bluuebunny/crossref_metadata_2025 huggingface dataset:
Nomogram models for the prognosis of cervical cancer: A SEER-based study
Authors: Jiang Kaijun , Ai Yiqin , Li Yanqing , Jia Lianyin
Published: October 2022

Background

Cervical cancer (CC) is one of the most common cancers in women. This study aimed to investigate the clinical and non-clinical features that may affect the prognosis of patients with CC and to develop accurate prognostic models with respect to overall survival (OS) and cancer-specific survival (CSS).

Methods

We identified 11,148 patients with CC from the SEER (Surveillance, Epidemiology, and End Results) database from 2010 to 2016. Univariate and multivariate Cox regression models were used to identify potential predictors of patients’ survival outcomes (OS and CSS). We selected meaningful independent parameters and developed nomogram models for 1-, 3-, and 5-year OS and CSS via R tools. Model performance was evaluated by C-index and receiver operating characteristic curve. Furthermore, calibration curves were plotted to compare the predictions of nomograms with observed outcomes, and decision curve analysis (DCA) and clinical impact curves (CICs) were used to evaluate the clinical effectiveness of the nomograms.

Results

All eligible patients (n=11148) were randomized at a 7:3 ratio into training (n=7803) and validation (n=3345) groups. Ten variables were identified as common independent predictors of OS and CSS: insurance status, grade, histology, chemotherapy, metastasis number, tumor size, regional nodes examined, International Federation of Obstetrics and Gynecology stage, lymph vascular space invasion (LVSI), and radiation. The C-index values for OS (0.831 and 0.824) and CSS (0.844 and 0.841) in the training cohorts and validation cohorts, respectively, indicated excellent discrimination performance of the nomograms. The internal and external calibration plots indicated excellent agreement between nomogram prediction and actual survival, and the DCA and CICs reflected favorable potential clinical effects.

Conclusions

We constructed nomograms that could predict 1-, 3-, and 5-year OS and CSS in patients with CC. These tools showed near-perfect accuracy and clinical utility; thus, they could lead to better patient counseling and personalized and tailored treatment to improve clinical prognosis.
Immune checkpoint inhibitors plus capecitabine and oxaliplatin in unresectable or advanced biliary tract cancer patients: A retrospective study
Authors: Zhao Jie , Guo Yongzhong , Ding Wenzhou , Han Guoyong , Jiang Chuanwei , Yang Chao , Hu Yuanchang , Zhang Long , Wu Chen , Ni Ming , Kong Xiangyi , Huang Tian , Zhang Chuanyong , Xia Yongxiang
Published: October 2022

Objective

Immune checkpoint inhibitors (ICIs) have recently been increasingly used in cancer treatment, whereas their clinical application in biliary tract cancer (BTC) patients is uncommon. This study aimed to evaluate the efficacy and safety of ICIs plus capecitabine and oxaliplatin (CAPOX) in the treatment of BTC patients.

Methods

This retrospective study reviewed 26 unresectable or advanced BTC patients who received ICIs plus CAPOX. The treatment continued until disease progression, uncontrollable adverse event (AE) occurrence, intolerable toxicity occurrence, or voluntary withdrawal.

Results

The median treatment cycles were 5.5 [interquartile range (IQR): 3.8–8.0]. Complete response, partial response, stable disease, and progressive disease rates were 0.0%, 46.2%, 23.1%, and 30.8%, respectively. Objective response rate (ORR) and disease control rate (DCR) were 46.2% and 69.2%, correspondingly. Regarding survival, the median progression-free survival (PFS) and overall survival (OS) were 6.1 (95% CI: 4.4–7.7) months and 16.5 (95% CI: 5.0–28.0) months; moreover, the 1-year PFS and OS rates were 21.5% and 54.3%, respectively. An Eastern Cooperative Oncology Group (ECOG) score of 1–3 (vs. 0) was associated with declined DCR, PFS, and OS (all p < 0.050). The most common AEs of ICIs plus CAPOX were thrombocytopenia (61.5%), neutropenia (26.9%), and reactive cutaneous capillary endothelial proliferation (RCCEP) (23.1%). Moreover, 13 (50.0%) patients suffered from grade 3–4 AEs, including thrombocytopenia (50.0%), neutropenia (7.7%), liver dysfunction (7.7%), and RCCEP (3.8%). Notably, the majority of AEs were controllable.

Conclusion

ICIs plus CAPOX chemotherapy exhibit a good efficacy and a manageable safety profile in the treatment of patients with unresectable or advanced BTC.
Prioritizing key synergistic circulating microRNAs for the early diagnosis of biliary tract cancer
Authors: Su Fei , Gao Ziyu , Liu Yueyang , Zhou Guiqin , Gao Wei , Deng Chao , Liu Yuyu , Zhang Yihao , Ma Xiaoyan , Wang Yongxia , Guan Lili , Zhang Yafang , Liu Baoquan
Published: October 2022

Biliary tract cancer (BTC) is a highly aggressive malignant tumor. Serum microRNAs (ser-miRNAs) serve as noninvasive biomarkers to identify high risk individuals, thereby facilitating the design of precision therapies. The study is to prioritize key synergistic ser-miRNAs for the diagnosis of early BTC. Sampling technology, significant analysis of microarrays, Pearson Correlation Coefficients, t-test, decision tree, and entropy weight were integrated to develop a global optimization algorithm of decision forest. The source code is available at https://github.com/SuFei-lab/GOADF.git. Four key synergistic ser-miRNAs were prioritized and the synergistic classification performance was better than the single miRNA’ s. In the internal feature evaluation dataset, the area under the receiver operating characteristic curve (AUC) for each single miRNA was 0.8413 (hsa-let-7c-5p), 0.7143 (hsa-miR-16-5p), 0.8571 (hsa-miR-17-5p), and 0.9365 (hsa-miR-26a-5p), respectively, whereas the synergistic AUC value increased to 1.0000. In the internal test dataset, the single AUC was 0.6500, 0.5125, 0.6750, and 0.7500, whereas the synergistic AUC increased to 0.8375. In the independent test dataset, the single AUC was 0.7280, 0.8313, 0.8957, and 0.8303, and the synergistic AUC was 0.9110 for discriminating between BTC patients and healthy controls. The AUC for discriminating BTC from pancreatic cancer was 0.9000. Hsa-miR-26a-5p was a predictor of prognosis, patients with high expression had shorter survival than those with low expression. In conclusion, hsa-let-7c-5p, hsa-miR-16-5p, hsa-miR-17-5p, and hsa-miR-26a-5p may act as key synergistic biomarkers and provide important molecular mechanisms that contribute to pathogenesis of BTC.
Case report: Atypical teratoid/rhabdoid tumor of the lateral ventricle in a male adolescent (case-based review and diagnostic challenges in developing countries)
Authors: Karim Akzhol , Shaikhyzada Kundyz , Suleimenova Assel , Ibraimov Bakytkali , Nurgaliev Dair , Poddighe Dimitri
Published: October 2022

Atypical teratoid/rhabdoid tumor (AT/RT) is a rare and highly malignant central nervous system (CNS) embryonal neoplasm: it accounts for <2% of all pediatric CNS tumors and occurs mainly in infants and young children. The primary site of this tumor is usually the posterior cranial fossa. Supratentorial and, in detail, latero-ventricular location is extremely uncommon, especially in adolescents. This tumor is characterized by rapid growth and spread in cerebrospinal fluid and, therefore, it is characterized by a poor prognosis. Neurological signs and symptoms are related the location of the tumor. The radiological features of AT/RT are nonspecific. Immunohistochemical staining for loss of nuclear integrase interactor 1 (INI1) expression is considered a reliable criterion for the diagnosis of this type of tumor. AT/RT has been linked to mutations of SMARCB1 or, rarely, SMARCA4 genes, which function as tumor suppressor genes. Currently, there is no validated protocol of treatment for children with AT/RT, and multimodality treatment (consisting of surgery, chemotherapy, and radiation therapy) is considered. In this case report, we describe a 15-year-old adolescent with an AT/RT of the left lateral ventricle. Despite the late diagnosis, the multimodal therapeutic approach provided a good outcome for our patient at 21 months’ follow-up. Based on our case-based review, early diagnosis and a multimodal approach to treatment play a key role in improving the survival of patients with this diagnosis. Implementing a system supporting pathological and molecular analyses for developing countries and, in general, for non-academic centers is of primary importance to timely diagnose and treat rare tumors, such as AT/RT.
Prediction model based on preoperative CT findings for carotid artery invasion in patients with head and neck masses
Authors: Zhao Yanfeng , Bao Dan , Wang Xiaoyi , Lin Meng , Li Lin , Zhu Zheng , Zhao Xinming , Luo Dehong
Published: October 2022

Objectives

To investigate the performance of a model in predicting carotid artery (CA) invasion in patients with head and neck masses using computed tomography (CT).

Methods

This retrospective study included patients with head and neck masses who underwent CT and surgery between January 2013 and July 2021. Patient characteristics and ten CT features were assessed by two radiologists. The patients were randomly allocated to a training cohort (n=106) and a validation cohort (n=109). Independent risk factors for CA invasion were assessed by univariate and multivariate logistic regression analyses. The predictive model was established as a nomogram using the training cohort. In addition, the calibration, discrimination, reclassification, and clinical application of the model were assessed in the validation cohort.

Results

A total of 215 patients were evaluated, including 54 patients with CA invasion. Vascular wall deformation (odds ratio [OR], 7.17; p=0.02) and the extent of encasement to the CA (OR, 1.02; p<0.001) were independent predictors of CA invasion in the multivariable analysis in the training cohort. The performance of the model was similar between the training and validation cohort, with an area under the receiver operating characteristic curve of 0.93 (95% confidence intervals [CI], 0.88-0.98) and 0.88 (95% CI, 0.80-0.96) (p=0.07), respectively. The calibration curve showed a good agreement between the predicted and actual probabilities.

Conclusion

A predictive model for carotid artery invasion can be defined based on features that come from patient characteristics and CT data to help in improve surgical planning and invasion evaluation.
Delta radiomics model for the prediction of progression-free survival time in advanced non-small-cell lung cancer patients after immunotherapy
Authors: Xie Dong , Xu Fangyi , Zhu Wenchao , Pu Cailing , Huang Shaoyu , Lou Kaihua , Wu Yan , Huang Dingpin , He Cong , Hu Hongjie
Published: October 2022

Objective

To assess the validity of pre- and posttreatment computed tomography (CT)-based radiomics signatures and delta radiomics signatures for predicting progression-free survival (PFS) in stage III-IV non-small-cell lung cancer (NSCLC) patients after immune checkpoint inhibitor (ICI) therapy.

Methods

Quantitative image features of the largest primary lung tumours were extracted on CT-enhanced imaging at baseline (time point 0, TP0) and after the 2nd-3rd immunotherapy cycles (time point 1, TP1). The critical features were selected to construct TP0, TP1 and delta radiomics signatures for the risk stratification of patient survival after ICI treatment. In addition, a prediction model integrating the clinicopathologic risk characteristics and phenotypic signature was developed for the prediction of PFS.

Results

The C-index of TP0, TP1 and delta radiomics models in the training and validation cohort were 0.64, 0.75, 0.80, and 0.61, 0.68, 0.78, respectively. The delta radiomics score exhibited good accuracy for distinguishing patients with slow and rapid progression to ICI treatment. The predictive accuracy of the combined prediction model was higher than that of the clinical prediction model in both training and validation sets (P<0.05), with a C-index of 0.83 and 0.70, respectively. Additionally, the delta radiomics model (C-index of 0.86) had a higher predictive accuracy compared to PD-L1 expression (C-index of 0.50) (P<0.0001).

Conclusions

The combined prediction model including clinicopathologic characteristics (tumour anatomical classification and brain metastasis) and the delta radiomics signature could achieve the individualized prediction of PFS in ICIs-treated NSCLC patients.
Immune checkpoint inhibitors in advanced and recurrent/metastatic cervical cancer
Authors: Han Xiling , Chang Wei-wei , Xia Xiaoping
Published: October 2022

Cervical cancer (CC) poses a serious threat to women’s health. Although many early-stage patients have a good prognosis, there are still a lack of effective therapies for advanced and recurrent/metastatic CC. In this context, immunotherapy and immune checkpoint inhibitors (ICIs) are particularly likely to play a role in the treatment of cervical tumors in a variety of disease settings. Some promising immune checkpoints include programmed cell death 1 (PD-1), programmed death ligand 1 (PD-L1) and cytotoxic T lymphocyte antigen 4 (CTLA-4), which exert immunomodulatory effects as negative regulators of T-cell activation and suppress immune responses in cervical cancer through cancer cell immune evasion. Initial trials of ICIs for CC have shown encouraging results in terms of objective response rate (ORR), progression-free survival (PFS), and overall survival (OS), both monotherapy and combination strategies. Meanwhile, human papillomavirus, vaginal microecology and intestinal microenvironment play an important role in CC, which provides new treatment directions. This review analyzed a number of completed or ongoing clinical trials of ICIs in the treatment of advanced and recurrent/metastatic CC. And we also analyzed the important relationship between vaginal microecology and intestinal microecology with CC and their related immunotherapy prospects.
Analysis of the effect of phototherapy on intestinal probiotics and metabolism in newborns with jaundice
Authors: Fan Sainan , Zhang Kun , Zhang Jiahui , Zhang Lei , Liu Lixiao , Lv Anping , Ma Yanan , Fang Xiaohui , Zheng Fang , Wu Zhimin , Zhang Jinping
Published: October 2022

Background

In clinical practice, oral probiotics are often given to children with hyperbilirubinaemia who receive phototherapy, but the exact mechanism of the action of the probiotics on hyperbilirubinaemia remains unclear. It is unclear how the effects of phototherapy on the probiotic flora in the neonatal gut, in particular.

Materials and methods

Fifty newborns who needed phototherapy from June 2018 to June 2020 were selected as the study subjects, and five healthy newborns in the same period were used as controls to analyse the changes in probiotic bacteria in their faeces.

Results

1. In the intestinal tracts of newborns, Bifidobacterium is the main probiotic strain, with a small amount of Lactobacillus. There were probiotic species changes in the neonatal intestinal microbiota after phototherapy for 24 and 48 h. The amount of Bifidobacterium and Lactobacillus decreased significantly (P < 0.05). 2. A correlation analysis of probiotic species and bile acid metabolism indexes showed that Bifidobacterium was positively correlated with many metabolites (P < 0.05), such as chenodeoxycholic acid, hyodeoxycholic acid, cholic acid, allocholic acid, and β-cholic acid. It was also negatively correlated with many metabolites (P < 0.05), such as glycocholic acid, sodium, sodium tudca, and chenodeoxycholic acid. Lactobacillus was negatively correlated with metabolites (P < 0.05) such as α-sodium cholate and β-cholic acid. 3. A correlation analysis between the changes in probiotics and intestinal short-chain fatty acid metabolites after phototherapy showed that acetic acid, butyric acid, caproic acid, and propionic acid decreased and were significantly correlated with Bifidobacterium (P < 0.05). 4. After phototherapy, 17 metabolites changed significantly (P < 0.05). This correlated with many probiotics (P < 0.05). The significantly changed probiotics in this study showed a significant correlation with some intestinal metabolites (P < 0.05).

Conclusion

It was found that phototherapy can significantly affect the intestinal probiotic flora and the metabolic indicators of newborns, which may be an important reason for the side effects of phototherapy, and also provides the theoretical basis for the provision of probiotics to newborns with jaundice.
Efficacy of the growing rod technique on kyphotic early-onset scoliosis
Authors: Cao Jiang , Zhang Xuejun , Cao Jun , Gao Rongxuan , Guo Dong
Published: October 2022

Objective

To explore the application of the growing rod (GR) technique in the treatment of kyphotic early-onset scoliosis (KEOS) and analyze its surgical efficacy and safety.

Methods

The clinical data of 30 children with KEOS who received GR treatment at our department between January 2016 and December 2019 were analyzed retrospectively. There were 18 cases with normal kyphosis (normal kyphosis group) and 12 cases with excessive kyphosis (excessive kyphosis group). Both groups received GR treatment, and all patients received anteroposterior and lateral spine X-ray examinations before, after the initial surgery, and at the final follow-up. The surgical conditions and imaging parameters of the two groups were compared, and the complications were recorded.

Results

There was no statistical difference in the Cobb angle of the major curve, apical vertebral translation (AVT), and trunk shift (TS) between the two groups before, after the first surgery, and at the final follow-up (P> 0.05). The Cobb angle of the major curve, the AVT, and the TS in both groups after the first surgery were lower than before the first surgery (P< 0.05), but there was no statistical difference between the two groups (P> 0.05). At the final follow-up, there were increases in both the Cobb angle and the AVT (P< 0.05), while the TS decreased in comparison with findings after the first surgery (P< 0.05). Before and after the first surgery and at the final follow-up appointment, there was a statistical difference in the degree of thoracic kyphosis (TK) between the two groups (P< 0.05), while there was no statistical difference in terms of lumbar lordosis (LL), the proximal junctional angle (PJA), and the distal junctional angle (DJA) (P> 0.05). After the first surgery, TK and LL showed a significant moderate response in both groups (P< 0.05), while there was no significant difference in TK, LL, PJA, and DJA compared with the results at the final follow-up (P> 0.05).

Conclusions

The use of the GR technique can improve kyphosis in KEOS treatment.
Farnesoid-X receptor as a therapeutic target for inflammatory bowel disease and colorectal cancer
Authors: Zhou Mengjiao , Wang Danfeng , Li Xiang , Cao Ying , Yi Chengxue , Wiredu Ocansey Dickson Kofi , Zhou Yuling , Mao Fei
Published: October 2022

Farnesoid-X receptor (FXR), as a nuclear receptor activated by bile acids, is a vital molecule involved in bile acid metabolism. Due to its expression in immune cells, FXR has a significant effect on the function of immune cells and the release of chemokines when immune cells sense changes in bile acids. In addition to its regulation by ligands, FXR is also controlled by post-translational modification (PTM) activities such as acetylation, SUMOylation, and methylation. Due to the high expression of FXR in the liver and intestine, it significantly influences intestinal homeostasis under the action of enterohepatic circulation. Thus, FXR protects the intestinal barrier, resists bacterial infection, reduces oxidative stress, inhibits inflammatory reactions, and also acts as a tumor suppressor to impair the multiplication and invasion of tumor cells. These potentials provide new perspectives on the treatment of intestinal conditions, including inflammatory bowel disease (IBD) and its associated colorectal cancer (CRC). Moreover, FXR agonists on the market have certain organizational heterogeneity and may be used in combination with other drugs to achieve a greater therapeutic effect. This review summarizes current data on the role of FXR in bile acid metabolism, regulation of immune cells, and effects of the PTM of FXR. The functions of FXR in intestinal homeostasis and potential application in the treatment of IBD and CRC are discussed.
MFDA: Multiview fusion based on dual-level attention for drug interaction prediction
Authors: Lin Kaibiao , Kang Liping , Yang Fan , Lu Ping , Lu Jiangtao
Published: October 2022

Drug-drug interaction prediction plays an important role in pharmacology and clinical applications. Most traditional methods predict drug interactions based on drug attributes or network structure. They usually have three limitations: 1) failing to integrate drug features and network structures well, resulting in less informative drug embeddings; 2) being restricted to a single view of drug interaction relationships; 3) ignoring the importance of different neighbors. To tackle these challenges, this paper proposed a multiview fusion based on dual-level attention to predict drug interactions (called MFDA). The MFDA first constructed multiple views for the drug interaction relationship, and then adopted a cross-fusion strategy to deeply fuse drug features with the drug interaction network under each view. To distinguish the importance of different neighbors and views, MFDA adopted a dual-level attention mechanism (node level and view level) to obtain the unified drug embedding for drug interaction prediction. Extensive experiments were conducted on real datasets, and the MFDA demonstrated superior performance compared to state-of-the-art baselines. In the multitask analysis of new drug reactions, MFDA obtained higher scores on multiple metrics. In addition, its prediction results corresponded to specific drug reaction events, which achieved more accurate predictions.
Effects of CYP2C19 genetic polymorphisms on the cure rates of H. pylori in patients treated with the proton pump inhibitors: An updated meta-analysis
Authors: Zhao Xianghong , Zhang Zhongqiu , Lu Fang , Xiong Mengqiu , Jiang Liping , Tang Ke , Fu Min , Wu Yu , He Bangshun
Published: October 2022

Background: The cure rates of Helicobacter pylori (H. pylori) treatment using a proton pump inhibitor (PPI) are gradually decreasing due to antibiotic resistance, poor compliance, high gastric acidity, and cytochrome P450 2C19 (CYP2C19) polymorphism, and the effects of PPI depend on metabolic enzymes, cytochrome P450 enzymes. The aim of this meta-analysis was to determine whether CYP2C19 polymorphisms affect H. pylori cure rates in patients treated with different proton pump inhibitors (PPIs) according to stratified analysis.

Materials and methods: The literature was searched with the key words “H. pylori” and “CYP2C19” in PubMed, CNKI, and Wanfang up to 31 May 2022, and the studies were limited to clinical observational or randomized controlled trials (RCTs). Finally, seven RCTs and 29 clinical observational studies met the inclusion criteria and were used for the meta-analysis via STATA version 16.

Results: The cure rates were significantly different between genotypes of homozygous extensive metabolizers (EM) and poor metabolizers (PM) (OR = 0.58, 95% CI: 0.47–0.71) and between EM and heterozygous extensive metabolizers (IM) (OR = 0.71, 95% CI: 0.59–0.86), but not between IM and PM. Moreover, there was a significantly lower H. pylori cure rate in EM subjects than that in IM subjects when treated with omeprazole (66.4% vs. 84.1%), lansoprazole (76.1% vs. 85.6%), but not rabeprazole, esomeprazole, or pantoprazole. In addition, there was a significantly lower H. pylori cure rate in EM subjects than that in IM subjects when treated with a PPIs for 7 days (77.4% vs. 82.1%), but not 14 days (85.4% vs. 90.0%).

Conclusion: Carriers of CYP2C19 loss-of-function variant alleles (IM and PM) exhibit a significantly greater cure rate of H. pylori than noncarriers (EM) regardless of other factors (84.7% vs. 79.2%). In addition, pantoprazole- and rabeprazole-based quadruple therapy for H. pylori treatment is less dependent on the CYP2C19 genotype and should be prioritized in Asian populations with H. pylori.
Multiple lump solutions of the (2+1)-dimensional sawada-kotera-like equation
Authors: Qi Feng-Hua , Li Shuang , Li Zhenhuan , Wang Pan
Published: October 2022

In this paper, 1-lump solution and 2-lump solution of a (2 + 1)-dimensional Sawada-Kotera-like equation are obtained by means of the Hirota’s bilinear method and long wave limit method. The propagation orbits, velocities and the collisions among waves are analyzed. By setting the parameter values, the dynamic characteristics of the obtained solutions are shown in 3D and density plots. These conclusions enrich the dynamical theory of higher-dimensional nonlinear dispersive wave equations.
The Research of Declining Factor and a New Model of Decline Rate for Gas Well Production in Low Permeability Reservoir
Authors: Wang Hua , Wu Yong , Fu Yu , Zhang Yunjun
Published: October 2022

The decline rate of gas wells varies with production time and is related to reservoir and working system. A typical single well numerical model of low permeability gas wells is established. The variation law of decline rate and its main influencing factors are studied by single factor analysis method. The results show that there are two stages of rapid and slow decline for the decline rate of gas wells, and the decline rate tends to be stable after the gas wells entering the decline period of 2–3 years; the decline rate increases with the increase of permeability, gas saturation and wellhead pressure, and decreases with the increase of porosity and well-controlled reserves; the decline rate in late production does not change with the change of reservoir thickness, initial production allocation and formation pressure. Then the decline rate model is and Then the decline rate model and the non-linear model of each factor are established by using response surface method are used to predict the decline rate quickly and accurately. According to the prediction model, the larger the well-controlled reserves, the smaller the permeability and the smaller the decline rate. In order to reduce production decline rate in gas well production process, it is suggested that the influence of various parameters on production decline rate should be considered comprehensively, and the well-controlled reserves of gas well should be increased as far as possible.
Review of Processing Pathological Vectorcardiographic Records for the Detection of Heart Disease
Authors: Vondrak Jaroslav , Penhaker Marek
Published: October 2022

Vectorcardiography (VCG) is another useful method that provides us with useful spatial information about the electrical activity of the heart. The use of vectorcardiography in clinical practice is not common nowadays, mainly due to the well-established 12-lead ECG system. However, VCG leads can be derived from standard 12-lead ECG systems using mathematical transformations. These derived or directly measured VCG records have proven to be a useful tool for diagnosing various heart diseases such as myocardial infarction, ventricular hypertrophy, myocardial scars, long QT syndrome, etc., where standard ECG does not achieve reliable accuracy within automated detection. With the development of computer technology in recent years, vectorcardiography is beginning to come to the forefront again. In this review we highlight the analysis of VCG records within the extraction of functional parameters for the detection of heart disease. We focus on methods of processing VCG functionalities and their use in given pathologies. Improving or combining current or developing new advanced signal processing methods can contribute to better and earlier detection of heart disease. We also focus on the most commonly used methods to derive a VCG from 12-lead ECG.
Construction of a highly saturated genetic map and identification of quantitative trait loci for leaf traits in jujube
Authors: Yan Fenfen , Luo Yujia , Bao Jingkai , Pan Yiling , Wang Jiurui , Wu Cuiyun , Liu Mengjun
Published: October 2022

Chinese jujube (Ziziphus jujuba Mill.), a member of the genus Ziziphus, which comes under the family Rhamnaceae, is the most important species in terms of its economic, ecological, and social benefits. To dissect the loci associated with important phenotypical traits and analyze their genetic and genomic information in jujube, a whole-genome resequencing (WGR) based highly saturated genetic map was constructed using an F1 hybrid population of 140 progeny individuals derived from the cross of ‘JMS2’ × ‘Jiaocheng 5’. The average sequencing depth of the parents was 14.09× and that of the progeny was 2.62×, and the average comparison efficiency between the sample and the reference genome was 97.09%. Three sets of genetic maps were constructed for a female parent, a male parent, and integrated. A total of 8,684 markers, including 8,158 SNP and 526 InDel markers, were evenly distributed across all 12 linkage groups (LGs) in the integrated map, spanning 1,713.22 cM with an average marker interval of 0.2 cM. In terms of marker number and density, this is the most saturated genetic map of jujube to date, nearly doubling that of the best ones previously reported. Based on this genetic map and phenotype data from 2019 to 2021, 31 leaf trait QTLs were identified in the linkage groups (LG1, 15; LG3, 1; LG5, 8; LG7, 4; LG8, 1, and LG11, 2), including 17 major QTLs. There were 4, 8, 14, and 5 QTLs that contributed to leaf length, leaf width, leaf shape index, and leaf area, respectively. Six QTLs clusters were detected on LG1 (8.05 cM–9.52 cM; 13.12 cM–13.99 cM; 123.84 cM–126.09 cM), LG5 (50.58 cM–50.86 cM; 80.10 cM–81.76 cM) and LG11 (35.98 cM–48.62 cM). Eight candidate genes were identified within the QTLs cluster regions. Annotation information showed that 4 genes (LOC107418196, LOC107418241, LOC107417968, and LOC112492570) in these QTLs are related to cell division and cell wall integrity. This research will provide a valuable tool for further QTL analysis, candidate gene identification, map-based gene cloning, comparative mapping, and marker-assisted selection (MAS) in jujube.
Cloning, characterization and functional analysis of NtMYB306a gene reveals its role in wax alkane biosynthesis of tobacco trichomes and stress tolerance
Authors: Yu Jing , Lei Bo , Zhao Huina , Wang Bing , Kakar Kaleem U. , Guo Yushuang , Zhang Xiaolian , Jia Mengao , Yang Hui , Zhao Degang
Published: October 2022

Trichomes are specialized hair-like organs found on epidermal cells of many terrestrial plants, which protect plant from excessive transpiration and numerous abiotic and biotic stresses. However, the genetic basis and underlying mechanisms are largely unknown in Nicotiana tabacum (common tobacco), an established model system for genetic engineering and plant breeding. In present study, we identified, cloned and characterized an unknown function transcription factor NtMYB306a from tobacco cultivar K326 trichomes. Results obtained from sequence phylogenetic tree analysis showed that NtMYB306a-encoded protein belonged to S1 subgroup of the plants’ R2R3-MYB transcription factors (TFs). Observation of the green fluorescent signals from NtMYB306a-GFP fusion protein construct exhibited that NtMYB306a was localized in nucleus. In yeast transactivation assays, the transformed yeast containing pGBKT7-NtMYB306a construct was able to grow on SD/-Trp-Ade+X-α-gal selection media, signifying that NtMYB306a exhibits transcriptional activation activity. Results from qRT-PCR, in-situ hybridization and GUS staining of transgenic tobacco plants revealed that NtMYB306a is primarily expressed in tobacco trichomes, especially tall glandular trichomes (TGTs) and short glandular trichomes (SGTs). RNA sequencing (RNA-seq) and qRT-PCR analysis of the NtMYB306a-overexpressing transgenic tobacco line revealed that NtMYB306a activated the expression of a set of key target genes which were associated with wax alkane biosynthesis. Gas Chromatography–Mass Spectrometry (GC-MS) exhibited that the total alkane contents and the contents of n-C28, n-C29, n-C31, and ai-C31 alkanes in leaf exudates of NtMYB306a-OE lines (OE-3, OE-13, and OE-20) were significantly greater when compared to WT. Besides, the promoter region of NtMYB306a contained numerous stress-responsive cis-acting elements, and their differential expression towards salicylic acid and cold stress treatments reflected their roles in signal transduction and cold-stress tolerance. Together, these results suggest that NtMYB306a is necessarily a positive regulator of alkane metabolism in tobacco trichomes that does not affect the number and morphology of tobacco trichomes, and that it can be used as a candidate gene for improving stress resistance and the quality of tobacco.
Morphological and physiological variation of soybean seedlings in response to shade
Authors: Wu Yushan , Chen Ping , Gong Wanzhuo , Gul Hina , Zhu Junqi , Yang Feng , Wang Xiaochun , Yong Taiwen , Liu Jiang , Pu Tian , Yan Yanhong , Yang Wenyu
Published: October 2022

Soybean (Glycine max) is a legume species that is widely used in intercropping. Quantitative analyses of plasticity and genetic differences in soybean would improve the selection and breeding of soybean in intercropping. Here, we used data of 20 varieties from one year artificial shading experiment and one year intercropping experiment to characterize the morphological and physiological traits of soybean seedlings grown under shade and full sun light conditions. Our results showed that shade significantly decreased biomass, leaf area, stem diameter, fraction of dry mass in petiole, leaf mass per unit area, chlorophyll a/b ratio, net photosynthetic rate per unit area at PAR of 500 μmol m–2 s–1 and 1,200 μmol m–2 s–1 of soybean seedling, but significantly increased plant height, fraction of dry mass in stem and chlorophyll content. Light × variety interaction was significant for all measured traits, light effect contributed more than variety effect. The biomass of soybean seedlings was positively correlated with leaf area and stem diameter under both shade and full sunlight conditions, but not correlated with plant height and net photosynthetic rate. The top five (62.75% variation explained) most important explanatory variables of plasticity of biomass were that the plasticity of leaf area, leaf area ratio, leaflet area, plant height and chlorophyll content, whose total weight were 1, 0.9, 0.3, 0.2, 0.19, respectively. The plasticity of biomass was positively correlated with plasticity of leaf area and leaflet area but significant negative correlated with plasticity of plant height. The principal component one account for 42.45% variation explain. A cluster analysis further indicated that soybean cultivars were classified into three groups and cultivars; Jiandebaimaodou, Gongdou 2, and Guixia 3 with the maximum plasticity of biomass. These results suggest that for soybean seedlings grown under shade increasing the capacity for light interception by larger leaf area is more vital than light searching (plant height) and light conversion (photosynthetic rate).
Landscape of biomolecular condensates in heat stress responses
Authors: Londoño Vélez Violeta , Alquraish Fatema , Tarbiyyah Ibrahim , Rafique Fareena , Mao Duruo , Chodasiewicz Monika
Published: October 2022

High temperature is one of the abiotic stresses that plants face and acts as a major constraint on crop production and food security. Plants have evolved several mechanisms to overcome challenging environments and respond to internal and external stimuli. One significant mechanism is the formation of biomolecular condensates driven by liquid–liquid phase separation. Biomolecular condensates have received much attention in the past decade, especially with regard to how plants perceive temperature fluctuations and their involvement in stress response and tolerance. In this review, we compile and discuss examples of plant biomolecular condensates regarding their composition, localization, and functions triggered by exposure to heat. Bioinformatic tools can be exploited to predict heat-induced biomolecular condensates. As the field of biomolecular condensates has emerged in the study of plants, many intriguing questions have arisen that have yet to be solved. Increased knowledge of biomolecular condensates will help in securing crop production and overcoming limitations caused by heat stress.
Physicochemical and biological factors determining the patchy distribution of soil water repellency among species of dominant vegetation in loess hilly region of China
Authors: Chai Xiaohong , Xu Xuexuan , Li Lushan , Wang Weiwei , Li Shuo , Geming Palixiati , Qu Yuanyuan , Zhang Qi , Ren Xiuzi , Xu Yuanhui , Li Mengyao
Published: October 2022

Soil water repellency (SWR) is a physical phenomenon whereby water cannot penetrate or has difficulty penetrating the soil surface. There are many factors involved in its occurrence, but the main factors controlling its emergence in loess remain unclear. In this work, we have studied numerous physicochemical and biological factors functioning in different dominant vegetations (Pinus tabulaeformis Carr., Robinia pseudoacacia L., and Hippophae rhamnoides L.) in a loess hilly region by gas chromatography–mass spectrometry (GC-MS) and high-throughput sequencing techniques. We observed that more than 75% of the soils under Robinia and Hippophae are categorized as slightly or strongly water repellent, while nearly 50% of the soils under Pinus are categorized as severely to extremely water repellent. The relative concentrations of total free lipids in the soil in the same water-repellency class were Pinus > Robinia > Hippophae, where fatty acids, alkanols, and sterols were positively correlated with SWR, whereas alkanes were not. For the abundance and diversity index of bacterial and fungal communities, the three species ranked in the following order: Robinia ≈ Hippophae > Pinus. Thus, solvent-extractable polar waxes were indicated to be better preserved in water-repellent soils under Pinus due to lower microbial diversity than Robinia and Hippophae. Here, we demonstrate polar waxes to be the principal factor controlling SWR. Moreover, the dominant phyla of fungi varied greatly than those of bacteria under three vegetation types. Correlation analysis showed that the abundance of Actinobacteria in dominant bacteria increased with SWR. Nonmetric multidimensional scaling suggested the fungal community in different water-repellent soils under Pinus to vary more than those under Robinia and Hippophae. The indicator species mainly belonged to Actinobacteria in bacteria and Basidiomycota in fungi at the phylum level; this finding was further supported by the linear discriminant analysis (LDA) effect size (LEfSe). Additionally, GC-MS identified a small amount of ergosterol, a specific biomarker of fungi under Pinus. These pieces of evidence collectively reveal that severe to extreme SWR occurs under Pinus and appears to be the most influenced by fungi and actinomycetes when the topsoil is close to air drying. However, there is a need for further testing on different plant species or land use.
The rhizosphere microbiome improves the adaptive capabilities of plants under high soil cadmium conditions
Authors: Fan Wenjun , Deng Jinmei , Shao Li , Jiang Shiming , Xiao Tangfu , Sun Weimin , Xiao Enzong
Published: October 2022

Cadmium (Cd) contamination of agricultural soils poses a potential public health issue for humans. Phytoremediation-based accumulating plants are an effective and sustainable technology for Cadmium remediation of contaminated agricultural soil. The rhizosphere microbiome can promote the growth and Cadmium accumulation in hyperaccumulators, but its taxonomic and functional traits remain elusive. The present study used two ecotypes of Sedum alfredii, an accumulating ecotype (AE) and a non-accumulating ecotype (NAE), as model plants to investigate the rhizosphere microbiome assemblages and influence on plant growth under high cadmium conditions. Our results showed that distinct root microbiomes assembled in association with both ecotypes of S. alfredii and that the assemblages were based largely on the lifestyles of the two ecotypes. In addition, we demonstrated that the functions of the microbes inhabiting the rhizosphere soils were closely associated with root-microbe interactions in both ecotypes of S. alfredii. Importantly, our results also demonstrated that the rhizosphere microbiome assembled in the AE rhizosphere soils contributed to plant growth and cadmium uptake under high cadmium conditions through functions such as nitrogen fixation, phosphorus solubilization, indole acetic acid (IAA) synthesis, and siderophore metabolism. However, this phenomenon was not clearly observed in the NAE. Our results suggest that the rhizosphere microbiome plays important roles in biogeochemical nutrient and metal cycling that can contribute to host plant fitness.
Genetic dissection of QTLs for starch content in four maize DH populations
Authors: Zhang Xiaolei , Wang Min , Zhang Changzheng , Dai Changjun , Guan Haitao , Zhang Ruiying
Published: October 2022

Starch is the principal carbohydrate source in maize kernels. Understanding the genetic basis of starch content (SC) benefits greatly in improving maize yield and optimizing end-use quality. Here, four double haploid (DH) populations were generated and were used to identify quantitative trait loci (QTLs) associated with SC. The phenotype of SC exhibited continuous and approximate normal distribution in each population. A total of 13 QTLs for SC in maize kernels was detected in a range of 3.65–16.18% of phenotypic variation explained (PVE). Among those, only some partly overlapped with QTLs previously known to be related to SC. Meanwhile, 12 genes involved in starch synthesis and metabolism located within QTLs were identified in this study. These QTLs will lay the foundation to explore candidate genes regulating SC in maize kernel and facilitate the application of molecular marker-assisted selection for a breeding program to cultivate maize varieties with a deal of grain quality.
Nitric oxide promotes energy metabolism and protects mitochondrial DNA in peaches during cold storage
Authors: Ren Yuanyuan , Zhu Shuhua
Published: October 2022

The mitochondria are important organelles related to energy metabolism and are susceptible to oxidative damage. In this experiment, peaches (Prunus persica) were treated with distilled water (as the control), 15 μmol L−1 of nitric oxide (NO), and 20 μmol L−1 of carboxy-PTIO (NO scavenger). The changes in mitochondrial physiological indicators, energy metabolism process, and mitochondrial DNA (mtDNA) damage and repair were quantified. Compared with the control, NO treatment reduced mitochondrial oxygen consumption and the reactive oxygen species content, increased mitochondrial respiration control rate, and promoted energy metabolism by influencing the activities of citrate synthase, aconitase, isocitrate dehydrogenase, and α‐ketoglutarate dehydrogenase in the tricarboxylic acid cycle and ATPase activity in peach mitochondria. NO treatment also maintained the relative copy number of mtDNA and the relative amplification of long PCR in peaches, decreased the level of 8-hydroxy-2 deoxyguanosine, and upregulated the expression of PpOGG1, PpAPE1, and PpLIG1. These results indicated that exogenous NO treatment (15 μmol L−1) could reduce mtDNA oxidative damage, maintain mtDNA molecular integrity, and inhibit mtDNA copy number reduction by reducing the reactive oxygen species content, thereby promoting mitochondrial energy metabolism and prolonging the storage life of peaches at low temperatures.
DIANA: A deep learning-based paprika plant disease and pest phenotyping system with disease severity analysis
Authors: Ilyas Talha , Jin Hyungjun , Siddique Muhammad Irfan , Lee Sang Jun , Kim Hyongsuk , Chua Leon
Published: October 2022

The emergence of deep neural networks has allowed the development of fully automated and efficient diagnostic systems for plant disease and pest phenotyping. Although previous approaches have proven to be promising, they are limited, especially in real-life scenarios, to properly diagnose and characterize the problem. In this work, we propose a framework which besides recognizing and localizing various plant abnormalities also informs the user about the severity of the diseases infecting the plant. By taking a single image as input, our algorithm is able to generate detailed descriptive phrases (user-defined) that display the location, severity stage, and visual attributes of all the abnormalities that are present in the image. Our framework is composed of three main components. One of them is a detector that accurately and efficiently recognizes and localizes the abnormalities in plants by extracting region-based anomaly features using a deep neural network-based feature extractor. The second one is an encoder–decoder network that performs pixel-level analysis to generate abnormality-specific severity levels. Lastly is an integration unit which aggregates the information of these units and assigns unique IDs to all the detected anomaly instances, thus generating descriptive sentences describing the location, severity, and class of anomalies infecting plants. We discuss two possible ways of utilizing the abovementioned units in a single framework. We evaluate and analyze the efficacy of both approaches on newly constructed diverse paprika disease and pest recognition datasets, comprising six anomaly categories along with 11 different severity levels. Our algorithm achieves mean average precision of 91.7% for the abnormality detection task and a mean panoptic quality score of 70.78% for severity level prediction. Our algorithm provides a practical and cost-efficient solution to farmers that facilitates proper handling of crops.
Disentangling leaf-microbiome interactions in Arabidopsis thaliana by network mapping
Authors: Li Kaihang , Cheng Kexin , Wang Haochen , Zhang Qi , Yang Yan , Jin Yi , He Xiaoqing , Wu Rongling
Published: October 2022

The leaf microbiota plays a key role in plant development, but a detailed mechanism of microbe-plant relationships remains elusive. Many genome-wide association studies (GWAS) have begun to map leaf microbes, but few have systematically characterized the genetics of how microbes act and interact. Previously, we integrated behavioral ecology and game theory to define four types of microbial interactions – mutualism, antagonism, aggression, and altruism, in a microbial community assembly. Here, we apply network mapping to identify specific plant genes that mediate the topological architecture of microbial networks. Analyzing leaf microbiome data from an Arabidopsis GWAS, we identify several heritable hub microbes for leaf microbial communities and detect 140–728 SNPs (Single nucleotide polymorphisms) responsible for emergent properties of microbial network. We reconstruct Bayesian genetic networks from which to identify 22–43 hub genes found to code molecular pathways related to leaf growth, abiotic stress responses, disease resistance and nutrition uptake. A further path analysis visualizes how genetic variants of Arabidopsis affect its fecundity through the internal workings of the leaf microbiome. We find that microbial networks and their genetic control vary along spatiotemporal gradients. Our study provides a new avenue to reveal the “endophenotype” role of microbial networks in linking genotype to end-point phenotypes in plants. Our integrative theory model provides a powerful tool to understand the mechanistic basis of structural-functional relationships within the leaf microbiome and supports the need for future research on plant breeding and synthetic microbial consortia with a specific function.