bluuebunny/crossref_metadata_2025_split huggingface dataset:
Senescent cells develop PDK4-dependent hypercatabolism and form an acidic microenvironment to drive cancer resistance
Authors: Dou Xuefeng , Long Qilai , Liu Shuning , Zou Yejun , Fu Da , Chen Xue , Xu Qixia , Wang Changxu , Ren Xiaohui , Zhang Guilong , Fu Qiang , Campisi Judith , Zhao Yuzheng , Sun Yu 
Published: August 2022

Abstract
Cellular senescence is a state of stable growth arrest, usually accompanied by development of the senescence-associated secretory phenotype (SASP). Although senescent cells remain metabolically active, little is known about their metabolic landscape and in vivo pathophysiological implications. Here we show that expression of the pyruvate dehydrogenase (PDH) inhibitory enzyme, pyruvate dehydrogenase kinase 4 (PDK4), is significantly upregulated in human senescent stromal cells. Preferentially expressed upon genotoxicity-induced senescence (GIS), PDK4 is negatively correlated with posttreatment survival of cancer patients. Upon cellular senescence, PDK4 shifts glucose metabolic flux from oxidative phosphorylation to aerobic glycolysis, causing enhanced lactate production and forming an acidic microenvironment. However, distinct from the cancer cell-featured Warburg effect, senescent cells maintain an intensive use of pyruvate through the tricarboxylic acid cycle (TCA), displaying increased respiration and redox activity, indicative of a special form of metabolic reprogramming. Conditioned media from PDK4+ stromal cells change global expression and promote malignancy of recipient cancer cells in vitro and accelerate tumor progression in vivo. Pharmacologically targeting PDK4 restrains the adverse effects of PDK4 in cell-based assays, while promoting tumor regression and extending posttreatment survival in preclinical trials. Together, our study substantiates the hypercatabolic nature of senescent cells, and reveals a metabolic link between senescence-associated acidic microenvironment and age-related pathologies including but not limited to cancer.
Regulation of BMP genes, EMC production and deposition through TGFβ/Smad Signaling in Human Trabecular Meshwork for progression of glaucoma disease
Authors: Choudhari Jyoti Kant , Chatterjee Tanushree 
Published: August 2022

Abstract
Glaucoma is a chronic neurological condition that causes damage to retinal ganglion cells and nerve fibres. The transforming growth factor pathway may have a role in disease progression, but its mechanism and regulation are unknown. We explored the molecular mechanisms behind glaucoma onset and progression utilising a network and systems biology approach. First, we manually curated a glaucoma-related seed network. Simulation results reveal increasing BMP gene expression, EMC production, and gene transcription regulation. When glaucoma and control data are compared, gene expression analysis reveals that 21 of these 40 genes are downregulated, and 19 are upregulated. HLA-DPA1, COL3A1, TGFB3, LEFTY2, and ARHGEF6 are the most important genes that were upregulated, while RGMA, GADD45B, LAMMB3, ZFP36, and CEBPD are the most important genes that were downregulated. The miRNA target prediction and their expression studies revealed 37 miRNA targets, including 13 miRNA targets that were downregulated and 15 that were upregulated. For the regulation of gene expression, 7 transcription factors, including STAT3, ZNF263, NR3C1, CTCF, TCF4, FOS, and EGR1, have been revealed to regulate more than 2 DEGs genes. We further analysed the drug availability; 41 drugs for 14 gene targets and 1032 compounds for ten gene targets have been identified from the drug bank and ChEMBL for the novel targets. Furthermore, we identified BP words most significantly associated with the extracellular matrix, SMAD protein signal, and BMP signalling pathway. The preferred gene-affecting pathway that includes MAPK, TGF-beta, and other cancer-related pathways was discovered. The involvement of TGF in the development of glaucoma may be studied to shed new light on therapeutic targets and discover new drugs to target disease progression
Diabetes-related screw loosening: the distinction of surgical sites and the relationship among diabetes, implant stabilization and clinical outcomes
Authors: Wang Tianji , Wang Jing , Hu Xiaofan , Xiang Geng , Wu Zixiang , Ma Zhensheng , Li Tianqing , Chen Yu , Zhao Xiong , Zhang Yang , Ma Tiancheng , Ren Jingjuan , Lei Wei , Feng Yafei 
Published: August 2022

Abstract
Introduction.
Diabetes mellitus (DM) is correlated with poor clinical outcomes in spinal surgery. However, the effect of it on screw stabilization has not been investigated. The aim of this study was to evaluate the screw loosening rate and postoperative outcomes in diabetic patients and to identify potential risk factors associated with loosening.
Methods.
Two hundred and forty-three patients who received cervical or lumbar internal fixation between 2015 and 2019 were enrolled in this study. Screw loosening was assessed on radiography, and clinical outcomes were evaluated by the improvement of Visual Analog Scale (VAS), Oswestry Disability Index (ODI) or Japanese Orthopaedic Association (JOA) scores. The relationship of DM, screw loosening and clinical outcomes were analyzed with chi-square tests and regression analyses.
Results.
One hundred and twenty-two patients (50.2%) with diabetes were included in this study. Diabetes led to the increase of the rate of screw loosening in the lumbar spine, while the loosening rate did not vary significantly in the cervical spine. The occurrence of screw loosening in the lumbar spine was more likely to be associated with clinical outcomes for motor performance including walking and sitting. However, no significant effect on JOA and VAS scores in the cervical spine of screw loosening was found. Moreover, the history of DM affected the outcomes of the patients who underwent spinal surgery.
Conclusions.
DM had an adverse effect on screw stabilization. The impaired improvement of clinical outcomes in diabetics after spinal surgery was related to screw loosening. In addition to the direct effects on operative wounds and neural function, the impact on the screws due to DM was also worth noting.
Direct observation of bandgap opening at the metasurface of nano-scale highly oriented pyrolytic graphite
Authors: Chaiyachad Sujinda , Singsen Sirisak , Eknapakul Tanachat , Jindata Warakorn , Jaisuk Chutchawan , Fevre Patrick Le , Bertran Francois , Lu Donghui , Huang Yaobo , Nakajima Hideki , Liewrian Watchara , Fongkaew Ittipon , Meevasana Worawat 
Published: August 2022

Abstract
By using angle-resolved photoemission spectroscopy (ARPES), we study the electronic structure of highly oriented pyrolytic graphite (HOPG). In contrast to the pristine HOPG, band gap opening of approximately 100 meV is directly observed at the surface of nano-scale HOPG square pattern. Our Raman data and density functional theory calculations suggest that the bandgap opening is likely caused by tensile strain induced from the patterning. We believe that this surface engineering of HOPG will not only be useful for enhancing terahertz devices but also provides a route for modifying other materials/metasurfaces for optoelectronics applications.
Apical periodontitis in endodontically-treated teeth, association between the presence of missed canals and the quality of endodontic treatment in a Colombian population: A Cross-sectional study
Authors: Fuentes Bibiana Yorley Blanco , Monsalve Jaime Omar Moreno , Herrera Uriel Mesa , Amoroso-Silva Pablo Andres , Alves Flavio Rodrigues Ferreira , Marceliano-Alves Marília F. 
Published: August 2022

AbstractObjective:A high prevalence of post-treatment-apical periodontitis has been evidenced in 2D studies, associated to variables commonly evaluated as quality of endodontic treatment; currently, using CBCT the presence of missed canals is also one of the relevant variables associated to the failure of endodontic treatment. The objective was to evaluate the quality of endodontic treatment and the frequency of missed canals associated with teeth presenting apical periodontitis (AP) through CBCT in a Colombian sub-population.Methods:A cross-sectional study was conducted. CBCT scans with endodontically treated tooth (n = 318), were selected from 1100 exams from Colombian individuals between January 2017 and January 2020. The scans were taken using J Morita X550 CBCT Scanners (J Morita Corporation, Osaka, Japan), with voxel size between 0.125 and 0.20 mm. All endodontically treated teeth were analyzed for quality of treatment, the presence of missed canals and AP. All samples were independently analyzed by two endodontics specialists and an oral and maxillofacial radiology specialist. Chi-square or Fisher`s test and odds ratio calculation were applied to identify the association and risk relationship between the presence of AP and the study variables; P values <0.05 were considered statistically significant.Results:Missed canals were found in 18.61% (86/462) and 95.3% were associated with AP. The frequency of AP was 62.34% (288/462) for all the evaluated teeth. AP was found in 27.43 % (79/462) of the teeth with adequate endodontic treatment in contrast with 72.57% (209/462) of the teeth with inadequate ones (P <0.01). The frequency of missed canals was highest in upper molars with 55.23% (58/105), with 96.55% presenting with AP. The second mesiobuccal canal was the most frequently missed canal, 88.52% (54/61), with AP in 90.74% (49/54) of the cases.Conclusion:There was a high risk of teeth with missed canal presenting AP. More than half of the teeth with missed canals were maxillary molars, the MB2 the most frequent missed canal, with apical periodontitis.
Phylogenetic diversity of microbial communities and physicochemical properties along a vertical soil section of Lam Pokhari Lake in Eastern Himalayas.
Authors: Sinha Shruti , Ankulkar Rutuja , Kandekar Avinash , Mirza Yasmin 
Published: August 2022

Abstract
It is well documented that the microbes found in soil are key drivers of various environmental processes such as nutrient cycling, soil formation and production of key enzymes and metabolites. There is a possibility of infinite number of microbes being buried in the layers of soil that formed over timescales of hundreds and thousands of years. However, there are few studies till date which correlate the depth and physicochemical properties of soil with the microbial population inhabiting that soil. In this study, an investigation of eleven samples along a 100 cm vertical section of soil from Lam Pokhari Lake, Eastern Himalayas, India was done by Sanger sequencing and Field emission scanning electron microscope-energy dispersive X-ray spectroscopy (FESEM-EDS). Further, the distribution of culturable bacteria and fungi was studied. Bacteria belonging to four different phyla- Firmicutes, Actinobacteria, Beta-proteobacteria and Gamma-proteobacteria were present in the soil samples as inferred from 16s rDNA gene sequencing. Internal transcribed spacer (ITS) gene sequencing revealed the presence of fungi belonging to Ascomycota and Basidiomycota. Lastly, the particle size was obtained and the homogeneity of the samples was assessed by FESEM and imaging. EDS was used for obtaining the composition of seventeen elements in the soil samples. The weight percentage of oxygen and silicon was the highest in all the samples. Each sample showed a characteristic microbial distribution, particle size and elemental profile, which validated the use of a multidisciplinary approach to study soil samples.
Robust bounded control scheme for quadrotor vehicles under high dynamic disturbances
Authors: Betancourt J. , Castillo P. , Garcı́a P. , Balaguer V. , Lozano R. 
Published: August 2022

Abstract
In this paper, an optimal bounded robust control algorithm for secure autonomous navigation in quadcopter vehicles is proposed. The controller is developed combining two parts; one dedicated to stabilize the closed-loop system and the second one for dealing and estimating external disturbances as well unknown nonlinearities {inherent to the real system's operations}. For bounding the energy used by the system during a mission and, without losing its robustness properties, the quadratic problem formulation is used considering the actuators system constraints. The resulting optimal bounded control scheme improves considerably the stability and robustness of the closed-loop system and at the same time bounds the motor control inputs. The controller is validated in real-time flights and in unconventional conditions for high wind-gusts and LoE - Loss of Effectiveness- in two rotors. The experimental results demonstrate the good performance of the proposed controller in both scenarios.
Transient Crosslinking Mass Spectrometry: Taking Conformational Snapshots of Proteins
Authors: Yang Lei , Xie Yuxin , Wang Jiawen , Zou Guiqing , Ruan Xujun , Wang Yan , Xia Dandan , Sun Huiyong , Xu Xiaowei , Zheng Qiuling , Hao Haiping 
Published: August 2022

Abstract
Protein structural analysis at the very moment of target binding or sensing incoming stimuli sheds light on how protein functions diversely with time or pathological conditions. To understand it, we need to intercept and see the intermediate conformation. Although conventional methods offer high resolution structural analysis, they do not address puzzling dynamic conformational changes. Herein, we developed a transient crosslinking mass spectrometry involving a novel photoreactive crosslinker that can capture intermediate conformers. The designed non-specific reactivity increased the crosslinking site diversity, thereby enhancing the resolution and broadening the scope of mass spectrometric-based structural analysis. A time-resolved crosslinking strategy was developed to take conformational snapshots for calmodulin, an important calcium sensor, and revealed the structural basis of its dynamic conformational response to calcium binding and target interaction. Therefore, the designed transient crosslinking makes short-lived conformers visible, which has the potential to tackle the question how variations in protein’s conformation change functions.
Quantum adversarial metric learning model based on triplet loss function
Authors: Hou Yan-Yan , Li Jian , Chen Xiu-Bo , Ye Chong-Qiang 
Published: August 2022

Abstract
Metric learning plays an essential role in image analysis and classification, and it has attracted more and more attention. In this paper, we propose a quantum adversarial metric learning (QAML) model based on the triplet loss function, where samples are embedded into the high-dimensional Hilbert space and the optimal metric is obtained by minimizing the triplet loss function. The QAML model employs entanglement and interference to build superposition states for triplet samples so that only one parameterized quantum circuit is needed to calculate sample distances, which reduces the demand for quantum resources. Considering the QAML model is fragile to adversarial attacks, an adversarial sample generation strategy is designed based on the quantum gradient ascent method, effectively improving the robustness against the functional adversarial attack. Simulation results show that the QAML model can effectively distinguish samples of MNIST and Iris datasets and has higher robustness over the general quantum metric learning. The QAML model is a fundamental research problem of machine learning. As a subroutine of classification and clustering tasks, the QAML model opens an avenue for exploring quantum advantages in machine learning.
Investigating Long-term Prognostication of CT-based Radiomics for Subgroup of High-risk Localized Prostate Cancer Patients Treated by Whole-pelvic Radiotherapy
Authors: Leung Wan Shun , Lam Sai Kit , Wong Po Tsz , Ng Ka Yan , Tam Cheuk Hong , Lee Tsz Ching , Chow Kin Chun , Chow Yan Kate , Tam Victor CW , Lee Shara WY , Lim Mei Ying , Wu Q Jackie , Cai Jing 
Published: August 2022

Abstract
Background
To investigate capability of planning computed tomography (CT)-based radiomics for prediction of long-term prognostication, for the first time, in subgroup of high-risk localized prostate cancer (PCa) patients treated by whole-pelvic radiotherapy (WPRT).
Methods
A total of 64 high-risk localized PCa patients [training cohort (n = 45) and validation cohort (n = 19)] were enrolled. The planning CT and clinical data were collected. The least absolute shrinkage selection operator (LASSO) was used for model training in conjunction with 3-fold cross validation. The predictive performance of the model was assessed using the Area-under-the-curve (AUC) values generated from receiver operating characteristic analysis. The resultant radiomics signature was used for calculation of radiomics score (Rad-score) for every patients. A cut-off of the Rad-score was suggested for classification of the risk of having progression within 6 years, based on the evaluation of model accuracy, sensitivity, and specificity.
Results
The model incorporated 2 features: the run entropy of gray level run length matrix after Laplacian of Gaussian (LoG) filtering with a sigma value of 2 mm (RE-GLRLMσ2mm); and the small area emphasis of gray level size zone matrix after LoG filtering with a sigma value of 4.5 mm (SAE-GLSZMσ4.5mm). AUC values of the training and testing cohorts were 0.76 and 0.71, respectively. With the cut-off as the third-quartile value for stratification into high-risk and low-risk group, the respective accuracy, sensitivity, and specificity of the radiomics signature were 77.8%, 83.3% and 55.6% in the training cohort and 84.2%, 86.7% and 75% in the testing cohort.
Conclusions
Radiomics signature based on pre-treatment planning CT images can be used as a potential biomarker for differentiating the risk of 6-year disease progression in high-risk localized PCa patients treated with WPRT. Further development is warranted that may help to support clinical decisions about follow-up and treatment options in this subgroup of patients.
The protective effect of mushroom consumption on depressive symptom in Korean population
Authors: Park Sung Keun , Oh Chang-Mo , Ryoo Jae-Hong , Jung Ju Young 
Published: August 2022

Abstract
Mushrooms are nutraceutical food with health benefit. However, data is still limited in identifying the protective effect of mushroom consumption on depressive symptom. In a cohort of 87,822 Korean, we longitudinally assessed the risk of depressive symptom according to mushrooms consumption. Study participants were categorized into 5 groups by the frequency of one serving size of mushrooms (30 g) as follows: rare/never, <1/month, 1/month-1/week, 1-3/week, ≥ 3/week. The development of depressive symptom was determined in Center for epidemiological studies-depression (CES-D) scale ≥ 16. Cox proportional hazards model was used to calculate adjusted hazard ratio (HR) and 95% confidence intervals (CI) for depressive symptom (adjusted HR [95% CI]). Subgroup analysis was performed for gender and age. Compared with group with rare/never consumption, groups with mushrooms consumption ≥ one serving size/month had the significantly decreased levels in adjusted HR and 95% CI for depressive symptom (rare/never consumption: reference, < 1/month: 0.92 [0.83 - 1.02], 1/month-1/week: 0.88 [0.83 – 0.94], 1-3/week: 0.88 [0.82 – 0.94], ≥ 3/week: 0.86 [0.80 – 0.93]). This association was similarly observed in both gender and age subgroup analyses. However, women and participants ≥ age of 40 showed the more prominent association than men and participants < age of 40.
Tailoring of performance characteristics of green tyre tread formulation using thermally exfoliated graphite/ carbon black binary filler system via scalable and competent method
Authors: Bijina V , Jandas P J , Jose Jesvin , N Muhammad Ajnas , K Abhitha , John Honey 
Published: August 2022

Abstract
The present study is proposing an eco-friendly, green tyre tread formulation possessing excellent output properties in terms of abrasion resistance, mechanical, rolling resistance and heat buildup properties. A standard formulation was prepared with a nominal amount of carbon black (CB) filler and tried to reduce the filler loading to a minimum value without compromising the performance characteristics. The simultaneous reduction in aromatic oil content also tried to make the formulation eco-friendly. To compensate for the effect of changes in the formulation a binary hybrid filler system was prepared by the partial replacement of CB using graphite. To ensure the maximum dispersion, a filler masterbatch of graphite was prepared within natural rubber matrix (NR) as (50/50) composition and incorporated into the compound master batch. The effect of thermal exfoliation of graphite on the dispersion thereby the performance of the composite was also analyzed. The graphite was thermally treated for a sudden thermal shock for 15 minutes at various temperatures ranging from 400–550 ˚C. Rolling resistance and heat build-up were recorded 45% and 53% reduction respectively for the formulations with thermally exfoliated graphite in comparison with the standard formulation. Abrasion resistance showed 18% improvement and significant improvement in mechanical and thermal properties are also reported.
Induce male sterility by CRISPR/Cas9-mediated mitochondrial genome editing in tobacco
Authors: Chang Yanzi , Liu Baolong , Jiang Yanyan , Cao Dong , Liu Yongju , Li Yun 
Published: August 2022

Abstract
Genome editing has become more and more popular in animal and plant systems following the emergence of CRISPR/Cas9 technology. However, target sequence modification by CRISPR/Cas9 has not been reported in the plant mitochondrial genome, mtDNA. In plants, a type of male sterility known as cytoplasmic male sterility (CMS) has been associated with certain mitochondrial genes, but few genes have been confirmed by direct mitochondrial gene-targeted modifications. Here, the CMS-associated gene (mtatp9) in tobacco was cleaved using mitoCRISPR/Cas9 with a mitochondrial localization signal. The male-sterile mutant, with aborted stamens, exhibited only 70% of the mtDNA copy number of the wild type and exhibited an altered percentage of heteroplasmic mtatp9 alleles; otherwise, the mutant was similar in phenotype to the CMS tobacco caused by disturbance of mtatp9. Transcriptomic analyses showed that glycolysis, tricarboxylic acid cycle metabolism and the oxidative phosphorylation pathway, which are all related to aerobic respiration, were inhibited in stamens of the male-sterile gene-edited mutant. In addition, overexpression of the synonymous mutations dsmtatp9 could restore fertility to the male-sterile mutant. Our results strongly suggest that mutation of mtatp9 causes CMS and that mitoCRISPR/Cas9 can be used to modify the mitochondrial genome of plants.