efforts have been made to identify the genes/loci associated with quality traits and resistance to pathogens in greater yam(Bredeson et al.展开更多
The long-term evolutionary arms race between plants and path-ogens has shaped the abundant immune receptor repertoires in plants to counteract pathogens(Jones et al.,2024).Plant nucleotide-binding leucine-rich repeat ...The long-term evolutionary arms race between plants and path-ogens has shaped the abundant immune receptor repertoires in plants to counteract pathogens(Jones et al.,2024).Plant nucleotide-binding leucine-rich repeat proteins(NLRs)represent the largest family of intracellular immune receptors,responsible for the detection of rapidly evolving pathogen-secreted effec-tors and the initiation of effector-triggered immunity(ETI).展开更多
Background:Few studies have shown nomograms that may predict disease-specific survival(DSS)probability after curative D2 gastrectomy for advanced gastric cancer(AGC),particularly among Chinese patients.This study soug...Background:Few studies have shown nomograms that may predict disease-specific survival(DSS)probability after curative D2 gastrectomy for advanced gastric cancer(AGC),particularly among Chinese patients.This study sought to develop an elaborative nomogram that predicts long-term DSS for AGC in Chinese patients.Methods:A retrospective study was conducted on 6753 AGC patients undergoing D2 gastrectomy between January 1,2000 and December 31,2012 from three large medical hospitals in China.We assigned patients from Sun Yat-sen University Cancer Center to the training set,and patients from the First Affiliated Hospital of China Medical University and Tianjin Medical University Cancer Hospital to two separate external validation sets.A multivariate survival analysis was performed using Cox proportional hazards regression model in a training set,and a nomogram was constructed.Harrell’s C-index was used to evaluate discrimination and calibration plots were used to validate similarities between survival probabilities predicted by the nomogram model and actual survival rates in two validation sets.Results:The multivariate Cox regression model identified age,tumor size,location,Lauren classification,lymphatic/venous invasion,depth of invasion,and metastatic lymph node ratio as covariates associated with survival.In the training set,the nomogram exhibited superior discrimination power compared with the 8th American Joint Com-mittee on Cancer TNM classification(Harrell’s C-index,0.82 vs.0.74;P<0.001).In two validation sets,the nomogram’s discrimination power was also excellent relative to TNM classification(C-index,0.83 vs.0.75 and 0.81 vs.0.74,respec-tively;P<0.001 for both).After calibration,the nomogram produced survival predictions that corresponded closely with actual survival rate.Conclusions:The established nomogram was able to predict 3-,5-,and 10-year DSS probabilities for AGC patients.Validation revealed that this nomogram exhibited excellent discrimination and calibration capacity,suggesting its clinical utility.展开更多
Arbuscular mycorrhizal symbiosis(AMS)is an ancient plant-fungus relationship that is widely distributed in terrestrial plants.The formation of symbiotic structures and bidirectional nutrient exchange requires the regu...Arbuscular mycorrhizal symbiosis(AMS)is an ancient plant-fungus relationship that is widely distributed in terrestrial plants.The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes.However,the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood.In this study,a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato,an emerging AMS model.The annotation of the tomato genome was improved by a multiple-platform sequencing strategy.A total of 3,174 protein-coding genes were upregulated during AMS,42%of which were alternatively spliced.Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms.Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants.However,these orthogroups were absent or not induced in monocots and/or non-AMS hosts,suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module.Additionally,we detected 587 lncRNAs,ten miRNAs,and 146 circRNAs that responded to AMS,which were incorporated to establish a tomato AMSresponsive,competing RNA-responsive endogenous RNA(ceRNA)network.Finally,a tomato symbiotic transcriptome database(TSTD,https://efg.nju.edu.cn/TSTD)was constructed to serve as a resource for deep deciphering of the AMS regulatory network.These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.展开更多
基金the State Key Project of Research and Development Plan,No.2017YFC0108300 and No.2017YFC01083032018 Special Funds for the Cultivation of Guangdong College Students'Scientific and Technological Innovation(Climbing Program Special Funds),No.pdjha0094
文摘BACKGROUND Gastrointestinal stromal tumors(GISTs) are the most common mesenchymal tumor type in the gastrointestinal system. Presently, various classification systems to prognosticate GISTs have been proposed.AIM To evaluate the application value of four different risk stratification systems for GISTs.METHODS Patients who were diagnosed with GISTs and underwent surgical resection at four hospitals from 1998 to 2015 were identified from a database. Risk of recurrence was stratified by the modified National Institute of Health(NIH)criteria, the Armed Forces Institute of Pathology(AFIP) criteria, the Memorial Sloan Kettering Cancer Center(MSKCC) prognostic nomogram, and the contour maps. Receiver operating characteristic(ROC) curves were established to compare the four abovementioned risk stratification systems based on the area under the curve(AUC).RESULTS A total of 1303 patients were included in the study. The mean age of the patients was 55.77 ± 13.70 yr; 52.3% of the patients were male. The mean follow-up period was 64.91 ± 35.79 mo. Approximately 67.0% the tumors were located in the stomach, and 59.5% were smaller than 5 cm; 67.3% of the patients had a mitotic count ≤ 5/50 high-power fields(HPFs). Thirty-four tumors ruptured before and during surgery. Univariate analysis demonstrated that tumor size > 5 cm(P <0.05), mitotic count > 5/50 HPFs(P < 0.05), non-gastric location(P < 0.05), and tumor rupture(P < 0.05) were significantly associated with increased recurrence rates. According to the ROC curve, the AFIP criteria showed the largest AUC(0.754).CONCLUSION According to our data, the AFIP criteria were associated with a larger AUC than the NIH modified criteria, the MSKCC nomogram, and the contour maps, which might indicate that the AFIP criteria have better accuracy to support therapeutic decision-making for patients with GISTs.
文摘背景与目的目前鲜有文献报道接受D2根治性切除术的进展期胃癌(advanced gastric cancer,AGC)患者的疾病特异性生存(disease?specific survival,DSS)预测系统,尤其针对中国胃癌患者。本研究拟构建一种精准预测中国进展期胃癌患者预后的列线图(Nomogram)模型。方法回顾性纳入2000年1月1日至2012年12月31日间在中国三家大型医院接受D2胃切除术的6753例AGC患者。中山大学肿瘤防治中心患者作为训练集,中国医科大学附属第一医院和天津医科大学肿瘤医院患者作为两个独立的外部验证集。在训练集中采用Cox比例风险回归模型进行多因素生存分析,并构建Nomogram模型,在验证集中通过Harrell’s C-index和校准曲线评价该模型的准确性、实际生存情况和模型预测的一致性。结果 Cox回归模型显示年龄、肿瘤大小、部位、Lauren分型、淋巴管/血管浸润、肿瘤浸润深度和淋巴结转移率为患者预后相关因素。在训练集中,Nomogram模型的预测准确度较美国癌症研究联合会(American Joint Committee on Cancer,AJCC)TNM癌症分期系统(第8版)更高(C-index,0.82 vs. 0.74,P <0.001)。在两个验证集中,亦出现类似的结果(C-index分别为0.83 vs. 0.75和0.81 vs. 0.74;两者均P <0.001)。校准曲线显示Nomogram模型预测的患者生存与和实际生存高度接近。结论本研究构建的Nomogram模型能够预测AGC患者的3年、 5年和10年疾病特异性生存,经外部验证显示其具有较高的准确性和区分效能,预示潜在的临床应用前景。
基金supported by the National Natural Science Foundation of China(32172089 and 32270241)the Jiangsu Key Laboratory for the Research and Utilization of Plant Resources(JSPKLB202207)+1 种基金the National Administration of Traditional Chinese Medicine High-level Key Discipline Construction Project(grant no.zyyzdxk-2023293)Fundamental Research Funds for the Central Universities from Nanjing Agricultural University.Z.-Q.S.is supported by the Outstanding Young Teacher of the"QingLan Project"of Jiangsu Province.
文摘Dear Editor,Dioscorea alata L.(2n=2x=40,3x=60,and 4x=80)is a perennial,tangled,herbaceous vine in the Dioscoreaceae family that migrated from Asia to Africa and America via the Indian Ocean and the Caribbean(Sharif et al.,2020).The rich starch and crude protein in its inflated tuber(commonly known as the greater yam)make this plant an essential crop in the tropical and subtropical regions of Southeast Asia,Africa,and Latin America(Sharif et al.,2020).Moreover,D.alata,D.cayenensis and D.rotundata represent the three major food crops among 11 cultivated yam species,whereas the other eight are often referred to as"minor yams"(Lebot et al.,2023).The global production of yam tubers reached 75 million tons in 2021(Food and Agriculture Organization Statistical Database,2022),indicating their importance in the food supply.A high-quality reference genome serves as an essential resource for the molecular breeding of crops to improve their quality and resistance to pathogens.With the recent publication of a chromosome-level genome,efforts have been made to identify the genes/loci associated with quality traits and resistance to pathogens in greater yam(Bredeson et al.
基金supported by the Outstanding Young Teacher of the“QingLan Project”of Jiangsu Province.
文摘The long-term evolutionary arms race between plants and path-ogens has shaped the abundant immune receptor repertoires in plants to counteract pathogens(Jones et al.,2024).Plant nucleotide-binding leucine-rich repeat proteins(NLRs)represent the largest family of intracellular immune receptors,responsible for the detection of rapidly evolving pathogen-secreted effec-tors and the initiation of effector-triggered immunity(ETI).
基金supported by the Natural Science Foundation of Guangdong Province(No.2015A030313089)the Major Program of Collaborative Innovation of Guangzhou(No.201508030042).
文摘Background:Few studies have shown nomograms that may predict disease-specific survival(DSS)probability after curative D2 gastrectomy for advanced gastric cancer(AGC),particularly among Chinese patients.This study sought to develop an elaborative nomogram that predicts long-term DSS for AGC in Chinese patients.Methods:A retrospective study was conducted on 6753 AGC patients undergoing D2 gastrectomy between January 1,2000 and December 31,2012 from three large medical hospitals in China.We assigned patients from Sun Yat-sen University Cancer Center to the training set,and patients from the First Affiliated Hospital of China Medical University and Tianjin Medical University Cancer Hospital to two separate external validation sets.A multivariate survival analysis was performed using Cox proportional hazards regression model in a training set,and a nomogram was constructed.Harrell’s C-index was used to evaluate discrimination and calibration plots were used to validate similarities between survival probabilities predicted by the nomogram model and actual survival rates in two validation sets.Results:The multivariate Cox regression model identified age,tumor size,location,Lauren classification,lymphatic/venous invasion,depth of invasion,and metastatic lymph node ratio as covariates associated with survival.In the training set,the nomogram exhibited superior discrimination power compared with the 8th American Joint Com-mittee on Cancer TNM classification(Harrell’s C-index,0.82 vs.0.74;P<0.001).In two validation sets,the nomogram’s discrimination power was also excellent relative to TNM classification(C-index,0.83 vs.0.75 and 0.81 vs.0.74,respec-tively;P<0.001 for both).After calibration,the nomogram produced survival predictions that corresponded closely with actual survival rate.Conclusions:The established nomogram was able to predict 3-,5-,and 10-year DSS probabilities for AGC patients.Validation revealed that this nomogram exhibited excellent discrimination and calibration capacity,suggesting its clinical utility.
基金supported by the National Natural Science Foundation of China(31770245,32070243,and 32170218)supported by the Jiangsu Excellent Postdoctoral Funding(2022ZB45)supported by the Outstanding Young Teacher of“QingLan Project”of Jiangsu Province.
文摘Arbuscular mycorrhizal symbiosis(AMS)is an ancient plant-fungus relationship that is widely distributed in terrestrial plants.The formation of symbiotic structures and bidirectional nutrient exchange requires the regulation of numerous genes.However,the landscape of RNAome during plant AMS involving different types of regulatory RNA is poorly understood.In this study,a combinatorial strategy utilizing multiple sequencing approaches was used to decipher the landscape of RNAome in tomato,an emerging AMS model.The annotation of the tomato genome was improved by a multiple-platform sequencing strategy.A total of 3,174 protein-coding genes were upregulated during AMS,42%of which were alternatively spliced.Comparative-transcriptome analysis revealed that genes from 24 orthogroups were consistently induced by AMS in eight phylogenetically distant angiosperms.Seven additional orthogroups were specifically induced by AMS in all surveyed dicot AMS host plants.However,these orthogroups were absent or not induced in monocots and/or non-AMS hosts,suggesting a continuously evolving AMS-responsive network in addition to a conserved core regulatory module.Additionally,we detected 587 lncRNAs,ten miRNAs,and 146 circRNAs that responded to AMS,which were incorporated to establish a tomato AMSresponsive,competing RNA-responsive endogenous RNA(ceRNA)network.Finally,a tomato symbiotic transcriptome database(TSTD,https://efg.nju.edu.cn/TSTD)was constructed to serve as a resource for deep deciphering of the AMS regulatory network.These results help elucidate the reconfiguration of the tomato RNAome during AMS and suggest a sophisticated and evolving RNA layer responsive network during AMS processes.
