bluuebunny/crossref_metadata_2025_split huggingface dataset:
Pretreatment with Bifidobacterium longum BAA2573 ameliorates dextran sulfate sodium (DSS)-induced colitis by modulating gut microbiota
Authors: Lin Qiong , Hao Wu-Juan , Zhou Ren-Min , Huang Cui-Lan , Wang Xu-Yang , Liu Yan-Shan , Li Xiao-Zhong 
Published: June 2023

ObjectivesInflammatory bowel disease (IBD) is a chronic lifelong inflammatory disease. Probiotics such as Bifidobacterium longum are considered to be beneficial to the recovery of intestinal inflammation by interaction with gut microbiota. Our goals were to define the effect of the exclusive use of BAA2573 on dextran sulfate sodium (DSS)-induced colitis, including improvement of symptoms, alleviation of histopathological damage, and modulation of gut microbiota.MethodsIn the present study, we pretreated C57BL/6J mice with Bifidobacterium longum BAA2573, one of the main components in an over-the-counter (OTC) probiotic mixture BIFOTO capsule, before modeling with DSS. 16S rDNA sequencing and liquid chromatography–tandem mass spectrometry (LC-MS/MS)-based non-targeted metabolomic profiling were performed with the collected feces.ResultsWe found that pretreatment of Bifidobacterium longum BAA2573 given by gavage significantly improved symptoms and histopathological damage in DSS-induced colitis mice. After the BAA2573 intervention, 57 genera and 39 metabolites were significantly altered. Pathway enrichment analysis demonstrated that starch and sucrose metabolism, vitamin B6 metabolism, and sphingolipid metabolism may contribute to ameliorating colitis. Moreover, we revealed that the gut microbiome and metabolites were interrelated in the BAA2573 intervention group, while Alistipes was the core genus.ConclusionOur study demonstrates the impact of BAA2573 on the gut microbiota and reveals a possible novel adjuvant therapy for IBD patients.
Discovery of anti-SARS-CoV-2 secondary metabolites from the heartwood of Pterocarpus santalinus using multi-informative molecular networking
Authors: Wasilewicz Andreas , Zwirchmayr Julia , Kirchweger Benjamin , Bojkova Denisa , Cinatl Jindrich , Rabenau Holger F. , Rollinger Judith M. , Beniddir Mehdi A. , Grienke Ulrike 
Published: June 2023

A pigment-depleted extract from the heartwood of Pterocarpus santalinus L. f. (PS-DE) showed promising anti-SARS-CoV-2 activity with an IC50 of 29.9 μg/mL in Caco-2-F03 cells. To determine the potential active constituents within the extract prior to isolation, multi-informative molecular network (MN) was applied. Therefore, the extract was separated by high-performance counter-current chromatography (HPCCC) into 11 fractions which were subsequently tested for anti-SARS-CoV-2 activity and analysed by UPLC-tandem mass spectrometry (MS2). The resulting MN combines the bioactivity data of the fractions with the MS2 data. The MN analysis led to the targeted isolation of seven compounds including one pterocarpan (7) reported for the first time as constituent of P. santalinus and four so far undescribed natural products (NPs) that belong to the compound classes of arylpropanes (9), isoflavanones (10) coumestans (16) and 3-arylcoumarins (17), respectively. In total, 15 constituents from the heartwood of P. santalinus and one synthetic isoflavonoid that is structurally related to the natural metabolites were tested for anti-SARS-CoV-2 activity. Thereby, the two pterocarpans (−)-homopterocarpin (5) and (−)-medicarpin (2), the stilbene (E)-pterostilbene (1) and the isoflavonoid 7-O-methylgenistein (11) showed a distinct antiviral activity with IC50 values of 17.2, 33.4, 34.7, and 37.9 µM, respectively, and no cytotoxic effects against Caco-2-F03 cells (CC50 &gt; 100 µM). In addition, a structure-activity relationship (SAR) was proposed indicating structural requirements of pterocarpans for anti-SARS-CoV-2 activity. The herein presented results support the implementation of multi-informative molecular networks as powerful tool for dereplication and targeted isolation of bioactive NPs.
Investigation of FGF21 mRNA levels and relative mitochondrial DNA copy number levels and their relation in nonalcoholic fatty liver disease: a case-control study
Authors: Houshmand Massoud , Zeinali Vahide , Hosseini Amirhossein , Seifi Atena , Danaei Bardia , Kamfar Sharareh 
Published: June 2023

Background: Although the exact mechanisms of nonalcoholic fatty liver disease (NAFLD) are not fully understood, numerous pieces of evidence show that the variations in mitochondrial DNA (mtDNA) level and hepatic Fibroblast growth factor 21 (FGF21) expression may be related to NAFLD susceptibility.Objectives: The main objective of this study was to determine relative levels of mtDNA copy number and hepatic FGF21 expression in a cohort of Iranian NAFLD patients and evaluate the possible relationship.Methods: This study included 27 NAFLD patients (10 with nonalcoholic fatty liver (NAFL) and 17 with non-alcoholic steatohepatitis (NASH)) and ten healthy subjects. Total RNA and genomic DNA were extracted from liver tissue samples, and then mtDNA copy number and FGF21 expression levels were assessed by quantitative real-time PCR.Results: The relative level of hepatic mtDNA copy number was 3.9-fold higher in patients than in controls (p &lt; 0.0001). NAFLD patients showed a 2.9-fold increase in hepatic FGF21 expression compared to controls (p &lt; 0.013). Results showed that hepatic FGF21 expression was positively correlated with BMI, serum ALT, and AST levels (p &lt; 0.05). The level of mitochondrial copy number and hepatic FGF21 expression was not significantly associated with stages of change in hepatic steatosis. Finally, there was a significant correlation between FGF21 expression and mitochondrial copy number in NAFLD patients (p = 0.027).Conclusion: Our findings suggest a considerable rise of hepatic FGF21 mRNA levels and mtDNA-CN and show a positive correlation between them in the liver tissue of NAFLD patients.
Dietary glycemic index, glycemic load, and renal cancer risk: findings from prostate, lung, colorectal, and ovarian cancer trial
Authors: Qi Honggang , Xia Dan , Xu Xin 
Published: June 2023

BackgroundDietary glycemic index (GI) or glycemic load (GL) has been associated with the development of many cancers, but the evidence for renal cancer is still limited. The aim of the present study was to investigate the association between GI or GL and renal cancer risk in the Prostate, Lung, Colorectal, and Ovarian Cancer (PLCO) Screening Trial.MethodsThe cohort for our analysis consisted of 101,190 participants. GI and GL were calculated from the FFQ data using previously published reference values. Multivariate-adjusted hazard ratios (HRs) and 95% confidence intervals (CIs) were estimated using Cox regression model after adjusting for most known renal cancer risk factors.ResultsDuring a median of 12.2 years of follow-up, 443 incident renal cancer cases occurred. Higher dietary GI was significantly associated with a higher risk of renal cancer (HRQ3vsQ1: 1.38; 95% CI: 1.09–1.74; p for trend = 0.008). There was no significant association between dietary GL and renal cancer risk (HRQ3vsQ1 = 1.12, 95% CI = 0.79–1.59, p for trend = 0.591). Spline regression plot revealed a higher risk of renal cancer with a higher GI but not GL. There was no statistical evidence for nonlinearity (p for nonlinearity &gt;0.05).ConclusionIn summary, findings of this large-scale prospective cohort study suggested that dietary GI may be associated with the risk of renal cancer. If confirmed in other populations and settings, dietary GI could be considered as a modifiable risk factor for renal cancer prevention.
PARP-1: a critical regulator in radioprotection and radiotherapy-mechanisms, challenges, and therapeutic opportunities
Authors: Li Wen-Hao , Wang Fei , Song Gui-Yuan , Yu Qing-Hua , Du Rui-Peng , Xu Ping 
Published: June 2023

Background: Since its discovery, poly (ADP-ribose) polymerase 1 (PARP-1) has been extensively studied due to its regulatory role in numerous biologically crucial pathways. PARP inhibitors have opened new therapeutic avenues for cancer patients and have gained approval as standalone treatments for certain types of cancer. With continued advancements in the research of PARP inhibitors, we can fully realize their potential as therapeutic targets for various diseases.Purpose: To assess the current understanding of PARP-1 mechanisms in radioprotection and radiotherapy based on the literature.Methods: We searched the PubMed database and summarized information on PARP inhibitors, the interaction of PARP-1 with DNA, and the relationships between PARP-1 and p53/ROS, NF-κB/DNA-PK, and caspase3/AIF, respectively.Results: The enzyme PARP-1 plays a crucial role in repairing DNA damage and modifying proteins. Cells exposed to radiation can experience DNA damage, such as single-, intra-, or inter-strand damage. This damage, associated with replication fork stagnation, triggers DNA repair mechanisms, including those involving PARP-1. The activity of PARP-1 increases 500-fold on DNA binding. Studies on PARP-1-knockdown mice have shown that the protein regulates the response to radiation. A lack of PARP-1 also increases the organism’s sensitivity to radiation injury. PARP-1 has been found positively or negatively regulate the expression of specific genes through its modulation of key transcription factors and other molecules, including NF-κB, p53, Caspase 3, reactive oxygen species (ROS), and apoptosis-inducing factor (AIF).Conclusion: This review provides a comprehensive analysis of the physiological and pathological roles of PARP-1 and examines the impact of PARP-1 inhibitors under conditions of ionizing radiation exposure. The review also emphasizes the challenges and opportunities for developing PARP-1 inhibitors to improve the clinical outcomes of ionizing radiation damage.
An improved approach for rapid filter convergence of GNSS satellite real-time orbit determination
Authors: Zhou Liqin , Fan Lei , Li Zongnan , Fang Xinqi , Shi Chuang 
Published: June 2023

Introduction: The real-time precise satellite orbit of Global Navigation Satellite System (GNSS) usually takes a long time to converge to a stable state using the filter method. The ultra-rapid orbit products are helpful to improve convergence speed by introducing them as external constraints. Reasonably determination of stochastic model of the constraint equation from the ultra-rapid products is the key for a better performance of convergence whereas it has not been well solved.Methods: We propose to establish the stochastic model of the orbit constraint equation by analyzing the differences between the predicted part of the ultra-rapid orbit and the filter orbit after convergence. To improve the orbit accuracy during the convergence, the constant stochastic model of the constraint equation is first determined for each system by averaging the root mean square (RMS) time-series of the differences between predicted orbit from the ultra-rapid products and the SRIF orbit after convergence in different time ranges. Besides, a time-dependent stochastic model of the constraint equation is then determined by analyzing the variation of the RMS time-series. To validate the proposed method, a month of multi-constellation data collected from 80 globally distributed stations is processed using the Square Root Information Filter (SRIF) algorithm.Results: Orbit results without introducing external orbit constraints show that the convergence time in the radial direction is 13.75, 15.25 and 17.75 h for GPS, Galileo and BDS-3 satellite, respectively. For the scheme of constant stochastic model using the average RMS over 6 h, results show that there is no significant convergence phenomenon for each system in all directions. The one-dimensional (1D) RMS during the constraint period is improved by 86.5%, 84.8%, 96.8% for GPS, Galileo and BDS-3 satellites when compared to the results without introducing external orbit constraints. As for the scheme of time-dependent stochastic model, results show that the quadratic function is suitable for modeling the RMS time-series for each system, and the accuracy of results during the constraint period has a further improvement of 1.3%, 3.7% in 1D direction for GPS, BDS-3 satellites when compared to the constant stochastic model using the average RMS over 6 h. In addition, the orbit accuracy with external orbit constraint is slightly better than those without external orbit constraint after the constraint period.Discussion: The above results show that when introducing the ultra-rapid product as the external constraint, there is basically no convergence phenomenon for GNSS satellite, while the orbit accuracy for time-dependent stochastic model has further improvement than constant stochastic model. These results indicate that the proposed method can significantly improve the convergence performance without damaging the orbit accuracy after convergence, and time-dependent stochastic model is better than constant stochastic model.
Antioxidant and Anti-atherogenic Properties of Prosopis strombulifera and Tessaria absinthioides Aqueous Extracts: Modulation of NADPH Oxidase-Derived Reactive Oxygen Species
Authors: Quesada Isabel , de Paola Matilde , Alvarez María Soledad , Hapon María Belén , Gamarra-Luques Carlos , Castro Claudia 
Published: June 2023

Graphical AbstractSchematic representation of the effect of P. strombulifera or T. absinthioide decoctions on VSMC and ApoE-KO mice. The combination of antimitogenic effect and antioxidant capacity of the extracts is effective to increase antioxidant status and reduce atheroma development modulating NADPH oxidase expression.
Novel predator-induced phenotypic plasticity by hemoglobin and physiological changes in the brain of Xenopus tropicalis
Authors: Mori Tsukasa , Machida Kazumasa , Kudou Yuki , Kimishima Masaya , Sassa Kaito , Goto-Inoue Naoko , Minei Ryuhei , Ogura Atsushi , Kobayashi Yui , Kamiya Kentaro , Nakaya Daiki , Yamamoto Naoyuki , Kashiwagi Akihiko , Kashiwagi Keiko 
Published: June 2023

Organisms adapt to changes in their environment to survive. The emergence of predators is an example of environmental change, and organisms try to change their external phenotypic systems and physiological mechanisms to adapt to such changes. In general, prey exhibit different phenotypes to predators owing to historically long-term prey-predator interactions. However, when presented with a novel predator, the extent and rate of phenotypic plasticity in prey are largely unknown. Therefore, exploring the physiological adaptive response of organisms to novel predators is a crucial topic in physiology and evolutionary biology. Counterintuitively, Xenopus tropicalis tadpoles do not exhibit distinct external phenotypes when exposed to new predation threats. Accordingly, we examined the brains of X. tropicalis tadpoles to understand their response to novel predation pressure in the absence of apparent external morphological adaptations. Principal component analysis of fifteen external morphological parameters showed that each external morphological site varied nonlinearly with predator exposure time. However, the overall percentage change in principal components during the predation threat (24 h) was shown to significantly (p &lt; 0.05) alter tadpole morphology compared with that during control or 5-day out treatment (5 days of exposure to predation followed by 5 days of no exposure). However, the adaptive strategy of the altered sites was unknown because the changes were not specific to a particular site but were rather nonlinear in various sites. Therefore, RNA-seq, metabolomic, Ingenuity Pathway Analysis, and Kyoto Encyclopedia of Genes and Genomes analyses were performed on the entire brain to investigate physiological changes in the brain, finding that glycolysis-driven ATP production was enhanced and ß-oxidation and the tricarboxylic acid cycle were downregulated in response to predation stress. Superoxide dismutase was upregulated after 6 h of exposure to new predation pressure, and radical production was reduced. Hemoglobin was also increased in the brain, forming oxyhemoglobin, which is known to scavenge hydroxyl radicals in the midbrain and hindbrain. These suggest that X. tropicalis tadpoles do not develop external morphological adaptations that are positively correlated with predation pressure, such as tail elongation, in response to novel predators; however, they improve their brain functionality when exposed to a novel predator.
Overlapping exposure effects of pathogen and dimethoate on honeybee (Apis mellifera Linnaeus) metabolic rate and longevity
Authors: Pent Kaarel , Naudi Sigmar , Raimets Risto , Jürison Margret , Liiskmann Egle , Karise Reet 
Published: June 2023

Introduction: Declines in honeybee abundance have been observed worldwide during last decades. This is partly due to plant protection agents used in intensive farming, landscaping and infrastructure maintenance. Another type of factors negatively affecting honeybees is the spread of diseases caused by different pathogens and pests. Lately, more focus has been paid to the interactions between different overlapping stressors affecting honeybee health, the combination of these often being more detrimental compared to individual stressors. The most widely used stress-evaluating methods take into account lethal- or motorial changes of the individuals or colonies. Comparatively little honeybee research has examined changes in initial recovery potential and physiological symptoms of toxification. The aim of this study was to examine the combined effect of Nosema apis and N. ceranae (according to a newer classification Vairimorpha apis and V. ceranae), the common causes of nosemosis in the honeybee Apis mellifera L., with the insecticide dimethoate.Methods: In this study, honeybee mortality and metabolic rate were used to assess the combined effects interactions of Nosema ssp. and dimethoate.Results: Our results showed that exposure to the low concentration of either dimethoate, either one or both species of Nosema ssp as single factors or in the combination had no significant effect on honeybee metabolic rate. The mortality increased with the two Nosema spp., as well as with infection by N. ceranae alone. The effect of dimethoate was observed only in combination with N. apis infection, which alone had no effect on individual honeybee mortality.Conclusion: This study demonstrates that the overlapping exposure to a non-lethal concentration of a pesticide and a pathogen can be hidden by stronger stressor but become observable with milder stressors.
Synergistic effects of methyl jasmonate treatment and propagation method on Norway spruce resistance against a bark-feeding insect
Authors: Berggren Kristina , Nordkvist Michelle , Björkman Christer , Bylund Helena , Klapwijk Maartje J. , Puentes Adriana 
Published: June 2023

Utilizing plants with enhanced resistance traits is gaining interest in plant protection. Two strategies are especially promising for increasing resistance against a forest insect pest, the pine weevil (Hylobius abietis): exogenous application of the plant defense hormone methyl jasmonate (MeJA), and production of plants through the clonal propagation method somatic embryogenesis (SE). Here, we quantified and compared the separate and combined effects of SE and MeJA on Norway spruce resistance to pine weevil damage. Plants produced via SE (emblings) and nursery seedlings (containerized and bare-root), were treated (or not) with MeJA and exposed to pine weevils in the field (followed for 3 years) and in the lab (with a non-choice experiment). Firstly, we found that SE and MeJA independently decreased pine weevil damage to Norway spruce plants in the field by 32-33% and 53-59%, respectively, compared to untreated containerized and bare-root seedlings. Secondly, SE and MeJA together reduced damage to an even greater extent, with treated emblings receiving 86-87% less damage when compared to either untreated containerized or bare-root seedlings in the field, and by 48% in the lab. Moreover, MeJA-treated emblings experienced 98% lower mortality than untreated containerized seedlings, and this high level of survival was similar to that experienced by treated bare-root seedlings. These positive effects on survival remained for MeJA-treated emblings across the 3-year experimental period. We conclude that SE and MeJA have the potential to work synergistically to improve plants’ ability to resist damage, and can thus confer a strong plant protection advantage. The mechanisms underlying these responses merit further examination.
Genome-wide identification and analysis of glyceraldehyde-3-phosphate dehydrogenase family reveals the role of GmGAPDH14 to improve salt tolerance in soybean (Glycine max L.)
Authors: Zhao Xunchao , Wang Jie , Xia Ning , Qu Yuewen , Zhan Yuhang , Teng Weili , Li Haiyan , Li Wenbin , Li Yongguang , Zhao Xue , Han Yingpeng 
Published: June 2023

IntroductionGlyceraldehyde-3-phosphate dehydrogenase (GAPDH) is an essential key enzyme in the glycolytic pathway and plays an important role in stress responses. Although GAPDH family genes have been found in different plant species, the determination of their gene family analysis and their functional roles in soybean are still unknown. MethodsIn this study, gene sequence and expression data were obtained using online tools, and systematic evolution, expression profile analysis, and qRT-PCR analysis were conducted.Results and DiscussionHere a total of 16 GmGAPDH genes were identified on nine chromosomes, which were classified into three clusters. Additionally, all GmGAPDH genes harbor two highly conserved domains, including Gp_dh_N (PF00044) and Gp_dh_C (PF02800). The qRTPCR analysis also showed that most GmGAPDH genes significantly responded to multiple abiotic stresses, including NaHCO3, polyethylene glycol, cold, and salt. Among them, GmGAPDH14 was extraordinarily induced by salt stress. The GmGAPDH14 gene was cloned and overexpressed through soybean hair roots. The overexpressed transgenic soybean plants of the GmGAPDH14 gene have also shown better growth than that of control plants. Moreover, the overexpressed transgenic plants of GmGAPDH14 gene had higher activities of superoxide dismutase but lower malonaldehyde (MDA) content than those of control plants under salt stress. Meanwhile, a total of four haplotypes were found for the GmGAPDH14 gene, and haplotypes 2, 3, and 4 were beneficial for the tolerance of soybean to salt stress. These results suggest that the GmGAPDH14 gene might be involved in the process of soybean tolerance to salt stress. The results of this study will be valuable in understanding the role of GAPDH genes in the abiotic stress response of soybean.