bluuebunny/crossref_metadata_2025_split huggingface dataset:
A cyclical deep learning based framework for simultaneous inverse and forward design of nanophotonic metasurfaces
Authors: Mall Abhishek , Patil Abhijeet , Sethi Amit , Kumar Anshuman 
Published: November 2020

AbstractThe conventional approach to nanophotonic metasurface design and optimization for a targeted electromagnetic response involves exploring large geometry and material spaces. This is a highly iterative process based on trial and error, which is computationally costly and time consuming. Moreover, the non-uniqueness of structural designs and high non-linearity between electromagnetic response and design makes this problem challenging. To model this unintuitive relationship between electromagnetic response and metasurface structural design as a probability distribution in the design space, we introduce a framework for inverse design of nanophotonic metasurfaces based on cyclical deep learning (DL). The proposed framework performs inverse design and optimization mechanism for the generation of meta-atoms and meta-molecules as metasurface units based on DL models and genetic algorithm. The framework includes consecutive DL models that emulate both numerical electromagnetic simulation and iterative processes of optimization, and generate optimized structural designs while simultaneously performing forward and inverse design tasks. A selection and evaluation of generated structural designs is performed by the genetic algorithm to construct a desired optical response and design space that mimics real world responses. Importantly, our cyclical generation framework also explores the space of new metasurface topologies. As an example application of the utility of our proposed architecture, we demonstrate the inverse design of gap-plasmon based half-wave plate metasurface for user-defined optical response. Our proposed technique can be easily generalized for designing nanophtonic metasurfaces for a wide range of targeted optical response.
Lung transcriptome of a COVID-19 patient and systems biology predictions suggest impaired surfactant production which may be druggable by surfactant therapy
Authors: Islam Abul Bashar Mir Md. Khademul , Khan Md. Abdullah-Al-Kamran 
Published: November 2020

AbstractAn incomplete understanding of the molecular mechanisms behind impairment of lung pathobiology by COVID-19 complicates its clinical management. In this study, we analyzed the gene expression pattern of cells obtained from biopsies of COVID-19-affected patient and compared to the effects observed in typical SARS-CoV-2 and SARS-CoV-infected cell-lines. We then compared gene expression patterns of COVID-19-affected lung tissues and SARS-CoV-2-infected cell-lines and mapped those to known lung-related molecular networks, including hypoxia induced responses, lung development, respiratory processes, cholesterol biosynthesis and surfactant metabolism; all of which are suspected to be downregulated following SARS-CoV-2 infection based on the observed symptomatic impairments. Network analyses suggest that SARS-CoV-2 infection might lead to acute lung injury in COVID-19 by affecting surfactant proteins and their regulators SPD, SPC, and TTF1 through NSP5 and NSP12; thrombosis regulators PLAT, and EGR1 by ORF8 and NSP12; and mitochondrial NDUFA10, NDUFAF5, and SAMM50 through NSP12. Furthermore, hypoxia response through HIF-1 signaling might also be targeted by SARS-CoV-2 proteins. Drug enrichment analysis of dysregulated genes has allowed us to propose novel therapies, including lung surfactants, respiratory stimulants, sargramostim, and oseltamivir. Our study presents a distinct mechanism of probable virus induced lung damage apart from cytokine storm.
Teleconnection between the Asian Polar Vortex and surface PM2.5 in China
Authors: Zhou Lihua , Zhang Jing , Zheng Xiaohui , Zhu Siguang , Hu Yueming 
Published: November 2020

AbstractAtmospheric fine particulate matter (PM2.5) pollutions are of particular concern because of their direct and indirect harm to humans and organisms. China has suffered from severe air pollution for the past ten years, related to heavy pollution emissions and compounded by the effects of atmospheric circulation. This study applied statistical methods, observational data of ground pollutants, and meteorological data to analyze the impact of large-scale atmospheric circulations on PM2.5 pollution over China. Empirical orthogonal function (EOF) analysis was used to evaluate the main PM2.5 patterns and total contributions of the leading four EOFs. The results indicate that the total contributions of the leading four EOFs accounted for 50.5% of the total variance, reflecting four main types of PM2.5 pollution, namely, overall pollution phase, north–south phase, east–west phase and north–center–south phase, with contributions of 28.4%, 9.7%, 6.5% and 5.9%, respectively. We selected indices of the Asian Polar Vortex (APV) to analyze the impact of large-scale atmospheric circulations on PM2.5 pollution over China. The most pronounced APV control occurred in Beijing and its surroundings, specifically, along the Bohai Sea and the Northeast Plain.
Early vascular ageing biomarkers in osteoporotic outpatients: a pilot study
Authors: Gaudio Agostino , Xourafa Anastasia , Zanoli Luca , Rapisarda Rosario , Catalano Antonino , Signorelli Salvatore Santo , Castellino Pietro 
Published: November 2020

AbstractOsteoporosis and atherosclerosis are significant public health problems that often coexist, especially in the elderly. Although some studies have reported an age-dependent relationship, others have suggested a causal relationship between osteoporosis and atherosclerosis. The aim of our study was to evaluate the cardiovascular risk in a population of patients with osteoporosis by measuring carotid intima-media thickness (cIMT) and carotid-femoral pulse wave velocity (cf-PWV). A total of 58 patients with osteoporosis and an equal number of healthy control subjects were enrolled. All subjects underwent (1) a bone densitometry examination using dual X-ray absorptiometry, (2) a vascular evaluation for the measurements of cIMT and cf-PWV and (3) a blood sample for the evaluation of lipids and phosphocalcic metabolism. Patients with osteoporosis had a significant increase in cIMT and cf-PWV. There was also a significant inverse correlation between the femoral neck BMD and cf-PWV values. In conclusion, osteoporotic outpatients have earlier vascular ageing, with an increase of arterial stiffness. These data support a possible association between osteoporosis and atherosclerosis independent of age.
Modelling the potential for soil carbon sequestration using biochar from sugarcane residues in Brazil
Authors: Lefebvre David , Williams Adrian , Meersmans Jeroen , Kirk Guy J. D. , Sohi Saran , Goglio Pietro , Smith Pete 
Published: November 2020

AbstractSugarcane (Saccharum officinarum L.) cultivation leaves behind around 20 t ha−1 of biomass residue after harvest and processing. We investigated the potential for sequestering carbon (C) in soil with these residues by partially converting them into biochar (recalcitrant carbon-rich material). First, we modified the RothC model to allow changes in soil C arising from additions of sugarcane-derived biochar. Second, we evaluated the modified model against published field data, and found satisfactory agreement between observed and predicted soil C accumulation. Third, we used the model to explore the potential for soil C sequestration with sugarcane biochar in São Paulo State, Brazil. The results show a potential increase in soil C stocks by 2.35 ± 0.4 t C ha−1 year−1 in sugarcane fields across the State at application rates of 4.2 t biochar ha−1 year−1. Scaling to the total sugarcane area of the State, this would be 50 Mt of CO2 equivalent year−1, which is 31% of the CO2 equivalent emissions attributed to the State in 2016. Future research should (a) further validate the model with field experiments; (b) make a full life cycle assessment of the potential for greenhouse gas mitigation, including additional effects of biochar applications on greenhouse gas balances.
Gut microbiota and metabolic health among overweight and obese individuals
Authors: Kim Mi-Hyun , Yun Kyung Eun , Kim Jimin , Park Eunkyo , Chang Yoosoo , Ryu Seungho , Kim Hyung-Lae , Kim Han-Na 
Published: November 2020

AbstractAlthough obesity is associated with numerous diseases, the risks of disease may depend on metabolic health. Associations between the gut microbiota, obesity, and metabolic syndrome have been reported, but differences in microbiomes according to metabolic health in the obese population have not been explored in previous studies. Here, we investigated the composition of gut microbiota according to metabolic health status in obese and overweight subjects. A total of 747 overweight or obese adults were categorized by metabolic health status, and their fecal microbiota were profiled using 16S ribosomal RNA gene sequencing. We classified these adults into a metabolically healthy group (MH, N = 317) without any components of metabolic syndrome or a metabolically unhealthy group (MU, N = 430) defined as having at least one metabolic abnormality. The phylogenetic and non-phylogenetic alpha diversity for gut microbiota were lower in the MU group than the MH group, and there were significant differences in gut microbiota bacterial composition between the two groups. We found that the genus Oscillospira and the family Coriobacteriaceae were associated with good metabolic health in the overweight and obese populations. This is the first report to describe gut microbial diversity and composition in metabolically healthy and unhealthy overweight and obese individuals. Modulation of the gut microbiome may help prevent metabolic abnormalities in the obese population.
The mode of action of plant associated Burkholderia against grey mould disease in grapevine revealed through traits and genomic analyses
Authors: Esmaeel Qassim , Jacquard Cédric , Sanchez Lisa , Clément Christophe , Ait Barka Essaid 
Published: November 2020

AbstractPlant-associated Burkholderia spp. have been shown to offer a promising alternative method that may address concerns with ecological issue associated with pesticide overuse in agriculture. However to date, little work has studied the role of Burkholderia species as biocontrol agents for grapevine pathogens. To this end, two Burkholderia strains, BE17 and BE24 isolated from the maize rhizosphere in France, were investigated to determine their biocontrol potential and their ability to induce systemic resistance against grey mould disease in grapevine. Results showed the capacity of both strains to inhibit spore germination and mycelium growth of Botrytis cinerea. Experimental inoculation with BE17 and BE24 showed a significant protection of bacterized-plantlets against grey mould compared to the non-bacterized control. BE17 and BE24-bacterized plants accumulated more reactive oxygen species and an increased callose deposition was observed in leaves of bacterized plantlets compared to the control plantlets. In bacterized plants, gene expression analysis subsequent to B. cinerea challenge showed that strains BE17 and BE24 significantly increased the relative transcript level of pathogenesis-related (PR) proteins PR5 and PR10, two markers involved in the Salicylic acid (SA)-signaling pathway. Furthermore, in silico analysis of strains revealed the presence of genes involved in plant growth promotion and biocontrol highlighting the attractiveness of these strains for sustainable agricultural applications.
The effect of smoking on chronic inflammation, immune function and blood cell composition
Authors: Elisia Ingrid , Lam Vivian , Cho Brandon , Hay Mariah , Li Michael Yu , Yeung Michelle , Bu Luke , Jia William , Norton Nancy , Lam Stephen , Krystal Gerald 
Published: November 2020

AbstractSmoking is the number one risk factor for cancer mortality but only 15–20% of heavy smokers develop lung cancer. It would, therefore, be of great benefit to identify those at high risk early on so that preventative measures can be initiated. To investigate this, we evaluated the effects of smoking on inflammatory markers, innate and adaptive immune responses to bacterial and viral challenges and blood cell composition. We found that plasma samples from 30 heavy smokers (16 men and 14 women) had significantly higher CRP, fibrinogen, IL-6 and CEA levels than 36 non-smoking controls. Whole blood samples from smokers, incubated for 7 h at 37 °C in the absence of any exogenous stimuli, secreted significantly higher levels of IL-8 and a number of other cytokines/chemokines than non-smokers. When challenged for 7 h withE. coli,whole blood samples from smokers secreted significantly lower levels of many inflammatory cytokines/chemokines. However, when stimulated with HSV-1, significantly higher levels of both PGE2and many cytokines/chemokines were secreted from smokers’ blood samples than from controls. In terms of blood cell composition, red blood cells, hematocrits, hemoglobin levels, MCV, MCH, MCHC, Pct and RDW levels were all elevated in smokers, in keeping with their compromised lung capacity. As well, total leukocytes were significantly higher, driven by increases in granulocytes and monocytes. In addition, smokers had lower NK cells and higher Tregs than controls, suggesting that smoking may reduce the ability to kill nascent tumor cells. Importantly, there was substantial person-to person variation amongst smokers with some showing markedly different values from controls and others showing normal levels of many parameters measured, indicating the former may be at significantly higher risk of developing lung cancer.
Paracoccidioides brasiliensis downmodulates α3 integrin levels in human lung epithelial cells in a TLR2-dependent manner
Authors: de Barros Bianca Carla Silva Campitelli , Almeida Bruna Rocha , Suzuki Erika 
Published: November 2020

AbstractParacoccidioidomycosis (PCM) is the most prevalent systemic mycosis in Latin America and may be caused by the species Paracoccidioides brasiliensis. In the lungs, this fungus interacts with epithelial cells, activating host cell signalling pathways, resulting in the production of inflammatory mediators. This event may be initiated through the activation of Pattern-Recognition Receptors such as Toll-like Receptors (TLRs). By interacting with cell wall components, TLR2 is frequently related to fungal infections. In this work, we show that, after 24 h post-infection with P. brasiliensis, A549 lung epithelial cells presented higher TLR2 levels, which is important for IL-8 secretion. Besides, integrins may also participate in pathogen recognition by host cells. We verified that P. brasiliensis increased α3 integrin levels in A549 cells after 5 h of infection and promoted interaction between this receptor and TLR2. However, after 24 h, surprisingly, we verified a decrease of α3 integrin levels, which was dependent on direct contact between fungi and epithelial cells. Likewise, we observed that TLR2 is important to downmodulate α3 integrin levels after 24 h of infection. Thus, P. brasiliensis can modulate the host inflammatory response by exploiting host cell receptors and cell signalling pathways.
The secondary structural difference between Lewy body and glial cytoplasmic inclusion in autopsy brain with synchrotron FTIR micro-spectroscopy
Authors: Araki Katsuya , Yagi Naoto , Ikemoto Yuka , Hayakawa Hideki , Fujimura Harutoshi , Moriwaki Taro , Nagai Yoshitaka , Murayama Shigeo , Mochizuki Hideki 
Published: November 2020

AbstractLewy bodies (LBs) and glial cytoplasmic inclusions (GCIs) are specific aggregates found in Parkinson’s disease (PD) and multiple system atrophy (MSA), respectively. These aggregates mainly consist of α-synuclein (α-syn) and have been reported to propagate in the brain. In animal experiments, the fibrils of α-syn propagate similarly to prions but there is still insufficient evidence to establish this finding in humans. Here, we analysed the protein structure of these aggregates in the autopsy brains of patients by synchrotron Fourier-transform infrared micro-spectroscopy (FTIRM) analysis without extracting or artificially amplifying the aggregates. As a result, we found that the content of the β-sheet structure in LBs in patients with PD was significantly higher than that in GCIs in patients with MSA (52.6 ± 1.9% in PD vs. 38.1 ± 0.9% in MSA, P < 0.001). These structural differences may provide clues to the differences in phenotypes of PD and MSA.
A combination of fuzzy Delphi method and hybrid ANN-based systems to forecast ground vibration resulting from blasting
Authors: Huang Jiandong , Koopialipoor Mohammadreza , Armaghani Danial Jahed 
Published: November 2020

AbstractThis study presents a new input parameter selection and modeling procedure in order to control and predict peak particle velocity (PPV) values induced by mine blasting. The first part of this study was performed through the use of fuzzy Delphi method (FDM) to identify the key input variables with the deepest influence on PPV based on the experts’ opinions. Then, in the second part, the most effective parameters on PPV were selected to be applied in hybrid artificial neural network (ANN)-based models i.e., genetic algorithm (GA)-ANN, particle swarm optimization (PSO)-ANN, imperialism competitive algorithm (ICA)-ANN, artificial bee colony (ABC)-ANN and firefly algorithm (FA)-ANN for the prediction of PPV. Many hybrid ANN-based models were constructed according to the most influential parameters of GA, PSO, ICA, ABC and FA optimization techniques and 5 hybrid ANN-based models were proposed to predict PPVs induced by blasting. Through simple ranking technique, the best hybrid model was selected. The obtained results revealed that the FA-ANN model is able to offer higher accuracy level for PPV prediction compared to other implemented hybrid models. Coefficient of determination (R2) results of (0.8831, 0.8995, 0.9043, 0.9095 and 0.9133) and (0.8657, 0.8749, 0.8850, 0.9094 and 0.9097) were obtained for train and test stages of GA-ANN, PSO-ANN, ICA-ANN, ABC-ANN and FA-ANN, respectively. The results showed that all hybrid models can be used to solve PPV problem, however, when the highest prediction performance is needed, the hybrid FA-ANN model would be the best choice.
Gene-regulatory network analysis of ankylosing spondylitis with a single-cell chromatin accessible assay
Authors: Yu Haiyan , Wu Hongwei , Zheng Fengping , Zhu Chengxin , Yin Lianghong , Dai Weier , Liu Dongzhou , Tang Donge , Hong Xiaoping , Dai Yong 
Published: November 2020

AbstractA detailed understanding of the gene-regulatory network in ankylosing spondylitis (AS) is vital for elucidating the mechanisms of AS pathogenesis. Assaying transposase-accessible chromatin in single cell sequencing (scATAC-seq) is a suitable method for revealing such networks. Thus, scATAC-seq was applied to define the landscape of active regulatory DNA in AS. As a result, there was a significant change in the percent of CD8+ T cells in PBMCs, and 37 differentially accessible transcription factor (TF) motifs were identified. T cells, monocytes-1 and dendritic cells were found to be crucial for the IL-17 signaling pathway and TNF signaling pathway, since they had 73 potential target genes regulated by 8 TF motifs with decreased accessibility in AS. Moreover, natural killer cells were involved in AS by increasing the accessibility to TF motifs TEAD1 and JUN to induce cytokine-cytokine receptor interactions. In addition, CD4+ T cells and CD8+ T cells may be vital for altering host immune functions through increasing the accessibility of TF motifs NR1H4 and OLIG (OLIGI and OLIG2), respectively. These results explain clear gene regulatory variation in PBMCs from AS patients, providing a foundational framework for the study of personal regulomes and delivering insights into epigenetic therapy.
Co-blending modification of activated coke using pyrolusite and titanium ore for low-temperature NOx removal
Authors: Yang Lin , Yao Lu , Lai Yuguo , Jiang Xia , Jiang Wenju 
Published: November 2020

AbstractActivated coke (AC) has great potential in the field of low-temperature NO removal (DeNOx), especially the branch prepared by blending modification. In this study, the AC-based pyrolusite and/or titanium ore blended catalysts were prepared and applied for DeNOx. The results show blending pyrolusite and titanium ore promoted the catalytic performance of AC (Px@AC, Tix@AC) clearly, and the co-blending of two of them showed a synergistic effect. The (P/Ti-1/2)15@AC performed the highest NO conversion of 66.4%, improved 16.9% and 16.0% respectively compared with P15@AC and Ti15@AC. For the (P/Ti-1/2)15@AC DeNOx, its relative better porous structure (SBET = 364 m2/g, Vmic = 0.156 cm3/g) makes better mass transfer and more active sites exposure, stronger surface acidity (C–O, 19.43%; C=O, 4.16%) is more favorable to the NH3 adsorption, and Ti, Mn and Fe formed bridge structure fasted the lactic oxygen recovery and electron transfer. The DeNOx of (P/Ti-1/2)15@AC followed both the E–R and L–H mechanism, both the gaseous and adsorbed NO reacted with the activated NH3 due to the active sites provided by both the carbon and titanium.
Ecological corridors for the amphibians and reptiles in the Natura 2000 sites of Romania
Authors: Sahlean Tiberiu C. , Papeș Monica , Strugariu Alexandru , Gherghel Iulian 
Published: November 2020

AbstractLandscape heterogeneity and fragmentation are key challenges for biodiversity conservation. As Earth’s landscape is increasingly dominated by anthropogenic land use, it is clear that broad-scale systems of nature reserves connected by corridors are needed to enable the dispersal of flora and fauna. The European Union currently supports a continent-wide network of protected areas, the Natura 2000 program, but this program lacks the necessary connectivity component. To examine whether a comprehensive network could be built in order to protect amphibians and reptiles, two taxonomic groups sensitive to environmental changes due to their physiological constrains and low dispersal capacity, we used species’ distribution maps, the sites of community interest (SCIs) in Romania, and landscape resistance rasters. Except Vipera ursinii rakosiensis, all amphibians and reptiles had corridors mapped that, when assembled, provided linkages for up to 27 species. Natura 2000 species were not good candidates for umbrella species as these linkages covered only 17% of the corridors for all species. Important Areas for Connectivity were identified in the Carpathian Mountains and along the Danube River, further confirming these regions as hot spots for biodiversity in Europe, where successful linkages are most likely. In the end, while such corridors may not be created just for amphibians and reptiles, they can easily be incorporated into more complex linkages with corridors for more charismatic species, therefore enhancing the corridors’ value in terms of quality and structure.