UBE2C as an Immune-Related Biomarker for Breast Cancer:A Study Based on Multiple Databases

Objective To screen the target gene UBE2C and explore its prognostic value and immune correlation in breast cancer(BRCA)using multiple databases..Methods The microarray expression datasets of BRCA were downloaded from the Gene Expresssion Omnibus database(GEO)and analyzed to obtain differentially expressed genes(DEGs).Hub genes were obtained by constructing and visualizing the protein-protein interaction network of DEGs.Then the key gene UBE2C was determined using R language,STRING,and Cytoscape,and the differential expression of UBE2C was verified using the external datasets,The Cancer Genome Atlas(TCGA),and quantitative real-time PCR(qRT-PCR).The prognostic value and immunological correlation of UBE2C in BRCA were explored using R language,TIMER,and Gene Set Enrichment Analysis(GSEA).Results The expression of UBE2C was differentially upregulated in BRCA,as verified by TCGA and qRT-PCR.Prognostic analysis revealed that UBE2C served as an independent prognostic factor.High expression of UBE2C was associated with decreased immune infiltration levels of B cells,CD4+T cells,CD8+T cells,macrophages,and myeloid dendritic cells in BRCA tissue.The expression of UBE2C in BRCA showed a significant correlation with PDCD1,CD274,and CTLA4 expressions.There was a positive correlation between the expression of UBE2C and the tumor mutational burden and microsatellite instability.GSEA demonstrated that UBE2C expression significantly enriched 786 immune-related gene sets.Conclusions UBE2C expression in BRCA tissues can predict the survivals and prognosis of BRCA patients.Also,it is closely related to the BRCA immune microenvironment and can predict the effecacy of immunotherapy in BRCA patients.Therefore,UBE2C may be an potential immune-related prognostic biomarker for BRCA.

Diagnosis and treatment of refractory infectious diseases using nanopore sequencing technology:Three case reports

BACKGROUND Infectious diseases are still one of the greatest threats to human health,and the etiology of 20%of cases of clinical fever is unknown;therefore,rapid identification of pathogens is highly important.Traditional culture methods are only able to detect a limited number of pathogens and are time-consuming;serologic detection has window periods,false-positive and false-negative problems;and nucleic acid molecular detection methods can detect several known pathogens only once.Three-generation nanopore sequencing technology provides new options for identifying pathogens.CASE SUMMARY Case 1:The patient was admitted to the hospital with abdominal pain for three days and cessation of defecation for five days,accompanied by cough and sputum.Nanopore sequencing of the drainage fluid revealed the presence of orallike bacteria,leading to a clinical diagnosis of bronchopleural fistula.Cefoperazone sodium sulbactam treatment was effective.Case 2:The patient was admitted to the hospital with fever and headache,and CT revealed lung inflammation.Antibiotic treatment for Streptococcus pneumoniae,identified through nanopore sequencing of cerebrospinal fluid,was effective.Case 3:The patient was admitted to our hospital with intermittent fever and an enlarged neck mass that had persisted for more than six months.Despite antibacterial treatment,her symptoms worsened.The nanopore sequencing results indicate that voriconazole treatment is effective for Aspergillus brookii.The patient was diagnosed with mixed cell type classical Hodgkin's lymphoma with infection.CONCLUSION Three-generation nanopore sequencing technology allows for rapid and accurate detection of pathogens in human infectious diseases.

肿瘤重症患者急性呼吸衰竭专家共识(2023版)

目的本共识的制定旨在为肿瘤重症患者合并呼吸衰竭的临床处理中常见问题提供基于临床证据的推荐意见。方法采用人群、干预、比较和预后(Population,Intervention,Comparison,and Outcome,PICO)原则对肿瘤重症患者呼吸衰竭的诊断和处理提出6个重要临床问题,基于文献检索和证据整合形成推荐意见。采用推荐意见分级评价、制定与评估(Grading of Recommendation Assessment,Development and Evaluation,GRADE)的方法讨论每个问题并经专家组讨论后形成共识意见。结果共识专家组形成了如下推荐意见。强推荐:(1)宏基因组二代测序可能有助于临床医师快速诊断合并呼吸衰竭的肿瘤重症患者的肺部感染;(2)体外膜肺(Extracorporeal Membrane Oxygenation,ECMO)不作为合并急性呼吸窘迫综合征的肿瘤重症患者常规挽救方案,多学科会诊后高选择性患者可能受益于ECMO治疗;(3)与标准化疗相比,免疫检查点抑制剂治疗增加肿瘤患者肺毒性的发生率;(4)接受机械通气的肿瘤患者如预计通气时间超过14天,早期气管切开可能使患者获益;(5)高流量氧疗和无创通气可以作为肿瘤合并呼吸衰竭的重症患者的一线氧疗方案。弱推荐:(6)对于癌肿压迫所致呼吸衰竭的肿瘤重症患者,如多学科会诊后考虑肿瘤对于药物潜在敏感,可采用紧急化疗作为挽救治疗。结论基于已有证据形成的推荐意见可指导肿瘤合并呼吸衰竭患者的诊断和治疗并改善预后。

Methods for improving colorectal cancer annotation efficiency for artificial intelligence-observer training

BACKGROUND Missing occult cancer lesions accounts for the most diagnostic errors in retrospective radiology reviews as early cancer can be small or subtle,making the lesions difficult to detect.Secondobserver is the most effective technique for reducing these events and can be economically implemented with the advent of artificial intelligence(AI).AIM To achieve appropriate AI model training,a large annotated dataset is necessary to train the AI models.Our goal in this research is to compare two methods for decreasing the annotation time to establish ground truth:Skip-slice annotation and AI-initiated annotation.METHODS We developed a 2D U-Net as an AI second observer for detecting colorectal cancer(CRC)and an ensemble of 5 differently initiated 2D U-Net for ensemble technique.Each model was trained with 51 cases of annotated CRC computed tomography of the abdomen and pelvis,tested with 7 cases,and validated with 20 cases from The Cancer Imaging Archive cases.The sensitivity,false positives per case,and estimated Dice coefficient were obtained for each method of training.We compared the two methods of annotations and the time reduction associated with the technique.The time differences were tested using Friedman’s two-way analysis of variance.RESULTS Sparse annotation significantly reduces the time for annotation particularly skipping 2 slices at a time(P<0.001).Reduction of up to 2/3 of the annotation does not reduce AI model sensitivity or false positives per case.Although initializing human annotation with AI reduces the annotation time,the reduction is minimal,even when using an ensemble AI to decrease false positives.CONCLUSION Our data support the sparse annotation technique as an efficient technique for reducing the time needed to establish the ground truth.

甲状腺乳头状癌中央区淋巴结转移的危险因素分析

目的探讨甲状腺乳头状癌(PTC)中央区淋巴结转移(CLNM)的危险因素。方法选取2016年8月—2018年12月在锦州医科大学附属第一医院行手术治疗的303例PTC患者临床资料,回顾性分析患者性别、年龄、体重指数(BMI)、肿瘤最大直径、肿瘤数量、肿瘤位置、被膜侵犯情况、甲状腺球蛋白抗体(TgAb)及促甲状腺激素(TSH)等因素对CLNM的影响。结果303例患者中,116例发生CLNM,总转移率为39.27%。单因素分析结果显示,性别、年龄、BMI、肿瘤最大直径、肿瘤数量、是否被膜侵犯及CLNM率比较,差异有统计学意义(P<0.05)。多因素Logistic回归分析显示,性别[O^R=0.454(95%CI:0.224,0.921)]、年龄[O^R=0.957(95%CI:0.936,0.978)]、肿瘤最大直径[O^R=1.438(95%CI:1.117,1.852)]及被膜侵犯[O^R=0.399(95%CI:0.230,0.691)]是PTC患者发生CLNM的危险因素。受试者工作特征曲线显示,年龄为45.5岁、肿瘤最大直径为0.75cm时约登指数最大,对应的曲线下面积分别为0.643和0.691,敏感性分别为0.620(95%CI:0.580,0.706)和0.695(95%CI:0.632,0.750),特异性分别为0.682(95%CI:0.580,0.706)和0.720(95%CI:0.632,0.750)。结论PTC发生CLNM与多个因素有关,当患者为男性、年龄<45.5岁、肿瘤最大直径≥0.75 cm及存在被膜侵犯时,CLNM发生可能性大,建议行中央区淋巴结清扫。

Prognostic predictors in patients with sepsis after gastrointestinal tumor surgery:A retrospective study

BACKGROUND There have been different reports on mortality of sepsis;however,few focus on the prognosis of patients with sepsis after surgery.AIM To study the clinical features and prognostic predictors in patients with sepsis after gastrointestinal tumor surgery in intensive care unit(ICU).METHODS We retrospectively screened patients who underwent gastrointestinal tumor surgery at Peking University Cancer Hospital from January 2015 to December 2019.Among them,181 patients who were diagnosed with sepsis in ICU were included in our study.Survival was analysed by the Kaplan-Meier method.Univariate and multivariate adjusted analyses were performed to identify predictors of prognosis.RESULTS The 90-d all-cause mortality rate was 11.1%in our study.Univariate analysis showed that body mass index(BMI),shock within 48 h after ICU admission,leukocyte count,lymphocyte to neutrophil ratio,international normalized ratio,creatinine,procalcitonin,lactic acid,oxygenation index,and sequential organ failure assessment(SOFA)score within 24 h after ICU admission might be all significantly associated with the prognosis of sepsis after gastrointestinal tumor surgery.In multiple analysis,we found that BMI≤20 kg/m^(2),lactic acid after ICU admission,and SOFA score within 24 h after ICU admission might be independent risk predictors of the prognosis of sepsis after gastrointestinal tumor surgery.Compared with SOFA score,SOFA score combined with BMI and lactic acid might have higher predictive ability(area under the receiver operating characteristic curve,0.859;95%confidence interval,0.789-0.929).CONCLUSION Lactic acid and SOFA score within 24 h after ICU admission are independent risk predictors of the prognosis of sepsis after gastrointestinal tumor surgery.SOFA score combined with BMI and lactic acid might have good predictive value.

Improving the accuracy and consistency of clinical target volume delineation for rectal cancer by an education program

BACKGROUND Accurate target volume delineation is the premise for the implementation of precise radiotherapy.Inadequate target volume delineation may diminish tumor control or increase toxicity.Although several clinical target volume(CTV)delineation guidelines for rectal cancer have been published in recent years,significant interobserver variation(IOV)in CTV delineation still exists among radiation oncologists.However,proper education may serve as a bridge that connects complex guidelines with clinical practice.AIM To examine whether an education program could improve the accuracy and consistency of preoperative radiotherapy CTV delineation for rectal cancer.METHODS The study consisted of a baseline target volume delineation,a 150-min education intervention,and a follow-up evaluation.A 42-year-old man diagnosed with stage IIIC(T3N2bM0)rectal adenocarcinoma was selected for target volume delineation.CTVs obtained before and after the program were compared.Dice similarity coefficient(DSC),inclusiveness index(IncI),conformal index(CI),and relative volume difference[ΔV(%)]were analyzed to quantitatively evaluate the disparities between the participants’delineation and the standard CTV.Maximum volume ratio(MVR)and coefficient of variation(CV)were calculated to assess the IOV.Qualitative analysis included four common controversies in CTV delineation concerning the upper boundary of the target volume,external iliac area,groin area,and ischiorectal fossa.RESULTS Of the 18 radiation oncologists from 10 provinces in China,13 completed two sets of CTVs.In quantitative analysis,the average CTV volume decreased from 809.82 cm3 to 705.21 cm3(P=0.001)after the education program.Regarding the indices for geometric comparison,the mean DSC,IncI,and CI increased significantly,whileΔV(%)decreased remarkably,indicating improved agreement between participants’delineation and the standard CTV.Moreover,an 11.80%reduction in MVR and 18.19%reduction in CV were noted,demonstrating a smaller IOV in delineation after the education program.Regarding qualitative analysis,the greatest variations in baseline were observed at the external iliac area and ischiorectal fossa;61.54%(8/13)and 53.85%(7/13)of the participants unnecessarily delineated the external iliac area and the ischiorectal fossa,respectively.However,the education program reduced these variations.CONCLUSION Wide variations in CTV delineation for rectal cancer are present among radiation oncologists in China's Mainland.A well-structured education program could improve delineation accuracy and reduce IOVs.

Consolidation chemotherapy with capecitabine after neoadjuvant chemoradiotherapy in high-risk patients with locally advanced rectal cancer:Propensity score study

BACKGROUND The effects of consolidation chemotherapy(CC) in neoadjuvant therapy in locally advanced rectal cancer(LARC) have been explored. However, the optimal neoadjuvant chemoradiotherapy(NCRT) and surgery interval, regimen, and cycles of chemotherapy remains unclear.AIM To evaluate the effects of one to two cycles of CC with capecitabine on high-risk patients with LARC without extending NCRT and surgery interval.METHODS We retrospectively evaluated high-risk patients with LARC, who were defined as having at least one of the following factors by magnetic resonance imaging: depth of invasion beyond the muscularis propria of more than 5 mm(c T3c-c T3d), T4, meso-rectal fascia or extramural vascular invasion positive, and treatment date between January 2015 and July 2019 in our center. Patients were divided into the CC and non-CC group according to whether they received CC(capecitabine 1000 mg/m^(2) twice daily from days 1 to 14 every 21 d) after NCRT. Propensity score matching(PSM) and inverse probability of treatment weight(IPTW) were used to balance the differences between the two groups. The main outcome was the complete response(CR) rate.RESULTS A total of 265 patients were enrolled: 136 patients in the CC group and 129 patients in the non-CC group. The median interval was 70 d(range, 37-168). The CR rate was 24.3% and 16.3%(P = 0.107) in the CC and non-CC groups’ original samples, respectively. After PSM and IPTW, the CR rate in the CC group was higher than that in non-CC group(27.6% vs 16.2%, P = 0.045;25.9% vs 16.3%, P = 0.045). The median follow-up was 39.8 mo(range, 2.9-74.8), and there were no differences in 3-year non-regrowth disease-free survival nor overall survival in the original samples(73.2% vs 71.9%, P = 0.913;92.3% vs 86.7%, P = 0.294), PSM(73.2% vs 73.5%, P = 0.865;92.5% vs 89.3%, P = 0.612), and IPTW(73.8% vs 72.1%, P = 0.913;92.4% vs 87.4%, P = 0.294). There was also no difference in grade 2 or higher acute toxicity during neoadjuvant therapy in the two groups(49.3% vs 53.5%, P = 0.492).CONCLUSION One to two cycles of CC with capecitabine after NCRT was safe and increased the CR rate in highrisk LARC but failed to improve the long-term outcomes.

Nomogram for predicting the prognosis of tumor patients with sepsis after gastrointestinal surgery

BACKGROUND There were few studies on the prognosis of tumor patients with sepsis after gastrointestinal surgery and there was no relevant nomogram for predicting the prognosis of these patients.AIM To establish a nomogram for predicting the prognosis of tumor patients with sepsis after gastrointestinal surgery in the intensive care unit(ICU).METHODS A total of 303 septic patients after gastrointestinal tumor surgery admitted to the ICU at Peking University Cancer Hospital from January 1, 2013 to December 31, 2020 were analysed retrospectively. The model for predicting the prognosis of septic patients was established by the R software package.RESULTS The most common infection site of sepsis after gastrointestinal surgery in the ICU was abdominal infection. The 90-d all-cause mortality rate was 10.2% in our study group. In multiple analyses, we found that there were statistically significant differences in tumor type, septic shock, the number of lymphocytes after ICU admission, serum creatinine and total operation times among tumor patients with sepsis after gastrointestinal surgery(P < 0.05). These five variables could be used to establish a nomogram for predicting the prognosis of these septic patients. The nomogram was verified, and the initial C-index was 0.861. After 1000 internal validations of the model, the C-index was 0.876, and the discrimination was good. The correction curve indicated that the actual value was in good agreement with the predicted value.CONCLUSION The nomogram based on these five factors(tumor type, septic shock, number of lymphocytes, serum creatinine, and total operation times) could accurately predict the prognosis of tumor patients with sepsis after gastrointestinal surgery.

Correlation of PRPS1 and JAB1 expression in the bone marrow tissue of acute leukemia with the apoptosis and invasion of tumor cells

Objective:To study the correlation of PRPS1 and JAB1 expression in the bone marrow tissue of acute leukemia with the apoptosis and invasion of tumor cells.Methods:Patients who were diagnosed with acute leukemia by bone marrow aspiration biopsy in Edong medical group Huangshi central hospital between February 2015 and December 2017 were selected as the AL group of the research, and patients who received bone marrow aspiration biopsy and were without significant abnormality in Edong medical group Huangshi central hospital during the same period were selected as the control group of the research. RNA was extracted to determine the mRNA expression of PRPS1, JAB1, apoptosis genes and invasion genes, and protein was extracted to determine the protein expression of PRPS1 and JAB1.Results:Both mRNA expression and protein expression of PRPS1 and JAB1 in bone marrow tissues of AL group were significantly higher than those of control group;AuroraA, Bcl-2,β-catenin, MMP2, MMP9, N-cadherin and Msi2 mRNA expression in bone marrow tissues of AL group were significantly higher than those of control group whereas Bax, C/EBP , RUNX3 and TIMP3 mRNA expression were significantly lower than those of control group, and the PRPS1 and JAB1 mRNA expression in bone marrow tissues of AL group were positively correlated with AuroraA, Bcl-2,β-catenin, MMP2, MMP9, N-cadherin and Msi2 mRNA expression, and negatively correlated with Bax, C/EBP , RUNX3 and TIMP3 mRNA expression.Conclusion:The high expression of PRPS1 and JAB1 in the bone marrow tissue of acute leukemia can inhibit cell apoptosis and promote cell invasion.

Highly Stretchable and Conductive Hybrid Fibers for High-performance Fibrous Electrodes and All-solid-state Supercapacitors

The development of lightweight,flexible,and stretchable energy storage systems is essential for state-of-the-art electronic devices.We propose a new and broad strategy to fabricate a stretchable and conductive GO/CNTs-TPU fiber electrode by direct wet spinning,from which a flexible fibrous supercapacitor is fabricated.The fibrous electrode exhibits a high strength of 11.68 MPa,high conductivity of 342 S/cm,and high specific capacitances(21.8 mF/cm,36.45 F/cm^3,and 95 F/g).The specific capacitance of the assembled all-solid-state hybrid fiber-shaped supercapacitor reaches 14.3 F/cm^3.After 5000 charge-discharge cycles,97%of the capacitance of the hybrid supercapacitor is maintained.These high-strength electrochemical electrode materials could be potential candidates for applications in practical and large-scale energy storage systems and textile clothes.

EntityManager： Managing Dirty Data Based on Entity Resolution

Data quality is important in many data-driven applications, such as decision making, data analysis, and data mining. Recent studies focus on data cleaning techniques by deleting or repairing the dirty data, which may cause information loss and bring new inconsistencies. To avoid these problems, we propose EntityManager, a general system to manage dirty data without data cleaning. This system takes real-world entity as the basic storage unit and retrieves query results according to the quality requirement of users. The system is able to handle all kinds of inconsistencies recognized by entity resolution. We elaborate the EntityManager system, covering its architecture, data model, and query processing techniques. To process queries efficiently, our system adopts novel indices, similarity operator and query optimization techniques. Finally, we verify the efficiency and effectiveness of this system and present future research challenges.

O2iJoin： An Efficient Index-Based Algorithm for Overlap Interval Join

Time intervals are often associated with tuples to represent their valid time in temporal relations, where overlap join is crucial for various kinds of queries. Many existing overlap join algorithms use indices based on tree structures such as quad-tree, B＋-tree and interval tree. These algorithms usually have high CPU cost since deep path traversals are unavoidable, which makes them not so competitive as data-partition or plane-sweep based algorithms. This paper proposes an efficient overlap join algorithm based on a new two-layer flat index named as Overlap Interval Inverted Index （i.e., O2i Index）. It uses an array to record the end points of intervals and approximates the nesting structures of intervals via two functions in the first layer, and the second layer uses inverted lists to trace all intervals satisfying the approximated nesting structures. With the help of the new index, the join algorithm only visits the must-be-scanned lists and skips all others. Analyses and experiments on both real and synthetic datasets show that the proposed algorithm is as competitive as the state-of-the-art algorithms.

COSSET＋： Crowdsourced Missing Value Imputation Optimized by Knowledge Base

Missing value imputation with crowdsourcing is a novel method in data cleaning to capture missing values that could hardly be filled with automatic approaches. However, the time cost and overhead in crowdsourcing are high. Therefore, we have to reduce cost and guarantee the accuracy of crowdsourced imputation. To achieve the optimization goal, we present COSSET+, a crowdsourced framework optimized by knowledge base. We combine the advantages of both knowledge-based filter and crowdsourcing platform to capture missing values. Since the amount of crowd values will affect the cost of COSSET+, we aim to select partial missing values to be crowdsourced. We prove that the crowd value selection problem is an NP-hard problem and develop an approximation algorithm for this problem. Extensive experimental results demonstrate the efficiency and effectiveness of the proposed approaches.

Impacts of Dirty Data on Classification and Clustering Models:An Experimental Evaluation

Data quality issues have attracted widespread attentions due to the negative impacts of dirty data on data mining and machine learning results.The relationship between data quality and the accuracy of results could be applied on the selection of the appropriate model with the consideration of data quality and the determination of the data share to clean.However,rare research has focused on exploring such relationship.Motivated by this,this paper conducts an experimental comparison for the effects of missing,inconsistent,and conflicting data on classification and clustering models.FYom the experimental results,we observe that dirty-data impacts are related to the error type,the error rate,and the data size.Based on the findings,we suggest users leverage our proposed metrics,sensibility and data quality inflection point,for model selection and data cleaning.

FrepJoin:an efficient partition-based algorithm for edit similarity join

String similarity join(SSJ) is essential for many applications where near-duplicate objects need to be found. This paper targets SSJ with edit distance constraints. The existing algorithms usually adopt the filter-andrefine framework. They cannot catch the dissimilarity between string subsets, and do not fully exploit the statistics such as the frequencies of characters. We investigate to develop a partition-based algorithm by using such statistics.The frequency vectors are used to partition datasets into data chunks with dissimilarity between them being caught easily. A novel algorithm is designed to accelerate SSJ via the partitioned data. A new filter is proposed to leverage the statistics to avoid computing edit distances for a noticeable proportion of candidate pairs which survive the existing filters. Our algorithm outperforms alternative methods notably on real datasets.