bluuebunny/crossref_metadata_2025 huggingface dataset:
Sodium New Houttuyfonate Inhibits Cancer-Promoting Fusobacterium nucleatum (Fn) to Reduce Colorectal Cancer Progression
Authors: Jia Fengjing , Yu Qun , Zhao Ling , Shen Yunhui , Guo Haidong , He Feng
Published: December 2022

Colorectal cancer (CRC) is a major cause of morbidity and mortality worldwide. Recent studies showed that the common anaerobe Fusobacterium nucleatum (Fn) is closely associated with a higher risk for carcinogenesis, metastasis, and chemoresistance of CRC. However, there is no specific antimicrobial therapy for CRC treatment. Herbal medicine has a long history of treating diseases with remarkable effects and is attracting extensive attention. In this study, we tested six common phytochemicals for their antimicrobial activities against Fn and whether anti-Fn phytochemicals can modulate CRC development associated with Fn. Among these antimicrobials, we found that SNH showed the highest antimicrobial activity and little cytotoxicity toward cancer cells and normal cells in vitro and in vivo. Mechanistically, SNH may target membrane-associated FadA, leading to FadA oligomerization, membrane fragmentation and permeabilization. More importantly, SNH blocked the tumor-promoting activity of Fn and Fn-associated cancer-driven inflammation, thus improving the intestinal barrier damaged by Fn. SNH reduced Fn load in the CRC-cells-derived mice xenografts with Fn inoculation and significantly inhibited CRC progression. Our data suggest that SNH could be used for an antimicrobial therapy that inhibits Fn and cancer-driven inflammation of CRC. Our results provide an important foundation for future gut microbiota-targeted clinical treatment of CRC.
Real World Cost-Effectiveness Analysis of Population Screening for BRCA Variants among Ashkenazi Jews Compared with Family History-Based Strategies
Authors: Michaelson-Cohen Rachel , Cohen Matan J. , Cohen Carmit , Greenberg Dan , Shmueli Amir , Lieberman Sari , Tomer Ariela , Levy-Lahad Ephrat , Lahad Amnon
Published: December 2022

Identifying carriers of pathogenic BRCA1/BRCA2 variants reduces cancer morbidity and mortality through surveillance and prevention. We analyzed the cost-effectiveness of BRCA1/BRCA2 population screening (PS) in Ashkenazi Jews (AJ), for whom carrier rate is 2.5%, compared with two existing strategies: cascade testing (CT) in carrier’s relatives (≥25% carrier probability) and international family history (IFH)-based guidelines (>10% probability). We used a decision analytic-model to estimate quality-adjusted life-years (QALY) gained, and incremental cost-effectiveness ratio for PS vs. alternative strategies. Analysis was conducted from payer-perspective, based on actual costs. Per 1000 women, the model predicted 21.6 QALYs gained, a lifetime decrease of three breast cancer (BC) and four ovarian cancer (OC) cases for PS vs. CT, and 6.3 QALYs gained, a lifetime decrease of 1 BC and 1 OC cases comparing PS vs. IFH. PS was less costly compared with CT (−3097 USD/QALY), and more costly than IFH (+42,261 USD/QALY), yet still cost-effective, from a public health policy perspective. Our results are robust to sensitivity analysis; PS was the most effective strategy in all analyses. PS is highly cost-effective, and the most effective screening strategy for breast and ovarian cancer prevention. BRCA testing should be available to all AJ women, irrespective of family history.
Microporous Ceramics Based on β-Tricalcium Phosphate
Authors: Safronova Tatiana , Grigorev Grigorii , Shatalova Tatiana , Roslyakov Ilya , Platonov Vadim , Khayrutdinova Dinara
Published: December 2022

Microporous ceramic material, based on β-tricalcium phosphate β-Ca3(PO4)2 with grain size 2–5 μm, pore size smaller than 10 mm, and density 1.22 g/cm3 corresponding to ~40% of the theoretical density (3.07 g/cm3) of β-Ca3(PO4)2, was obtained from a powder mixture with a given molar ratio Ca/P = 1.5 after firing at 1100 °C. A homogenized powder mixture of synthetic dicalcium hydrogen phosphates with the molar ratio Ca/P = 1 and calcium citrate tetrahydrate Ca3(C6H5O7)2·4H2O with the molar ratio Ca/P = ∞ was used for microporous ceramic preparation. The phase composition of calcium phosphate powder, synthesized from an aqueous solution of phosphoric acid H3PO4 and calcium carbonate CaCO3 powder, included brushite CaHPO4·2H2O as the predominant phase. Formation of β-tricalcium phosphate β-Ca3(PO4)2 during firing occurred due to the heterophase interaction of the products of thermal decomposition of the components of the starting powder mixture, namely, calcium pyrophosphate Ca2P2O7 and calcium oxide CaO. The formation of arch-like structures from β-tricalcium phosphate β-Ca3(PO4)2 grains, which were tightly sintered together, hindered the shrinkage of ceramics. The microporous ceramics obtained, based on β-tricalcium phosphate β-Ca3(PO4)2, can be recommended as a biocompatible and biodegradable material for treatment of bone defects and as a substrate for bone-cell cultivation.
Amphiboreality and Distribution of Snailfishes (Cottiformes: Liparidae) in the Arctic and the North Atlantic
Authors: Chernova Natalia V.
Published: December 2022

The marine ichthyofauna of the Arctic Ocean has an ancestral origin from the Pacific Ocean and, to a lesser extent, from the Atlantic Ocean, which is explained by the amphiboreal concept, developed on groups of fish and invertebrates. Snailfishes (Liparidae) of the Arctic and the North Atlantic are analyzed in the context of this amphiboreal concept. The review is based on the data of many years of research on their taxonomy using various material of morphological differences/similarities of the taxa and patterns of species distribution against the background of biogeographic representations. For the Arctic area, 33 species of the family are known: Liparis (5), Careproctus (21), Paraliparis (2), Rhodichthys (2), and Psednos (3). For the Atlantic fauna, with the same number of species, their composition differs: Liparis (6), Careproctus (3), Paraliparis (12), Psednos (11), and Eutelichthys (1). The amphiboreal concept explains the speciation of Liparis and the majority of Careproctus as the result of trans-Arctic preglacial migrations. For other (deep-sea) species, the hypothesis of a transoceanic dispersal route is applicable; it passed from the North Pacific through the Southern Ocean and then north across the Atlantic.
Semantic Representation of the Intersection of Criminal Law & Civil Tort
Authors: Spyropoulos Alexandros Z. , Kornilakis Angelos , Makris Georgios C. , Bratsas Charalampos , Tsiantos Vassilis , Antoniou Ioannis
Published: December 2022

The more complex and globalized social structures become, the greater the need for new ways of exchanging information and knowledge. Legal science is a field that needs to be codified to allow the interoperability between people and states, as well as between humans and machines. The objective of this work is to develop an ontology in order to describe two different pillars of codified law (civil and criminal) and be able to depict the interaction between them. To answer the above question, we examine the Greek Criminal Law as depicted in the Greek Penal Code (ΠΚ) and the way its articles can be analyzed. Then we examine Tort as described in the Greek Civil Code (AΚ) and link the two codifications through the concepts of illegality and damage, both being prerequisites of tortious liability. Following that, through the Protégé application, a legal ontology is created in the OWL semantic language, while finally, four articles of the Penal Code are codified in the ontology and a presentation of their relation to the civil tort is required from a reasoning algorithm.
Similarities in Bacterial Uropathogens and Their Antimicrobial Susceptibility Profile in Diabetics and Their Non-Diabetic Caregivers at a National Diabetes Management and Research Centre, Accra-Ghana
Authors: Owusu Enid , Adjei Henrietta , Afutu Emmanuel
Published: December 2022

Background: Diabetes mellitus has some damaging effects on the genitourinary system and has been found to have adverse effects on the host immune system, resulting in higher risk of infections including urinary tract infections (UTI). Incidences of UTI caused by bacteria have been increasingly reported globally and the abuse of antibiotics leading to evolving resistant strains of antibiotics is a public health challenge for the management of this condition. Information on the difference in types of bacterial agents causing UTI in diabetic patients and non-diabetic individuals, and their susceptibility profiles, will facilitate effective management among these groups of patients. Therefore, this study aimed at determining the difference in prevalence of UTI, the causative bacteria, and their antimicrobial susceptibility profiles in diabetic patients and non-diabetic individuals at a diabetes management center. Methods: This was a prospective cross-sectional study conducted amongst 100 diagnosed diabetic patients and 100 non-diabetic individuals. Urine sample was collected aseptically and analyzed microbiologically for the presence of urinary tract bacterial pathogens. Drug susceptibility testing was conducted on the isolates by the Kirby Bauer method to ascertain the antibiotic susceptibility patterns. Results: Among the diabetic and non-diabetic individuals, urinary tract bacterial pathogens were observed in 28.0% and 26.0% of samples, respectively. The organisms were in the following proportions for diabetic and non-diabetic individuals, respectively: E. coli (14/28, 50% and 8/26, 30.7%), S. aureus (2/28, 7.1% and 4/26, 15.4%), K. pneumoniae (4/28, 14.3% and 8/26, 30.7%), K. ozoenae (2/28, 7.14% and 0/26, 0%), K. oxytoca (0/28, 0% and 4/26, 15.4%) and C. urealyticum (6/28, 21.4% and 2/26, 7.69%). The difference between the proportions of bacteria isolated was, however, not statistically significant (p-value = 0.894). Bacteria isolated from both diabetic and non-diabetic individuals were highly susceptible to most of the antibiotics tested, especially nitrofurantoin, cefuroxime, ceftriaxone, and cefotaxime. Conclusion: This study has shown that similarities exist in prevalence of UTI, the causative bacteria, and their antimicrobial susceptibility patterns amongst diabetic patients and non-diabetic individuals at a diabetes management center. These data will help in the management of UTI among these individuals.
Texture Analysis to Enhance Drone-Based Multi-Modal Inspection of Structures
Authors: Nooralishahi Parham , Ramos Gabriel , Pozzer Sandra , Ibarra-Castanedo Clemente , Lopez Fernando , Maldague Xavier P. V.
Published: December 2022

The drone-based multi-modal inspection of industrial structures is a relatively new field of research gaining interest among companies. Multi-modal inspection can significantly enhance data analysis and provide a more accurate assessment of the components’ operability and structural integrity, which can assist in avoiding data misinterpretation and providing a more comprehensive evaluation, which is one of the NDT4.0 objectives. This paper investigates the use of coupled thermal and visible images to enhance abnormality detection accuracy in drone-based multi-modal inspections. Four use cases are presented, introducing novel process pipelines for enhancing defect detection in different scenarios. The first use case presents a process pipeline to enhance the feature visibility on visible images using thermal images in pavement crack detection. The second use case proposes an abnormality classification method for surface and subsurface defects using both modalities and texture segmentation for piping inspections. The third use case introduces a process pipeline for road inspection using both modalities. A texture segmentation method is proposed to extract the pavement regions in thermal and visible images. Further, the combination of both modalities is used to detect surface and subsurface defects. The texture segmentation approach is employed for bridge inspection in the fourth use case to extract concrete surfaces in both modalities.
Multispectral Spaceborne Proxies of Predisposing Forest Structure Attributes to Storm Disturbance—A Case Study from Germany
Authors: Garamszegi Balázs , Jung Christopher , Schindler Dirk
Published: December 2022

Windstorms are among the primary drivers of forest disturbances. Although they are inherent part of the natural ecosystem processes, they severely impact managed forests. Modeling approaches serve as key tools for the evaluation of disturbance risk and different predisposing factors. However, data availability on relevant forest attributes can be problematic on a larger scale. While spaceborne remote sensing has already proven itself as a tool for disturbance detection, its use in relation to predisposing forest attributes remains underexploited. The present work explores multispectral object-based proxy predictors for statistical wind disturbance modeling based on the publicly available Sentinel-2 imagery and recorded damage polygons from the pan-European FORWIND database. Potential predictors were tested in logistic and random forests (RF) regression models for both disturbance occurrence and severity for a case study of a major storm event in Northern Germany from 2017. The results reveal a general potential of the derived spaceborne variables to be used as proxy variables to critical predisposing forest attributes. The presented proxy variables also outperformed a set of publicly available derived spatial data products for modeling both disturbance occurrence and severity. Model accuracies were moderate (reaching AUC = 0.76 for logistic regression fit and AUC = 0.69 for predictive accuracy of RF models), yet falling within the range of reported results in previous studies from the field. Limitations of the spectral satellite imagery as a single information source were acknowledged; however, the results indicate the further potential of spaceborne imagery applications in disturbance modeling, assessment and resulting mapping of disturbance susceptibility at different spatial scales. Considering the growing spatiotemporal availability of high-resolution spaceborne data, we propose that a model representation of post-disturbance forest patterns could improve the understanding of complex disturbance regimes and recurrent susceptibility.
Rapid Estimation of Decameter FPAR from Sentinel-2 Imagery on the Google Earth Engine
Authors: Wang Yiting , Zhan Yinggang , Xie Donghui , Liu Jinghao , Huang Haiyang , Zhao Dan , Xiao Zihang , Zhou Xiaode
Published: December 2022

As a direct indicator of vegetation photosynthesis, the fraction of absorbed photosynthetically active radiation (FPAR) serves as a critical input in a series of land surface models. While existing satellite FPAR products are generally at coarse resolutions ranging from 250 m to 1 km, operational FPAR products at fine resolution are urgently needed in studying land surface processes at the plot scale. However, existing methods for estimating fine-resolution FPAR were mainly designed for Landsat data, and few studies have attempted to develop algorithms for Sentinel-2 data. In particular, the operational estimation of decameter FPAR has a higher requirement for the algorithms in terms of generalizability, efficiency, accuracy, and adaptability to Sentinel-2 data. In this paper, we developed a retrieval chain on the Google Earth Engine (GEE) platform to estimate FPAR by learning the relationship between MODIS FPAR and Sentinel-2 surface reflectance. Scale-consistent multilinear models were used to model the relationship between MODIS FPAR and Sentinel-2 surface reflectance, and the model coefficients were regressed from the selected training samples. To account for the spectral and spatial characteristics of the Sentinel-2 data, we designed criteria for selecting training samples and compared different band combinations. Three strategies for band combination were used: (1) green, red, and near infrared (NIR) bands at 10 m resolution (i.e., three bands); (2) green, red, NIR, and red edge (RE) 1, RE2, and RE3 bands at 20 m resolution (i.e., five bands); and (3) green, red, NIR, RE1, RE2, RE3, shortwave infrared1 (SWIR1) and SWIR2 bands at 20 m resolution (i.e., eight bands). Meanwhile, the official Sentinel Application Platform (SNAP) method has also been implemented to estimate the Sentinel FPAR at 10 m and 20 m resolutions for comparison. Both methods were applied to the western Guanzhong area, Shaanxi Province, China, for FPAR estimation of all cloud-free Sentinel-2 images in 2021. The results show that the scaling-based method using five bands at 20 m resolution was the most accurate compared to the in situ measurements (RMSE = 0.076 and R² = 0.626), which outperformed the SNAP method at 10 m and 20 m resolutions and the scaling-based method using other strategies. The results of the scaling-based method using all three strategies were highly consistent with the MODIS FPAR product, while the SNAP method systematically underestimated FPAR values compared to the MODIS FPAR products. The proposed method is more ready-to-use and more efficient than SNAP software. Considering that the service of the MODIS sensor is overdue, the proposed method can be extended to alternatives to MODIS products, such as VIIRS and Sentinel-3 data.
Effects of Plot Size on Airborne LiDAR-Derived Metrics and Predicted Model Performances of Subtropical Planted Forest Attributes
Authors: Li Chungan , Lin Xin , Dai Huabing , Li Zhen , Zhou Mei
Published: December 2022

Investigating the impact of field plot size on the performance of estimation models for forest inventory attributes could help optimize the technical schemes for an operational airborne LiDAR-assisted forest resource inventory. However, few studies on the topic have focused on subtropical forests. In this study, 104 rectangular plots of 900 m2 (subdivided into nine quadrats with an area of 10 × 10 m) in subtropical planted forests (Chinese fir, pine, eucalyptus, and broad-leaved forest, 2–56 years old) were used to establish four datasets with six different plot sizes (100, 200, 300, 400, 600, and 900 m2) by combining quadrats. The differences in the LiDAR-derived metrics and forest attributes between plots of different sizes were statistically analyzed. Based on the multivariate power models with stable structures, the differences in estimation accuracies of the stand volume (VOL) and basal area (BA) using plot data of different sizes were compared. The results indicated that: (1) the mean differences in LiDAR-derived metrics of the plots of different sizes in all forest types were small, and most of them had no statistically significant differences (α = 0.05) between the plots of different sizes and the 900 m2 plots; however, the standard deviation of the difference increased rapidly with decreasing plot size; (2) except for the maximal tree height of the plots, the other forest attributes, including the mean tree height, diameter at breast height, BA, and VOL of all forest types, showed no statistically significant differences between the plots of different sizes and the 900 m2 plots; and (3) with increasing plot size, the accuracies of VOL and BA estimations improved markedly, and the effects of plot size on the estimation accuracies of the different forest attributes and different forest types were essentially the same. Spatial averaging resulted in the variations in the independent variables (LiDAR variables) and dependent variables (forest attributes) decreasing gradually with the increasing plot size, which was the main reason for the model’s accuracy improving. In applying airborne LiDAR to a large-scale subtropical planted forest inventory, the plot size should be at least 600 m2 for all forest types.
Root Production and Microbe-Derived Carbon Inputs Jointly Drive Rapid Soil Carbon Accumulation at the Early Stages of Forest Succession
Authors: Liu Ruiqiang , He Yanghui , Du Zhenggang , Zhou Guiyao , Zhou Lingyan , Wang Xinxin , Li Nan , Yan Enrong , Feng Xiaojuan , Liang Chao , Zhou Xuhui
Published: December 2022

Plants and microbes are the primary drivers in affecting the formation and accrual of soil organic carbon (SOC) for natural ecosystems. However, experimental evidence elucidating their underlying mechanisms for SOC accumulation remains elusive. Here, we quantified plant and microbial contributions to SOC accrual in successional subtropical forests by measuring leaf-, root-, and microbial biomarkers, root and leaf litter inputs, and microbial C decomposition. The long-term monitoring results showed that SOC accumulated rapidly at the early-successional stage, but changed little at the mid- and late-successional stages. SOC accrual rate was positively correlated with fine-root production and microbial C turnover, but negatively with annual litterfall. Biomarker data exhibited that the rapid SOC accumulation was jointly driven by root- and microbe-derived C inputs from the early- to mid-successional stages. In contrast, aboveground litterfall considerably contributed to soil C accrual from the mid- to late-successional stages compared to belowground processes, although SOC accumulation is low. Our study revealed the importance of root production and microbial anabolism in SOC accrual at the early stages of forest succession. Incorporating these effects of belowground C inputs on SOC formation and accumulation into earth system models might improve model performance and projection of long-term soil C dynamics.
Application of Length-Based Assessment Methods to Elucidate Biological Reference Points of Black Pomfret Stock in the Bay of Bengal, Bangladesh
Authors: Barua Suman , Liu Qun , Alam Mohammed Shahidul , Schneider Petra , Mozumder Mohammad Mojibul Hoque
Published: December 2022

The black pomfret (Parastromateus niger) is one of the high-income-generating carangid fish species and the only known member of its genus. This study aims to identify existing gaps in stock status and population demography of this species and provide viable management recommendations to enhance the sustainability of this fishery. Therefore, three methodological approaches have been used in this study; TropFishR to present the current exploitation status, the length-based spawning potential ratio (LB-SPR) to quantify stock spawning biomass, and Froese’s sustainability indicators (LBI) to establish a basic standard for sustainable management of the fishery. In the length-weight relationship of black pomfret, an allometric growth pattern (b = 2.19) was found. The VBGF life history parameters for black pomfret were L∞ = 55.25 cm, K = 0.54 year−1, and based on LCCC analysis, the total mortality (Z = 1.61 year−1), natural mortality (M = 0.69 year−1) and fishing mortality (F = 0.91 year−1) are calculated. The result reveals that this fishery is currently suffering from overexploitation and the stock’s spawning biomass (SPR = 13%) is below the limit reference point because most of the catch (82%) was found to be under the maturity level. Based on the results, this study recommended strictly maintaining the mesh size of the net to ensure not to catch immature fish with a length smaller than 30.63 cm, recommended the length to catch be between 29 and 35 cm, and reducing fishing pressure by one-third to ensure the sustainability of the black pomfret fishery.
Genome-Wide Identification of WRKY Family Genes and the Expression Profiles in Response to Nitrogen Deficiency in Poplar
Authors: Chen Yao , Kong Xiangge , Yang Le , Fu Mingyue , Zhang Sheng
Published: December 2022

The fast-growing arbor poplar is widely distributed across the world and is susceptible to nitrogen availability. The WRKY transcription factor is an important regulatory node of stress tolerance as well as nutrient utilization. However, the potential response mechanism of WRKY genes toward nitrogen is poorly understood. Therefore, the identification of WRKY genes on the Populus trichocarpa genome was performed, and 98 PtWRKYs (i.e., PtWRKY1 to PtWRKY98) were identified. Phylogenetic analysis and the promoter cis-acting element detection revealed that PtWRKYs have multiple functions, including phosphorus and nitrogen homeostasis. By constructing multilayer-hierarchical gene regulatory networks (ML-hGRNs), it was predicted that many WRKY transcription factors were involved in the nitrogen response, such as PtWRKY33 and PtWRKY95. They mainly regulated the expression of primary nitrogen-responsive genes (NRGs), such as PtNRT2.5A, PtNR2 and PtGLT2. The integrative analysis of transcriptome and RT-qPCR results show that the expression levels of 6 and 15 PtWRKYs were regulated by nitrogen availability in roots and leaves, respectively, and those were also found in ML-hGRN. Our study demonstrates that PtWRKYs respond to nitrogen by regulating NRGs, which enriches the nitrate-responsive transcription factor network and helps to uncover the hub of nitrate and its related signaling regulation.
Identifying the Genetic Basis of Mineral Elements in Rice Grain Using Genome-Wide Association Mapping
Authors: Islam A. S. M. Faridul , Mustahsan Wardah , Tabien Rodante , Awika Joseph M. , Septiningsih Endang M. , Thomson Michael J.
Published: December 2022

Mineral malnutrition is a major problem in many rice-consuming countries. It is essential to know the genetic mechanisms of accumulation of mineral elements in the rice grain to provide future solutions for this issue. This study was conducted to identify the genetic basis of six mineral elements (Cu, Fe, K, Mg, Mn, and Zn) by using three models for single-locus and six models for multi-locus analysis of a genome-wide association study (GWAS) using 174 diverse rice accessions and 6565 SNP markers. To declare a SNP as significant, −log10(P) ≥ 3.0 and 15% FDR significance cut-off values were used for single-locus models, while LOD ≥ 3.0 was used for multi-locus models. Using these criteria, 147 SNPs were detected by one or two GWAS methods at −log10(P) ≥ 3.0, 48 of which met the 15% FDR significance cut-off value. Single-locus models outperformed multi-locus models before applying multi-test correction, but once applied, multi-locus models performed better. While 14 (~29%) of the identified quantitative trait loci (QTLs) after multiple test correction co-located with previously reported genes/QTLs and marker associations, another 34 trait-associated SNPs were novel. After mining genes within 250 kb of the 48 significant SNP loci, in silico and gene enrichment analyses were conducted to predict their potential functions. These shortlisted genes with their functions could guide future experimental validation, helping us to understand the complex molecular mechanisms controlling rice grain mineral elements.
Significance of Identifying Key Genes Involved in HBV-Related Hepatocellular Carcinoma for Primary Care Surveillance of Patients with Cirrhosis
Authors: Li Yaqun , Li Jianhua , He Tianye , Song Yun , Wu Jian , Wang Bin
Published: December 2022

Cirrhosis is frequently the final stage of disease preceding the development of hepatocellular carcinoma (HCC) and is one of the risk factors for HCC. Preventive surveillance for early HCC in patients with cirrhosis is advantageous for achieving early HCC prevention and diagnosis, thereby enhancing patient prognosis and reducing mortality. However, there is no highly sensitive diagnostic marker for the clinical surveillance of HCC in patients with cirrhosis, which significantly restricts its use in primary care for HCC. To increase the accuracy of illness diagnosis, the study of the effective and sensitive genetic biomarkers involved in HCC incidence is crucial. In this study, a set of 120 significantly differentially expressed genes (DEGs) was identified in the GSE121248 dataset. A protein–protein interaction (PPI) network was constructed among the DEGs, and Cytoscape was used to extract hub genes from the network. In TCGA database, the expression levels, correlation analysis, and predictive performance of hub genes were validated. In total, 15 hub genes showed increased expression, and their positive correlation ranged from 0.80 to 0.90, suggesting they may be involved in the same signaling pathway governing HBV-related HCC. The GSE10143, GSE25097, GSE54236, and GSE17548 datasets were used to investigate the expression pattern of these hub genes in the progression from cirrhosis to HCC. Using Cox regression analysis, a prediction model was then developed. The ROC curves, DCA, and calibration analysis demonstrated the superior disease prediction accuracy of this model. In addition, using proteomic analysis, we investigated whether these key hub genes interact with the HBV-encoded oncogene X protein (HBx), the oncogenic protein in HCC. We constructed stable HBx-expressing LO2-HBx and Huh-7-HBx cell lines. Co-immunoprecipitation coupled with mass spectrometry (Co-IP/MS) results demonstrated that CDK1, RRM2, ANLN, and HMMR interacted specifically with HBx in both cell models. Importantly, we investigated 15 potential key genes (CCNB1, CDK1, BUB1B, ECT2, RACGAP1, ANLN, PBK, TOP2A, ASPM, RRM2, NEK2, PRC1, SPP1, HMMR, and DTL) participating in the transformation process of HBV infection to HCC, of which 4 hub genes (CDK1, RRM2, ANLN, and HMMR) probably serve as potential oncogenic HBx downstream target molecules. All these findings of our study provided valuable research direction for the diagnostic gene detection of HBV-related HCC in primary care surveillance for HCC in patients with cirrhosis.
Identification and Functional Characterization of CYP4D2 Putatively Associated with β-Cypermethrin Detoxification in Phortica okadai
Authors: Wang Lingjun , Tang Hongri , Xie Zhimei , Li Di , Yin Changzhu , Luo Bo , Yan Rong , Sun Wei , Liu Hui
Published: December 2022

Phortica okadai, a polyphagous pest, serves as a vector for Thelazia callipaeda in China. Currently, there are no effective control strategies for this vector. Agricultural pest control may cause P. okadai to become a threat due to the development of pesticide resistance. Cytochrome P450s (CYP450) plays a significant role in detoxifying xenobiotics in insects. In this study, we performed RNA sequencing of P. okadai exposed to β-cypermethrin for 0 and 1 h and then gene cloning of the five up-regulated CYP450 genes. Three CYP450 genes were successfully cloned, and their expression patterns in different developmental stages and in different tissues were analyzed by RT-qPCR. Pocyp4d2 was observed to have the highest expression in the midgut (fold change 2.82 for Pocyp4d2, 2.62 for Pocyp49a1, and 1.77 for Pocyp28d2). Functional analysis was carried out according to overexpression in S2 cells from the pfastbac1 vector and RNAi with siRNA. The results of the CCK8 assay indicated that the overexpression of the recombinant protein PoCYP4D2 suppressed the decrease in S2 cell viability due to β-cypermethrin. The expression levels of PoCYP4D2 decreased significantly, and the mortality rates increased from 6.25% to 15.0% at 3 h and from 15.0% to 27.5% at 6 h after Pocyp4d2-siRNA injection. These results suggest that Pocyp4d2 may be an essential key gene in the metabolism of β-cypermethrin in P. okadai. This study constitutes a foundation to explore further the functions of P. okadai CYP450 genes in insecticide metabolism.
Gene Networks and Pathways Involved in LPS-Induced Proliferative Response of Bovine Endometrial Epithelial Cells
Authors: Najafi Mojtaba , Guo Yongzhi , Andersson Göran , Humblot Patrice , Bongcam-Rudloff Erik
Published: December 2022

Lipopolysaccharide (LPS) is a component of the outer membrane of Gram-negative bacteria involved in the pathogenic processes leading to mastitis and metritis in animals such as dairy cattle. LPS causes cell proliferation associated with endometrium inflammation. Former in vitro studies have demonstrated that LPS induces an intense stimulation of the proliferation of a pure population of bovine endometrial epithelial cells. In a follow-up transcriptomic study based on RNA-sequencing data obtained after 24 h exposure of primary bovine endometrial epithelial cells to 0, 2, and 8 μg/mL LPS, 752 and 727 differentially expressed genes (DEGs) were detected between the controls and LPS-treated samples that encode proteins known to be associated with either proliferation or apoptosis, respectively. The present bioinformatic analysis was performed to decipher the gene networks involved to obtain a deeper understanding of the mechanisms underlying the proliferative and apoptosis processes. Our findings have revealed 116 putative transcription factors (TFs) and the most significant number of interactions between these TFs and DEGs belong to NFKβ1, TP53, STAT1, and HIF1A. Moreover, our results provide novel insights into the early signaling and metabolic pathways in bovine endometrial epithelial cells associated with the innate immune response and cell proliferation to Escherichia coli-LPS infection. The results further indicated that LPS challenge elicited a strong transcriptomic response, leading to potent activation of pro-inflammatory pathways that are associated with a marked endometrial cancer, Toll-like receptor, NFKβ, AKT, apoptosis, and MAPK signaling pathways. This effect may provide a mechanistic explanation for the relationship between LPS and cell proliferation.
Effectiveness of Convalescent Plasma Therapy in COVID-19 Patients with Hematological Malignancies: A Systematic Review
Authors: Shibeeb Sapha , Ajaj Ilham , Al-Jighefee Hadeel , Abdallah Atiyeh M.
Published: December 2022

Background: Immunocompromised patients, including those with hematological malignancies, are at a high risk of developing severe coronavirus disease 2019 (COVID-19) complications. Currently, there is a limited number of systematic reviews into the efficacy of convalescent plasma therapy (CPT) use in the treatment of COVID-19 patients with hematological malignancies. Therefore, the aim of this review was to systematically appraise the current evidence for the clinical benefits of this therapy in COVID-19 patients with hematological malignancies. Methods: A comprehensive search was conducted up to April 2022, using four databases: PubMed, Web of Science, Science Direct, and Scopus. Two reviewers independently assessed the quality of the included studies. Data collection analysis was performed using Microsoft Excel 365 and GraphPad Prism software. Results: 18 studies met the inclusion criteria; these records included 258 COVID-19 patients who had hematological malignancies and were treated with CPT. The main findings from the reviewed data suggest that CPT may be associated with improved clinical outcomes, including (a) higher survival rate, (b) improved SARS-CoV-2 clearance and presence of detectable anti-SARS-CoV-2 antibodies post CP transfusion, and (c) improved hospital discharge time and recovery after 1 month of CPT. Furthermore, treatment with convalescent plasma was not associated with the development of adverse events. Conclusions: CPT appears to be an effective supportive therapeutic option for hematological malignancy patients infected with COVID-19. To our knowledge, this is one of the first systematic reviews of the clinical benefits of CPT in COVID-19 patients with hematological malignancies.
Enhanced Production of Apocarotenoids by Salicylic Acid Elicitation in Cell Suspension Cultures of Saffron (Crocus sativus L.)
Authors: Moradi Azar , Zarinkamar Fatemeh , Mita Giovanni , Caretto Sofia , De Paolis Angelo
Published: December 2022

A cell suspension culture of saffron (Crocus sativus L.) was previously established from style-derived calli to obtain an in vitro system for crocin, an uncommon and valuable water-soluble apocarotenoid, and carotenoid production suitable for future scaling up. To shed more light on the correlation between apocarotenoid biosynthesis and key-gene expression, in this study, SA was used at 0.5 mM concentration to elicit crocin production and the effects on carotenoid production were analyzed after 6, 12, 24, and 48 h. HPLC-DAD analysis was used for total crocin quantification as well as the other carotenoids zeaxanthin, β-carotene and lutein. Quantitative RT-PCR was used to analyze the transcript levels of saffron apocarotenoid biosynthetic key genes PSY (phytoene synthase), BCH1 (β-carotene hydroxylase), and CCD2 (carotenoid cleavage dioxygenase) after SA elicitation. In saffron suspension-cultured cells elicited by SA, the carotenoid biosynthetic pathway was mostly enhanced toward crocin biosynthesis, known to exert strong biological activity and therapeutic effects, rather than lutein or xanthins. SA increased BCH1 and CCD2 gene expression 15.6 and 3.3 times, respectively, compared to the control at 24 h after elicitation. Although a dynamic change of metabolite contents and gene expression was observed during the 48 h time course in response to SA elicitation, the changes of zeaxanthin and crocin were consistent with the regulation of the corresponding genes BCH and CCD2 during the time course. In conclusion, the effects of SA on regulation of gene expression in the apocarotenoid pathway could be successfully applied for the biotechnological production of crocin.
Effect of Leaf Extract from Lycium barbarum on Preservation of Cherry Tomato Fruit
Authors: Bu Hubai , Ma Yujia , Ge Beilei , Sha Xiaorong , Ma Ying , Zhang Ping , Jin Lei
Published: December 2022

The preservation of cherry tomatoes is a challenge for farmers, sellers, and processors. In recent years, natural extracts of plants have been increasingly used for the preservation of fruits and vegetables. In this study, we investigated the effect of treatment with goji berry (Lycium barbarum) leaf extract on the postharvest freshness of cherry tomatoes, and we determined the active ingredients, antioxidant capacity, and antifungal activity of the extract. Goji leaf extracts were tested at different concentrations (0.2–1.0 g/L) to assess their effects on preserving the freshness of cherry tomatoes at 5 °C and 20 °C. The goji berry leaf extract was rich in polysaccharides, saponins, polyphenols, and other active ingredients (1.11–45.83 mg/g), and the antioxidant capacity and antifungal activity were outstanding. Treatments with 0.2, 0.4, and 0.6 g/L of goji berry leaf extract at 20 °C helped to preserve tomato fruit, where 0.4 g/L was the most effective, followed by 0.2 and 0.6 g/L. However, 0.8 and 1.0 g/L had no effect. Treatment with 1.0 g/L of goji berry leaf extract at 5 °C effectively reduced the loss of quality of tomato fruit. This treatment maintained the firmness and color of the tomatoes and maintained the levels of nutrients such as vitamin C, total acids, and total soluble solids. The next most effective doses were 0.8 g/L and 0.6 g/L. Cherry tomatoes treated with goji berry leaf extract could be stored for 21 days at 20 °C and for 35 days at 5 °C. Compared with the control groups treated with distilled water and no treatment, the storage period was extended by 3–6 days at 20 °C and by 7–14 days at 5 °C. The results obtained in this study provide a theoretical basis for extending the storage period of cherry tomatoes using goji berry leaf extract and the development of natural preservatives as well as enhancing the utilization of germplasm resources.
Identification and Functional Analysis of Transcription Factor NF-Y Family during Flower Bud Dormancy in Prunus mume
Authors: Gao Feng , Huang Xiao , Segbo Silas , Coulibaly Daouda , Wang Rui , Ma Chengdong , Bai Yang , Zhou Pengyu , Tan Wei , Ma Yufan , Ni Zhaojun , Shi Ting , Gao Zhihong
Published: December 2022

NF-Y transcription factor consists of three subsets, A, B, and C, which play various roles during biological processes in plants, particularly in growth and development, stress response, and microorganism interactions. The current study was exhaustively conducted on the NF-Y gene family in Prunus mume (Japanese apricot). We identified 27 PmNF-Y genes that were distributed on eight chromosomes of the Japanese apricot genome, and which were divided into three subgroups according to their phylogenetic relationship. Protein replication analysis showed that the Ka/Ks ratio of one pair of tandem repeats and two pairs of segmental repeats was less than 1. Cis-acting elements upstream of PmNF-Y genes were divided into four distinct categories: light response, growth metabolism, stress, and hormones, among which the numbers of hormone and light-responsive cis-acting elements were higher. RNA-seq analysis revealed that most of the genes were expressed with slight variation in various tissues. Interestingly, some genes were expressed differently during dormancy. During dormancy with exogenous hormones and low temperature, the qRT-PCR results showed that these differentially expressed genes had specific expression responses under GA4, ABA, MeJA, and low-temperature treatments. Therefore, these findings could provide a novel theoretical foundation for future research into the function and molecular regulation mechanism of the NF-Y gene family in the Prunus species.
Impact of Beauveria bassiana and Metarhizium anisopliae on the Metabolic Interactions between Cucumber (Cucumis sativus L.) and Cucumber Mosaic Virus (CMV)
Authors: Shaalan Roshan , Ibrahim Ludmilla , As-sadi Falah , El Kayal Walid
Published: December 2022

In natural systems, plant–endophyte interactions are important for reducing abiotic and biotic stresses in plants by producing a variety of metabolites that protect plants from pathogens and herbivores. Biocontrol strategies are increasingly being used as a viable alternative to chemical pesticides. Entomopathogenic fungi (EPF) are one of them, and they have been touted as a successful method for biological pest control in plants. Because EPF strains are sensitive to environmental conditions when sprayed, the recently discovered endophytic behavior of several EPF strains has improved their management. Cucumber mosaic virus (CMV) is one of the most common and serious plant viruses worldwide, infecting over 1200 plant species and being spread by more than 80 aphid species. CMV control is directed towards the use of chemical insecticides to eradicate its insect vectors. Endophytic EPF is currently being studied to control plant virus infection, and antagonistic effects have been reported. Metabolomics is an emerging research field for plant metabolite profiling and is employed to study plant–endophyte interactions. In the present research, metabolomics approaches were conducted to gain information into mechanisms involved in defense against CMV in endophytes Beauveria bassiana and Metarhizium anisopliae (EPF)-treated diseased cucumber plants. In addition, CMV-induced metabolic changes in cucumber plants were investigated. Our analysis indicated large differences in cucumber metabolites due to endophytes application. In total, six hundred and thirty-one metabolites were differentially expressed in endophyte-treated CMV diseased cucumber plants. Regulation of different kinds of amino acids, organic acids, and phenylpropanoids metabolites could provide insight about plant defense mechanism against CMV pathogen. Important metabolites were found to be regulated in diseased cucumber plants due to fungal endophytes treatment that could possibly confer tolerance to CMV disease.
Examining the Auditory Selective Attention Switch in a Child-Suited Virtual Reality Classroom Environment
Authors: Breuer Carolin , Loh Karin , Leist Larissa , Fremerey Stephan , Raake Alexander , Klatte Maria , Fels Janina
Published: December 2022

The ability to focus ones attention in different acoustical environments has been thoroughly investigated in the past. However, recent technological advancements have made it possible to perform laboratory experiments in a more realistic manner. In order to investigate close-to-real-life scenarios, a classroom was modeled in virtual reality (VR) and an established paradigm to investigate the auditory selective attention (ASA) switch was translated from an audio-only version into an audiovisual VR setting. The new paradigm was validated with adult participants in a listening experiment, and the results were compared to the previous version. Apart from expected effects such as switching costs and auditory congruency effects, which reflect the robustness of the overall paradigm, a difference in error rates between the audio-only and the VR group was found, suggesting enhanced attention in the new VR setting, which is consistent with recent studies. Overall, the results suggest that the presented VR paradigm can be used and further developed to investigate the voluntary auditory selective attention switch in a close-to-real-life classroom scenario.
Freshwater as a Sustainable Resource and Generator of Secondary Resources in the 21st Century: Stressors, Threats, Risks, Management and Protection Strategies, and Conservation Approaches
Authors: Bănăduc Doru , Simić Vladica , Cianfaglione Kevin , Barinova Sophia , Afanasyev Sergey , Öktener Ahmet , McCall Grant , Simić Snežana , Curtean-Bănăduc Angela
Published: December 2022

This paper is a synthetic overview of some of the threats, risks, and integrated water management elements in freshwater ecosystems. The paper provides some discussion of human needs and water conservation issues related to freshwater systems: (1) introduction and background; (2) water basics and natural cycles; (3) freshwater roles in human cultures and civilizations; (4) water as a biosphere cornerstone; (5) climate as a hydrospheric ‘game changer’ from the perspective of freshwater; (6) human-induced stressors’ effects on freshwater ecosystem changes (pollution, habitat fragmentation, etc.); (7) freshwater ecosystems’ biological resources in the context of unsustainable exploitation/overexploitation; (8) invasive species, parasites, and diseases in freshwater systems; (9) freshwater ecosystems’ vegetation; (10) the relationship between human warfare and water. All of these issues and more create an extremely complex matrix of stressors that plays a driving role in changing freshwater ecosystems both qualitatively and quantitatively, as well as their capacity to offer sustainable products and services to human societies. Only internationally integrated policies, strategies, assessment, monitoring, management, protection, and conservation initiatives can diminish and hopefully stop the long-term deterioration of Earth’s freshwater resources and their associated secondary resources.
Patterns of Changes in Respiratory Muscle Strength over 1 Year in Non-Sarcopenia, Sarcopenia, and Severe Sarcopenia
Authors: Sawaya Yohei , Hirose Tamaki , Ishizaka Masahiro , Shiba Takahiro , Sato Ryo , Kubo Akira , Urano Tomohiko
Published: December 2022

In this prospective longitudinal cohort study, we explored the characteristics of older people with lower respiratory muscle strength, according to sarcopenia severity, over the course of 1 year. The maximum expiratory pressure (MEP), grip strength, walking speed, and skeletal muscle mass index of 58 participants (28 men, 30 women; mean age, 76.9 ± 7.7 years) were measured at baseline and at the 1-year follow-up. Participants were classified into a decreased MEP group (n = 29; MEP decreased by ≥10% after 1 year) and a non-decreased MEP group (n = 29; MEP decreased by <10%). Sarcopenia status in the mild direction at baseline was significantly associated with MEP decline after one year. Repeated two-way analysis of variance showed significant main effects of measurement time (p < 0.001) and severity of sarcopenia (p = 0.026), as well as a significant interaction effect (p = 0.006). Surprisingly, MEP decreased significantly in the non-sarcopenia and sarcopenia groups, but not in the severe sarcopenia group. Thus, individuals without sarcopenia and those with moderate sarcopenia at baseline are predisposed to MEP decline and should be closely monitored for signs of such decline and associated adverse events.