Effects of dairy processing sludge and derived biochar on greenhouse gas emissions from Danish and Irish soils.

Globally, to ensure food security bio-based fertilizers must replace a percentage of chemical fertilizers. Such replacement must be deemed sustainable from agronomic and greenhouse gas (GHG) emission perspectives. For agronomic performance several controlled protocols are in place but not for testing GHG emissions. Herein, a pre-screening tool is presented to examine GHG emissions from bio-waste as fertilizers. The various treatments examined are as follows: soil with added mineral nitrogen (N, 140 kg N ha-1) fertilizer (MF), the same amount of MF combined with dairy processing sludge (DS), sludge-derived biochar produced at 450 °C (BC450) and 700 °C (BC700) and untreated control (CK). These treatments were combined with Danish (sandy loam) or Irish (clay loam) soils, with carbon dioxide (CO2), methane (CH4) and nitrous oxide (N2O) emissions and soil inorganic-N contents measured on selected days. During the incubation, biochar mitigated N2O emissions by regulating denitrification. BC450 reduced N2O emissions from Danish soil by 95.5% and BC700 by 97.7% compared to emissions with the sludge application, and for Irish soil, the N2O reductions were 93.6% and 32.3%, respectively. For both soils, biochar reduced CO2 emissions by 50% as compared to the sludge. The lower N2O reduction potential of BC700 for Irish soil could be due to the high soil organic carbon and clay content and pyrolysis temperature. For the same reasons emissions of N2O and CO2 from Irish soil were significantly higher than from Danish soil. The temporal variation in N2O emissions was correlated with soil inorganic-N contents. The CH4 emissions across treatments were not significantly different. This study developed a simple and cost-effective pre-screening method to evaluate the GHG emission potential of new bio-waste before its field application and guide the development of national emission inventories, towards achieving the goals of circular economy and the European Green Deal.

Prediction of Individual Lymph Node Metastatic Status in Esophageal Squamous Cell Carcinoma Using Routine Computed Tomography Imaging: Comparison of Size-Based Measurements and Radiomics-Based Models.

BACKGROUND: Lymph node status is vital for prognosis and treatment decisions for esophageal squamous cell carcinoma (ESCC). This study aimed to construct and evaluate an optimal radiomics-based method for a more accurate evaluation of individual regional lymph node status in ESCC and to compare it with traditional size-based measurements. METHODS: The study consecutively collected 3225 regional lymph nodes from 530 ESCC patients receiving upfront surgery from January 2011 to October 2015. Computed tomography (CT) scans for individual lymph nodes were analyzed. The study evaluated the predictive performance of machine-learning models trained on features extracted from two-dimensional (2D) and three-dimensional (3D) radiomics by different contouring methods. Robust and important radiomics features were selected, and classification models were further established and validated. RESULTS: The lymph node metastasis rate was 13.2% (427/3225). The average short-axis diameter was 6.4 mm for benign lymph nodes and 7.9 mm for metastatic lymph nodes. The division of lymph node stations into five regions according to anatomic lymph node drainage (cervical, upper mediastinal, middle mediastinal, lower mediastinal, and abdominal regions) improved the predictive performance. The 2D radiomics method showed optimal diagnostic results, with more efficient segmentation of nodal lesions. In the test set, this optimal model achieved an area under the receiver operating characteristic curve of 0.841-0.891, an accuracy of 84.2-94.7%, a sensitivity of 65.7-83.3%, and a specificity of 84.4-96.7%. CONCLUSIONS: The 2D radiomics-based models noninvasively predicted the metastatic status of an individual lymph node in ESCC and outperformed the conventional size-based measurement. The 2D radiomics-based model could be incorporated into the current clinical workflow to enable better decision-making for treatment strategies.

Paclitaxel plus cisplatin and 5-fluorouracil induction chemotherapy for locally advanced borderline-resectable esophageal squamous cell carcinoma: a phase II clinical trial.

PURPOSE: This phase II trial aimed to assess the safety and efficacy of paclitaxel in combination with cisplatin and 5-fluorouracil (TPF) induction chemotherapy followed by surgery for locally advanced borderline-resectable esophageal squamous cell carcinoma (BR-ESCC). METHODS: Patients with primary tumor or bulky lymph nodes that might invade nearby organs were eligible. Treatment started with 2-3 cycles of TPF induction chemotherapy, followed by surgery if the tumor was assessed resectable, or by radical concurrent chemoradiotherapy if unresectable. The primary endpoint was pathologically proven complete resection (R0) rate. RESULTS: From July 2014 to February 2019, a total of 47 patients were enrolled. After TPF chemotherapy, 27 patients (57.4%) received surgery and 11 patients (23.4%) received radical concurrent chemoradiotherapy. R0 resection was confirmed in 25 patients (53.2%, 95% confidence interval (CI) 38.9-67.5%). Pathologic complete response was confirmed in four patients (8.5%). The median overall survival (OS) and progression-free survival (PFS) for all patients were 33.3 months and 20.3 months, respectively. The median OS was significantly more favorable in surgery group than in chemoradiotherapy and chemotherapy alone group [33.3 months vs 14.1 months, hazard ratio 0.32 (95% CI 0.12-0.88), p = 0.027]. During induction chemotherapy, the most common grade 3 or 4 toxicities were neutropenia (29.8%), leucopenia (21.3%) and stomatitis (4.3%). No serious postoperative complications were observed in patients undergoing surgery. CONCLUSIONS: The treatment strategy of induction chemotherapy followed by surgery is promising for patients with locally advanced BR-ESCC. To further improve the R0 resection rate, more effective induction chemotherapy regimens need to be explored. TRIAL REGISTRATION: ClinicalTrials.gov identifier: NCT02976909.

Using Genomics Feature Selection Method in Radiomics Pipeline Improves Prognostication Performance in Locally Advanced Esophageal Squamous Cell Carcinoma-A Pilot Study.

PURPOSE: To evaluate the prognostic value of baseline and restaging CT-based radiomics with features associated with gene expression in esophageal squamous cell carcinoma (ESCC) patients receiving neoadjuvant chemoradiation (nCRT) plus surgery. METHODS: We enrolled 106 ESCC patients receiving nCRT from two institutions. Gene expression profiles of 28 patients in the training set were used to detect differentially expressed (DE) genes between patients with and without relapse. Radiomic features that were correlated to DE genes were selected, followed by additional machine learning selection. A radiomic nomogram for disease-free survival (DFS) prediction incorporating the radiomic signature and prognostic clinical characteristics was established for DFS estimation and validated. RESULTS: The radiomic signature with DE genes feature selection achieved better performance for DFS prediction than without. The nomogram incorporating the radiomic signature and lymph nodal status significantly stratified patients into high and low-risk groups for DFS (p < 0.001). The areas under the curve (AUCs) for predicting 5-year DFS were 0.912 in the training set, 0.852 in the internal test set, 0.769 in the external test set. CONCLUSIONS: Genomics association was useful for radiomic feature selection. The established radiomic signature was prognostic for DFS. The radiomic nomogram could provide a valuable prediction for individualized long-term survival.

Evaluation of Fibrin Sealant in Prevention of Cervical Anastomotic Leakage After McKeown Esophagectomy: A Single-Center, Retrospective Study.

BACKGROUND: Anastomotic leakage remains an issue after esophagectomy for patients with esophageal or esophagogastric junction cancer. Previous studies have indicated that the intraoperative application of fibrin sealant may reduce the incidence of postoperative anastomotic leakage. This retrospective study was aimed to evaluate the efficacy and safety of fibrin sealant in the prevention of anastomotic leakage in patients undergoing McKeown esophagectomy. METHODS: We designed a single-center, retrospective study. Between January 2018 and December 2019, 227 patients with esophageal or esophagogastric junction cancer undergoing McKeown esophagectomy performed by our team were retrospectively identified, of whom 86 patients were included in the FS group and 141 patients were included in the control group. Intraoperatively, 2.5 ml of porcine fibrin sealant was applied circumferentially to the cervical anastomosis after the anastomosis was created in the FS group. The primary outcome was the incidence of cervical anastomotic leakage within the first three months after surgery. RESULTS: The differences in baseline clinical characteristics between the two groups were not significant except for a history of drinking. In the FS group, the postoperative cervical anastomotic leakage rate was lower (FS group: 4.7% [4 of 82] vs. control group: 19.9% [28 of 141], p < 0.01). Multivariate logistic regression showed that the intraoperative application of fibrin sealant was an independent protective factor for anastomotic leakage (OR 0.169, 95% CI 0.055-0.515, p = 0.002). CONCLUSIONS: The intraoperative application of fibrin sealant could possibly prevent cervical anastomotic leakage after McKeown esophagectomy with satisfactory safety. Further prospective clinical trials are warranted.

Phenotypic profiling and prognostic significance of immune infiltrates in esophageal squamous cell carcinoma.

The tumor microenvironment (TME) of esophageal squamous cell carcinoma (ESCC) impacts tumor progression but is poorly understood. We obtained tumor tissues from 279 patients after esophagectomy and characterized the TME in intraepithelial and stromal regions using multiplex fluorescent immunohistochemistry (mfIHC). A heterogeneous immune population infiltrating tumor and the uninvolved esophageal tissue were observed. The infiltration of intraepithelial programmed death ligand 1 (PD-L1)-positive tumor-associated macrophages (TAMs) and stromal granzyme B+ activated cytotoxic T cells (aCTLs) correlated with both prolonged overall survival (OS) and disease-free survival (DFS). The intraepithelial memory T cell infiltration predicted longer OS, while intraepithelial and stromal regulatory T cell (Treg) infiltration was associated with shortened OS and DFS, respectively. Multivariate models combining immune infiltrates and clinicopathological factors outperformed tumor-node-metastasis (TNM) stage in predicting OS and DFS at 3 and 5 years. The infiltration of Treg inversely correlated with that of the antitumor effectors including CTLs, aCTLs, and natural killer (NK) cells. Intraepithelial memory T cell infiltration also negatively correlated with PD-L1 expression. In spatial analysis, intraepithelial dendritic cell (DC)-memory T cell engagement increased in high PD-L1+ TAM infiltration group. The characterization of the TME revealed a complex interplay between immune populations and may be employed to stratify patient for prognosis prediction and immunotherapy.

Computed tomography-based deep-learning prediction of neoadjuvant chemoradiotherapy treatment response in esophageal squamous cell carcinoma.

BACKGROUND: Deep learning is promising to predict treatment response. We aimed to evaluate and validate the predictive performance of the CT-based model using deep learning features for predicting pathologic complete response to neoadjuvant chemoradiotherapy (nCRT) in esophageal squamous cell carcinoma (ESCC). MATERIALS AND METHODS: Patients were retrospectively enrolled between April 2007 and December 2018 from two institutions. We extracted deep learning features of six pre-trained convolutional neural networks, respectively, from pretreatment CT images in the training cohort (n = 161). Support vector machine was adopted as the classifier. Validation was performed in an external testing cohort (n = 70). We assessed the performance using the area under the receiver operating characteristics curve (AUC) and selected an optimal model, which was compared with a radiomics model developed from the training cohort. A clinical model consisting of clinical factors only was also built for baseline comparison. We further conducted a radiogenomics analysis using gene expression profiles to reveal underlying biology associated with radiological prediction. RESULTS: The optimal model with features extracted from ResNet50 achieved an AUC and accuracy of 0.805 (95% CI, 0.696-0.913) and 77.1% (65.6%-86.3%) in the testing cohort, compared with 0.725 (0.605-0.846)) and 67.1% (54.9%-77.9%) for the radiomics model. All the radiological models showed better predictive performance than the clinical model. Radiogenomics analysis suggested a potential association mainly with WNT signaling pathway and tumor microenvironment. CONCLUSIONS: The novel and noninvasive deep learning approach could provide efficient and accurate prediction of treatment response to nCRT in ESCC, and benefit clinical decision making of therapeutic strategy.

Assessment of Intratumoral and Peritumoral Computed Tomography Radiomics for Predicting Pathological Complete Response to Neoadjuvant Chemoradiation in Patients With Esophageal Squamous Cell Carcinoma.

Importance: For patients with locally advanced esophageal squamous cell carcinoma, neoadjuvant chemoradiation has been shown to improve long-term outcomes, but the treatment response varies among patients. Accurate pretreatment prediction of response remains an urgent need. Objective: To determine whether peritumoral radiomics features derived from baseline computed tomography images could provide valuable information about neoadjuvant chemoradiation response and enhance the ability of intratumoral radiomics to estimate pathological complete response. Design, Setting, and Participants: A total of 231 patients with esophageal squamous cell carcinoma, who underwent baseline contrast-enhanced computed tomography and received neoadjuvant chemoradiation followed by surgery at 2 institutions in China, were consecutively included. This diagnostic study used single-institution data between April 2007 and December 2018 to extract radiomics features from intratumoral and peritumoral regions and established intratumoral, peritumoral, and combined radiomics models using different classifiers. External validation was conducted using independent data collected from another hospital during the same period. Radiogenomics analysis using gene expression profile was done in a subgroup of the training set for pathophysiological explanation. Data were analyzed from June to December 2019. Exposures: Computed tomography-based radiomics. Main Outcomes and Measures: The discriminative performances of radiomics models were measured by area under the receiver operating characteristic curve. Results: Among the 231 patients included (192 men [83.1%]; mean [SD] age, 59.8 [8.7] years), the optimal intratumoral and peritumoral radiomics models yielded similar areas under the receiver operating characteristic curve of 0.730 (95% CI, 0.609-0.850) and 0.734 (0.613-0.854), respectively. The combined model was composed of 7 intratumoral and 6 peritumoral features and achieved better discriminative performance, with an area under the receiver operating characteristic curve of 0.852 (95% CI, 0.753-0.951), accuracy of 84.3%, sensitivity of 90.3%, and specificity of 79.5% in the test set. Gene sets associated with the combined model mainly involved lymphocyte-mediated immunity. The association of peritumoral area with response identification might be partially attributed to type I interferon-related biological process. Conclusions and Relevance: A combination of peritumoral radiomics features appears to improve the predictive performance of intratumoral radiomics to estimate pathological complete response after neoadjuvant chemoradiation in patients with esophageal squamous cell carcinoma. This study underlines the significant application of peritumoral radiomics to assess treatment response in clinical practice.

Fibrin sealant for esophageal anastomosis: A phase II study.

BACKGROUND: Esophagectomy is a pivotal curative modality for localized esophageal or esophagogastric junction cancer (EC or EJC). Postoperative anastomotic leakage (AL) remains problematic. The use of fibrin sealant (FS) may improve the strength of esophageal anastomosis and reduce the incidence of AL. AIM: To assess the efficacy and safety of applying FS to prevent AL in patients with EC or EJC. METHODS: In this single-arm, phase II trial (Clinicaltrial.gov identifier: NCT03529266), we recruited patients aged 18-80 years with resectable EC or EJC clinically staged as T1-4aN0-3M0. An open or minimally invasive McKeown esophagectomy was performed with a circular stapled anastomosis. After performing the anastomosis, 2.5 mL of porcine FS was applied circumferentially. The primary endpoint was the proportion of patients with AL within 3 mo. RESULTS: From June 4, 2018, to December 29, 2018, 57 patients were enrolled. At the data cutoff date (June 30, 2019), three (5.3%) of the 57 patients had developed AL, including two (3.5%) with esophagogastric AL and one (1.8%) with gastric fistula. The incidence of anastomotic stricture and other major postoperative complications was 1.8% and 17.5%, respectively. The median time needed to resume oral feeding after operation was 8 d (Interquartile range: 7.0-9.0 d). No adverse events related to FS were recorded. No deaths occurred within 90 d after surgery. CONCLUSION: Perioperative sealing with porcine FS appears safe and may prevent AL after esophagectomy in patients with resectable EC or EJC. Further phase III studies are warranted.

Comparison of Outcomes Between McKeown and Sweet Esophagectomy in the Elderly Patients for Esophageal Squamous Cell Carcinoma: A Propensity Score-Matched Analysis.

The aim of this study was to compare the perioperative outcomes and long-term survival rates of the McKeown and Sweet procedures in patients with esophageal cancer younger than 70 years or older than 70 years. A total of 1432 consecutive patients with esophageal squamous cell carcinoma (ESCC) who received surgery at Sun Yat-sen University Cancer Center from January 2009 to October 2012 were analyzed. Propensity score matching was used to balance the clinical characteristics of the patients who underwent different surgical approaches, and 275 and 71 paired cases were matched among those younger and older than 70 years, respectively. The prognosis and postoperative outcomes were compared between the McKeown and the Sweet esophagectomy. For patients younger than 70 years, those who underwent the McKeown procedure had better overall survival (OS) than those in the Sweet group (log rank = 4.467; P = .035). However, no significant difference in disease-free survival and OS was observed between two approaches for the elderly patients (log rank = 1.562; P = .211 and log rank = 0.668; P = .414, respectively). Cox regression analysis revealed that McKeown approach was a positive prognostic factor compared to the Sweet approach for patients younger than 70 years in univariable analysis (HR = 0.790; 95% CI, 0.625-0.997; P = .047), whereas the surgical approach was not significantly related to the prognosis in the elderly patients. For patients older than 70 years, the occurrence of anastomotic fistula increased in those who underwent the McKeown procedure (23.9% vs 11.3%, P = .038, for the McKeown and Sweet esophagectomy, respectively). The McKeown approach increases the OS in younger patients with ESCC. However, for patients older than 70 years, the Sweet approach was proven to be an effective therapy, given the better perioperative outcomes and similar long-term survival compared with patients in the McKeown group.

Clinical predictors of pathologically response after neoadjuvant chemoradiotherapy for esophageal squamous cell carcinoma: long term outcomes of a phase II study.

BACKGROUND: A pathologically complete response (pCR) or near pCR to neoadjuvant chemoradiotherapy (NCRT) might imply a better prognosis in patients with esophageal cancer. The aim of the study is to identify clinical factors associated with a pCR or near pCR. METHODS: We retrospectively analyzed 40 patients with radical esophagectomy after NCRT for esophageal squamous cell carcinoma (ESCC) from January 2001 to December 2006 in Sun Yat-sen University Cancer Center. Clinical factors included age, gender, weight loss, dysphagia, drinking status, smoking status, tumor location, tumor length, tumor grade, cT status, cN status, the regimen of chemotherapy and the interval between NCRT and surgery as potential predictors for a pCR or near pCR. Logistic regression was used to estimate the independent factors for a pCR or near pCR. RESULTS: After surgical resection, 22.5% of the patients obtained the pCR. Patients with pCR had a better prognosis than those with non-pCR. However, there was no statistically significantly difference between the two groups (P=0.124). We separated the patients into pCR or near pCR (good responders, GRs) and poor responders (PR) based on the histology. GR showed better overall survival (OS) than PR (P=0.014). Univariate analysis indicated that short tumor length, good tumor grade and never drinking were associated with GR to NCRT. Using logistic regression analysis, good tumor grade was the only independent factor for the GR to NCRT (P=0.021). Cox regression revealed that weight loss, drinking status and GR were independent factors in ESCC patients with radical esophagectomy after NCRT. CONCLUSIONS: Our study indicated that good tumor grade were an independent significant factor for the GR to NCRT. Weight loss, drinking status and GR were independent factors in patients with radical esophagectomy after NCRT. GR may improve OS of ESCC patients receiving NCRT.

DdrB stimulates single-stranded DNA annealing and facilitates RecA-independent DNA repair in Deinococcus radiodurans.

The bacterium Deinococcus radiodurans can survive extremely high exposure to ionizing radiation. The repair mechanisms involved in this extraordinary ability are still being investigated. ddrB is one gene that is highly up-regulated after irradiation, and it has been proposed to be involved in RecA-independent repair in D. radiodurans. Here we cloned, expressed and characterized ddrB in order to define its roles in the radioresistance of D. radiodurans. DdrB preferentially binds to single-stranded DNA. Moreover, it interacts directly with single-stranded binding protein of D. radiodurans DrSSB, and stimulates single-stranded DNA annealing even in the presence of DrSSB. The post-irradiation DNA repair kinetics of a ddrB/recA double mutant were compared to ddrB and recA single mutants by pulsed-field gel electrophoresis (PFGE). DNA fragment rejoining in the ddrB/recA double mutant is severely compromised, suggesting that DdrB-mediated single-stranded annealing plays a critical role in the RecA-independent DNA repair of D. radiodurans.

Characteristics of nuclease activity of the SbcCD complex from Deinococcus radiodurans.

The bacterium Deinococcus radiodurans is extremely resistant to the intense ionizing irradiation which causes extensive DNA double-strand breaks (DSBs). The deinococcal SbcCD complex (drSbcCD) is required for DSB repair. The drSbcC and drSbcD genes were cloned and overexpressed in Escherichia coli cells, respectively. The nearly homogeneous drSbcC and drSbcD proteins were purified and reconstituted to form a stable complex in vitro. The drSbcCD complex has an ATP-independent 3'-->5' exonuclease activity to cleave both dsDNA and ssDNA substrates in the presence of either Mn(2+) or Mg(2+) ion. The drSbcCD complex also has an ATP-independent endonuclease activity. It can cleave the circular ssDNA, nick the supercoiled circular dsDNA, cleave the 3' flap DNA substrate at the site of the single-strand branch adjacent to duplex DNA, and cleave the hairpin DNA taking no account of the DNA end free or not. It is a kind of secondary structure-specific endonuclease. The drSbcCD complex still has a 3'-->5' exonuclease activity when the DNA termini are blocked by the proteins. These results suggest that the drSbcCD complex takes part in the metabolism of DNA, and its nuclease activities may play important roles in DNA repair process.

Evolution of double MutT/Nudix domain-containing proteins: similar domain architectures from independent gene duplication-fusion events.

The MutT/Nudix superfamily proteins repair DNA damage and play a role in human health and disease. In this study, we examined two different cases of double MutT/Nudix domain-containing proteins from eukaryotes and prokaryotes. Firstly, these double domain proteins were discovered in Drosophila, but only single Nudix domain proteins were found in other animals. The phylogenetic tree was constructed based on the protein sequence of Nudix_N and Nudix_C from Drosophila, and Nudix from other animals. The phylogenetic analysis suggested that the double Nudix domain proteins might have undergone a gene duplication-speciation-fusion process. Secondly, two genes of the MutT family, DR0004 and DR0329, were fused by two mutT gene segments and formed double MutT domain protein genes in Deinococcus radiodurans. The evolutionary tree of bacterial MutT proteins suggested that the double MutT domain proteins in D. radiodurans probably resulted from a gene duplication-fusion event after speciation. Gene duplication-fusion is a basic and important gene innovation mechanism for the evolution of double MutT/Nudix domain proteins. Independent gene duplication-fusion events resulted in similar domain architectures of different double MutT/Nudix domain proteins.

Pleiotropic effects of RecQ in Deinococcus radiodurans.

In Deinococcus radiodurans, there is a unique RecQ homolog (DR1289) with three-tandem HRDC domains. Deletion of drrecQ resulted in a low doubling rate and sensitivity to hydrogen peroxide. Here, we used cDNA microarray and biochemical assays to explore the physiological changes in the drrecQ mutant. The expressions of genes with predicted functions involved in iron homeostasis, antioxidant system, electron transport, and energy metabolism were significantly altered in response to drrecQ disruption. More reactive oxygen species (ROS) was accumulated in drrecQ mutant strain when compared to wild type. In addition, ICP-MS results showed that the intracellular level of iron was relatively higher, whereas the concentration of manganese was lower in drrecQ mutant than in wild type. Furthermore, our microarray data and pulsed-field gel results showed that DNA suffered more damage in drrecQ mutant than in wild type under 20 mM hydrogen peroxide stress. These results suggested that drrecQ is a gene of pleiotropic functions and contributes to the extraordinary resistance of D. radiodurans against stresses.