bluuebunny/crossref_metadata_2025_split huggingface dataset:
Deep learning of stochastic contagion dynamics on complex networks
Authors: Murphy Charles , Laurence Edward , Allard Antoine 
Published: July 2020

Abstract
Forecasting the evolution of contagion dynamics is still an open problem to which mechanistic models only offer a partial answer. To remain mathematically and/or computationally tractable, these models must rely on simplifying assumptions, thereby limiting the quantitative accuracy of their predictions and the complexity of the dynamics they can model. Here, we propose a complementary approach based on deep learning where the effective local mechanisms governing a dynamic are learned automatically from time series data. Our graph neural network architecture makes very few assumptions about the dynamics, and we demonstrate its accuracy using stochastic contagion dynamics of increasing complexity on static and temporal networks. By allowing simulations on arbitrary network structures, our approach makes it possible to explore the properties of the learned dynamics beyond the training data. Our results demonstrate how deep learning offers a new and complementary perspective to build effective models of contagion dynamics on networks.
Operation Optimization of Integrated Energy Systems Based on Heat Storage Characteristics of Heating Network
Authors: PAN Ersheng , LI Hui , WANG Zhidong , PENG Dong , ZHAO Lang , WANG Yongli , Huang Feifei , MA Yang 
Published: July 2020

Abstract
Background With the rapid development of multi-energy technology and the wide application of electric-heat integrated energy system (IES), multi-energy network optimization has become an important research direction of multi-energy joint supply in recent years.Compared with electric energy, heat energy has the characteristics of delay in transmission time and fuzzy body temperature, which makes the heating system more flexible to participate in IES. Methods An operation optimization model for the electric-heat IES that takes into account the heat storage characteristics of the heating network is proposed to address the operation cost of the electric-heat IES. Firstly, the virtual energy storage characteristics of the heating network are proposed based on the characteristics of the transmission time delay of the heat system and the somatic blurring of user temperature. Then, the model of the dynamic transfer of energy in the heat system was built. Based on this, an operation optimization model of the electric-heat IES is established. And the Monte Carlo Simulation embedded Quantum Particle Swarm Optimization (MCS-QPSO) algorithm is proposed to solve the model. Results This paper takes a park in Northwest China as a simulation case to prove the effectiveness of the model. The analysis of the case shows that the model can optimize the output of energy supply equipment, so that the output equipment can maintain high efficiency. The mode changes the energy purchase strategy according to the price change of different energy. The results show that the proposed model can effectively utilize the virtual energy storage characteristics of the heating network to achieve energy transfer across time, thus reducing the operation cost of the IES. Conclusions In this paper, the operation optimization model of the electric heating IES is established based on the incubation period of the heating network and the virtual energy storage characteristics. The model can not only achieve the coordination and complementarity between the electric and thermal systems in time and space, but also improve the energy efficiency and reduce operation cost of the system.
Association Between Functional Disability and Depressive Symptoms Among Older Adults in Rural China: A Cross-Sectional Study
Authors: Rong Jian , Ge Yanhong , Wang Xueqin , Chen Guimei , Ding Hong 
Published: July 2020

Abstract
Background: The association between functional disability and depressive symptoms among elderly people in rural China is not clear. This study explored the relationship between functional disability and depressive symptoms, focusing on whether an interactive association between functional disability, demographic characteristics and depressive symptoms exists among older adults in rural Anhui, China.Methods: A cross-sectional survey study was conducted with multi-stage stratified random sampling. The 30-item Geriatric Depression Scale and WHO Disability Assessment Schedule 2.0 were used to evaluate depressive symptoms and functional disability, respectively. The data were analyzed using SPSS statistics 25.0 program with chi-square test, Mann-Whitney U test, binary logistic regression analysis, and classification and regression tree model.Results: The prevalence of depressive symptoms in 3336 older people was 52.94%. After adjustment, subjects who had problems in participation (adjusted odds ratio [AOR]=3.499, 95% confidence interval [CI]:2.385-4.987), life activities (AOR=1.683, 95% CI: 1.370-2.066), getting along (AOR=1.616, 95% CI: 1.299-2.010), and mobility (AOR=1.842, 95% CI: 1.503-2.258) had an increased depressive symptoms risk. However, cognition (AOR=0.785, 95% CI: 0.647-0.953) negatively correlated with depressive symptoms. Additionally, the interactive association between functional disability dimensions, various variables and depressive symptoms were identified for the first time. Those who had problems in mobility, getting along and were unemployed, the possibility of having depressive symptoms was the highest.Conclusions: Special attention should be paid to unemployed older adults, and those with problems in participation, life activities, getting along, and mobility and no problems in cognition to maintain a good psychological state. Our findings may be greatly significant for developing more targeted and effective mental health prevention and intervention measures for older adults in rural areas.
Comprehensive Analysis of NAC Transcription Factor Family in Pearl Millet Uncovers Drought and Salinity Stress Responsive NAC in Pearl Millet (Pennisetum Glaucum)
Authors: Dudhate Ambika , Shinde Harshraj , Yu Pei , Tsugama Daisuke , Gupta Shashi Kumar , Liu Shenkui , Takano Tetsuo 
Published: July 2020

Abstract
Background: Pearl millet (Pennisetum glaucum) is a cereal crop that possesses the ability to withstand drought, salinity and high temperature stresses. The NAC [NAM (No Apical Meristem), ATAF1 and (Arabidopsis thaliana Activation Factor 1), and CUC2 (Cup-shaped Cotyledon)] transcription factor family is one of the largest transcription factor families in plants. NAC family members are known to regulate plant growth and abiotic stress tolerance. Currently, no reports are available on the functions of the NAC family in pearl millet. Results: Our genome-wide analysis found 151 NAC transcription factor genes (PgNACs) in the pearl millet genome. Phylogenetic analysis divided these NAC transcription factors into 11 groups (A-K). Three PgNACs (-073, -29, and -151) were found to be membrane-associated transcription factors (MTF). Seventeen other conserved motifs were found in PgNACs. Based on the similarity of PgNACs to NAC proteins in other species, the functions of PgNACs were predicted. In total, 88 microRNA target sites were predicted in 59 PgNACs. A previously performed transcriptome analysis suggests that the expression of 30 and 42 PgNACs are affected by salinity stress and drought stress, respectively. The expression of 36 randomly selected PgNACs was examined by quantitative reverse transcription-PCR. Many of these genes showed diverse salt- and drought-responsive expression patterns in roots and leaves. These results confirm that PgNACs are potentially involved in regulating abiotic stress tolerance in pearl millet.Conclusion: The pearl millet genome contains 151 NAC transcription factor genes that can be classified into 11 groups. Many of these genes are either upregulated or downregulated by either salinity or drought stress and may therefore contribute to establishing stress tolerance in pearl millet.
Remarkable Shift In Structural And Functional Properties of An Animal Charcoal Polluted Soil Accentuated By Inorganic Nutrients Amendment
Authors: Salam Lateef , Obayori Oluwafemi S. 
Published: July 2020

Abstract
The effects of carbon-free mineral medium (CFMM) amendment on hydrocarbon degradation and microbial community structure and function in an animal charcoal polluted soil was monitored for six weeks in field moist microcosms consisting of CFMM treated soil (FN4) and an untreated control (FN1). Gas chromatographic analysis of hydrocarbon fractions revealed the removal 84.02% and 82.38% and 70.09% and 70.14% aliphatic and aromatic fractions in FN4 and FN1 microcosms in 42 days. Shotgun metagenomic analysis of the two metagenomes revealed a remarkable shift in the microbial community structure of FN4 metagenome with 92.97% of the population belonging to the phylum Firmicutes and its dominant representative genera Anoxybacillus (64.58%), Bacillus (21.47%) and Solibacillus (2.39%). In untreated FN1 metagenome, the phyla Proteobacteria (56.12%), Actinobacteria (23.79%), Firmicutes (11.20%); and the genera Xanthobacter (9.73%), Rhizobium (7.49%) and Corynebacterium (7.35%) were preponderant. Functional annotation of putative ORFs from the two metagenomes revealed the detection of degradation genes for benzoate (pcaD, mhpF, aliB, benD-xylL, benC-xylZ, badH, had, dmpD, ligC, CMLE, pcaL, acd), xylene (mhpF, benD-xylL, benC-xylZ, dmpD, cymB, cmtB), chlorocyclohexane/chlorobenzene (dehH, dhaA, linC, linX, pcpC), toluene (bbsG, bbsC, bbsD, tsaC1), and several others in FN1 metagenome. In FN4 metagenome, only seven hydrocarbon degradation genes namely dmpH, mhpD, bphH, nemA and three others were detected. This study has revealed that CFMM amendment negatively impacts the structural and functional properties of the animal charcoal polluted soil. It also revealed that intrinsic bioremediation of the polluted soil could be enhanced via addition of water and aeration.
WITHDRAWN: PYCR1 Promotes Proliferation, Invasion and Drug-Resistance of Lung Cancer Cells by Regulating STAT3-Mediated PI3K/AKT and NF-κB Signaling Pathway
Authors: Yu Zhanwu , Wang Gebang , Zhang Chenlei , Liu Yu , Chen Wei , Wang Haoyou , Liu Hongxu 
Published: July 2020

Abstract

Background: Aberrant expression of PYCR1 has been proved to be one of the most pivotal regulators of tumor progress and metastasis. However, the detailed role of PYCR1 in promotion of NSCLC progress is not investigated thoroughly. The present study was aimed to thoroughly investigate the effect of PYCR1 in the growth of NSCLC and the underlying mechanisms, so that provide valuable theoretical basis for efficient treatment of NSCLC. Methods: The expressions of PYCR1 and its target genes and downstream signals were respectively determined by Western-blot assay and RT-qPCR experiment. Cell growth of NSCLC cells was investigated using the CCK-8 kit while the proliferation assay was performed with the help of EDU staining. The NSCLC-bearing mice mode was established to evaluate the effect of PYCR1 on the progress of NSCLC and the underlying mechanisms in vivo.Results: It was firstly demonstrated that the PYCR1 was overexpressed in lung cancer tissues and cells and overexpression of PYCR1 contributed to significantly enhanced proliferation, invasion, and drug-resistance of cancer cells and progress of NSCLC tissues. Further studies revealed that up-regulation of PYCR1 level resulted to the elevation of bioactivity of STAT3. Additionally, the positive correlation between the expression of PYCR1 and STAT3 indicated that the PYCR1 promotes the growth of NSCLC through targeting regulation the STAT3 levels. Furthermore, activation of STAT3 by PYCR1 was proved to be able of awaking the PI3K/AKT and NF-κB signaling pathway, which was extremely important to the metabolism, proliferation, cell survival, and growth of many cancer cell types.Conclusion: In conclusion, our study demonstrated that PYCR1 was specifically overexpressed in lung cancer and closely related to rapid progress and drug-resistance thorough regulating the STAT3-mediated PI3K/AKT and NF-κB signaling pathway. It may provide a valuable strategy for treatment of malignant lung cancer.
C1q/TNF-Related Protein-9 Attenuates Palmitic Acid-Induced Endothelial Cell Senescence via Increasing Autophagy
Authors: Lee Jiwoo , Yoo Jee Hee , Kim Hwi Seung , Cho Yun Kyung , Lee Yoo La , Lee Woo Je , Jung Chang Hee , Park Joong-Yeol 
Published: July 2020

Abstract
Background: Autophagy is an important process in the pathogenesis of atherosclerosis. C1q/tumor necrosis factor-related protein 9 (CTRP9) is the closest adiponectin paralog. CTRP9 has purported anti-aging and anti-atherogenic effects, but its roles in autophagy and endothelial senescence are unknown. The aim of this study was to evaluate whether CTRP9 prevents palmitic acid (PA)-induced endothelial senescence by promoting autophagy.Methods: After no treatment or pre-treatment of human umbilical vein endothelial cells with CTRP9 prior to PA treatment, the level of senescence was measured by senescence associated acidic β-galactosidase staining and the level of hyperphosphorylated pRB protein. Autophagy was evaluated by LC3 conversion and the level of p62/SQSTM1, a protein degraded during autophagy. Autophagosome–lysosome fusion was detected by fluorescence microscopy.Results: Pre-treatment with CTRP9 attenuated PA-induced endothelial senescence. CTRP9 increased the conversion of LC3-I to LC3-II, and decreased the level of p62 in time- and dose-dependent manners. Although both CTRP9 and PA treatment increased the LC3 conversion, treatment of PA increased p62 and decreased the fusion of autophagosomes and lysosomes, which represented decreased autophagic flux. However, pre-treatment with CTRP9 recovered the autophagic flux inhibited by PA. AMP-activated kinase (AMPK) activation was involved in LC3 conversion and decreased p62 induced by CTRP9.Conclusion: CTRP9 inhibits PA-induced endothelial senescence by recovering autophagy and autophagic flux through AMPK activation.
NEMO-Binding Domain Peptide Ameliorates Alveolar Hypercoagulation and Fibrinolytic Inhibition in Lipopolysaccharide-Induced Acute Respiratory Distress Syndrome via NF-κB Signaling Pathway in Mice
Authors: WANG Yahui , WU Yanqi , LIU Bo , YANG Huilin , QIAN Hong , CHENG Yumei , LI Xiang , YANG Guixia , ZHENG Xinghao , shen Feng 
Published: July 2020

Abstract
Background It was confirmed that alveolar hypercoagulation and fibrinolytic inhibition were associated with refractory hypoxemia in acute respiratory distress syndrome (ARDS), and NF-κB pathway was involved in this process. The purpose of the present study is to explore the effects and relevant mechanisms exerted by NEMO-binding domain peptide (NBDP) to alleviate alveolar hypercoagulation and fibrinolytic inhibition aroused by lipopolysaccharide in ARDS mice. Materials and Methods Adult male BALB/c mice inhaled lipopolysaccharide (LPS, mg/L) to induce ARDS. 30 minutes before LPS administration, we treated the mice with increasing concentrations of intratracheally inhaled NBDP or saline aerosol. Six hours after LPS treatment, bronchoalveolar lavage fluids (BALF) were collected and then all mice were executed. We checked coagulation and fibrinolysis associated factors in lung tissues and in BALF as well. We simultaneously observed the activation of NF-κB signaling pathway as well. Results NBDP pretreatment dose-dependently inhibited either the expressions of tissue factor (TF) and plasminogen activator inhibitor (PAI) 1 in lung tissues or the secretions of TF, PAI-1, thrombin-antithrombin complex (TAT) and promoted activated protein C (APC) secretion in BALF induced by LPS. LPS-induced high expression of pulmonary procollagen peptide type Ⅲ (PⅢP) was also declined by NBDP pretreatment in dose-dependent manner. Western blotting showed that NBDP pretreatment obviously attenuated LPS-induced IKKα/β, Iκα and NF-κB p65 activation. LPS-induced p65 DNA binding activity was inhibited by NBDP pretreatment either. We also noticed NBDP protected mice against LPS-induced lung injury in a dose-dependent manner.Conclusions Our experimental findings demonstrate that NBDP dose-dependently ameliorated LPS-induced alveolar hypercoagulation and fibrinolytic inhibition through inhibiting NF-κB signaling pathway. NBDP is expected to be a new therapeutic target to correct the abnormalities of alveolar coagulation and fibrinolysis in ARDS.
Fabrication of Chitosan-Polyvinyl Alcohol and Silk Electrospun Fiber Seeded with Differentiated Keratinocyte for Skin Tissue Regeneration in Animal Wound Model
Authors: Fathi Afshin , Khanmohammadi Mehdi , Goodarzi Arash , Mobarakeh Zahra Taherian , Saremi Jamileh , Arabpour Zohre , Ai Jafar 
Published: July 2020

Abstract
Hybrid fibrous mat containing cell interactive molecules offers the ability to deliver the cells and drugs in wound bed, which will help to achieve a high therapeutic treatment. In this study, a co-electrospun hybrid of polyvinyl alcohol (PVA), chitosan (Ch) and silk fibrous mat was developed and their wound healing potential by localizing bone marrow mesenchymal stem cells (MSCs)-derived keratinocytes on it was evaluated in vitro and in vivo. The fabricated fibrous Ch-PVA + Silk hydrogels were characterized for their structural, mechanical and biochemical properties. The shape uniformity and pore size of fibers showed smooth and homogenous structures of them. Fourier transform infrared spectroscopy (FTIR) verified all typical absorption characteristics of Ch-PVA + Silk polymers as well as Ch-PVA or pure PVA substrates. The contact angle and wettability measurement of fibers showed that mats found moderate hydrophilicity by addition of Ch and silk substrates compared with PVA alone. The mechanical features of Ch-PVA + Silk fibrous mats increase significantly through co-electrospun process as well as hybridization of these synthetic and natural polymers. Higher degrees of cellular attachment and proliferation obtained on Ch-PVA + Silk fibers compared with PVA and Ch-PVA fibers. In terms of the capability of Ch-PVA + Silk fibers and MSC-derived keratinocytes, histological analysis and skin regeneration results showed this novel fibrous construct could be suggested as a skin substitute in the repair of injured skin and regenerative medicine applications.
A Real-Time PCR Assay for Rapid Identification of Inducible and Acquired Clarithromycin Resistance in Mycobacterium Abscessus
Authors: Sharma Meenu Kaushal , La Yanni , Janella Debra , Soualhine Hafid 
Published: July 2020

Abstract
Background: Mycobacterium abscessus is a rapidly growing mycobacteria involved in severe infections of the lung, skin, or soft tissue. Macrolides such as clarithromycin are the recommended first line drugs for treatment of M. abscessus infections. However, M. abscessus has dual mechanisms of resistance to macrolides, making treatment by macrolides difficult. A functional erm(41) gene confers for inducible resistance while acquired mutations on the 23S rRNA rrl gene confer for constitutive resistance. Methods: We have developed a real-time PCR assay to detect both inducible and acquired resistance to clarithromycin, and compared the results to traditional erm(41) and rrl sequencing and phenotypic susceptibility testing using Sensititre™ plates. Results: Of the total 126 M. abscessus isolates tested, truncated erm(41) was found in 23/126 (18.3%) of the samples, 27/126 (21.4%) had a T28C mutation in erm(41), and 2/126 (1.6%) had an acquired A2058C mutation in rrl. The phenotypic results correlated with the expected sequencing results in 121/126 samples (96%). Phenotypic testing compared to real-time PCR resolved 2 of these discrepancies by showing the existence of both erm(41) alleles in the isolates that sequencing missed. One culture was found to be mixed with two M. abscessus subspecies as per hsp65 sequencing and 2 isolates had discordance between molecular and phenotypic results. It was presumed that 3 isolates showed discrepancy between sequencing and real-time PCR but one culture was mixed and other 2 detected both alleles by real-time PCR leading to 100% concordance when compared to sequencing. Conclusion: In conclusion, real-time PCR is more accurate for detection of both acquired and induced clarithromycin resistance, specifically when mixed genic profiles are present in a sample.
Artificial Intelligence-guided Prediction of Dental Dosesprior Toplanning of Head and Neck Radiotherapy: Technical Development and Pilot Study of Feasibility
Authors: Chan Jason W. , Hohenstein Nicole , Carpenter Colin , Pattison Adam J. , Morin Olivier , Valdes Gilmer , Thompson Maria , Perkins Jennifer , Solberg Timothy D. , Yom Sue S. 
Published: July 2020

Abstract
Background: The aim of this research was to develop a novel artificial intelligence (AI)-guided clinical decision support (CDS) system, to predict radiation doses to subsites of the mandibleusing diagnostic CT scans acquired before planning of head and neck radiotherapy (RT). Methods: A dose classifier was trained using RT plans from 86 oropharyngeal cancer patients; thetest set consisted of an additional 20 plans.The classifier was trained topredictwhether mandible subsites would receive a mean dose >50Gy.The AI predictionswere prospectively evaluated and compared to those of a specialist head and neck radiation oncologist for 9 patients.Positive predictive value (PPV), negative predictive value (NPV), Pearson’s correlation coefficient, and Lin's concordance correlation coefficient were calculated to compare the AIpredictions to those of the physician. Results: In the test dataset, the AIpredictions had a PPVof 0.95 and NPVof 0.88.For 9 patients evaluated prospectively, there was a strong correlation between the predictions of the AIalgorithm and physician (p = 0.72, p < 0.001).Comparing the AI algorithm versus the physician, the PPVs were 0.82 versus0.25, and the NPVs were 0.94versus 1.0,respectively.Concordance between physician estimatesand final planned doses was 0.62;this was 0.71 between AI-based estimates and final planned doses. Conclusions: An AI-guidedCDStool to predict dental dosimetry prior to head and neck RT was built, validated, and prospectively tested.AI-guided decision supportincreasedprecision and accuracy ofdental dose estimates and improved the quality of pre-RTdental assessment.