bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-native Brachiaria humidicola with biological nitrification inhibition capacity stimulates in situ grassland N2O emissions
Authors: Xie Lu , Liu Deyan , Chen Zengming , Niu Yuhui , Meng Lei , Ding Weixin 
Published: March 2023

IntroductionBrachiaria humidicola, a tropical grass, could release root exudates with biological nitrification inhibition (BNI) capacity and reduce soil nitrous oxide (N2O) emissions from grasslands. However, evidence of the reduction effect in situ in tropical grasslands in China is lacking.MethodsTo evaluate the potential effects of B. humidicola on soil N2O emissions, a 2-year (2015–2017) field experiment was established in a Latosol and included eight treatments, consisting of two pastures, non-native B. humidicola and a native grass, Eremochloa ophiuroide, with four nitrogen (N) application rates. The annual urea application rates were 0, 150, 300, and 450 kg N ha−1.ResultsThe average 2-year E. ophiuroides biomass with and without N fertilization were 9.07–11.45 and 7.34 t ha−1, respectively, and corresponding values for B. humidicola increased to 31.97–39.07 and 29.54 t ha−1, respectively. The N-use efficiencies under E. ophiuroide and B. humidicola cultivation were 9.3–12.0 and 35.5–39.4%, respectively. Annual N2O emissions in the E. ophiuroides and B. humidicola fields were 1.37 and 2.83 kg N2O-N ha−1, respectively, under no N fertilization, and 1.54–3.46 and 4.30–7.19 kg N2O-N ha−1, respectively, under N fertilization.DiscussionsAccording to the results, B. humidicola cultivation increased soil N2O emissions, especially under N fertilization. This is because B. humidicola exhibited the more effective stimulation effect on N2O production via denitrification primarily due to increased soil organic carbon and exudates than the inhibition effect on N2O production via autotrophic nitrification. Annual yield-scaled N2O emissions in the B. humidicola treatment were 93.02–183.12 mg N2O-N kg−1 biomass, which were significantly lower than those in the E. ophiuroides treatment. Overall, our results suggest that cultivation of the non-native grass, B. humidicola with BNI capacity, increased soil N2O emissions, while decreasing yield-scaled N2O emissions, when compared with native grass cultivation.
Functional metagenomics uncovers nitrile-hydrolysing enzymes in a coal metagenome
Authors: Achudhan Arunmozhi Bharathi , Kannan Priya , Saleena Lilly M. 
Published: March 2023

Introduction: Nitriles are the most toxic compounds that can lead to serious human illness through inhalation and consumption due to environmental pollution. Nitrilases can highly degrade nitriles isolated from the natural ecosystem. In the current study, we focused on the discovery of novel nitrilases from a coal metagenome using in silico mining.Methods: Coal metagenomic DNA was isolated and sequenced on the Illumina platform. Quality reads were assembled using MEGAHIT, and statistics were checked using QUAST. Annotation was performed using the automated tool SqueezeMeta. The annotated amino acid sequences were mined for nitrilase from the unclassified organism. Sequence alignment and phylogenetic analyses were carried out using ClustalW and MEGA11. Conserved regions of the amino acid sequences were identified using InterProScan and NCBI-CDD servers. The physicochemical properties of the amino acids were measured using ExPASy’s ProtParam. Furthermore, NetSurfP was used for 2D structure prediction, while AlphaFold2 in Chimera X 1.4 was used for 3D structure prediction. To check the solvation of the predicted protein, a dynamic simulation was conducted on the WebGRO server. Ligands were extracted from the Protein Data Bank (PDB) for molecular docking upon active site prediction using the CASTp server.Results and discussion:In silico mining of annotated metagenomic data revealed nitrilase from unclassified Alphaproteobacteria. By using the artificial intelligence program AlphaFold2, the 3D structure was predicted with a per-residue confidence statistic score of about 95.8%, and the stability of the predicted model was verified with molecular dynamics for a 100-ns simulation. Molecular docking analysis determined the binding affinity of a novel nitrilase with nitriles. The binding scores produced by the novel nitrilase were approximately similar to those of the other prokaryotic nitrilase crystal structures, with a deviation of ±0.5.
Drug repurposing using meta-analysis of gene expression in Alzheimer’s disease
Authors: Jang Ha Young , Oh Jung Mi , Kim In-Wha 
Published: March 2023

IntroductionAlzheimer’s disease and other forms of dementia are disease that bring an increased global burden. However, the medicine developed to date remains limited. The purpose of this study is to predict drug repositioning candidates using a computational method that integrates gene expression profiles on Alzheimer’s disease and compound-induced changes in gene expression levels.MethodsGene expression data on Alzheimer’s disease were obtained from the Gene Expression Omnibus (GEO) and we conducted a meta-analysis of their gene expression levels. The reverse scores of compound-induced gene expressions were computed based on the reversal relationship between disease and drug gene expression profiles.ResultsReversal genes and the candidate compounds were identified by the leave-one-out cross-validation procedure. Additionally, the half-maximal inhibitory concentration (IC50) values and the blood-brain barrier (BBB) permeability of candidate compounds were obtained from ChEMBL and PubChem, respectively.ConclusionNew therapeutic target genes and drug candidates against Alzheimer’s disease were identified by means of drug repositioning.
A phase I dose-escalation study of neoantigen-activated haploidentical T cell therapy for the treatment of relapsed or refractory peripheral T-cell lymphoma
Authors: Chen Yuan , Zhao Hu , Luo Jing , Liao Youping , Dan Xu , Hu Guoyu , Gu Weiyue 
Published: March 2023

Peripheral T-cell lymphoma (PTCL) is a type of highly heterogeneous non-Hodgkin lymphoma with a poor prognosis and lack of effective targeted therapies. Adoptive T-cell therapy has been successfully used in the treatment of B-cell malignancies. We first used adoptive transfer of haploidentical T cells activated by patient-specific neoantigens in vitro to treat an elderly patient with refractory angioimmunoblastic T-cell lymphoma (AITL) in 2017, and the patient achieved long-term complete remission (CR). Here we report on early results from this first-in-human phase 1 clinical trial that aims to assess the safety and tolerability of neoantigen-activated haploidentical T cell therapy (NAHTC) for relapsed/refractory PTCL.Clinical trial registrationhttp://www.chictr.org.cn/index.aspx, identifier [ChiCTR1800017440].
Adjuvant therapy for cholangiocarcinoma after surgery and prognosis factors for cholangiocarcinoma: A single-center retrospective cohort study
Authors: Sun Zhongquan , Han Xin , You Wanlu , Tang Jinlong , Xu Juehua , Ye Binglin , Li Tengfei , Zhang Yixin , Chen Kai , Ding Yuan , Wang Weilin 
Published: March 2023

BackgroundCholangiocarcinoma (CCA) is a highly heterogeneous malignant tumor, and more than 60% of patients have recurrence and metastasis after surgery. The efficacy of postoperative adjuvant therapy for CCA remains unclear. This study aimed to explore whether adjuvant therapy benefits patients with CCA and examine the independent prognostic factors for overall survival (OS) and progression-free survival (PFS).MethodsPatients with CCA undergoing surgery were retrospectively enrolled in this study from June 2016 to June 2022. The chi-square test or Fisher exact test was used to analyze the correlation between clinicopathologic characteristics. Survival curves were plotted using the Kaplan-Meier method, and the Cox regression model was used for univariate and multivariate analysis to search for independent prognostic factors.ResultsOf the 215 eligible patients, 119 patients received adjuvant therapy, and the other 96 patients did not. The median follow-up was 37.5 months. The median OS of CCA patients with and without adjuvant therapy was 45 and 18 months (P &lt; 0.001), respectively. The median PFS of CCA patients with and without adjuvant therapy was 34 and 8 months (P &lt; 0.001), respectively. The Cox univariate and multivariate regression analysis showed that preoperative aspartate transaminase and carbohydrate antigen 19-9, microvascular invasion, lymph node metastasis, differentiation degree, and adjuvant therapy were independent prognostic factors for OS (all P values &lt; 0.05). Preoperative carbohydrate antigen 125, microvascular invasion, lymph node metastasis, differentiation degree, and adjuvant therapy were independent prognostic factors for PFS (all P values &lt; 0.05). The stratified analysis by TMN stage detected significant differences in the early stages (median OS [mOS]: P = 0.0128; median PFS [mPFS]: P = 0.0209) and advanced stages (mOS and mPFS: both P values &lt; 0.001). Adjuvant therapy was also identified as a significantly favorable prognostic factor for OS and PFS in the early stages and advanced stages.ConclusionPostoperative adjuvant therapy can improve the prognosis of patients with CCA, even in the early stages and advanced stages. All data suggest that adjuvant therapy should be incorporated into the treatment of CCA in all cases, where appropriate.
Emergency department use by patients who received chimeric antigen receptor T cell infusion therapy
Authors: Lipe Demis N. , Qdaisat Aiham , Chaftari Patrick , Wattana Monica K. , Krishnamani Pavitra P. , Reyes-Gibby Cielito , Yeung Sai-Ching J. 
Published: March 2023

BackgroundChimeric antigen receptor T cell infusion (CAR T) therapy has revolutionized the treatment of hematologic malignancies, but treatment-related toxicities are of concern. Understanding the timing and reasons for which patients present to the emergency department (ED) after CAR T therapy can assist with the early recognition and management of toxicities.MethodsA retrospective observational cohort study was conducted for patients who had undergone CAR T therapy in the past 6 months and visited the ED of The University of Texas MD Anderson Cancer Center between 04/01/2018 and 08/01/2022. The timing of presentation after CAR T product infusion, patient characteristics, and outcomes of the ED visit were examined. Survival analyses were conducted using Cox proportional hazards regression and Kaplan-Meier estimates.ResultsDuring the period studied, there were 276 ED visits by 168 unique patients. Most patients had diffuse large B-cell lymphoma (103/168; 61.3%), multiple myeloma (21/168; 12.5%), or mantle cell lymphoma (16/168; 9.5%). Almost all 276 visits required urgent (60.5%) or emergent (37.7%) care, and 73.5% of visits led to admission to the hospital or observation unit. Fever was the most frequent presenting complaint, reported in 19.6% of the visits. The 30-day and 90-day mortality rates after the index ED visits were 17.0% and 32.2%, respectively. Patients who had their first ED visit &gt;14 days after CAR T product infusion had significantly worse overall survival (multivariable hazard ratio 3.27; 95% confidence interval 1.29–8.27; P=0.012) than patients who first visited the ED within 14 days of CAR T product infusion.ConclusionCancer patients who receive CAR T therapy commonly visit the ED, and most are admitted and/or require urgent or emergent care. During early ED visits patients mainly present with constitutional symptoms such as fever and fatigue, and these early visits are associated with better overall survival.
Diagnosis of benign and malignant thyroid nodules by a dual-layer spectral detector CT-based nomogram
Authors: Yi Rongqi , Li Ting , Xie Gang , Li Kang 
Published: March 2023

IntroductionPreoperative diagnosis of benign and malignant thyroid nodules is crucial for appropriate clinical treatment and individual patient management. In this study, a double-layer spectral detector computed tomography (DLCT)-based nomogram for the preoperative classification of benign and malignant thyroid nodules was developed and tested. MethodsA total of 405 patients with pathological findings of thyroid nodules who underwent DLCT preoperatively were retrospectively recruited. They were randomized into a training cohort (n=283) and a test cohort (n=122). Information on clinical features, qualitative imaging features and quantitative DLCT parameters was collected. Univariate and multifactorial logistic regression analyses were used to screen independent predictors of benign and malignant nodules. A nomogram model based on the independent predictors was developed to make individualized predictions of benign and malignant thyroid nodules. Model performance was evaluated by calculating the area under the receiver operating characteristic curve (AUC), calibration curve and decision curve analysis(DCA). ResultsStandardized iodine concentration in the arterial phase, the slope of the spectral hounsfield unit(HU) curves in the arterial phase, and cystic degeneration were identified as independent predictors of benign and malignant thyroid nodules. After combining these three metrics, the proposed nomogram was diagnostically effective, with AUC values of 0.880 for the training cohort and 0.884 for the test cohort. The nomogram showed a better fit (all p &gt; 0.05 by Hosmer−Lemeshow test) and provided a greater net benefit than the simple standard strategy within a large range of threshold probabilities in both cohorts. DiscussionThe DLCT-based nomogram has great potential for the preoperative prediction of benign and malignant thyroid nodules. This nomogram can be used as a simple, noninvasive, and effective tool for the individualized risk assessment of benign and malignant thyroid nodules, helping clinicians make appropriate treatment decisions.
Robotic natural orifice specimen extraction surgery versus conventional robotic resection for patients with colorectal neoplasms
Authors: Li Linye , Liu Kuijie , Li Tiegang , Zhou Jiangjiao , Xu Shu , Yu Nanhui , Guo Zhushu , Yao Hongliang 
Published: March 2023

BackgroundLaparoscopic natural orifice specimen extraction surgery (NOSES) has been widely used in colorectal neoplasms. However, only a few studies have focused on robotic NOSES. This study compared the short-term clinical outcomes and long-term survival outcomes between robotic NOSES and conventional robotic resection (CRR) groups.MethodsFrom March 2016 to October 2018, a consecutive of 143 patients who underwent robotic sigmoid and rectal resection at the Department of Gastrointestinal Surgery, The Second Xiangya Hospital, Central South University, were considered for inclusion in this study. Propensity-score matching (PSM) was conducted to account for differences in the baseline characteristics. After PSM, 39 patients were included in the robotic NOSES group, and 39 patients in the CRR group. The baseline characteristics between the two groups were all balanced and comparable.ResultsPatients in the NOSES group experienced less intraoperative blood loss (p=0.001), lower requirements for additional analgesia (p=0.020), shorter time to first flatus (p=0.010), and a shorter time to first liquid diet (p=0.003) than the CRR group. The 3-year overall survival rates (NOSES: 92.3% vs. CRR: 89.7% p=1.000) and 3-year disease-free survival rates (NOSES: 82.1% vs. CRR: 84.6% p=0.761) between the two groups were comparable.ConclusionRobotic natural orifice specimen extraction surgery is a safe and feasible surgery for patients with colorectal neoplasms. Robotic NOSES is associated with better short-term clinical outcomes and similar long-term survival outcomes to conventional robotic resection.
Case report: Prader–Willi syndrome and inflammatory arthritis—An important consideration
Authors: Marelli Luca , Dallos Tomáš , Miserocchi Elisabetta , Nucci Paolo , Tombolini Beatrice , De Lucia Orazio , Gattinara Maurizio , Caporali Roberto , Marino Achille 
Published: March 2023

BackgroundPrader–Willi syndrome (PWS) is a multisystemic genetically determined disorder. Musculoskeletal manifestations are common in most patients. We report the cases of two children with PWS who developed inflammatory arthritis, complicated with chronic anterior bilateral uveitis in one case. To our knowledge, no previous reports of such an association exist.Case presentationCase 1 was of a 3-year-old girl diagnosed with PWS who developed arthritis of the right knee with morning stiffness, joint swelling, and limited range of motion. Other causes of arthritis were ruled out. Increased inflammatory markers, antinuclear antibody (ANA) positivity, and hypertrophic synovitis on ultrasound confirmed the diagnosis of inflammatory arthritis compatible with juvenile idiopathic arthritis (JIA). Despite the treatment with methotrexate, arthritis progressed, and etanercept was added. The patient reached and maintained articular remission while on combined MTX and etanercept treatment during 9 years of follow-up. Case 2 was of a 6-year-old boy diagnosed with PWS who developed arthritis of the right knee. Laboratory investigations showed mildly increased acute phase reactants, microcytic anemia, and ANA positivity at high titer (titer 1:1,280). Infectious and other causes of arthritis were excluded. Ultrasound confirmed the presence of joint effusion and synovial thickening, and synovial fluid analysis was consistent with inflammatory arthrosynovitis (white blood cell count of 14,200/µl) compatible with JIA. Shortly after the diagnosis, the ophthalmologic evaluation revealed the presence of bilateral anterior uveitis. Despite MTX and topical corticosteroid, ocular inflammation persisted and adalimumab was added. At the last follow-up, 9 months later, the child experienced inactivity of arthritis and uveitis with normal growth.ConclusionsWe aim to raise awareness of this possible association among pediatricians since arthritis might be underestimated due to high pain tolerance, behavioral disturbances, and other musculoskeletal abnormalities in PWS patients.
Retroperitoneal kaposiform hemangioendothelioma with kasabach-merritt phenomenon in children: A case report and review of the literature
Authors: Huo Junming , Chen Song , Li Jing , Liu Chengjun 
Published: March 2023

ObjectiveTo investigate the clinical features, diagnosis and treatment methods and prognosis of retroperitoneal Kaposiform hemangioendothelioma (R-KHE) in children.MethodsThe clinical data of an infant with R-KHE was retrospectively analyzed. Literature on R-KHE in pediatrics were retrieved in databases including Wanfang, CNKI and PubMed as of April 2022.ResultsA 1 month and 6 days female infant with R-KHE was reported. After the diagnosis was confirmed by biopsy and pathological examination, the patient was treated by interventional embolization, and a combined therapy with glucocorticoid, vincristine, sirolimus and propranolol. The patient has been followed up for 1 year and 2 months, and is still alive with tumor. Through literature search, a total of 15 children, together with the case in our report, were included. The main manifestations were diversity among those patients. 14 cases have combined Kasabach-Merritt phenomenon (KMP). 6 cases accepted surgery plus drug therapy. 4 cases accepted only surgery, and 4 cases only accepted drug therapy. While drug therapy plus radiotherapy were employed to 1 case. Improvement was observed in 11 cases, with significantly reduced tumor and survival with tumor. Tumor disappeared completely in 2 cases. While 2 cases suffered death.ConclusionR-KHE has diverse clinical presentations and non-specificity in symptoms and imaging examinations, and most cases accompanied with KMP. Methods for R-KHE treatment include surgical resection, interventional embolization and drug therapy. Close attention needs to be paid to the adverse reactions of the drug during the course of treatment.
Cinnamomi ramulus inhibits cancer cells growth by inducing G2/M arrest
Authors: Li Jing , Huang Hsi-Yuan , Lin Yang-Chi-Dung , Zuo Huali , Tang Yun , Huang Hsien-Da 
Published: March 2023

Introduction:Cinnamomi ramulus (CR) is one of the most widely used traditional Chinese medicine (TCM) with anti-cancer effects. Analyzing transcriptomic responses of different human cell lines to TCM treatment is a promising approach to understand the unbiased mechanism of TCM.Methods: This study treated ten cancer cell lines with different CR concentrations, followed by mRNA sequencing. Differential expression (DE) analysis and gene set enrichment analysis (GSEA) were utilized to analyze transcriptomic data. Finally, the in silico screening results were verified by in vitro experiments.Results: Both DE and GSEA analysis suggested the Cell cycle pathway was the most perturbated pathway by CR across these cell lines. By analyzing the clinical significance and prognosis of G2/M related genes (PLK1, CDK1, CCNB1, and CCNB2) in various cancer tissues, we found that they were up-regulated in most cancer types, and their down-regulation showed better overall survival rates in cancer patients. Finally, in vitro experiments validation on A549, Hep G2, and HeLa cells suggested that CR can inhibit cell growth by suppressing the PLK1/CDK1/ Cyclin B axis.Discussion: This is the first study to apply transcriptomic analysis to investigate the cancer cell growth inhibition of CR on various human cancer cell lines. The core effect of CR on ten cancer cell lines is to induce G2/M arrest by inhibiting the PLK1/CDK1/Cyclin B axis.