bluuebunny/crossref_metadata_2025_split huggingface dataset:
Theoretical and experimental analysis of circularly polarized luminescence spectrophotometers for artifact-free measurements using a single CCD camera.
Authors: baguenard bruno , Bensalah-Ledoux amina , Guy Laure , Riobé François , Maury Olivier , Guy Stephan 
Published: July 2022

Abstract
We demonstrate the feasibility of artifact-free measurements of Circularly Polarised Luminescence (CPL) spectra on an
imaging spectrometer. The polarization is spatially separated on two
measurement channels using an achromatic quarter-wave plate associated with a
polarizing beam splitter. The two channels are then imaged on a spectrometer to
give the left and right circularly polarized spectra. The artifacts have been highlighted via the Mueller formalism and verified experimentally. As they add spectral contributions from either the shape of the luminescence or its derivative, they are almost impossible to eliminate by pre-calibration.
We show that, at the cost of a second measurement that reverses the role of the two measuring arms, these artifacts are reduced in proportion to the stability of the lamp. The experimental results show the ability of our setup to measure CPL spectra on different kind of molecules in an accurate way with a dramatic (3 orders of magnitude) reduction in the recording time compared to a standard step by step measurement.
Integration of in vivo exposure and network pharmacology to investigate the pharmacodynamic material basis and action mechanism of Sinomenii Caulis in the treatment of myocardial infarction
Authors: Yang Cui , Guo Xiaodan , Li Yangling , Chen Jiayun , Zhu Chunyan , Wang Hao , Yang Xinyi , Huang Zhengrong , Wu Caisheng 
Published: July 2022

Abstract
Background
It is generally believed that the materials basis of traditional Chinese medicine (TCM) are chemical substances and their metabolites entering the systemic circulation or target organs. In this case, analyzing and screening the possible pharmacodynamic substances of drugs from the perspective of in vivo exposure might provide the basis or direction for network pharmacology, a powerful tool for exploring the bioactive components and potential targets of TCM. Based on these, this study aims to develop a novel strategy to quickly screen out the pharmacodynamic substances and mechanisms of TCM in diseases, and further applied it to the pharmacodynamic substances and action mechanism study of Sinomenii Caulis (SC) in treating myocardial infarction (MI).
Methods
Firstly, ultra-high performance liquid chromatography tandem high resolution mass spectrometry (UPLC-HRMS) technology was used to study the exposed components of SC in mice. According to the main exposed components, the key genes, proteins, and mechanisms of SC in MI were predicted by network pharmacology. Finally, the effects of SC and its main pharmacodynamic substances on MI were evaluated by building a model of MI in vivo, and the possible key proteins were docked and verified by molecular docking or western blotting.
Results
The analysis of substances exposed in vivo revealed that the main exposed substances in mice were sinomenine, magnoflorine, menisperine, and their metabolites. Network pharmacology and molecular docking, combined with exposure to substances of SC in vivo, revealed that sinomenine was the potential pharmacodynamic substance of SC. By establishing a mouse model of MI in vivo, it was found that sinomenine had the same therapeutic effect on MI as SC containing the same dose of sinomenine. By western blotting and molecular docking, sinomenine was found to play a therapeutic role by inhibiting AKT phosphorylation.
Conclusions
The study indicates that the rational combination of exposure research in vivo and network pharmacology might be beneficial to discover the pharmacodynamic substances and their mechanisms of TCM. Meanwhile, this is a pioneer report that sinomenine, the main exposed substance of SC, had the same therapeutic effect on MI as SC containing the same dose of and inhibited AKT phosphorylation.
Cortistatin prevents glucocorticoid-associated osteonecrosis of the femoral head via the GHSR1a/Akt pathway
Authors: Li Weiwei , Gao Yuan , You Yunhao , Zhang Pengfei , Liu Zhicheng , Yu Ruixuan , Jin Gaoxin , Zhao Yunpeng , Xia Yanni , Li Yuhua 
Published: July 2022

Abstract
Long-term use of glucocorticoids (GCs) is known to be a predominant cause of osteonecrosis of the femoral head (ONFH). Moreover, GCs can mediate apoptosis of various cell types by exaggerating oxidative stress. Previous studies have reported that the AKT pathway might be closely associated with apoptosis and metabolism of osteoblasts in ONFH mediated by GCs. We have previously found that cortistatin (CST) antagonizes oxidative stress and improves cell metabolism as well as apoptosis in several conditions. In this study, we detected that local and systemic CST expression levels were diminished in patients with ONFH compared with femoral neck fracture (FNF). In addition, a GC-induced rat ONFH model was established, which impaired bone quality and angiogenesis and improved osteoblastogenesis in the femoral head. Then, administration of CST attenuated these ONFH phenotypes in this model. Furthermore, osteoblast and endothelial cell lines were cultured and stimulated with dexamethasone (Dex) in the presence or absence of recombinant CST. As a result, Dex induced apoptosis and impaired anabolic metabolism of osteoblasts and suppressed tube formation as well as migration in endothelial cells, while additional treatment with CST reversed this damage to the cells. Moreover, blocking GHSR1a, a well-accepted receptor of CST, or blocking the AKT signaling pathway largely abolished the protective function of CST in Dex-induced disorder of the cells. Taken together, our results indicate that CST has the capability to prevent GC-induced apoptosis and metabolic disorder of osteoblasts in the pathogenesis of ONFH via the GHSR1a/AKT signaling pathway.
Universal compilation for quantum state tomography
Authors: Hai Vu Tuan , Binho Le 
Published: July 2022

Abstract
Universal compilation is a training process that compiles a trainable unitary into a target unitary. It has vast potential applications from depth-circuit compressing to device benchmarking and quantum error mitigation. Here we propose a universal compilation algorithm for quantum state tomography in low-depth quantum circuits. We apply the Fubini-Study distance as a trainable cost function and employ various gradient-based optimizations. We evaluate the performance of various trainable unitary topologies and the trainability of different optimizers for getting high efficiency and reveal the crucial role of the circuit depth in robust fidelity. The results are comparable with the shadow tomography method, a similar fashion in the field. Our work expresses the adequate capability of the universal compilation algorithm to maximize the efficiency in the quantum state tomography. Further, it promises applications in quantum metrology and sensing and is applicable in the near-term quantum computers for various quantum computing tasks.
Additional anterolateral ligament reconstruction helps patients improve dynamic postural stability in revision anterior cruciate ligament reconstruction
Authors: Lee Joon Kyu , Cho Seung Ik , Lee Dhong Won , Yang Sang Jin , Lee Donghwan , Kim Jin Goo 
Published: July 2022

Abstract
Introduction: The goal in treating anterior cruciate ligament (ACL) injury, especially in revision cases is to return to sports activity by regaining dynamic postural stability. Additional anterolateral ligament reconstruction (ALLR) is gaining attention to achieve this goal. The purpose was to evaluate the effects of additional ALLR in revision ACL reconstruction (RACLR). Methods: Patients who underwent RACLR between July 2015 and June 2018 were enrolled. The exclusion criteria were less than the 1-year follow-up, age older than 45 years, concomitant multiple ligament injuries, contralateral knee injury, subtotal or total meniscectomized state, and cartilage lesions worse than Outerbridge grade 3. Thirty-nine patients (20 patients; RACLR only (Group A), 19 patients; RACLR with additional ALLR (Group B)) were included. Clinical scores, isokinetic strength test, single-leg-hop for distance test (SLHDT), and Y-balance test (YBT) were checked preoperatively and 1-year postoperatively.Results: Limb symmetry index values in YBT showed significantly better results in Group B 1-year postoperatively, although there were no differences preoperatively between groups. Regarding clinical scores, isokinetic strength tests, and SLHDT, there were no differences between groups preoperatively or 1-year postoperatively.Conclusion: Additional ALLR in RACLR helped patients gain better dynamic postural stability at 1-year postoperative follow-up.
Peptains Block Retinal Ganglion Cell Death in Animal Models of Ocular Hypertension: Implications for Neuroprotection in Glaucoma
Authors: Nam Mi-Hyun , Stankowska Dorota , Johnson Gretchen , Nahomi Rooban , Pantcheva Mina , Nagaraj Ram H. 
Published: July 2022

Abstract
Ocular hypertension is a significant risk factor for vision loss in glaucoma due to the death of retinal ganglion cells (RGCs). This study investigated the effects of the antiapoptotic peptides peptain-1 and peptain-3a on RGC death in vitro in rat primary RGCs and in mouse models of ocular hypertension. Apoptosis was induced in primary rat RGCs by trophic factor deprivation for 48 h in the presence or absence of peptains. The effects of intravitreally injected peptains on RGC death were investigated in mice subjected to retinal ischemic/reperfusion (I/R) injury and elevated intraocular pressure (IOP). I/R injury was induced in mice by elevating the IOP to 120 mm Hg for one h, followed by rapid reperfusion. Ocular hypertension was induced in mice by injecting microbeads (MB) or silicone oil (SO) into the anterior chamber of the eye. Whole retinal flat mounts were immunostained with RGC and activated glial markers. Effects on anterograde axonal transport were determined by intravitreal injection of cholera toxin-B (CT-B). Peptain-1 and peptain-3a inhibited neurotrophic factor deprivation-mediated RGC apoptosis by 29% and 35%, respectively. I/R injury caused 52% RGC loss, but peptain-1 and peptain-3a restricted RGC loss to 13% and 16%, respectively. MB and injections resulted in 31% and 36% loss in RGCs following 6 weeks and 4 weeks of IOP elevation, respectively. Peptain-1 and peptain-3a inhibited RGC death; the loss was only 4% and 12% in MB-injected eyes and 16% and 15% in SO-injected eyes, respectively. Anterograde transport was defective in eyes with ocular hypertension, but this defect was substantially ameliorated in peptain-injected eyes. In addition, peptains suppressed ocular hypertension-mediated retinal glial activation. Peptains block RGC somal and axonal damage and neuroinflammation in animal models of glaucoma. Peptain-1 and − 3a have the potential to be developed as therapeutics against neurodegeneration in glaucoma.
Observer-based decentralized fuzzy control for connected nonlinear vehicle systems
Authors: Meng Li , Chen Yong , Hu Kun , Pan Chengwei , Mao Zhenhai 
Published: July 2022

Abstract
This article analyzes the tracking control of a type of connected nonlinear vehicle system, where the problem of hacker attacks and external disturbance is considered . A decentralized fuzzy control method based on observer is constructed. Specifically, first of all, the mathematical model of an automobile system with disturbance and false data injection attacks is built, which is composed of a head vehicle and N following vehicles. Then, in order to obtain prior knowledge of disturbance and states, a disturbance estimator on fuzzy sliding mode technique is proposed and a state observer is designed. Thirdly, an observer-based decentralized secure control strategy via fuzzy and backstepping control technique is designed to achieve the tracking control. Furthermore, the boundness of closed-loop signals and existence of appropriate safety distance between vehicles are certificated by Lyapunov theory. Finally, the potential of presented approaches are simultaneously illustrated by a numerical simulation and a semi-physical simulation.
Effectively Improving the Anti-corrosive Properties of Triazine-based Mixed Corrosion Inhibitors by the Adjustment of Bridge Heteroatoms: a Combined DFT and MD Simulation Study
Authors: Jia Xiao-yu , Xu Yan , WU QIONG , Zhu Wei-hua 
Published: July 2022

Abstract
In this study, to develop new advanced corrosion inhibitors with high corrosion inhibition efficiency at low concentration, a simple but effective strategy that is the adjustment of bridge heteroatoms in a mixed corrosion inhibitor named 2-(n-hexylamino)-4-(3-N,N-dimethylaminopropyl)amino-6-(2-aminobenzimidazol)-1,3,5-s-triazine (BDCT) was used to improve the anti-corrosive properties. Two series of new compounds were designed by adjusting three bridge N atoms in BDCT by different number of O and S atoms at three different positions. The molecular structures and different kinds of anti-corrosive properties of 14 designed compounds were investigated by the DFT and MD methods. The results showed that when compared to BDCT, the molecular area, electrophilicity, electronegativity, strength of feed-back bonding, softness, chemical reactivity and binding energy on the Fe(110) surface were improved obviously by the introduced bridge O and S atoms, leading to higher corrosion inhibition efficiency. This effect could be further enhanced with the increased number of them, and S atoms were found to better than O atoms obviously. The introduction positions of O and S atoms also made effects on anti-corrosive properties, introducing them at the R1 position was more helpful for improving anti-corrosive properties than R2 than R3. As a result, the compound with three bridge S atoms (B7) has the best anti-corrosive properties. The adsorption sites, type of bonding with metals and corrosion inhibition mechanism of BDCT were also changed completely by O and S atoms.
Investigation of Cyclo-Z Therapeutic Effect on Insulin Pathway in Alzheimer's Rat Model: Biochemical and Electrophysiological Parameters
Authors: Acun Alev Duygu , Kantar Deniz , Er Hakan , Erkan Orhan , Derin Narin , Yargıcoglu Piraye 
Published: July 2022

Abstract
Background
Cyclo (his-pro-CHP) plus zinc (Zn+ 2) (Cyclo-Z) is the only chemical agent known to stimulate IDE synthesis and reduction of inactive cellular insulin fragments.
Objectives
The aim of this study was to characterize the effects of Cyclo-Z on insulin pathway, memory functions and brain oscillations in the Alzheimer's disease (AD) rat model.
Methods
The rat model of AD was established by bilateral injection of Aβ42 oligomer (2,5nmol/10µl) into the lateral ventricles. Cyclo-Z (10mg Zn+ 2/kg and 0,2mg CHP/kg, daily) was administered orally by gavage for 21 days. At the end of the experimental period, memory tests and electrophysiological recordings were performed which followed by the biochemical analysis.
Results
Aβ42 oligomers led to a significant increase in fasting blood glucose, serum insülin, Homeostatic Model Assessment for Insulin Resistance(HOMA-IR) and phospho-tau-Ser356 levels. Moreover, Aβ42 oligomers caused a significant decrement in body weight, hippocampal insulin, brain insulin receptor substrate(IRS-Ser612), and glycogen synthase kinase-3 beta(GSK-3β) levels. Also, Aβ42 oligomers resulted in a significant reduction in memory. The Cyclo-Z treatment prevented the observed alterations in the ADZ group except for phospho-tau levels and attenuated the increased Aβ42 oligomers levels in the ADZ group. We also found that the Aβ42 oligomer decreased the left temporal spindle and delta power during ketamine anesthesia. Cyclo-Z treatment reversed the Aβ42 oligomer-related alterations in the left temporal spindle power.
Conclusions
Cyclo-Z prevents Aβ oligomer-induced changes in the insulin pathway, amyloid toxicity, and may contribute to the improvement of memory deficits and neural network dynamics in this rat model.
Binding organophosphate pesticides to acetylcholinesterase: Risk assessment using the Monte Carlo method
Authors: Toropova Alla P. , Toropov Andrey A. , Roncaglioni Alessandra , Benfenati Emilio 
Published: July 2022

Abstract
Binding to acetylcholinesterase may cause toxic effects in humans. Organophosphates simultaneously are both dangerous and useful substances: dangerous since they are employed in chemical warfare; and useful when they are applied as pesticides. Here we suggest the models for organophosphates binding to acetylcholinesterase developed via representing the molecular structure by a simplified molecular input-line entry system (SMILES) using so-called optimal SMILES-based descriptors calculated with the Monte Carlo technique using the CORAL software available on the Internet (http://www.insilico.eu/coral). Quantitative structure-activity relationships (QSARs) serve to develop predictive models for organophosphates. The predictive potential of these models is quite good: the determination coefficient for the validation set ranged from 0.87 to 0.90. These models were built up according to the principle "QSAR is a random event", i.e. predictive potential of an approach should be checked up with several splits of available data into the training and test sets. The special scheme of mechanistic interpretation definition is represented. The mechanistic interpretation is based on probabilities of molecular features to be in the sub-group of promoters of increase for endpoint or in sub-group of promoters of its' decrease.
The LMR-SSIGN-MAPS model Predicts Disease-free Survival in Patients with Localized Clear Cell Renal Cell Carcinoma
Authors: wen hongzhuang , zhang yong , Yang Zhan , Zhai Zhao , Wang Mingshuai , Shi Hongzhe , Chen Xi , Wahafu Wasilijiang , Guan Kaopeng , Wang Xiaolu 
Published: July 2022

Abstract

Background: To develop a comprehensive model for predicting disease-free survival (DFS) in patients with localized clear cell renal cell carcinoma (ccRCC). Methods: A retrospective analysis of 612 patients was performed between 2010 and 2015.The least absolute shrinkage and selection operator (LASSO) Cox regression analysis was performed to identify significant predictors. Furthermore, the multivariate Cox regression analysis was performed to reconfirm risk factors, then the prognosis model was constructed. The Harrell’s concordance index (C-index) was conducted to assess the model’s accuracy for predicting DFS in localized ccRCC.Results: The lymphocyte-to-monocyte ratio (LMR) (HR: 1.04, P = 0.009), the Mayo Clinic stage, size, grade, and necrosis score (SSIGN) (HR: 1.36, P < 0.001) and Mayo adhesive probability score (MAPS) (HR: 1.99, P＜0.001) were the significant risk factors screened by LASSO Cox regression and reconfirmed by multivariate Cox regression analysis in 44 variables. The LMR-SSIGN-MAPS model was constructed by combining the LMR, SSIGN, and MAPS. In the training and validation cohorts, the Harrell’s C-index was larger for the LMR-SSIGN-MAPS model (0.854, 0.848) than the SSIGN score (0.782, 0.772). The Kaplan-Meier survival analysis demonstrated the significant association between higher LMR-SSIGN-MAPS score and poorer DFS (P < 0.001) in the overall cohorts.Conclusions: The LMR-SSIGN-MAPS model which consists of preoperative inflammation biomarkers, perinephric adipose tissue image-based scoring system, and pathological features showed the strengths of easy-to-use and high predictability and might be also used as a promising prognosis model in predicting DFS for patients with localized ccRCC.
Functional modular networks identify the pivotal genes associated with morphine addiction and potential drug therapies
Authors: Jiang Yage , Wei Donglei , Xie Yubo 
Published: July 2022

Abstract
Background
Chronic morphine usage induces lasting molecular and microcellular adaptations in distinct brain areas, resulting in addiction-related behavioural abnormalities, drug-seeking, and relapse. Nonetheless, the mechanisms of action of the genes responsible for morphine addiction have not been exhaustively studied.
Methods
We obtained morphine addiction-related datasets from the GEO database and screened for differential genes (DEGs) by GEO2R analysis.WGCNA functional modularity constructs were analyzed for genes associated with clinical traits. Venn diagrams were filtered for intersecting common differential genes (CDEGs). Gene Ontology (GO) enrichment analysis and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis for functional annotation. Protein-protein interaction network (PPI) and CytoHubba were used to screen for hub genes (Hub). Potential treatments for morphine addiction were figured out with the help of an online database.
Results
65 common differential genes linked to morphine addiction were identified, and functional enrichment analysis showed that they were primarily involved in ion channel activity, protein transport, the oxytocin signalling pathway, neuroactive ligand-receptor interactions, and other signalling pathways. Based on the PPI network, ten Hub genes (Chn2, Olig2, Ugt8a, Cacnb2, Timp3, Fkbp5, Zbtb16, Tsc22d3, Isl1, and Slc2a1) were checked. In the data set GSE7762, all of the AUC values for the Hub gene ROC curves were greater than 0.8. We also used the DGIdb database to look for eight small-molecule drugs that might be useful for treating morphine addiction.
Conclusions
The Hub genes are crucial genes associated with morphine addiction in the mouse striatum, and morphine addiction is highly correlated with these genes. The oxytocin signalling pathway may play a vital role in developing morphine addiction.
Genome-wide identification and ABCE-class proposal of the MADS-box gene family in Salvia miltiorrhiza Bunge
Authors: Cui Ning , Guo Fengdan , Chen Weixu , Liao Baosheng , Chu Yang , Li Xiwen , Wang Ping 
Published: July 2022

Abstract
MADS-box transcription factors, as the heart of the classic ABCE model of floral development, play critical roles in several aspects of plant flowering. In recent years, to comprehensively utilise and improve the added value of Chinese herbal medicine, the non-medicinal part (flower) development of Salvia miltiorrhiza Bunge has been promoted, thereby focusing the attention of researchers on the flower organ of S. miltiorrhiza. However, an analysis of the complete MADS-box family along with a comprehensive expression profiling was still awaited after the completion of S. miltiorrhiza genome sequencing. This work systematically characterised S. miltiorrhiza MADS-box genes (SmiMADSes) and predicted those likely involved in the floral development of this medicinal plant. Seventy-two MADS-box genes were identified in the S. miltiorrhiza genome and categorised into MIKC*, MIKCc, Mα, Mβ and Mγ groups based on phylogeny. Genomic localisation analysis revealed that these genes were evenly localised on 10 genome scaffolds. The expression profiles of all the SmiMADSes were analysed in four organs and four flower tissues, as well as in the three stages of floral development. Transcripts for 13 genes accumulated preferentially in flowers. SmiMADS44 was specifically expressed in stems. SmiMADS57 and SmiMADS31 showed specific expressions in roots and leaves, respectively. Based on transcriptome data and homology with functionally validated ABCE class genes in Arabidopsis, a prediction was made to gain insight into ABCE-class SmiMADSes that were strongly expressed in all flowering stages of S. miltiorrhiza, including the following: SmiMADS65 and SmiMADS67 of A-class; SmiMADS26, SmiMADS28 and SmiMADS29 of B-class; SmiMADS45, SmiMADS50 and SmiMADS51 of C-class; and SmiMADS70, SmiMADS71 and SmiMADS72 of E-class. The results of this study lay a foundation for the further exploration of molecular and regulatory mechanisms controlling floral organ development and provide a basis for the selection of candidate genes for functional validation studies.