bluuebunny/crossref_metadata_2025 huggingface dataset:
Prediction of Progression to Severe Stroke in Initially Diagnosed Anterior Circulation Ischemic Cerebral Infarction
Authors: Wei Lai , Cao Yidi , Zhang Kangwei , Xu Yun , Zhou Xiang , Meng Jinxi , Shen Aijun , Ni Jiong , Yao Jing , Shi Lei , Zhang Qi , Wang Peijun
Published: June 2021

Purpose: Accurate prediction of the progression to severe stroke in initially diagnosed nonsevere patients with acute–subacute anterior circulation nonlacuna ischemic infarction (ASACNLII) is important in making clinical decision. This study aimed to apply a machine learning method to predict if the initially diagnosed nonsevere patients with ASACNLII would progress to severe stroke by using diffusion-weighted images and clinical information on admission.

Methods: This retrospective study enrolled 344 patients with ASACNLII from June 2017 to August 2020 on admission, and 108 cases progressed to severe stroke during hospitalization within 3–21 days. The entire data were randomized into a training set (n = 271) and an independent test set (n = 73). A U-Net neural network was employed for automatic segmentation and volume measurement of the ischemic lesions. Predictive models were developed and used for evaluating the progression to severe stroke using different feature sets (the volume data, the clinical data, and the combination) and machine learning methods (random forest, support vector machine, and logistic regression).

Results: The U-Net showed high correlation with manual segmentation in terms of Dice coefficient of 0.806 and R2 value of the volume measurements of 0.960 in the test set. The random forest classifier of the volume + clinical combination achieved the best area under the receiver operating characteristic curve of 0.8358 (95% CI 0.7321–0.9269), and the accuracy, sensitivity, and specificity were 0.7780 (0.7397–0.7945), 0.7695 (0.6102–0.9074), and 0.8686 (0.6923–1.0), respectively. The Shapley additive explanation diagram showed the volume variable as the most important predictor.

Conclusion: The U-Net was fully automatic and showed a high correlation with manual segmentation. An integrated approach combining clinical variables and stroke lesion volumes that were derived from the advanced machine learning algorithms had high accuracy in predicting the progression to severe stroke in ASACNLII patients.
Clinical Efficacy of Temozolomide and Its Predictors in Aggressive Pituitary Tumors and Pituitary Carcinomas: A Systematic Review and Meta-Analysis
Authors: Luo Mei , Tan Yiheng , Chen Wenli , Hu Bin , Wang Zongming , Zhu Diming , Jiao Haosen , Duan Chengbin , Zhu Yonghong , Wang Haijun
Published: June 2021

Background: A growing number of evidences suggest that TMZ applications can generate impressive benefits for APT and PC patients. However, the definite role of TMZ for individuals remains unclarified due to the variation between studies. And the predictive factors to alter its efficacy remain debatable.

Objective: To evaluate the long-term effectiveness and safety profile of TMZ in the treatment of pituitary malignancies, and delineate the predictors during its clinical employment.

Results: A literature retrieval was conducted from online databases for studies published up to December 31, 2020. Twenty one studies involving 429 patients were identified. TMZ exhibited 41% radiological overall response rate (rORR). The biochemical response rate was determinate in 53% of the functioning subset. Two-year and 4-year survival rate were 79 and 61%, respectively. TMZ prolonged the median PFS and OS as 20.18 and 40.24 months. TMZ-related adverse events occurred in 19% of patients. Regarding predictors of TMZ response, rORR was dramatically improved in patients with low/intermediate MGMT expression than those with high-MGMT (>50%) (p < 0.001). The benefit of TMZ varied according to functioning subtype of patients, with greater antitumor activities in functioning subgroups and fewer activities in non-functioning sets (p < 0.001). Notably, the concomitant therapy of radiotherapy and TMZ significantly increased the rORR (p = 0.007).

Conclusion: TMZ elicits clinical benefits with moderate adverse events in APT and PC patients. MGMT expression and clinical subtype of secreting function might be vital predictors of TMZ efficacy. In the future, the combination of radiotherapy with TMZ may further improve the clinical outcomes than TMZ monotherapy.
The Potential Role of Inflammation in Modulating Endogenous Hippocampal Neurogenesis After Spinal Cord Injury
Authors: Sefiani Arthur , Geoffroy Cédric G.
Published: June 2021

Currently there are approximately 291,000 people suffering from a spinal cord injury (SCI) in the United States. SCI is associated with traumatic changes in mobility and neuralgia, as well as many other long-term chronic health complications, including metabolic disorders, diabetes mellitus, non-alcoholic steatohepatitis, osteoporosis, and elevated inflammatory markers. Due to medical advances, patients with SCI survive much longer than previously. This increase in life expectancy exposes them to novel neurological complications such as memory loss, cognitive decline, depression, and Alzheimer’s disease. In fact, these usually age-associated disorders are more prevalent in people living with SCI. A common factor of these disorders is the reduction in hippocampal neurogenesis. Inflammation, which is elevated after SCI, plays a major role in modulating hippocampal neurogenesis. While there is no clear consensus on the mechanism of the decline in hippocampal neurogenesis and cognition after SCI, we will examine in this review how SCI-induced inflammation could modulate hippocampal neurogenesis and provoke age-associated neurological disorders. Thereafter, we will discuss possible therapeutic options which may mitigate the influence of SCI associated complications on hippocampal neurogenesis.
Research on the Structure of Peanut Allergen Protein Ara h1 Based on Aquaphotomics
Authors: Zhang Mengqi , Liu Liang , Yang Cui , Sun Zhongyu , Xu Xiuhua , Li Lian , Zang Hengchang
Published: June 2021

Peanut allergy is becoming a life-threatening disease that could induce severe allergic reactions in modern society, especially for children. The most promising method applied for deallergization is heating pretreatment. However, the mechanism from the view of spectroscopy has not been illustrated. In this study, near-infrared spectroscopy (NIRS) combined with aquaphotomics was introduced to help us understand the detailed structural changes information during the heating process. First, near-infrared (NIR) spectra of Ara h1 were acquired from 25 to 80°C. Then, aquaphotomics processing tools including principal component analysis (PCA), continuous wavelet transform (CWT), and two-dimensional correlation spectroscopy (2D-COS) were utilized for better understanding the thermodynamic changes, secondary structure, and the hydrogen bond network of Ara h1. The results indicated that about 55°C could be a key temperature, which was the structural change point. During the heating process, the hydrogen bond network was destroyed, free water was increased, and the content of protein secondary structure was changed. Moreover, it could reveal the interaction between the water structure and Ara h1 from the perspective of water molecules, and explain the effect of temperature on the Ara h1 structure and hydrogen-bonding system. Thus, this study described a new way to explore the thermodynamic properties of Ara h1 from the perspective of spectroscopy and laid a theoretical foundation for the application of temperature-desensitized protein products.
Construction and Validation of an Autophagy-Related Prognostic Signature and a Nomogram for Bladder Cancer
Authors: Yan Xin , Wu Hua-Hui , Chen Zhao , Du Guo-Wei , Bai Xiao-Jie , Tuoheti Kurerban , Liu Tong-Zu
Published: June 2021

Objective

Bladder cancer (BC) is one of the top ten cancers endangering human health but we still lack accurate tools for BC patients’ risk stratification. This study aimed to develop an autophagy-related signature that could predict the prognosis of BC. In order to provide clinical doctors with a visual tool that could precisely predict the survival probability of BC patients, we also attempted to establish a nomogram based on the risk signature.

Methods

We screened out autophagy-related genes (ARGs) combining weighted gene co-expression network analysis (WGCNA) and differentially expressed gene (DEG) in BC. Based on the screened ARGs, we performed survival analysis and Cox regression analysis to identify potential prognostic biomarkers. A risk signature based on the prognostic ARGs by multivariate Cox regression analysis was established, which was validated by using seven datasets. To provide clinical doctors with a useful tool for survival possibility prediction, a nomogram assessed by the ARG-based signature and clinicopathological features was constructed, verified using four independent datasets.

Results

Three prognostic biomarkers including BOC (P = 0.008, HR = 1.104), FGF7(P = 0.030, HR = 1.066), and MAP1A (P = 0.001, HR = 1.173) were identified and validated. An autophagy-related risk signature was established and validated. This signature could act as an independent prognostic feature in patients with BC (P = 0.047, HR = 1.419). We then constructed two nomograms with and without ARG-based signature and subsequent analysis indicated that the nomogram with ARG signature showed high accuracy for overall survival probability prediction of patients with BC (C-index = 0.732, AUC = 0.816). These results proved that the ARG signature improved the clinical net benefit of the standard model based on clinicopathological features (age, pathologic stage).

Conclusions

Three ARGs were identified as prognosis biomarkers in BC. An ARG-based signature was established for the first time, showing strong potential for prognosis prediction in BC. This signature was proven to improve the clinical net benefit of the standard model. A nomogram was established using this signature, which could lead to more effective prognosis prediction for BC patients.
GEFT Inhibits Autophagy and Apoptosis in Rhabdomyosarcoma via Activation of the Rac1/Cdc42-mTOR Signaling Pathway
Authors: Li Chunsen , Li Zhenzhen , Song Lingxie , Meng Lian , Xu Guixuan , Zhang Haijun , Hu Jianming , Li Feng , Liu Chunxia
Published: June 2021

Autophagy and apoptosis are dynamic processes that determine the fate of cells, and regulating these processes can treat cancer. GEFT is highly expressed in rhabdomyosarcoma (RMS), which accelerates the tumorigenicity and metastasis of RMS by activating Rac1/Cdc42 signaling, but the regulatory mechanisms of autophagy and apoptosis are unclear. In our study, we found that the RMS tissues had high Rac1, Cdc42, mTOR, and Bcl-2 expression levels and low Beclin1, LC3, and Bax expression levels compared with the normal striated muscle tissues (P < 0.05). In addition, multivariate analysis has proven that Rac1 is an independent prognostic factor (P < 0.05), and the high expression level of the Beclin1 protein was closely associated with the tumor diameter of the RMS patients (P = 0.044), whereas the high expression level of the LC3 protein was associated with the clinical stage of the RMS patients (P = 0.027). Furthermore, GEFT overexpression could inhibit autophagy and apoptosis in RMS. A Rac1/Cdc42 inhibitor was added, and the inhibition of autophagy and apoptosis decreased. Rac1 and Cdc42 could regulate mTOR to inhibit autophagy and apoptosis in RMS. Overall, these studies demonstrated that the GEFT–Rac1/Cdc42–mTOR pathway can inhibit autophagy and apoptosis in RMS and provide evidence for innovative treatments.
Prognostic Value of Eight-Gene Signature in Head and Neck Squamous Carcinoma
Authors: Liu Baoling , Su Quanping , Ma Jianhua , Chen Cheng , Wang Lijuan , Che Fengyuan , Heng Xueyuan
Published: June 2021

Head and neck cancer (HNC) is the fifth most common cancer worldwide. In this study, we performed an integrative analysis of the discovery set and established an eight-gene signature for the prediction of prognosis in patients with head and neck squamous cell carcinoma (HNSCC). Univariate Cox analysis was used to identify prognosis-related genes (with P < 0.05) in the GSE41613, GSE65858, and TCGA-HNSC RNA-Seq datasets after data collection. We performed LASSO Cox regression analysis and identified eight genes (CBX3, GNA12, P4HA1, PLAU, PPL, RAB25, EPHX3, and HLF) with non-zero regression coefficients in TCGA-HNSC datasets. Survival analysis revealed that the overall survival (OS) of GSE41613 and GSE65858 datasets and the progression-free survival(DFS)of GSE27020 and GSE42743 datasets in the low-risk group exhibited better survival outcomes compared with the high-risk group. To verify that the eight-mRNA prognostic model was independent of other clinical features, KM survival analysis of the specific subtypes with different clinical characteristics was performed. Univariate and multivariate Cox regression analyses were used to identify three independent prognostic factors to construct a prognostic nomogram. Finally, the GSVA algorithm identified six pathways that were activated in the intersection of the TCGA-HNSC, GSE65858, and GSE41613 datasets, including early estrogen response, cholesterol homeostasis, oxidative phosphorylation, fatty acid metabolism, bile acid metabolism, and Kras signaling. However, the epithelial–mesenchymal transition pathway was inhibited at the intersection of the three datasets. In conclusion, the eight-gene prognostic signature proved to be a useful tool in the prognostic evaluation and facilitate personalized treatment of HNSCC patients.
LncRNA FGD5-AS1 Facilitates the Radioresistance of Breast Cancer Cells by Enhancing MACC1 Expression Through Competitively Sponging miR-497-5p
Authors: Li Ji , Lei Changjiang , Chen Bineng , Zhu Qingfang
Published: June 2021

Background

LncRNA-FGD5-AS1, as an oncogene, participates in the development and progress of various cancers. However, the exact role and the molecular mechanisms by which FGD5-AS1 regulates radiosensitivity in breast cancer (BC) remains largely unknown.

Methods

We used X-Ray weekly-dose-increase method to establish radiation-resistance cell lines. Bioinformatics tools analyze the expression of FGD5-AS1 in breast cancer tissue and evaluated the relationship between FGD5-AS1 and clinic-pathological features. CCK-8 and colony formation were used to analyze cell proliferation. Western blotting and qPCR were applied to detect protein and gene expression, respectively. RNA interference was used to knock down the endogenous gene expression. Luciferase reporter system and immunoprecipitates were applied to verify the target of FGD5-AS1.

Result

FGD5-AS1 was overexpressed in BC tissues and radiation-resistance cell lines. Higher levels of FGD5-AS1 predicted poorer clinical characteristics and prognosis. Loss-of-function FGD5-AS1 sensitized BC cells to X-ray, meanwhile, the cell gained radiation-resistance when exogenous FGD5-AS1 was expressed. FGD5-AS1 depletion arrested cells at G0/G1 and triggers cell apoptosis. The starBase database (ENCORI), predicted binding site of miR-497-5p in FGD5-AS1 sequence, and luciferase reporter system and immunoprecipitates verified miR-497-5p was the target of FGD5-AS1. Furthermore, MACC1 was predicted and verified as the target of miR-497-5p. Loss-of-function FGD5-AS1 sensitized ionizing radiation was rescued by the up-regulation of MACC1 and the inhibition of miR-497.

Conclusion

FGD5-AS1 displays an oncogene profile in CRC; patients with high expression of FGD5-AS1 should benefit less from radiotherapy and need a more frequent follow-up. Besides, FGD5-AS1 may be a potential therapeutic target for CRC.
A Fibrinogen Alpha Fragment Mitigates Chemotherapy-Induced MLL Rearrangements
Authors: Eberle Julia , Wiehe Rahel Stefanie , Gole Boris , Mattis Liska Jule , Palmer Anja , Ständker Ludger , Forssmann Wolf-Georg , Münch Jan , Gebhardt J. Christof M. , Wiesmüller Lisa
Published: June 2021

Rearrangements in the Mixed Lineage Leukemia breakpoint cluster region (MLLbcr) are frequently involved in therapy-induced leukemia, a severe side effect of anti-cancer therapies. Previous work unraveled Endonuclease G as the critical nuclease causing initial breakage in the MLLbcr in response to different types of chemotherapeutic treatment. To identify peptides protecting against therapy-induced leukemia, we screened a hemofiltrate-derived peptide library by use of an enhanced green fluorescent protein (EGFP)-based chromosomal reporter of MLLbcr rearrangements. Chromatographic purification of one active fraction and subsequent mass spectrometry allowed to isolate a C-terminal 27-mer of fibrinogen α encompassing amino acids 603 to 629. The chemically synthesized peptide, termed Fα27, inhibited MLLbcr rearrangements in immortalized hematopoietic cells following treatment with the cytostatics etoposide or doxorubicin. We also provide evidence for protection of primary human hematopoietic stem and progenitor cells from therapy-induced MLLbcr breakage. Of note, fibrinogen has been described to activate toll-like receptor 4 (TLR4). Dissecting the Fα27 mode-of action revealed association of the peptide with TLR4 in an antagonistic fashion affecting downstream NFκB signaling and pro-inflammatory cytokine production. In conclusion, we identified a hemofiltrate-derived peptide inhibitor of the genome destabilizing events causing secondary leukemia in patients undergoing chemotherapy.
Cohort Profile: Chinese Cervical Cancer Clinical Study
Authors: Zhang Xi-Ru , Li Zhi-Qiang , Sun Li-Xin , Liu Ping , Li Zhi-Hao , Li Peng-Fei , Zhao Hong-Wei , Chen Bi-Liang , Ji Mei , Wang Li , Kang Shan , Lang Jing-He , Mao Chen , Chen Chun-Lin
Published: June 2021

Cervical cancer is the fourth most common cancer worldwide, but its incidence varies greatly in different countries. Regardless of incidence or mortality, the burden of cervical cancer in China accounts for approximately 18% of the global burden. The Chinese Cervical Cancer Clinical Study is a hospital-based multicenter open cohort. The major aims of this study include (i) to explore the associations of therapeutic strategies with complications as well as mid- and long-term clinical outcomes; (ii) to widely assess the factors which may have an influence on the prognosis of cervical cancer and then guide the treatment options, and to estimate prognosis using a prediction model for precise post-treatment care and follow-up; (iii) to develop a knowledge base of cervical clinical auxiliary diagnosis and prognosis prediction using artificial intelligence and machine learning approaches; and (iv) to roughly map the burden of cervical cancer in different districts and monitoring the trend in incidence of cervical cancer to potentially inform prevention and control strategies. Patients eligible for inclusion were those diagnosed with cervical cancer, whether during an outpatient visit or hospital admission, at 47 different types of medical institutions in 19 cities of 11 provinces across mainland China between 2004 and 2018. In a total, 63 926 patients with cervical cancer were enrolled in the cohort. Since the project inception, a large number of standardized variables have been collected, including epidemiological characteristics, cervical cancer-related symptoms, physical examination results, laboratory testing results, imaging reports, tumor biomarkers, tumor staging, tumor characteristics, comorbidities, co-infections, treatment and short-term complications. Follow-up was performed at least once every 6 months within the first 5 years after receiving treatment and then annually thereafter. At present, we are developing a cervical cancer imaging database containing Dicom files with data of computed tomography/magnetic resonance imaging examination. Additionally, we are also collecting original pathological specimens of patients with cervical cancer. Potential collaborators are welcomed to contact the corresponding authors, and anyone can submit at least one specific study proposal describing the background, objectives and methods of the study.
Lurbinectedin in Refractory Diffuse Malignant Peritoneal Mesothelioma: Report of Two Cases
Authors: Gros Louis , Szturz Petr , Diciolla Antonella , Kirchner Volker , Peters Solange , Schaefer Niklaus , Hubner Martin , Digklia Antonia
Published: June 2021

Mesothelioma is a malignancy of serosal membranes. Parietal pleura is the most common site, with peritoneum being the second most frequent location. Malignant peritoneal mesothelioma (MPM) is a rare and aggressive disease. The prognosis is often very poor with median overall survival ranging from 6 to 18 months in patients who are not candidates for cytoreductive surgery (CRS) with hyperthermic intraperitoneal chemotherapy (HIPEC) due to non-resectable disease or comorbid conditions. For patients with resectable disease, CRS and HIPEC have become the standard of care. However, for patients with unresectable malignant mesothelioma there is unfortunately no effective systemic treatment beyond the first line. Based on the results of a recent phase II trial, lurbinectedin has clinical activity and acceptable toxicity in the second- and third-line treatment of malignant pleural mesothelioma. However, until present, no data have been available for patients with MPM and for patients who become refractory after multiple treatment lines. We report on two patients with metastatic MPM who achieved durable disease control of 10+ and 8 months with lurbinectedin in the fourth and fifth treatment line, respectively.
Exploring the Mechanism Whereby Sinensetin Delays the Progression of Pulmonary Fibrosis Based on Network Pharmacology and Pulmonary Fibrosis Models
Authors: Xu Yong , Hang Wen-Lu , Zhou Xian-Mei , Wu Qi
Published: June 2021

The incidence of pulmonary fibrosis (PF), a progressively fatal disease, has increased in recent years. However, there are no effective medicines available. Previous results have shown that sinensetin probably has some curative effects on PF. Therefore, this paper aims to predict the targets of sinensetin using a network pharmacology method and to confirm its effects and functional targets in PF using a mouse PF model. First, network pharmacology analysis showed that sinensetin has 105 functional targets, and 1,698 gene targets closely relate to PF. The intersection of the functional targets and gene targets produced 52 targets for the treatment of PF with sinensetin. The PPIs (protein–protein interactions) led to several potential key target genes, including MAPK1, EGFR, SRC, and PTGS2. The results of GO and KEGG analyses suggested the crucial function of apoptosis in PF and its involvement in the PI3K signaling pathway. Subsequently, we tested the molecular docking of sinensetin with the PI3K protein using the AutoDock4 software. The results showed that sinensetin could fit well into several binding sites of the PI3K protein. Furthermore, we constructed a PF mouse model through one-off intratracheal instillation of bleomycin and then intragastrically administered different concentrations of sinensetin to the model mice. Twenty-eight days later, the mice were sacrificed, and the lung tissues, serum, and bronchoalveolar lavage fluid (BALF) were collected. The in vivo tests showed that the body weight of model mice increased slightly compared with that of PF mice after intragastric sinensetin. HE and Masson staining suggested a certain extent of reduction in the pathology of lung tissues. The expression of collagens I and III, as well as hydroxyproline in the lung tissues, was reduced to a certain extent. IL-6 levels in the serum and BALF decreased markedly. The expression of vimentin and α-SMA in pulmonary tissues decreased. Cell apoptosis, as well as P-PI3K and P-AKT levels, in lung tissues also reduced. In summary, network pharmacology and in vivo test results suggest sinensetin causes an effective delay in the progression of pulmonary fibrosis, and the functional mechanism is likely related to PI3K-AKT signaling.
He-Jie-Shen-Shi Decoction as an Adjuvant Therapy on Severe Coronavirus Disease 2019: A Retrospective Cohort and Potential Mechanistic Study
Authors: Hu Haibo , Wang Kun , Wang Li , Du Yanjun , Chen Juan , Li Yongchun , Fan Chuanbo , Li Ning , Sun Ying , Tu Shenghao , Lu Xuechao , Zhou Zhaoshan , Cui Huantian
Published: June 2021

Combination therapy using Western and traditional Chinese medicines has shown notable effects on coronavirus disease 2019 (COVID-19). The He-Jie-Shen-Shi decoction (HJSS), composed of Bupleurum chinense DC., Scutellaria baicalensis Georgi, Pinellia ternata (Thunb.) Makino, Glycyrrhiza uralensis Fisch. ex DC., and nine other herbs, has been used to treat severe COVID-19 in clinical practice. The aim of this study was to compare the clinical efficacies of HJSS combination therapy and Western monotherapy against severe COVID-19 and to study the potential action mechanism of HJSS. From February 2020 to March 2020, 81 patients with severe COVID-19 in Wuhan Tongji Hospital were selected for retrospective cohort study. Network pharmacology was conducted to predict the possible mechanism of HJSS on COVID-19-related acute respiratory distress syndrome (ARDS). Targets of active components in HJSS were screened using the Traditional Chinese Medicine Systems Pharmacology (TCMSP) and PharmMapper databases. The targets of COVID-19 and ARDS were obtained from GeneCards and Online Mendelian Inheritance in Man databases. The key targets of HJSS in COVID-19 and ARDS were obtained based on the protein–protein interaction network (PPI). Kyoto Encyclopedia of Genes and Genomes analysis (KEGG) was conducted to predict the pathways related to the targets of HJSS in COVID-19 and ARDS. A “herb-ingredient-target-pathway” network was established using Cytoscape 3.2.7. Results showed that the duration of the negative conversion time of nucleic acid was shorter in patients who received HJSS combination therapy. HJSS combination therapy also relieved fever in patients with severe COVID-19. Network pharmacology analysis identified interleukin (IL) 6, tumor necrosis factor (TNF), vascular endothelial growth factor A (VEGFA), catalase (CAT), mitogen-activated protein kinase (MAPK) 1, tumor protein p53 (TP53), CC-chemokine ligand (CCL2), MAPK3, prostaglandin-endoperoxide synthase 2 (PTGS2), and IL1B as the key targets of HJSS in COVID-19-related ARDS. KEGG analysis suggested that HJSS improved COVID-19-related ARDS by regulating hypoxia-inducible factor (HIF)-1, NOD-like receptor, TNF, T cell receptor, sphingolipid, PI3K-Akt, toll-like receptor, VEGF, FoxO, and MAPK signaling pathways. In conclusion, HJSS can be used as an adjuvant therapy on severe COVID-19. The therapeutic mechanisms may be involved in inhibiting viral replication, inflammatory response, and oxidative stress and alleviating lung injury. Further studies are required to confirm its clinical efficacies and action mechanisms.
Nonlinear Radiative Treatment of Hydromagnetic Non-Newtonian Fluid Flow Induced by a Nonlinear Convective-Boundary-Driven Curved Sheet With Dissipations and Chemical Reaction Effects
Authors: Sanni Kehinde Musodiq , Asghar Saleem , Rashid Saima , Chu Yu-Ming
Published: June 2021

This study investigates the flow of heat and mass transport of an incompressible MHD Cross fluid over a nonlinear curved stretching sheet. Heat transport incorporates viscous dissipation, radiative flux, and surface heating, whereas the fluid concentration is distressed with the first-order chemical reaction. A radially varying applied magnetic field is considered to examine the effect of Lorentz force and Ohmic heating. The rheology of the fluid is theoretically modeled and constitute a novel work for the completeness of shear thinning and thickening fluids over curved structure. Similarity method is utilized to reduce the governing system of PDE’s into ODE’s. Numerical computation through Runge-Kutta fourth order with shooting technique is implemented by the first initialized higher-order system into the first ODEs. The behaviors of the flow quantities—velocity, temperature, and concentration—are graphically analyzed against the parameters, including radius of curvature, fluid rheology, radiation, and rate of reactions. The numerical results are validated in comparison with the published results. Studies of Newtonian fluids on flat and curved surfaces are the special cases of this work. The results are useful in material processing and polymer dynamics involving stretchable materials.
Cloning and Expression of the Neuropeptide F and Neuropeptide F Receptor Genes and Their Regulation of Food Intake in the Chinese White Pine Beetle Dendroctonus armandi
Authors: Liu Bin , Fu Danyang , Gao Haiming , Ning Hang , Sun Yaya , Chen Hui , Tang Ming
Published: June 2021

Neuropeptide F (NPF) is an important signaling molecule that acts as a neuromodulator to regulate a diversity of physiological and behavioral processes from vertebrates to invertebrates by interaction with NPF receptors, which are G protein-coupled receptors (GPCR). However, nothing is known about NPF in Chinese white pine beetle, Dendroctonus armandi, a destructive pest of natural and coniferous forests in the middle Qinling Mountains of China. We have cloned and characterized cDNAs encoding one NPF precursor and two NPF receptors in D. armandi and made bioinformatics predictions according to the deduced amino acid sequences. They were highly similar to that of Dendroctonus ponderosa. The transcription levels of these genes were different between larvae and adults of sexes, and there were significant differences among the different developmental stages and tissues and between beetles under starvation and following re-feeding states. Additionally, downregulation of NPF and NPFR by injecting dsRNA into beetles reduced their food intake, caused increases of mortality and decreases of body weight, and also resulted in a decrease of glycogen and free fatty acid and an increase of trehalose. These results indicate that the NPF signaling pathway plays a significant positive role in the regulation of food intake and provides a potential target for the sustainable management of this pest.
Mitochondrial Adaptation to Diet and Swimming Activity in Gilthead Seabream: Improved Nutritional Efficiency
Authors: Perelló-Amorós Miquel , Fernández-Borràs Jaume , Sánchez-Moya Albert , Vélez Emilio J. , García-Pérez Isabel , Gutiérrez Joaquin , Blasco Josefina
Published: June 2021

Sustained exercise promotes growth in different fish species, and in gilthead seabream we have demonstrated that it improves nutrient use efficiency. This study assesses for differences in growth rate, tissue composition and energy metabolism in gilthead seabream juveniles fed two diets: high-protein (HP; 54% protein, 15% lipid) or high energy (HE; 50% protein, 20% lipid), under voluntary swimming (VS) or moderate-to-low-intensity sustained swimming (SS) for 6 weeks. HE fed fish under VS conditions showed lower body weight and higher muscle lipid content than HP fed fish, but no differences between the two groups were observed under SS conditions. Irrespective of the swimming regime, the white muscle stable isotopes profile of the HE group revealed increased nitrogen and carbon turnovers. Nitrogen fractionation increased in the HP fed fish under SS, indicating enhanced dietary protein oxidation. Hepatic gene expression markers of energy metabolism and mitochondrial biogenesis showed clear differences between the two diets under VS: a significant shift in the COX/CS ratio, modifications in UCPs, and downregulation of PGC1a in the HE-fed fish. Swimming induced mitochondrial remodeling through upregulation of fusion and fission markers, and removing almost all the differences observed under VS. In the HE-fed fish, white skeletal muscle benefited from the increased energy demand, amending the oxidative uncoupling produced under the VS condition by an excess of lipids and the pro-fission state observed in mitochondria. Contrarily, red muscle revealed more tolerant to the energy content of the HE diet, even under VS conditions, with higher expression of oxidative enzymes (COX and CS) without any sign of mitochondrial stress or mitochondrial biogenesis induction. Furthermore, this tissue had enough plasticity to shift its metabolism under higher energy demand (SS), again equalizing the differences observed between diets under VS condition. Globally, the balance between dietary nutrients affects mitochondrial regulation due to their use as energy fuels, but exercise corrects imbalances allowing practical diets with lower protein and higher lipid content without detrimental effects.
Optimizing Reservoir Computers for Signal Classification
Authors: Carroll Thomas L.
Published: June 2021

Reservoir computers are a type of recurrent neural network for which the network connections are not changed. To train the reservoir computer, a set of output signals from the network are fit to a training signal by a linear fit. As a result, training of a reservoir computer is fast, and reservoir computers may be built from analog hardware, resulting in high speed and low power consumption. To get the best performance from a reservoir computer, the hyperparameters of the reservoir computer must be optimized. In signal classification problems, parameter optimization may be computationally difficult; it is necessary to compare many realizations of the test signals to get good statistics on the classification probability. In this work, it is shown in both a spiking reservoir computer and a reservoir computer using continuous variables that the optimum classification performance occurs for the hyperparameters that maximize the entropy of the reservoir computer. Optimizing for entropy only requires a single realization of each signal to be classified, making the process much faster to compute.
De novo Transcriptome Assembly and Comparative Analysis Highlight the Primary Mechanism Regulating the Response to Selenium Stimuli in Oats (Avena sativa L.)
Authors: Liu Tao , Liu Xiaoting , Zhou Rangrang , Chen Hong , Zhang Huaigang , Zhang Bo
Published: June 2021

Selenium is an essential microelement for humans and animals. The specific processing technique of oats can maximize the preservation of its nutrients. In this study, to understand the genetic response of oats in a high-selenium environment, oats were treated with sodium selenate for 24 h, and transcriptome analysis was performed. A total of 211,485,930 clean reads composing 31.30 Gb of clean data were retained for four samples. After assembly, 186,035 unigenes with an average length of 727 bp were generated, and the N50 length was 1,149 bp. Compared with that in the control group, the expression of 7,226 unigenes in the treatment group was upregulated, and 2,618 unigenes were downregulated. Based on the sulfur assimilation pathway and selenocompound metabolic pathway, a total of 27 unigenes related to selenate metabolism were identified. Among them, the expression of both key genes APS (ATP sulfurylase) and APR (adenosine 5′-phosphosulfate reductase) was upregulated more than 1,000-fold under selenate treatment, while that of CBL (cystathionine-β-synthase) was upregulated 3.12-fold. Based on the transcriptome analysis, we suspect that the high-affinity sulfur transporter Sultr1;2 plays a key role in selenate uptake in oats. A preliminary regulatory mechanism explains the oat response to selenate treatment was ultimately proposed based on the transcriptome analysis and previous research.
Genome-Wide Association Studies Identifying Multiple Loci Associated With Alfalfa Forage Quality
Authors: Lin Sen , Medina Cesar Augusto , Norberg O. Steven , Combs David , Wang Guojie , Shewmaker Glenn , Fransen Steve , Llewellyn Don , Yu Long-Xi
Published: June 2021

Autotetraploid alfalfa is a major hay crop planted all over the world due to its adaptation in different environments and high quality for animal feed. However, the genetic basis of alfalfa quality is not fully understood. In this study, a diverse panel of 200 alfalfa accessions were planted in field trials using augmented experimental design at three locations in 2018 and 2019. Thirty-four quality traits were evaluated by Near Infrared Reflectance Spectroscopy (NIRS). The plants were genotyped using a genotyping by sequencing (GBS) approach and over 46,000 single nucleotide polymorphisms (SNPs) were obtained after variant calling and filtering. Genome-wide association studies (GWAS) identified 28 SNP markers associated with 16 quality traits. Among them, most of the markers were associated with fiber digestibility and protein content. Phenotypic variations were analyzed from three locations and different sets of markers were identified by GWAS when using phenotypic data from different locations, indicating that alfalfa quality traits were also affected by environmental factors. Among different sets of markers identified by location, two markers were associated with nine traits of fiber digestibility. One marker associated with lignin content was identified consistently in multiple environments. Putative candidate genes underlying fiber-related loci were identified and they are involved in the lignin and cell wall biosynthesis. The DNA markers and associated genes identified in this study will be useful for the genetic improvement of forage quality in alfalfa after the validation of the markers.
Peanut Leaf Wilting Estimation From RGB Color Indices and Logistic Models
Authors: Sarkar Sayantan , Ramsey A. Ford , Cazenave Alexandre-Brice , Balota Maria
Published: June 2021

Peanut (Arachis hypogaea L.) is an important crop for United States agriculture and worldwide. Low soil moisture is a major constraint for production in all peanut growing regions with negative effects on yield quantity and quality. Leaf wilting is a visual symptom of low moisture stress used in breeding to improve stress tolerance, but visual rating is slow when thousands of breeding lines are evaluated and can be subject to personnel scoring bias. Photogrammetry might be used instead. The objective of this article is to determine if color space indices derived from red-green-blue (RGB) images can accurately estimate leaf wilting for breeding selection and irrigation triggering in peanut production. RGB images were collected with a digital camera proximally and aerially by a unmanned aerial vehicle during 2018 and 2019. Visual rating was performed on the same days as image collection. Vegetation indices were intensity, hue, saturation, lightness, a∗, b∗, u∗, v∗, green area (GA), greener area (GGA), and crop senescence index (CSI). In particular, hue, a∗, u∗, GA, GGA, and CSI were significantly (p ≤ 0.0001) associated with leaf wilting. These indices were further used to train an ordinal logistic regression model for wilting estimation. This model had 90% accuracy when images were taken aerially and 99% when images were taken proximally. This article reports on a simple yet key aspect of peanut screening for tolerance to low soil moisture stress and uses novel, fast, cost-effective, and accurate RGB-derived models to estimate leaf wilting.
Regulatory Mechanisms of bHLH Transcription Factors in Plant Adaptive Responses to Various Abiotic Stresses
Authors: Qian Yuchen , Zhang Tongyao , Yu Yan , Gou Liangpeng , Yang Jingting , Xu Jia , Pi Erxu
Published: June 2021

Basic helix-loop-helix proteins (bHLHs) comprise one of the largest families of transcription factors in plants. They have been shown to be involved in responses to various abiotic stresses, such as drought, salinity, chilling, heavy metal toxicity, iron deficiency, and osmotic damages. By specifically binding to cis-elements in the promoter region of stress related genes, bHLHs can regulate their transcriptional expression, thereby regulating the plant’s adaptive responses. This review focuses on the structural characteristics of bHLHs, the regulatory mechanism of how bHLHs are involved transcriptional activation, and the mechanism of how bHLHs regulate the transcription of target genes under various stresses. Finally, as increasing research demonstrates that flavonoids are usually induced under fluctuating environments, the latest research progress and future research prospects are described on the mechanisms of how flavonoid biosynthesis is regulated by bHLHs in the regulation of the plant’s responses to abiotic stresses.
Expression Characterization of Flavonoid Biosynthetic Pathway Genes and Transcription Factors in Peanut Under Water Deficit Conditions
Authors: Kubra Ghulam , Khan Maryam , Munir Faiza , Gul Alvina , Shah Tariq , Hussain Adil , Caparrós-Ruiz David , Amir Rabia
Published: June 2021

Drought is one of the hostile environmental stresses that limit the yield production of crop plants by modulating their growth and development. Peanut (Arachis hypogaea) has a wide range of adaptations to arid and semi-arid climates, but its yield is prone to loss due to drought. Other than beneficial fatty acids and micronutrients, peanut harbors various bioactive compounds including flavonoids that hold a prominent position as antioxidants in plants and protect them from oxidative stress. In this study, understanding of the biosynthesis of flavonoids in peanut under water deficit conditions was developed through expression analysis and correlational analysis and determining the accumulation pattern of phenols, flavonols, and anthocyanins. Six peanut varieties (BARD479, BARI2011, BARI2000, GOLDEN, PG1102, and PG1265) having variable responses against drought stress have been selected. Higher water retention and flavonoid accumulation have been observed in BARI2011 but downregulation has been observed in the expression of genes and transcription factors (TFs) which indicated the maintenance of normal homeostasis. ANOVA revealed that the expression of flavonoid genes and TFs is highly dependent upon the genotype of peanut in a spatiotemporal manner. Correlation analysis between expression of flavonoid biosynthetic genes and TFs indicated the role ofAhMYB111andAhMYB7as an inhibitor forAhF3HandAhFLS, respectively, andAhMYB7, AhTTG1, andAhCSU2as a positive regulator for the expression ofAh4CL, AhCHS, and AhF3H, respectively. However,AhbHLHandAhGL3revealed nil-to-little relation with the expression of flavonoid biosynthetic pathway genes. Correlational analysis between the expression of TFs related to the biosynthesis of flavonoids and the accumulation of phenolics, flavonols, and anthocyanins indicated coregulation of flavonoid synthesis by TFs under water deficit conditions in peanut. This study would provide insight into the role of flavonoid biosynthetic pathway in drought response in peanut and would aid to develop drought-tolerant varieties of peanut.
An Efficient Brome mosaic virus-Based Gene Silencing Protocol for Hexaploid Wheat (Triticum aestivum L.)
Authors: Wang Yongqin , Chai Chenglin , Khatabi Behnam , Scheible Wolf-Rüdiger , Udvardi Michael K. , Saha Malay C. , Kang Yun , Nelson Richard S.
Published: June 2021

Virus-induced gene silencing (VIGS) is a rapid and powerful method to evaluate gene function, especially for species like hexaploid wheat that have large, redundant genomes and are difficult and time-consuming to transform. The Brome mosaic virus (BMV)-based VIGS vector is widely used in monocotyledonous species but not wheat. Here we report the establishment of a simple and effective VIGS procedure in bread wheat using BMVCP5, the most recently improved BMV silencing vector, and wheat genes PHYTOENE DESATURASE (TaPDS) and PHOSPHATE2 (TaPHO2) as targets. Time-course experiments revealed that smaller inserts (~100 nucleotides, nt) were more stable in BMVCP5 and conferred higher silencing efficiency and longer silencing duration, compared with larger inserts. When using a 100-nt insert and a novel coleoptile inoculation method, BMVCP5 induced extensive silencing of TaPDS transcript and a visible bleaching phenotype in the 2nd to 5th systemically-infected leaves from nine to at least 28 days post inoculation (dpi). For TaPHO2, the ability of BMVCP5 to simultaneously silence all three homoeologs was demonstrated. To investigate the feasibility of BMV VIGS in wheat roots, ectopically expressed enhanced GREEN FLUORESCENT PROTEIN (eGFP) in a transgenic wheat line was targeted for silencing. Silencing of eGFP fluorescence was observed in both the maturation and elongation zones of roots. BMVCP5 mediated significant silencing of eGFP and TaPHO2 mRNA expression in roots at 14 and 21 dpi, and TaPHO2 silencing led to the doubling of inorganic phosphate concentration in the 2nd through 4th systemic leaves. All 54 wheat cultivars screened were susceptible to BMV infection. BMVCP5-mediated TaPDS silencing resulted in the expected bleaching phenotype in all eight cultivars examined, and decreased TaPDS transcript was detected in all three cultivars examined. This BMVCP5 VIGS technology may serve as a rapid and effective functional genomics tool for high-throughput gene function studies in aerial and root tissues and in many wheat cultivars.
MrMYB6 From Chinese Bayberry (Myrica rubra) Negatively Regulates Anthocyanin and Proanthocyanidin Accumulation
Authors: Shi Liyu , Chen Xin , Wang Kang , Yang Minjie , Chen Wei , Yang Zhenfeng , Cao Shifeng
Published: June 2021

Anthocyanins and proanthocyanidins (PAs) are important flavonoids in Chinese bayberry (Morella rubra), which functions in fruit color and exhibits multiple health promoting and disease-preventing effects. To investigate the regulation of their biosynthesis in Chinese bayberries, we isolated and identified a subgroup 4 MYB transcription factor (TF), MrMYB6, and found MrMYB6 shared similar repressor domains with other MYB co-repressors of anthocyanin and PA biosynthesis after sequence analysis. Gene expression results revealed the transcripts of MrMYB6 were negatively correlated with the anthocyanin and insoluble PA contents and also with the gene expressions involved in anthocyanin biosynthesis and PA specific genes such as MrLAR and MrANR during the late ripening stages of bayberries. In addition, overexpression of MrMYB6 in tobacco inhibited the transcript levels of NtCHI, NtLAR, and NtANR2, resulting into a decline in the levels of anthocyanins and PAs in tobacco flowers. We further found that MrMYB6 interacted with MrbHLH1 and MrWD40-1 to form functional complexes that acted to directly repress the promoter activities of the PA-specific gene MrLAR and MrANR and the anthocyanin-specific gene MrANS and MrUFGT. Taken together, our results suggested that MrMYB6 might negatively regulate anthocyanin and PA accumulation in Chinese bayberry.
Who Believes in COVID-19 Conspiracy Theories in Croatia? Prevalence and Predictors of Conspiracy Beliefs
Authors: Tonković Mirjana , Dumančić Francesca , Jelić Margareta , Čorkalo Biruški Dinka
Published: June 2021

The COVID-19 pandemic has given rise to numerous new conspiracy theories related to the virus. This study aimed to investigate a range of individual predictors of beliefs in COVID-19 conspiracy theories that account for sociodemographic characteristics (age, gender, education, economic standard, the importance of religion, and political self-identification), distinctive motivational orientations (social dominance and authoritarianism), relevant social attitudes (sense of political powerlessness and trust in science and scientists), and perceived personal risk (perceived risk for self and family members, the concern of being infected, and the expected influence of pandemic on the economic standard of an individual). Participants were 1,060 adults recruited from the general public of Croatia. The sample was a probabilistic quota sample with gender, age, level of education, size of the dwelling, and region of the country as predetermined quotas. The regression model explained 42.2% of the individual differences in beliefs in COVID-19 conspiracy theories. Trust in science and scientists and political powerlessness were the strongest predictors, whereas fear of being infected had the weakest contribution in explaining the variance of the criterion. Additionally, results revealed that the relation of conventionalism (as a proxy of authoritarianism) with belief in COVID-19 conspiracies was mediated by trust in science and scientists. The relation between social dominance and belief in conspiracies was also partially mediated by trust in science. The results suggest that (re)building trust in science and lowering the sense of political helplessness might help in fighting potentially harmful false beliefs about the pandemic.