bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of organic fertilizer incorporation practices on crops yield, soil quality, and soil fauna feeding activity in the wheat-maize rotation system
Authors: Zhou Zhongkai , Zhang Siyu , Jiang Na , Xiu Weiming , Zhao Jianning , Yang Dianlin 
Published: November 2022

The decline in soil quality is becoming a significant process of soil degradation. Optimizing organic fertilizer incorporation practices in cropland is essential to enhancing crop productivity and soil health. However, that requires a comprehensive understanding of crop yield and soil quality reaction across an application gradient of organic fertilizer. We investigated the effect of organic fertilizer incorporation practices on crop yield, soil quality, and fauna feeding activity from fluvo-aquic soils on wheat (Triticum aestivum)-maize (Zea mays) rotation field. The six treatments included were unfertilized N control (UC), traditional chemical fertilizer application (TF, 600 N kg ha−1 year−1), and recommended chemical fertilization (RF, 400 N kg ha−1 year−1) with no organic fertilizer application rate, low-level 15.0 (RFLO), medium-level 30.0 (RFMO), and high-level 45.0 t ha−1 year−1(RFHO) application, respectively. The research findings show that the yield with organic fertilizer incorporation treatments increased 26.4%–44.6% for wheat and 12.5%–40.8% for maize compared to RF plots. The long-term organic fertilizer incorporation rate increased organic carbon from 54.7% to 110.6% versus UC plots and 27.9%–74.0% versus chemical fertilizer (TF and RF) treatments, and the total nitrogen content of soil increased from 41.8% to 59.2%, and 24.6%–39.2%. The long-term inorganic fertilizer combined with organic fertilizer incorporation practices significantly enhanced soil sucrose (30.1%–51.9%), urease (28.4%–38.3%), and β-1,4-glucosidase (34.6%–122.4%) activity. Still, nitrite reductase, polyphenol oxidase, and catalase significantly lower 27.3%–49.9%, 8.5%–26.3% and 23.3%–34.3% than single applications of inorganic N fertilizer groups. Meanwhile, the results showed that organic fertilizer incorporation practices improved soil fauna feeding activity by 35.2%–42.5%, and the excessive application of inorganic N fertilizer reduced the activity level of soil fauna.
Construction of an immune-related ceRNA network to screen for potential diagnostic markers for autism spectrum disorder
Authors: Sun Jing-Jing , Chen Bo , Yu Tao 
Published: November 2022

Purpose: The diagnosis of autism spectrum disorder (ASD) is reliant on evaluation of patients’ behavior. We screened the potential diagnostic and therapeutic targets of ASD through bioinformatics analysis.Methods: Four ASD-related datasets were downloaded from the Gene Expression Omnibus database. The “limma” package was employed to analyze differentially expressed messenger (m)RNAs, long non-coding (lnc)RNAs, and micro (mi)RNAs between ASD patients and healthy volunteers (HVs). We constructed a competing endogenous-RNA (ceRNA) network. Enrichment analyses of key genes were undertaken using the Gene Ontology database and Kyoto Encyclopedia of Genes and Genomes database. The ImmucellAI database was used to analyze differences in immune-cell infiltration (ICI) in ASD and HV samples. Synthetic analyses of the ceRNA network and ICI was done to obtain a diagnostic model using LASSO regression analysis. Analyses of receiver operating characteristic (ROC) curves were done for model verification.Results: The ceRNA network comprised 49 lncRNAs, 30 miRNAs, and 236 mRNAs. mRNAs were associated with 41 cellular components, 208 biological processes, 39 molecular functions, and 35 regulatory signaling pathways. Significant differences in the abundance of 10 immune-cell species between ASD patients and HVs were noted. Using the ceRNA network and ICI results, we constructed a diagnostic model comprising five immune cell-associated genes: adenosine triphosphate-binding cassette transporter A1 (ABCA1), DiGeorge syndrome critical region 2 (DGCR2), glucose-fructose oxidoreductase structural domain gene 1 (GFOD1), glutaredoxin (GLRX), and SEC16 homolog A (SEC16A). The diagnostic performance of our model was revealed by an area under the ROC curve of 0.923. Model verification was done using the validation dataset and serum samples of patients.Conclusion:ABCA1, DGCR2, GFOD1, GLRX, and SEC16A could be diagnostic biomarkers and therapeutic targets for ASD.
Construction and validation of an angiogenesis-related scoring model to predict prognosis, tumor immune microenvironment and therapeutic response in hepatocellular carcinoma
Authors: Tang Bo , Zhang Xinyuan , Yang Xiaozhou , Wang Wenling , Li Rongkuan , Liu Yu 
Published: November 2022

BackgroundHepatocellular carcinoma (HCC) is one of the most common malignant tumors in the world with high morbidity and mortality. Identifying an effective marker for predicting the prognosis and therapeutic response is extremely meaningful. Angiogenesis-related genes (ARGs) play important roles in the tumor progression and immune-suppressive microenvironment formation.MethodsThe differential expressed ARGs associated with the prognosis of HCC were identified in the TCGA dataset. Univariate Cox and least absolute shrinkage selection operator (LASSO) regression were applied to construct a ARGs Scoring model. The prognostic value of the ARGs Scoring model was assessed by Cox regression, Kaplan-Meier (KM) and ROC curve analyses. Then the model was further validated in an external dataset, ICGC dataset. The patients were split into two groups based on the ARGs Score and the clinical features were compared. TIMER, CIBERSORT and xCell algorithms were utilized to analyze the correlation between the ARGs Score and tumor immune microenvironment (TIME). Furthermore, we analyzed the efficacy of the model in predicting the therapeutic response for immunotherapy, targeted therapy and TACE treatment in different cohorts.ResultsA total of 97 differential expressed ARGs were identified relating to the prognosis of HCC patients from the TCGA dataset. Then the ARGs Scoring model based on a 9-gene signature was constructed using the Cox and LASSO regression analyses. Higher ARGs Score had a poor clinical outcome and was considered to be an independent prognostic predictor for HCC in the multivariate Cox analysis. The ARGs Score was related to the enrichment of various immune cells, such as CD4+ T cells, Treg, macrophage, neutrophil and dendritic cells, exhibiting a more immunosuppressive phenotype. Higher ARGs Score was correlated with higher expression of immune checkpoint genes and poor response to immunotherapy. Furthermore, higher ARGs Score indicated poor therapeutic response in the sorafenib and TACE treatment cohorts, individually.ConclusionsThe ARGs Scoring model exhibited robust predictive value for the prognosis and TIME for HCC patients. Higher ARGs Score indicated poor therapeutic response of the immunotherapy, sorafenib and TACE treatment. The ARGs Scoring model could be used as a biomarker to help physicians to develop more individualized treatment for HCC patients.
Comprehensive 18F-FDG PET-based radiomics in elevating the pathological response to neoadjuvant immunochemotherapy for resectable stage III non-small-cell lung cancer: A pilot study
Authors: Cui Yingpu , Lin Yaobin , Zhao Zerui , Long Hao , Zheng Lie , Lin Xiaoping 
Published: November 2022

PurposeTo develop a comprehensive PET radiomics model to predict the pathological response after neoadjuvant toripalimab with chemotherapy in resectable stage III non-small-cell lung cancer (NSCLC) patients.MethodsStage III NSCLC patients who received three cycles of neoadjuvant toripalimab with chemotherapy and underwent 18F-FDG PET/CT were enrolled. Baseline 18F-FDG PET/CT was performed before treatment, and preoperative 18F-FDG PET/CT was performed three weeks after the completion of neoadjuvant treatment. Surgical resection was performed 4–5 weeks after the completion of neoadjuvant treatment. Standardized uptake value (SUV) statistics features and radiomics features were derived from baseline and preoperative PET images. Delta features were derived. The radiologic response and metabolic response were assessed by iRECIST and iPERCIST, respectively. The correlations between PD-L1 expression, driver-gene status, peripheral blood biomarkers, and the pathological responses (complete pathological response [CPR]; major pathological response [MPR]) were assessed. Associations between PET features and pathological responses were evaluated by logistic regression.ResultsThirty patients underwent surgery and 29 of them performed preoperative PET/CT. Twenty patients achieved MPR and 16 of them achieved CPR. In univariate analysis, five SUV statistics features and two radiomics features were significantly associated with pathological responses. In multi-variate analysis, SUVmax, SUVpeak, SULpeak, and End-PET-GLDM-LargeDependenceHighGrayLevelEmphasis (End-GLDM-LDHGLE) were independently associated with CPR. SUVpeak and SULpeak performed better than SUVmax and SULmax for MPR prediction. No significant correlation, neither between the radiologic response and the pathological response, nor among PD-L1, driver gene status, and baseline PET features was found. Inflammatory response biomarkers by peripheral blood showed no difference in different treatment responses.ConclusionThe logistic regression model using comprehensive PET features contributed to predicting the pathological response after neoadjuvant toripalimab with chemotherapy in resectable stage III NSCLC patients.
Deep brain stimulation in Early Onset Parkinson's disease
Authors: Krause Patricia , Reimer Johanna , Kaplan Jonathan , Borngräber Friederike , Schneider Gerd-Helge , Faust Katharina , Kühn Andrea A. 
Published: November 2022

IntroductionSubthalamic Deep Brain Stimulation (STN-DBS) is a safe and well-established therapy for the management of motor symptoms refractory to best medical treatment in patients with Parkinson's disease (PD). Early intervention is discussed especially for Early-onset PD (EOPD) patients that present with an age of onset ≤ 45–50 years and see themselves often confronted with high psychosocial demands.MethodsWe retrospectively assessed the effect of STN-DBS at 12 months follow-up (12-MFU) in 46 EOPD-patients. Effects of stimulation were evaluated by comparison of disease-specific scores for motor and non-motor symptoms including impulsiveness, apathy, mood, quality of life (QoL), cognition before surgery and in the stimulation ON-state without medication. Further, change in levodopa equivalent dosage (LEDD) after surgery, DBS parameter, lead localization, adverse and serious adverse events as well as and possible additional clinical features were assessed.ResultsPD-associated gene mutations were found in 15% of our EOPD-cohort. At 12-MFU, mean motor scores had improved by 52.4 ± 17.6% in the STIM-ON/MED-OFF state compared to the MED-OFF state at baseline (p = 0.00; n = 42). These improvements were accompanied by a significant 59% LEDD reduction (p &lt; 0.001), a significant 6.6 ± 16.1 points reduction of impulsivity (p = 0.02; n = 35) and a significant 30 ± 50% improvement of QoL (p = 0.01). At 12-MFU, 9 patients still worked full- and 6 part-time. Additionally documented motor and/or neuropsychiatric features decreased from n = 41 at baseline to n = 14 at 12-MFU.ConclusionThe present study-results demonstrate that EOPD patients with and without known genetic background benefit from STN-DBS with significant improvement in motor as well as non-motor symptoms. In line with this, patients experienced a meaningful reduction of additional neuropsychiatric features. Physicians as well as patients have an utmost interest in possible predictors for the putative DBS outcome in a cohort with such a highly complex clinical profile. Longitudinal monitoring of DBS-EOPD-patients over long-term intervals with standardized comprehensive clinical assessment, accurate phenotypic characterization and documentation of clinical outcomes might help to gain insights into disease etiology, to contextualize genomic information and to identify predictors of optimal DBS candidates as well as those in danger of deterioration and/or non-response in the future.
Vestibular dysfunction is an important contributor to the aging of visuospatial ability in older adults–Data from a computerized test system
Authors: Zhang Xuehao , Huang Yan , Xia Yuqi , Yang Xiaotong , Zhang Yanmei , Wei Chaogang , Ying Hang , Liu Yuhe 
Published: November 2022

BackgroundA convergence of research supports a key role of the vestibular system in visuospatial ability. However, visuospatial ability may decline with age. This work aims to elucidate the important contribution of vestibular function to visuospatial ability in old adults through a computerized test system.MethodsPatients with a clinical history of recurrent vertigo and at least failed one vestibular test were included in this cross-sectional study. Healthy controls of three age groups: older, middle-aged, and young adults were also involved. Visuospatial cognitive outcomes including spatial memory, spatial navigation, and mental rotation of all the groups were recorded. Comparing the performance of the visuospatial abilities between patients and age-matched controls as well as within the controls.ResultsA total of 158 individuals were enrolled. Results showed that patients performed worse than the age-matched controls, with the differences in the forward span (p &lt; 0.001), the time of the maze 8 × 8 (p = 0.009), and the time of the maze 12 × 12 (p = 0.032) being significant. For the differences in visuospatial cognitive outcomes within the controls, the younger group had a significantly better performance than the other groups. The older group and the middle-aged group had comparable performances during all the tests.ConclusionsOlder patients with vestibular dysfunction had more difficulties during visuospatial tasks than age-matched controls, especially in spatial memory and spatial navigation. Within the controls, younger adults did much better than other age groups, while older adults behaved similarly to middle-aged adults. It is a valuable attempt to computerize the administration of tests for visuospatial ability.
Short-term and long-term outcomes in patients with cryptococcal meningitis after ventriculoperitoneal shunt placement
Authors: Wen Junxian , Yin Rui , Chang Jianbo , Chen Yihao , Dong Xiying , Cao Wei , Ma Xiaojun , Li Taisheng , Wei Junji 
Published: November 2022

ObjectiveThe purpose of this study was to assess the short-term and long-term outcomes of ventriculoperitoneal shunt (VPS) placement in patients with cryptococcal meningitis (CM).MethodsWe performed a retrospective analysis of all patients with CM admitted to the Peking Union Medical College Hospital from September 1990 to January 2021. We collected related clinical features to analyze the short- and long-term outcomes of VPS at 1 month and 1 year at least the following therapy, respectively. Overall survival (OS) was compared with all patients and a subgroup of critically ill cases by the Kaplan–Meier method with the log-rank test. Univariable and multivariable analyses were also performed using the Cox proportional hazard model to identify statistically significant prognostic factors.ResultsWe enrolled 98 patients, fifteen of whom underwent VPS. Those who received VPS had a lower cerebrospinal fluid (CSF) Cryptococcus burden (1:1 vs. 1:16; p = 0.046), lower opening pressures (173.3 mmH2 O vs. 224 mmH2O; p = 0.009) at lumbar punctures, and a lower incidence of critical cases (6.7 vs. 31.3%; p = 0.049). According to our long-term follow-up, no significant difference was shown in the Barthel Index (BI) between the two groups. Two patients in the VPS group suffered postoperative complications and had to go through another revision surgery. According to survival analysis, overall survival (OS) between the VPS and non-VPS groups was not significantly different. However, the Kaplan–Meier plots showed that critical patients with VPS had better survival in OS (p &lt; 0.009). Multivariable analyses for critical patients showed VPS was an independent prognostic factor.ConclusionA VPS could reduce the intracranial pressure (ICP), decrease the counts of Cryptococcus neoformans by a faster rate and reduce the number of critical cases. The VPS used in critical patients with CM has a significant impact on survival, but it showed no improvement in the long-term Barthel Index (BI) vs. the conservative treatment and could lead to postoperative complications.
Optimal modes of mind-body exercise for treating chronic non-specific low back pain: Systematic review and network meta-analysis
Authors: Shi Jian , Hu Zheng-Yu , Wen Yu-Rong , Wang Ya-Fei , Lin Yang-Yang , Zhao Hao-Zhi , Lin You-Tian , Wang Yu-Ling 
Published: November 2022

BackgroundThere were limited studies that directly compare the outcomes of various mind-body exercise (MBE) therapies on chronic non-specific low back pain (CNLBP).ObjectivesTo compare the efficacy of the four most popular MBE modes [Pilates, Yoga, Tai Chi (TC), and Qigong] in clinically CNLBP patients, we conducted a systematic review and network meta-analysis (NMA).MethodsWe searched databases for eligible randomized controlled trials (RCTs) (from origin to July 2022). RCTs were eligible if they included adults with CNLBP, and implemented one or more MBE intervention arms using Pilates, yoga, TC, and qigong. In addition, pain intensity and physical function were evaluated using validated questionnaires.ResultsNMA was carried out on 36 eligible RCTs involving 3,050 participants. The effect of exercise therapy on pain was in the following rankings: Pilates [Surface under cumulative ranking (SUCRA) = 86.6%], TC (SUCRA = 77.2%), yoga (SUCRA = 67.6%), and qigong (SUCRA = 64.6%). The effect of exercise therapy on function: Pilates (SUCRA = 98.4%), qigong (SUCRA = 61.6%,), TC (SUCRA = 59.5%) and yoga (SUCRA = 59.0%).ConclusionOur NMA shows that Pilates might be the best MBE therapy for CNLBP in pain intensity and physical function. TC is second only to Pilates in improving pain in patients with CNLBP and has the value of promotion. In the future, we need more high-quality, long-term follow-up RCTs to confirm our findings.Systematic review registrationhttps://www.crd.york.ac.uk/PROSPERO/display_record.php?RecordID=306905, identifier: CRD42022306905.
Development and validation of a prognostic 9-gene signature for colorectal cancer
Authors: Cui Junpeng , Guo Fangyu , Yu Yifan , Ma Zihuan , Hong Yuting , Su Junyan , Ge Yang 
Published: November 2022

IntroductionColorectal cancer (CRC) is one of the most prevalent cancers globally with a high mortality rate. Predicting prognosis using disease progression and cancer pathologic stage is insufficient, and a prognostic factor that can accurately evaluate patient prognosis needs to be developed. In this study, we aimed to infer a prognostic gene signature to identify a functional signature associated with the prognosis of CRC patients.MethodsFirst, we used univariate Cox regression, least absolute shrinkage and selection operator (lasso) regression, and multivariate Cox regression analyses to screen genes significantly associated with CRC patient prognosis, from colorectal cancer RNA sequencing data in The Cancer Genome Atlas (TCGA) database. We then calculated the risk score (RS) for each patient based on the expression of the nine candidate genes and developed a prognostic signature.ResultsBased on the optimal cut-off on the receiver operating characteristic (ROC) curve, patients were separated into high- and low-risk groups, and the difference in overall survival between the two groups was examined. Patients in the low-risk group had a better overall survival rate than those in the high-risk group. The results were validated using the GSE72970, GSE39582, and GSE17536 Gene Expression Omnibus (GEO) datasets, and the same conclusions were reached. ROC curve test of the RS signature also indicated that it had excellent accuracy. The RS signature was then compared with traditional clinical factors as a prognostic indicator, and we discovered that the RS signature had superior predictive ability.ConclusionThe RS signature developed in this study has excellent predictive power for the prognosis of patients with CRC and broad applicability as a prognostic indicator for patients.
Prognostic value of 18F-FDG PET/CT radiomic model based on primary tumor in patients with non-small cell lung cancer: A large single-center cohort study
Authors: Li Jihui , Zhang Bin , Ge Shushan , Deng Shengming , Hu Chunhong , Sang Shibiao 
Published: November 2022

ObjectivesIn the present study, we aimed to determine the prognostic value of the 18F-FDG PET/CT-based radiomics model when predicting progression-free survival (PFS) and overall survival (OS) in patients with non-small cell lung cancer (NSCLC).MethodsA total of 368 NSCLC patients who underwent 18F-FDG PET/CT before treatment were randomly assigned to the training (n = 257) and validation (n = 111) cohorts. Radiomics signatures from PET and CT images were obtained using LIFEx software, and then clinical and complex models were constructed and validated by selecting optimal parameters based on PFS and OS to construct radiomics signatures.ResultsIn the training cohort, the C-index of the clinical model for predicting PFS and OS in NSCLC patients was 0.748 and 0.834, respectively, and the AUC values ​​were 0.758 and 0.846, respectively. The C-index of the complex model for predicting PFS and OS was 0.775 and 0.881, respectively, and the AUC values ​​were 0.780 and 0.891, respectively. The C-index of the clinical model for predicting PFS and OS in the validation group was 0.729 and 0.832, respectively, and the AUC values ​​were 0.776 and 0.850, respectively. The C-index of the complex model for predicting PFS and OS was 0.755 and 0.867, respectively, and the AUC values ​​were 0.791 and 0.874, respectively. Moreover, decision curve analysis showed that the complex model had a higher net benefit than the clinical model.Conclusions18F-FDG PET/CT radiomics before treatment could predict PFS and OS in NSCLC patients, and the predictive power was higher when combined with clinical factors.