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Abstract Background Breast cancer is the most common malignant tumor in the world. Intraoperative frozen section of sentinel lymph nodes is an important basis for determining whether axillary lymph node dissection is required for breast cancer surgery. We propose an RRCART model based on a deep-learning network to identify metastases in 2362 frozen sections and count the wrongly identified sections and the associated reasons. The purpose is to summarize the factors that affect the accuracy of the artificial intelligence model and propose corresponding solutions. Methods We took the pathological diagnosis of senior pathologists as the gold standard and identified errors. The pathologists and artificial intelligence engineers jointly read the images and heatmaps to determine the locations of the identified errors on sections, and the pathologists found the reasons (false reasons) for the errors. Through NVivo 12 Plus, qualitative analysis of word frequency analysis and nodal analysis was performed on the error reasons, and the top-down error reason framework of “artificial intelligence RRCART model to identify frozen sections of breast cancer lymph nodes” was constructed based on the importance of false reasons. Results There were 101 incorrectly identified sections in 2362 slides, including 42 false negatives and 59 false positives. Through NVivo 12 Plus software, the error causes were node-coded, and finally, 2 parent nodes (high-frequency error, low-frequency error) and 5 child nodes (section quality, normal lymph node structure, secondary reaction of lymph nodes, micrometastasis, and special growth pattern of tumor) were obtained; among them, the error of highest frequency was that caused by normal lymph node structure, with a total of 45 cases (44.55%), followed by micrometastasis, which occurred in 30 cases (29.70%). Conclusions The causes of identification errors in examination of sentinel lymph node frozen sections by artificial intelligence are, in descending order of influence, normal lymph node structure, micrometastases, section quality, special tumor growth patterns and secondary lymph node reactions. In this study, by constructing an artificial intelligence model to identify the error causes of frozen sections of lymph nodes in breast cancer and by analyzing the model in detail, we found that poor quality of slices was the preproblem of many identification errors, which can lead to other errors, such as unclear recognition of lymph node structure by computer. Therefore, we believe that the process of artificial intelligence pathological diagnosis should be optimized, and the quality control of the pathological sections included in the artificial intelligence reading should be carried out first to exclude the influence of poor section quality on the computer model. For cases of micrometastasis, we suggest that by differentiating slices into high- and low-confidence groups, low-confidence micrometastatic slices can be separated for manual identification. The normal lymph node structure can be improved by adding samples and training the model in a targeted manner.

Abstract Background The efficacy of systemic therapy regimens, such as immune checkpoint inhibitors and tyrosine kinase inhibitors (IO‐TKI) and targeted therapy, for metastatic clear cell renal cell carcinoma (ccRCC) remains unpredictable due to the lack of effective biomarkers. Neutrophil extracellular trap (NET) plays an important role in promoting ccRCC. This study explores the NET predictive value of the efficacy in metastatic ccRCC. Methods In this retrospective study, patients with metastatic ccRCC who received targeted drugs and IO‐TKI were included. Immunofluorescence staining was utilized to quantify the levels of tissue NETs through cell counts of H3Cit(+) and MPO(+) cells. Results A total of 183 patients with metastatic ccRCC were enrolled, including 150 patients who received TKIs and 33 patients who received IO‐TKI. The levels of NETs in tumor tissue were significantly higher than in para‐tumor tissue (p

Abstract In silico interrogation of glioblastoma (GBM) in The Cancer Genome Atlas (TCGA) revealed upregulation of GNA12 (Gα12), encoding the alpha subunit of the heterotrimeric G-protein G12, concomitant with overexpression of multiple G-protein coupled receptors (GPCRs) that signal through Gα12. Glioma stem cell lines from patient-derived xenografts also showed elevated levels of Gα12. Knockdown (KD) of Gα12 was carried out in two different human GBM stem cell (GSC) lines. Tumors generated in vivo by orthotopic injection of Gα12KD GSC cells showed reduced invasiveness, without apparent changes in tumor size or survival relative to control GSC tumor-bearing mice. Transcriptional profiling of GSC-23 cell tumors revealed significant differences between WT and Gα12KD tumors including reduced expression of genes associated with the extracellular matrix, as well as decreased expression of stem cell genes and increased expression of several proneural genes. Thrombospondin-1 (THBS1), one of the genes most repressed by Gα12 knockdown, was shown to be required for Gα12-mediated cell migration in vitro and for in vivo tumor invasion. Chemogenetic activation of GSC-23 cells harboring a Gα12-coupled DREADD also increased THBS1 expression and in vitro invasion. Collectively, our findings implicate Gα12 signaling in regulation of transcriptional reprogramming that promotes invasiveness, highlighting this as a potential signaling node for therapeutic intervention.

Hard carbon is considered as the most commercially applicable anode for sodium-ion batteries. Lignin has the characteristics of sustainable, low cost, high carbon content (>60%) and abundant oxygen functional groups, which is expected to be used as a promising candidate precursor for low-cost hard carbons. The structure and electrochemical performances of hard carbons could be regulated by adjusting carbonization temperature. The microstructure and electrochemical performance of LDHC anode are highly dependent on the carbonization temperature. Increasing carbonization temperature could reduce specific surface area and improve initial coulombic efficiency. The slope and plateau capacity of the LDHC anode could also be adjusted by changing the carbonization temperature. The LDHC prepared at 1200 °C showed the best sodium-ion storage performance, with an initial coulombic efficiency of 78.9% and a reversible sodium-ion storage capacity of 284.7 mAh g−1.

Abstract Background Sorbus sensu stricto (Sorbus s.s.) is a genus with important economical values because of its beautiful leaves, and flowers and especially the colorful fruits. It belongs to the tribe Maleae of the family Rosaceae, and comprises about 90 species mainly distributed in China. There is on-going dispute about its infrageneric classification and species delimitation as the species are morphologically similar. With the aim of shedding light on the circumscription of taxa within the genus, phylogenetic analyses were performed using 29 Sorbus s.s. chloroplast (cp) genomes (16 newly sequenced) representing two subgenera and eight sections. Results The 16 cp genomes newly sequenced range between 159,646 bp and 160,178 bp in length. All the samples examined and 22 taxa re-annotated in Sorbus sensu lato (Sorbus s.l.) contain 113 unique genes with 19 of these duplicated in the inverted repeat (IR). Six hypervariable regions including trnR-atpA, petN-psbM, rpl32-trnL, trnH-psbA, trnT-trnL and ndhC-trnV were screened and 44–53 SSRs and 14–31 dispersed repeats were identified as potential molecular markers. Phylogenetic analyses under ML/BI indicated that Sorbus s.l. is polyphyletic, but Sorbus s.s. and the other five segregate genera, Aria, Chamaemespilus, Cormus, Micromeles and Torminalis are monophyletic. Two major clades and four sub-clades resolved with full-support within Sorbus s.s. are not consistent with the existing infrageneric classification. Two subgenera, subg. Sorbus and subg. Albocarmesinae are supported as monophyletic when S. tianschanica is transferred to subg. Albocarmesinae from subg. Sorbus and S. hupehensis var. paucijuga transferred to subg. Sorbus from subg. Albocarmesinae, respectively. The current classification at sectional level is not supported by analysis of cp genome phylogeny. Conclusion Phylogenomic analyses of the cp genomes are useful for inferring phylogenetic relationships in Sorbus s.s. Though genome structure is highly conserved in the genus, hypervariable regions and repeat sequences used are the most promising molecule makers for population genetics, species delimitation and phylogenetic studies.

Abstract The frozen section (FS) diagnoses of pathology experts are used in China to determine whether sentinel lymph nodes of breast cancer have metastasis during operation. Direct implementation of a deep neural network (DNN) in clinical practice may be hindered by misdiagnosis of the algorithm, which affects a patient's treatment decision. In this study, we first obtained the prediction result of the commonly used patch-DNN, then we present a relative risk classification and regression tree (RRCART) to identify the misdiagnosed whole-slide images (WSIs) and recommend them to be reviewed by pathologists. Applying this framework to 2362 WSIs of breast cancer lymph node metastasis, test on frozen section results in the mean area under the curve (AUC) reached 0.9851. However, the mean misdiagnosis rate (0.0248), was significantly higher than the pathologists’ misdiagnosis rate (p 0.01). However, the other low-accuracy group included most of the misdiagnoses of DNN models. Our research shows that the misdiagnosis from deep learning model can be further enriched by our method, and that the low-accuracy WSIs must be selected for pathologists to review and the high-accuracy ones may be ready for pathologists to give diagnostic reports.

RING finger E3 ligases play an important role in regulating plant growth and development by mediating substrate degradation. In this study, we identified TaGW2L, encoding a Grain width and weight2 (GW2)-like RING finger E3 ligase, as a novel positive regulator of heading date in wheat (Triticum aestivum L.). TaGW2L exhibited high amino acid sequence similarities with TaGW2 homoeologs, particularly in the conserved RING finger domain. Expression analysis indicated that TaGW2L was constitutively expressed in various wheat tissues. TaGW2L showed transactivation activity in yeast and could interact with the ubiquitin-conjugating enzymes E2s. An in vitro ubiquitination assay verified that TaGW2L possessed a similar E3 ligase activity to TaGW2. Overexpression of the TaGW2L-7A homoeolog in wheat led to a significantly earlier heading date under both natural conditions and long-day conditions. Transcriptome analysis revealed that multiple known genes positively regulating wheat heading were significantly upregulated in the TaGW2L-7A-overexpression plants compared with the wild-type control. Together, our findings shed light on the role of TaGW2L in wheat heading date and provide potential applications of TaGW2L for the adaptation improvement of crops.

Abstract Background Several models and markers were developed and found to predict outcome of advanced renal cell carcinoma. This study aimed to evaluate the prognostic value of the ratio of maximum to minimum tumor diameter (ROD) in metastatic clear cell renal cell carcinoma (mccRCC). Methods Patients with mccRCC (n = 213) treated with sunitinib from January 2008 to December 2018 were identified. Cutoff value for ROD was determined using receiver operating characteristic. Patients with different ROD scores were grouped and evaluated. Survival outcomes were estimated by Kaplan–Meier method. Results The optimal ROD cutoff value of 1.34 was determined for progression free survival (PFS) and overall survival (OS). Patients in ROD ≥ 1.34 group had shorter PFS (9.6 versus 17.7 months, p

Four Sorbus taxa endemic to China, S. arguta, S. guanxianensis, S. megalocarpa var. megalocarpa and S. megalocarpa var. cuneata, are morphologically similar to one another in having large brown fruits with persistent calyx and dense lenticels. In literature, either all of the four taxa were accepted, or two of them, S. arguta and S. megalocarpa var. cuneata, were treated as synonyms of S. megalocarpa var. megalocarpa, or S. guanxianensis alone was dubious. In this study, based on morphological comparison, S. arguta is reinstated for its relatively small inflorescence, small fruit and timing of flowering after leaves are unfolded. S. megalocarpa var. cuneata is confirmed as a synonym and S. guanxianensis is proposed as a new heterotypic synonym of S. megalocarpa.

IntroductionZinc (Zn) deficiency causes serious diseases in people who rely on cereals as their main food source. However, the grain zinc concentration (GZnC) in wheat is low. Biofortification is a sustainable strategy for reducing human Zn deficiency.MethodsIn this study, we constructed a population of 382 wheat accessions and determined their GZnC in three field environments. Phenotype data was used for a genome-wide association study (GWAS) using a 660K single nucleotide polymorphism (SNP) array, and haplotype analysis identified an important candidate gene for GZnC.ResultsWe found that GZnC of the wheat accessions showed an increasing trend with their released years, indicating that the dominant allele of GZnC was not lost during the breeding process. Nine stable quantitative trait loci (QTLs) for GZnC were identified on chromosomes 3A, 4A, 5B, 6D, and 7A. And an important candidate gene for GZnC, namely, TraesCS6D01G234600, and GZnC between the haplotypes of this gene showed, significant difference (P ≤ 0.05) in three environments.DiscussionA novel QTL was first identified on chromosome 6D, this finding enriches our understanding of the genetic basis of GZnC in wheat. This study provides new insights into valuable markers and candidate genes for wheat biofortification to improve GZnC.

Abstract Background Non-invasive, especially the urine-based diagnosis of prostate cancer (PCa) remains challenging. Although prostate cancer antigen (PSA) is widely used in prostate cancer screening, the false positives may result in unnecessary invasive procedures. PSA elevated patients are triaged to further evaluation of free/total PSA ratio (f/t PSA), to find out potential clinically significant PCa before undergoing invasive procedures. Genomic instability, especially chromosomal copy number variations (CNVs) were proved much more tumor specific. Here we performed a prospective study to evaluate the diagnostic value of CNV via urine-exfoliated cell DNA analysis in PCa. Methods We enrolled 28 PSA elevated patients (≥ 4 ng/ml), including 16 PCa, 9 benign prostate hypertrophy (BPH) and 3 prostatic intraepithelial neoplasia (PIN). Fresh initial portion urine was collected after hospital admission. Urine exfoliated cell DNA was analyzed by low coverage Whole Genome Sequencing, followed by CNV genotyping by the prostate cancer chromosomal aneuploidy detector (ProCAD). CNVs were quantified in absolute z-score (|Z|). Serum free/total PSA ratio (f/t PSA) was reported altogether. Results In patients with PCa, the most frequent CNV events were chr3q gain (n = 2), chr8q gain (n = 2), chr2q loss (n = 4), and chr18q loss (n = 3). CNVs were found in 81.2% (95% Confidence Interval (CI) 53.7–95.0%) PCa. No CNV was identified in BPH patients. A diagnosis model was established by incorporating all CNVs. At the optimal cutoff of |Z|≥ 2.50, the model reached an AUC of 0.91 (95% CI 0.83–0.99), a sensitivity of 81.2% and a specificity of 100%. The CNV approach significantly outperformed f/t PSA (AUC = 0.62, P = 0.012). Further analyses showed that the CNV positive rate was significantly correlated with tumor grade. CNVs were found in 90.9% (95% CI 57.1–99.5%) high grade tumors and 60.0% (95% CI 17.0–92.7%) low grade tumors. No statistical significance was found for patient age, BMI, disease history and family history. Conclusions Urine exfoliated cells harbor enriched CNV features in PCa patients. Urine detection of CNV might be a biomarker for PCa diagnosis, especially in terms of the clinically significant high-grade tumors.

Abstract Background We aimed to build a common terminology in the domain of cervical cancer, named Cervical Cancer Common Terminology (CCCT), that will facilitate clinical data exchange, ensure quality of data and support large scale data analysis. Methods The standard concepts and relations of CCCT were collected from ICD-10-CM Chinese Version, ICD-9-PC Chinese Version, officially issued commonly used Chinese clinical terms, Chinese guidelines for diagnosis and treatment of cervical cancer and Chinese medical book Lin Qiaozhi Gynecologic Oncology. 2062 cervical cancer electronic medical records (EMRs) from 16 hospitals, belong to different regions and hospital tiers, were collected for terminology enrichment and building common terms and relations. Concepts hierarchies, terms and relationships were built using Protégé. The performance of natural language processing results was evaluated by average precision, recall, and F1-score. The usability of CCCT were evaluated by terminology coverage. Results A total of 880 standard concepts, 1182 common terms, 16 relations and 6 attributes were defined in CCCT, which organized in 6 levels and 11 classes. Initial evaluation of the natural language processing results demonstrated average precision, recall, and F1-score percentages of 96%, 72.6%, and 88.5%. The average terminology coverage for three classes of terms, clinical manifestation, treatment, and pathology, were 87.22%, 92.63%, and 89.85%, respectively. Flexible Chinese expressions exist between regions, traditions, cultures, and language habits within the country, linguistic variations in different settings and diverse translation of introduced western language terms are the main reasons of uncovered terms. Conclusions Our study demonstrated the initial results of CCCT construction. This study is an ongoing work, with the update of medical knowledge, more standard clinical concepts will be added in, and with more EMRs to be collected and analyzed, the term coverage will be continuing improved. In the future, CCCT will effectively support clinical data analysis in large scale.

The development and production of bread wheat (Triticum aestivum L.) are widely affected by drought stress worldwide. Many NAC transcription factors (TFs) of stress-associated group (SNAC) are functionally proven to regulate drought tolerance. In this study, we identified 41 TaSNACs that were classified into 14 groups, and the expression of TaSNAC4-3D was induced in the leaf tissue via osmotic or abscisic acid (ABA) treatment. TaSNAC4-3D was localized to the nucleus through the transient expression assay, and the C-terminal region exhibited transcriptional activity via transactivation assays. TaSNAC4-3D was overexpressed in common wheat. The wheat plants with TaSNAC4-3D overexpression was more sensitive to drought stress compared with wild-type (WT) plants. The water loss rate showed no difference between transgenic lines and WT plants. However, drought stress increased H2O2 and O2– accumulation and promoted programmed cell death (PCD) in the leaf tissue of TaSNAC4-3D overexpression lines compared with WT plants. RNA-seq analysis was performed under well-watered and drought conditions, and four strong potential target genes, encoding senescence regulators, were identified by analyzing their promoters containing the NAC recognition sequence (NACRS). Based on these results, our findings revealed that TaSNAC4-3D negatively regulates drought tolerance by inducing oxidative damage in bread wheat.

Introduction: The pathological rare category of thyroid is a type of lesion with a low incidence rate and is easily misdiagnosed in clinical practice, which directly affects a patient’s treatment decision. However, it has not been adequately investigated to recognize the rare, benign, and malignant categories of thyroid using the deep learning method and recommend the rare to pathologists.Methods: We present an empirical decision tree based on the binary classification results of the patch-based UNet model to predict rare categories and recommend annotated lesion areas to be rereviewed by pathologists.Results: Applying this framework to 1,374 whole-slide images (WSIs) of frozen sections from thyroid lesions, we obtained an area under a curve of 0.946 and 0.986 for the test datasets with and without WSIs, respectively, of rare types. However, the recognition error rate for the rare categories was significantly higher than that for the benign and malignant categories (p < 0.00001). For rare WSIs, the addition of the empirical decision tree obtained a recall rate and precision of 0.882 and 0.498, respectively; the rare types (only 33.4% of all WSIs) were further recommended to be rereviewed by pathologists. Additionally, we demonstrated that the performance of our framework was comparable to that of pathologists in clinical practice for the predicted benign and malignant sections.Conclusion: Our study provides a baseline for the recommendation of the uncertain predicted rare category to pathologists, offering potential feasibility for the improvement of pathologists’ work efficiency.

BackgroundDespite the effectiveness of chemotherapy and targeted therapy for colorectal cancer, drug resistance drives therapy failure and tumor relapse. Increasing evidence has suggested that cancer cells can enter a reversible drug-tolerant persister state to survive chemotherapy or targeted agents. However, the traits and treatable vulnerabilities of anti-colorectal cancer drug-tolerant persister cells is not yet known.MethodsIn this study, we established 5-fluorouracil and AZ628-tolerant persister cell models in two colorectal cancer cell lines, namely HCT116 and SW620, and revealed the characteristics of colorectal cancer persister cells by cell viability assay and flow cytometry. We investigated the efficacy and mechanism of ferroptosis inducers RSL3 and FIN56 on persister cells, which are glutathione peroxidase 4 inhibitors. In the xenograft mouse model, we further evaluated the inhibitory effect of RSL3 on tumor regrowth.ResultsColorectal cancer persister cells, which were enriched in the residual cancer cell population, exhibited reduced drug sensitivity, were largely quiescent and expressed high levels of stem cell-related genes and mesenchymal markers but not epithelial markers. The persister cells were more sensitive and underwent ferroptosis induced by glutathione peroxidase 4 inhibitors. Mechanistically, glutathione peroxidase 4 and ferrous iron, which are pivotal ferroptosis regulators, were upregulated in residual cells or tumors, and were hence potential therapeutic targets of persister cells. In the xenograft model, we confirmed that inhibition of glutathione peroxidase 4 restrained tumor regrowth after discontinuation of anti-cancer drug treatment. Moreover, biopsies obtained from patients with colorectal cancer undergoing neoadjuvant chemoradiotherapy revealed upregulated glutathione peroxidase 4 and ferritin heavy chain 1. High glutathione peroxidase 4 expression correlates with a worse prognosis in colorectal cancer patients.ConclusionsOur work reveals that the upregulated glutathione peroxidase 4 and ferrous iron in anti-colorectal cancer drug-tolerant persister cells were potential therapeutic targets. Glutathione peroxidase 4 inhibition combined with chemotherapy or targeted therapy may be a promising therapy for colorectal cancer.

Drip irrigation is fundamental in water-saving agricultural greenhouses, especially in tomato (Solanum lycopersicum L.) greenhouses. However, a long-term drip irrigation has been observed to be associated with soil degradation, concerning both soil aggregate structure and soil microbial community. To evaluate how drip irrigation scheduling influences the soil structure and arbuscular mycorrhizal fungi (AMF), a long-term irrigation experiment was carried out in a tomato greenhouse in 2011, using an irrigation program with dripping water starting when the soil reached a suction of 20 kPa (D20), 30 kPa (D30) and 40 kPa (D40). In 2017, we tested the AMF community and soil aggregate composition by soil wet sieving. Aggregates of 0.25–1 mm represented the main class of aggregates (32.4%–43.1%) in this experiment. At D30, we measured the highest mean weight diameter (MWD) and soil organic carbon (SOC) and glomalin-related soil protein (GRSP) levels. Thus, D30 promoted soil aggregate stability in the greenhouse. According to the high-throughput sequencing results of AMF, Glomus at D30 was the main factor leading to a high soil aggregate stability, because its OTU relative abundance was significantly higher than those of Ambispora and Paraglomus. Through redundancy analysis, the GRSP concentration was positively correlated with the SOC and total N (TN) levels and with the presence of the genera Ambispora, Glomus and Paraglomus. This evidenced that AMF and SOC helped to increase GRSP concentration and aggregate stability. Therefore, initiating irrigation when the soil reaches a water suction of 30 kPa could promote soil aggregate stability by favoring AMF abundance.

BackgroundTesticular sex cord stromal tumours (TSCSTs) are rare, with few studies focusing on the metastatic TSCST prognosis. The value of treatments, including radical orchiectomy (RO) and retroperitoneal lymph node dissection (RPLND), in preventing metastasis is controversial. Additionally, metastatic TSCSTs are resistant to chemotherapy. We aimed to assess the effectiveness and safety of immunotherapy in metastatic TSCSTs after first-line chemotherapy.MethodsWe retrospectively screened patients with testicular tumours undergoing testis surgery between January 2005 and January 2019. Patients with TSCSTs who had undergone testis-sparing surgery (TSS) or RO were identified. The malignant type was defined as metastasis confirmed by pathology. Treatment responses, progression-free survival (PFS), overall survival (OS) and safety were analysed.ResultsAmong the 494 testicular tumour patients who received TSS or RO, 11 (2.2%) patients with histologically proven TSCSTs were identified. At the last follow-up, 7 patients survived without tumours, and 4 patients developed metastasis and received first-line cisplatin-based chemotherapy, with 1 of them achieving an objective response. Their PFS times were 1.5, 2.2, 9.0, and 17.0 months, respectively. Two patients received immune checkpoint inhibitors (ICIs) after developing chemotherapy resistance and achieved a partial response up to the last follow-up; one of them experienced Grade 1 adverse events, and the other experienced Grade 2 adverse events during immunotherapy. The median OS time of the 4 patients with metastatic TSCSTs was 32 months.ConclusionsTSCSTs are rare, and most are benign with a good prognosis. ICIs represent a promising option for improving clinical outcomes in metastatic TSCSTs.

BackgroundNon-metastatic renal cell carcinoma (RCC) with tumor thrombus showed a greater tendency for developing metastases after surgery. Early identification of patients with high risk of poor prognosis is especially important to explore adjuvant treatment of improving outcomes. Neutrophil-to-lymphocyte ratio (NLR) was a systemic inflammation marker and outcome predictor in RCC, reflecting the chaos in systemic immune status in cancer as myeloid cell expansion and lymphatic cell suppression. Neutrophil extracellular traps (NET) formation (NETosis) is the process of neutrophils generating an extracellular DNA net-like structure. NETosis in tumor was demonstrated to conduce to the subsequent metastases of tumor. However, the role of NLR for systemic immune status and tumor local immune infiltration, especially for neutrophil-associated NETs, in non-metastatic RCC with thrombus remains unclear.Patients and MethodsIn our clinical cohort, we enrolled the clinical, pathologic, and preoperative laboratory parameters of 214 RCC patients with tumor thrombus who were treated surgically. The clinical endpoint was defined as cancer-specific survival (CSS). In our basic research cohort, RNA-seq, TCR-seq, and scRNA-seq data were analyzed. Patients who reached the endpoint as recurrence-free survival (RFS) were defined as the “High-risk” group. Otherwise, they were separated into the “Low-risk” group.ResultsIn the clinical cohort, NLR≥4 was an independent risk factor for 203 localized RCC with tumor thrombus. In the basic research cohort, tumor thrombi were separated into NETosis-thrombi belonging to the “High-risk” group and non-NETosis-thrombi to the “Low-risk” group. NETs induced by tumor-derived G-CSF in tumor thrombus has a mechanistic role in unfavorable prognosis. Besides, NETs-score from single sample GSEA (ssGSEA) algorithm was an independent prognostic factor validated in the TCGA data. Apart from the neutrophils-associated NETosis, systemic immune perturbations of lymphocytes occurred in the “High-risk” group, represented with decreased TCR diversity and increasingly high proportion of CD4-positive effector memory T (Tem) cells, which indirectly represented the state of lymphopenia.ConclusionsOur findings firstly demonstrated that neutrophils-associated NETosis and systemic lymphocytes perturbations were considered as tumor progression in patients of localized RCC with tumor thrombus, which reflected NLR≥4 as an independent risk factor for patients.

The objective of this study was to assess the impact of different tillage and organic fertiliser regimes on soil carbon fractions and bacterial community composition within a maize–wheat cropping system. We conducted a six-year experiment on the Huang-Huai-Hai Plain of China. Six treatments were established: deep tillage (DT), shallow tillage (ST), no-tillage (NT), deep tillage with organic fertiliser (DTF), shallow tillage with organic fertiliser (STF), and no-tillage with organic fertiliser (NTF). Results indicated that during the winter wheat growing season, the highest contents of soil organic carbon (SOC) and easily-oxidised organic carbon (EOC) were in the STF treatment. During the summer maizegrowing season, the DTF treatment had the highest SOC and EOC contents. Compared with the other treatments, the NTF treatment had higher Chao1 and Shannon indices for bacteria; however, the relative abundance of Proteobacteria is highest in all treatments. A redundancy analysis (RDA) revealed that bacterial community composition was correlated with variation of the SOC, DOC, EOC, and microbial biomass carbon (MBC). Our results showed that combining the two components of the SOC fractions and bacterial community composition, STF practice in a maize–wheat rotation was a sustainable approach to optimising soil structure and improving soil quality.

The dearth of glioblastoma model systems that accurately recapitulate the disease remains a challenge. Here, the authors develop cancer avatars using genetically engineered human induced pluripotent cells.

Winter wheat and summer maize rotation is the main cropping pattern in the North China Plain (NCP). There are still problems with farmers’ production modes, including shallow tillage layers, single application of chemical fertilizer causing plow bottom layer thickening and soil pH decrease. A two-factor location experiment was conducted to investigate the effects of different tillage and fertilization patterns on the soil physical properties, soil organic carbon (SOC), nitrogen-use efficiency, and crop yield of wheat–maize rotation systems during the years 2018–2020. The different treatments were deep tillage + organic fertilizer (DTF), shallow tillage + organic fertilizer (STF), no tillage + organic fertilizer (NTF), deep tillage + nitrogen fertilizer (DT), shallow tillage + nitrogen fertilizer (ST), and no tillage + nitrogen fertilizer (NT). The results showed that STF treatment could effectively improve the physical properties of soil and, SOC content, and increase both the crop yield and revenue of farmers. In the STF treatment, soil water content was highest in the 0–20 cm layer (2018), which was 4.89–11.31% higher than that of the other treatments; additional organic fertilizer application reduced soil bulk and increased the proportion of −1, which were 1.02–12.94% and 2.29–9.87% higher than those of the other treatments. Therefore, the suggested planting method in the NCP is tillage of over 20 cm and additional organic fertilizer.

BackgroundFinding effective prognostic signatures is of great urgency due to the high risk of recurrence and progression of bladder cancer (BC). Although a lot of genetic alterations are involved in the carcinogenesis, none of them were referred in the current risk group stratifications. In this study, we aimed to find significant copy number variations (CNVs) to predict prognosis for BC patients.MethodsCNVs with high aberration frequencies in BC were explored by array-based comparative genomic hybridization in 65 tumor samples. Candidates were validated in independent groups of BC tumor samples (n=219) and urine samples (n=123). 3D digital PCR was applied for detecting accurate gene copy numbers in BC urine. In order to explore the prognostic value of candidate CNVs, all enrolled patients were followed up for the disease-free survival (DFS). Cox proportional hazards regression analysis was performed to find the independent prognostic factors for DFS.ResultsCNVs of CEP63, FOSL2 and PAQR6 with high aberration frequencies (67.7%, 56.9% and 60.0%, respectively) were found in BC tumors. Copy numbers of CEP63, FOSL2 and PAQR6 were gained in 219 tumor samples. CNVs of CEP63 and FOSL2 were correlated with advanced tumor stage and high grade. Retrospective analysis (median follow-up time: 69 months) revealed that CNVs of CEP63 and FOSL2 were independent prognostic factors for DFS of non-muscle-invasive bladder cancer (NMIBC) patients, while CNVs of FOSL2 and PAQR6 were independent prognostic factors for DFS of muscle-invasive bladder cancer (MIBC) patients. Models for predicting DFS were constructed based on CNVs of three genes. Patients with high prognostic indexes tended to have poor DFS. Prognostic index can also help to identify those with worse outcomes among high risk NMIBC patients. Copy number gains of CEP63 and FOSL2 in urine were found to be significantly correlated with poor DFS of NMIBC patients.ConclusionsCNVs of CEP63, FOSL2 and PAQR6 were capable of predicting DFS and may serve as promising signatures for prognosis of BC.

Background: The relationship between the size of the primary tumor and the prognosis of patients with metastatic renal cell carcinoma (mRCC) is unclear. In this study, we aimed to investigate the significance of the size of the primary tumor in mRCC. Methods: We retrospectively reviewed the data of patients with mRCC who underwent cytoreductive nephrectomy (CN) from 2006 to 2013 in a Chinese center (n = 96) and those in the Surveillance, Epidemiology, and End Results (SEER) database (from 2004 to 2015, n = 4403). Tumors less than 4 cm in size were defined as small. Prognostic factors were analyzed using univariate and multivariate Cox proportional hazards regression analyses. Results: Patients with small tumors had a longer overall survival than other patients, both in the Chinese cohort (median, 30.0 vs 24.0 months, P = 0.026) and the SEER cohort (median, 43.0 vs 23.0 months, P < 0.001). After adjusting for other significant prognostic factors, small tumor size was still an independent protective factor in the Chinese cohort (adjusted hazard ratio [HR], 0.793; 95% confidence interval [CI]: 0.587–0.998, P = 0.043). In the SEER cohort, multivariate analysis showed that small tumor size was also an independent protective factor (HR, 0.880; 95% CI: 0.654–0.987, P = 0.008). In addition, as a continuous variable, a 1 cm elevation in tumor size translated into a 3.8% higher risk of death (HR, 1.038; 95% CI, 1.029–1.046; P < 0.001). Conclusion: Patients with small tumors may have a favorable prognosis after CN for mRCC. Although CN is not a standard protocol in mRCC, small tumor size may be a candidate when we are deciding to perform CN because of the potential benefit for OS.

Abstract Background Previous related studies have mainly focused on renal cell carcinoma (RCC) with venous tumor thrombus, specifically inferior vena cava tumor thrombus with renal vein tumor thrombus (RVTT). However, only a few studies have focused on postoperative long-term survival of RCC patients exclusively with RVTT. Our aim was to investigate the independent prognostic factors for locally advanced RCC with RVTT in China. Methods Patients with locally advanced RCC with RVTT were enrolled for the study from January 2000 to December 2015. All patients underwent radical nephrectomy. Survival analysis was estimated using Kaplan-Meier. Univariable and multivariable survival analyses were performed using COX. Patients were divided into high-risk, middle-risk, and low-risk groups based on independent prognostic factors and then analyzed for survival. Results One hundred twenty-eight consecutive patients (103 men & 25 women) were enrolled with a median age of 61 years. Thrombi were all graded 0 using the Mayo system, of which 23 were friable. None of the thrombi detached during surgery. 121 patients were successfully followed up, with a median follow-up period of 47 months. Median overall survival was 127 months (95%CI: 101–153). The 5-year and 10-year cancer-specific survival (CSS) rate was 67.9 and 57.0%. 59 patients had recurrence with median time of 40 months. Friable thrombus, paraneoplastic syndrome (PNS), modified Fuhrman grade 3/4 and perirenal fat invasion were independent prognostic factors (p

Abstract Background β3‐αC loop is a highly conserved structural domain across oncogene families, which is a switch for kinase activity. There have been numerous researches on mutations within β3‐αC loop in EGFR, but relatively less in ERBB2, BRAF, and MAP2K1. In addition, previous studies mainly focus on β3‐αC deletion in EGFR, which is the most common type affecting kinase activity and driving lung cancer. Other mutation types are not well studied. Methods Here we analyzed the profile of β3‐αC loop mutations in a total of 10,000 tumor biopsy and/or ctDNA patient samples using hybridization capture‐based next‐generation sequencing. Results We identified 1616 mutations within β3‐αC loop in this cohort. Most mutations were located in EGFR, with less percentage in ERBB2, BRAF, and MAP2K1. EGFR β3‐αC deletions occurred at a high percentage of 96.7% and were all drug‐relevant. We also detected rare EGFR β3‐αC insertions and point mutations, most of which were related to EGFR TKIs resistance. ERBB2 β3‐αC deletions were only found in breast cancers and sensitive to EGFR/ERBB2 inhibitor. Moreover, BRAF and MAP2K1 mutations within β3‐αC loop also demonstrated drugs relevance. Conclusion Our study showed that oncogenic mutations within the β3‐αC loop of ERBB2, MAP2K1, and BRAF are analogous to that of EGFR, which have profound effect on drug response. Understanding the mutation profile within the β3‐αC loop is critical for targeted therapies.

The root tissues play important roles in water and nutrient acquisition, environmental adaptation, and plant development. In this study, a diversity panel of 388 wheat accessions was collected to investigate nine root system architecture (RSA) traits at the three-leaf stage under two growing environments: outdoor pot culture (OPC) and indoor pot culture (IPC). Phenotypic analysis revealed that root development was faster under OPC than that under IPC and a significant correlation was observed between the nine RSA traits. The 660K single-nucleotide polymorphism (SNP) chip was used for a genome-wide association study (GWAS). Significant SNPs with a threshold of −log10 (p-value) ≥ 4 were considered. Thus, 36 quantitative trait loci (QTLs), including 13 QTL clusters that were associated with more than one trait, were detected, and 31 QTLs were first identified. The QTL clusters on chromosomes 3D and 5B were associated with four and five RSA traits, respectively. Two candidate genes, TraesCS2A01G516200 and TraesCS7B01G036900, were found to be associated with more than one RSA trait using haplotype analysis, and preferentially expressed in the root tissues. These favourable alleles for RSA traits identified in this study may be useful to optimise the root system in wheat.

Introduction: Sequential therapy with vascular endothelial growth factor receptor-tyrosine kinase inhibitors (VEGFR-TKIs) is effective in some patients with metastatic renal cell carcinoma (mRCC) progressed from or were intolerant to a prior TKIs. Anlotinib is a multi-kinase inhibitor targeting VEGFR1/2/3, PDGFR and FGFR, which has demonstrated efficacy and safety in first-line treatment of mRCC. This study assessed the potential of anloitnib as second-line treatment for patients with mRCC after prior one VEGFR-TKI.Methods: This is a single-arm, open-label, phase 2 study. Patients progressed after or were intolerant to sorafenib or sunitinib were enrolled. Anlotinib was administrated orally 12 mg once daily for 14 days every 3 weeks. The primary endpoint was progression-free survival (PFS). Secondary endpoints included overall survival (OS), objective response rate (ORR), safety and quality of life (QoL).Results: Forty three patients were enrolled and 42 received anlotinib, of whom 32 progressed after and 10 were intolerant to sorafenib or sunitinib. Median PFS were 14.0 months (95% CI 8.3–20.3) and 8.5 months (95% CI 5.6–16.6) for overall population and patients progressed after a previous VEGFR-TKI, respectively. Median OS was 21.4 months (95% CI 16.0–34.5), confirmed ORR and DCR were 16.7 and 83.3% in overall population. The most common adverse events included diarrhea (47.6%), hypertension (45.2%), hand and foot syndrome (42.9%), and fatigue (40.5%). Grade 3 hematological adverse events occurred in four cases, while no grade 4 hematological adverse events was observed.Conclusions: Anlotinib showed promising efficacy as well as favorable safety as second-line treatment for patients with mRCC.Clinical Trial Registration:www.ClinicalTrials.gov, identifier: NCT02072044.

Abstract In transmitted X-ray tomography imaging, the acquired projections may be corrupted for various reasons, such as defective detector cells and beam-stop array scatter correction problems. In this study, we derive a consistency condition for cone-beam projections and propose a method to restore lost data in corrupted projections. In particular, the relationship of the geometry parameters in circular trajectory cone-beam computed tomography (CBCT) is utilized to convert an ultra-hyperbolic partial differential equation (PDE) into a second-order PDE. The second-order PDE is then transformed into a first-order ordinary differential equation in the frequency domain. The left side of the equation for the newly derived consistency condition is the projection derivative of the current and adjacent views, whereas the right side is the projection derivative of the geometry parameters. A projection restoration method is established based on the newly derived equation to restore corrupted data in projections in circular trajectory CBCT. The proposed method is tested in beam-stop array scatter correction, metal artifact reduction, and abnormal pixel correction cases to evaluate the performance of the consistency condition and corrupted projection restoration method. Qualitative and quantitative results demonstrate that the present method has considerable potential in restoring lost data in corrupted projections.

PTEN mutations are frequent in glioblastoma and often are associated with therapeutic resistance. Here, the authors demonstrate that PTEN regulates gene expression at the chromatin level by interacting with the histone chaperone DAXX and H3.3, and that DAXX inhibition inhibits PTEN-deficient GBM growth in vivo.

Most renal cell carcinoma (RCC) patients die from metastasis or recurrence after the spread of cancer to another organ, but the mechanisms underlying the intravascular survival of circulating tumor cells (CTCs) have not been completely deciphered. Additionally, although elevated plasma C-reactive protein (CRP) levels and thrombocytosis are strongly correlated and both indicate a poor prognosis for RCC patients, the bridge connecting inflammation and coagulation remains poorly understood. To explore the complicated relationship among inflammation, the coagulation system and CTC survival, we obtained viable CTC counts and clinical information from 106 treatment-naïve patients. In addition, we performed RNA sequencing on peripheral blood leukocytes from 21 of these patients. Patients with elevated CRP and fibrinogen (FIB) levels had higher CTC counts than patients with normal levels of these indexes. Each pair of the three variables (CTC count, CRP level and FIB level) was positively correlated. According to transcriptomic analysis of blood leukocytes, the functions of the 257 genes identified as being positively correlated with the CTC count indicated neutrophil extracellular trap (NET) formation. Indeed, gene set enrichment analysis (GSEA) suggested that NET formation or increased levels of NET markers would promote CTC viability. Additionally, the calculated NET score was positively correlated with the plasma FIB concentration, and both of these values were increased in patients with elevated CRP levels. Moreover, immunofluorescence staining showed that NETs were entangled with viable renal cancer cells and that the NET frameworks were decorated with NET-derived tissue factor (TF). Finally, analysis of 533 RCC samples from The Cancer Genome Atlas (TCGA) indicated that the NET score and TF value are independent prognostic factors for RCC patients. Collectively, NETs formed by intravascular neutrophils further activate the coagulation system. Both the DNA scaffold sprouted and fibrin net triggered by NETs anchor and shield CTCs from attack. Thus, degrading this framework maybe could destroy the double shelter of CTCs, the pioneers of metastasis.

Bread wheat is one of the most important crops in the world. However, osmotic stress significantly inhibits wheat growth and development, and reduces crop yield and quality. Plants respond to osmotic stress mainly through abscisic acid (ABA)-dependent and -independent pathways. In this study, root transcriptome profiles of wheat seedlings exposed to osmotic stress and exogenous ABA were analysed to identify osmotic-responsive genes belonging to the ABA-dependent or -independent pathways. We found that osmotic stress promoted proline biosynthesis in the ABA-dependent pathway, and trehalose biosynthesis is likely promoted among soluble sugars to maintain protein bioactivity under osmotic stress. In wheat roots subjected to osmotic stress, calcium ions, and glutathione exert their functions mainly through calcium-binding protein (CaM/CML) and glutathione-S-transferase, respectively, depending on both pathways. In addition, a complex relationship among phytohormones signal transduction was observed in response to osmotic stress. The findings of this study deepen our understanding of the molecular mechanisms of osmotic-stress resistance, and provide several candidate osmotic-responsive genes for further study.

The NAC genes, a large plant-specific family of transcription factors, regulate a wide range of pathways involved in development and response to biotic and abiotic stress. In this study, the NAC transcription factors were identified in 27 green plants, and the results showed that NAC transcription factors in plants undergo an appearance stage from water to land and a number expansion stage from gymnosperm to angiosperm. Investigating the evolutionary process of the NAC transcription factors from diploid species to hexaploid wheat revealed that tandem replications during the polyploidization process is an important event for increasing the number of NAC transcription factors in wheat. Then, the molecular characteristics, phylogenetic relationships, and expression patterns of 462 NAC transcription factors of hexaploid wheat (TaNACs) were analyzed. The protein structure results showed that TaNAC was relatively conservative at the N-terminal that contains five subdomains. All these TaNACs were divided into Group I and Group II by phylogenetic analysis, and the TaNACs in Group I should undergo strong artificial selection based on single nucleotide polymorphism (SNP) analysis. Through genome synteny and phylogenetic analysis, these TaNACs were classified into 88 groups and 9 clusters. The biased expression results of these TaNACs showed that there are 24 groups and 67 groups of neofunctionalization genes under biotic and abiotic stress, respectively, and 16 groups and 59 groups of subfunctionalization genes. This shows that neofunctionalization plays an important role in coping with different stresses. Our study provides new insights into the evolution of NAC transcription factors in hexaploid wheat.

Cotton is an important economic crop, used mainly for the production of textile fiber. Using a space mutation breeding technique, a novel photosensitive genetic male sterile mutant CCRI9106 was isolated from the wild-type upland cotton cultivar CCRI040029. To study the male sterile mechanisms of CCRI9106, histological and iTRAQ-facilitated proteomic analyses of anthers were performed. This data article contains data related to the research article titled iTRAQ-Facilitated Proteomic Profiling of Anthers From a Photosensitive Male Sterile Mutant and Wild-type Cotton (Gossypium hirsutum L.) [1]. This research article describes the iTRAQ-facilitated proteomic analysis of the wild-type and a photosensitive male sterile mutant in cotton. The report indicated that exine formation defect is the key reason for male sterility in mutant plant. The information presented here represents the tables and figures that detail the processing of the raw data obtained from iTRAQ analysis.

An amendment to this paper has been published and can be accessed via a link at the top of the paper.

As a superfamily of transcription factors, the tryptophan-arginine-lysine-tyrosine (WRKY) transcription factors have been found to be essential for abiotic and biotic stress responses in plants. Currently, only 76 WRKY transcription factors in wheat could be identified in the NCBI database, among which only a few have been functionally analyzed. Herein, a total of 188 WRKY transcription factors were identified from the wheat genome database, which included 123 full-length coding sequences, and all of them were used for detailed evolution studies. By bioinformatics analysis, a WRKY transcription factor, named TaWRKY146, was found to be the homologous gene of AtWRKY46, overexpression of which leads to hypersensitivity to drought and salt stress in Arabidopsis. Consequently, the full length of TaWRKY146 was cloned, and the expression levels of TaWRKY146 were found significantly up-regulated in the leaves and roots of wheat seedlings, which were subjected to osmotic stress. Overexpression of TaWRKY146 in Arabidopsis was shown to enhance drought tolerance by the induction of stomatal closure that reduced the transpiration rate. All these results provide a firm foundation for further identification of WRKY transcription factors with important functions in wheat.

In this paper, we reconstructed the positive operator-valued measure (POVM) of a photon-number-resolving detector (PNRD) based on a multi-pixel photon counter (MPPC) by means of quantum detector tomography (QDT) at 791 nm and 523 nm, respectively. MPPC is a kind of spatial-multiplexing PNRD with a silicon avalanche photodiode (Si-APD) array as the photon receiver. Experimentally, the quantum characteristics of MPPC were calibrated at 2 MHz at two different wavelengths. The POVM elements were given by QDT. The fidelity of the reconstructed POVM elements is higher than 99.96%, which testifies that the QDT is reliable to calibrate MPPC at different wavelengths. With QDT and associated Wigner functions, the quantum properties of MPPC can be calibrated more directly and accurately in contrast with those conventional methods of modeling detectors.

Necrotic death of macrophages has long been known to be present in atherosclerotic lesions but has not been studied. We examined the role of receptor interacting protein (RIP) 3, a mediator of necrotic cell death, in atherosclerosis and found that RIP3−/−;Ldlr−/− mice were no different from RIP3+/+;Ldlr−/− mice in early atherosclerosis but had significant reduction in advanced atherosclerotic lesions. Similar results were observed in Apoe−/− background mice. Bone marrow transplantation revealed that loss of RIP3 expression from bone-marrow-derived cells is responsible for the reduced disease progression. While no difference was found in apoptosis between RIP3−/−;Ldlr−/− and RIP3+/+;Ldlr−/− mice, electron microscopy revealed a significant reduction of macrophage primary necrosis in the advanced lesions of RIP3−/− mice. In vitro cellular studies showed that RIP3 deletion had no effect on oxidized low-density lipoprotein (LDL)-induced macrophage apoptosis, but prevented macrophage primary necrosis occurring in response to oxidized LDL under caspase inhibition or RIP3 overexpression conditions. RIP3-dependent necrosis is not postapoptotic, and the increased primary necrosis in advanced atherosclerotic lesions most likely resulted from the increase of RIP3 expression. Our data demonstrate that primary necrosis of macrophages is proatherogenic during advanced atherosclerosis development.

Wheat is one of the most important crops in the world, and osmotic stress has become one of the main factors affecting wheat production. Understanding the mechanism of the response of wheat to osmotic stress would be greatly significant. In the present study, isobaric tag for relative and absolute quantification (iTRAQ) was used to analyze the changes of protein expression in the wheat roots exposed to different osmotic stresses. A total of 2,228 expressed proteins, including 81 differentially expressed proteins, between osmotic stress and control, were found. The comprehensive analysis of these differentially expressed proteins revealed that osmotic stress increased the variety of expressed proteins and suppressed the quantity of expressed proteins in wheat roots. Furthermore, the proteins for detoxifying and reactive oxygen species scavenging, especially the glutathione system, played important roles in maintaining organism balance in response to osmotic stress in wheat roots. Thus, the present study comprehensively describes the protein expression changes in wheat roots in response to osmotic stress, providing firmer foundation to further study the mechanism of osmotic resistance in wheat.

Nature Communications 8:15223 doi: (2017); Published 12 May 2017; Updated 25 May 2018 The originally published version of this Article contained an error in Fig. 1. In panel d, the uppermost western blot was inadvertently inverted during typesetting of the figure. This has now been corrected in boththe PDF and HTML versions of the Article.

BackgroundPrevious transcriptome profiling studies have investigated the molecular mechanisms of pollen and anther development, and identified many genes involved in these processes. However, only 51 anther ESTs of Upland cotton (Gossypium hirsutum) were found in NCBI and there have been no reports of transcriptome profiling analyzing anther development in Upland cotton, a major fiber crop in the word.Methodology/principal findingNinety-eight hundred and ninety-six high quality ESTs were sequenced from their 3'-ends and assembled into 6,643 unigenes from a normalized, full-length anther cDNA library of Upland cotton. Combined with previous sequenced anther-related ESTs, 12,244 unigenes were generated as the reference genes for digital gene expression (DGE) analysis. The DGE was conducted on anthers that were isolated at tetrad pollen (TTP), uninucleate pollen (UNP), binucleate pollen (BNP) and mature pollen (MTP) periods along with four other tissues, i.e., roots (RO), stems (ST), leaves (LV) and embryos (EB). Through transcriptome profiling analysis, we identified 1,165 genes that were enriched at certain anther development periods, and many of them were involved in starch and sucrose metabolism, pentose and glucuronate interconversion, flavonoid biosynthesis, and ascorbate and aldarate metabolism.Conclusions/significanceWe first generated a normalized, full-length cDNA library from anthers and performed transcriptome profiling analysis of anther development in Upland cotton. From these results, 10,178 anther expressed genes were identified, among which 1,165 genes were stage-enriched in anthers. And many of these stage-enriched genes were involved in some important processes regulating anther development.