bluuebunny/crossref_metadata_2025_split huggingface dataset:
Catalytic production of low-carbon footprint sustainable natural gas
Authors: Si Xiaoqin , Lu Rui , Zhao Zhitong , Yang Xiaofeng , Wang Feng , Jiang Huifang , Luo Xiaolin , Wang Aiqin , Feng Zhaochi , Xu Jie , Lu Fang 
Published: January 2022

AbstractNatural gas is one of the foremost basic energy sources on earth. Although biological process appears as promising valorization routes to transfer biomass to sustainable methane, the recalcitrance of lignocellulosic biomass is the major limitation for the production of mixing gas to meet the natural gas composition of pipeline transportation. Here we develop a catalytic-drive approach to directly transfer solid biomass to bio-natural gas which can be suitable for the current infrastructure. A catalyst with Ni2Al3 alloy phase enables nearly complete conversion of various agricultural and forestry residues, the total carbon yield of gas products reaches up to 93% after several hours at relative low-temperature (300 degrees Celsius). And the catalyst shows powerful processing capability for the production of natural gas during thirty cycles. A low-carbon footprint is estimated by a preliminary life cycle assessment, especially for the low hydrogen pressure and non-fossil hydrogen, and technical economic analysis predicts that this process is an economically competitive production process.
Identification of a modular super-enhancer in murine retinal development
Authors: Honnell Victoria , Norrie Jackie L. , Patel Anand G. , Ramirez Cody , Zhang Jiakun , Lai Yu-Hsuan , Wan Shibiao , Dyer Michael A. 
Published: January 2022

AbstractSuper-enhancers are expansive regions of genomic DNA comprised of multiple putative enhancers that contribute to the dynamic gene expression patterns during development. This is particularly important in neurogenesis because many essential transcription factors have complex developmental stage– and cell–type specific expression patterns across the central nervous system. In the developing retina, Vsx2 is expressed in retinal progenitor cells and is maintained in differentiated bipolar neurons and Müller glia. A single super-enhancer controls this complex and dynamic pattern of expression. Here we show that deletion of one region disrupts retinal progenitor cell proliferation but does not affect cell fate specification. The deletion of another region has no effect on retinal progenitor cell proliferation but instead leads to a complete loss of bipolar neurons. This prototypical super-enhancer may serve as a model for dissecting the complex gene expression patterns for neurogenic transcription factors during development. Moreover, it provides a unique opportunity to alter expression of individual transcription factors in particular cell types at specific stages of development. This provides a deeper understanding of function that cannot be achieved with traditional knockout mouse approaches.
Reduced infant rhesus macaque growth rates due to environmental enteric dysfunction and association with histopathology in the large intestine
Authors: Hendrickson Sara M. , Thomas Archana , Prongay Kamm , Haertel Andrew J. , Garzel Laura M. , Gill Leanne , Barr Tasha , Rhoades Nicholas S. , Reader Rachel , Galan Mark , Carroll Julie M. , Roberts Charles T. , Gao Lina , Amanna Ian J. , Messaoudi Ilhem , Slifka Mark K. 
Published: January 2022

AbstractEnvironmental enteric dysfunction is associated with malnutrition as well as infant growth stunting and has been classically defined by villous blunting, decreased crypt-to-villus ratio, and inflammation in the small intestine. Here, we characterized environmental enteric dysfunction among infant rhesus macaques that are naturally exposed to enteric pathogens commonly linked to human growth stunting. Remarkably, despite villous atrophy and histological abnormalities observed in the small intestine, poor growth trajectories and low serum tryptophan levels were correlated with increased histopathology in the large intestine. This work provides insight into the mechanisms underlying this disease and indicates that the large intestine may be an important target for therapeutic intervention.
Ultra-low threshold lasing through phase front engineering via a metallic circular aperture
Authors: Wang Zhixin , Kapsalidis Filippos , Wang Ruijun , Beck Mattias , Faist Jérôme 
Published: January 2022

AbstractSemiconductor lasers with extremely low threshold power require a combination of small volume active region with high-quality-factor cavities. For ridge lasers with highly reflective coatings, an ultra-low threshold demands significantly suppressing the diffraction loss at the facets of the laser. Here, we demonstrate that introducing a subwavelength aperture in the metallic highly reflective coating of a laser can correct the phase front, thereby counter-intuitively enhancing both its modal reflectivity and transmissivity at the same time. Theoretical and experimental results manifest a decreasing in the mirror loss by over 40% and an increasing in the transmissivity by 104. Implementing this method on a small-cavity quantum cascade laser, room-temperature continuous-wave lasing operation at 4.5 μm wavelength with an electrical consumption power of only 143 mW is achieved. Our work suggests possibilities for future portable applications and can be implemented in a broad range of optoelectronic systems.
DeepNull models non-linear covariate effects to improve phenotypic prediction and association power
Authors: McCaw Zachary R. , Colthurst Thomas , Yun Taedong , Furlotte Nicholas A. , Carroll Andrew , Alipanahi Babak , McLean Cory Y. , Hormozdiari Farhad 
Published: January 2022

AbstractGenome-wide association studies (GWASs) examine the association between genotype and phenotype while adjusting for a set of covariates. Although the covariates may have non-linear or interactive effects, due to the challenge of specifying the model, GWAS often neglect such terms. Here we introduce DeepNull, a method that identifies and adjusts for non-linear and interactive covariate effects using a deep neural network. In analyses of simulated and real data, we demonstrate that DeepNull maintains tight control of the type I error while increasing statistical power by up to 20% in the presence of non-linear and interactive effects. Moreover, in the absence of such effects, DeepNull incurs no loss of power. When applied to 10 phenotypes from the UK Biobank (n = 370K), DeepNull discovered more hits (+6%) and loci (+7%), on average, than conventional association analyses, many of which are biologically plausible or have previously been reported. Finally, DeepNull improves upon linear modeling for phenotypic prediction (+23% on average).
Cancer cell-expressed BTNL2 facilitates tumour immune escape via engagement with IL-17A-producing γδ T cells
Authors: Du Yanyun , Peng Qianwen , Cheng Du , Pan Ting , Sun Wanwei , Wang Heping , Ma Xiaojian , He Ruirui , Zhang Huazhi , Cui Zhihui , Feng Xiong , Liu Zhiqiang , Zhao Tianxin , Hu Wenjun , Shen Lei , Jiang Wenyang , Gao Na , Martin Bradley N. , Zhang Cun-Jin , Zhang Zhanguo , Wang Chenhui 
Published: January 2022

AbstractTherapeutic blockade of the immune checkpoint proteins programmed cell death protein 1 (PD-1) and cytotoxic T lymphocyte antigen 4 (CTLA4) has transformed cancer treatment. However, the overall response rate to these treatments is low, suggesting that immune checkpoint activation is not the only mechanism leading to dysfunctional anti-tumour immunity. Here we show that butyrophilin-like protein 2 (BTNL2) is a potent suppressor of the anti-tumour immune response. Antibody-mediated blockade of BTNL2 attenuates tumour progression in multiple in vivo murine tumour models, resulting in prolonged survival of tumour-bearing mice. Mechanistically, BTNL2 interacts with local γδ T cell populations to promote IL-17A production in the tumour microenvironment. Inhibition of BTNL2 reduces the number of tumour-infiltrating IL-17A-producing γδ T cells and myeloid-derived suppressor cells, while facilitating cytotoxic CD8+ T cell accumulation. Furthermore, we find high BTNL2 expression in several human tumour samples from highly prevalent cancer types, which negatively correlates with overall patient survival. Thus, our results suggest that BTNL2 is a negative regulator of anti-tumour immunity and a potential target for cancer immunotherapy.
Mapping inhibitory sites on the RNA polymerase of the 1918 pandemic influenza virus using nanobodies
Authors: Keown Jeremy R. , Zhu Zihan , Carrique Loïc , Fan Haitian , Walker Alexander P. , Serna Martin Itziar , Pardon Els , Steyaert Jan , Fodor Ervin , Grimes Jonathan M. 
Published: January 2022

AbstractInfluenza A viruses cause seasonal epidemics and global pandemics, representing a considerable burden to healthcare systems. Central to the replication cycle of influenza viruses is the viral RNA-dependent RNA polymerase which transcribes and replicates the viral RNA genome. The polymerase undergoes conformational rearrangements and interacts with viral and host proteins to perform these functions. Here we determine the structure of the 1918 influenza virus polymerase in transcriptase and replicase conformations using cryo-electron microscopy (cryo-EM). We then structurally and functionally characterise the binding of single-domain nanobodies to the polymerase of the 1918 pandemic influenza virus. Combining these functional and structural data we identify five sites on the polymerase which are sensitive to inhibition by nanobodies. We propose that the binding of nanobodies at these sites either prevents the polymerase from assuming particular functional conformations or interactions with viral or host factors. The polymerase is highly conserved across the influenza A subtypes, suggesting these sites as effective targets for potential influenza antiviral development.
Food nanoparticles from rice vinegar: isolation, characterization, and antioxidant activities
Authors: Yu Zhaoshuo , Tan Ying , Luo Sihao , Zhou Jingru , Xu Tianhao , Zou Jianqiao , Ke Lijing , Yu Ji , Zhang Suyun , Zhou Jianwu , Rao Pingfan , Li Jiaxing 
Published: January 2022

AbstractAbundant nanostructures have been constantly found in various foods, like vinegar, tea, coffee, and milk. However, these structures largely remain unexplored and even been eliminated for stability reasons in food industry. Here we report the isolation, characterization, and antioxidant activities of food nanoparticles (NPs) carrying polyphenols from Chinese rice vinegar. Using a gel-chromatography-based isolation protocol, the vinegar was separated into three major fractions. They were identified as spherical NPs (P1), lollipop-like NPs (P2) and spherical microparticles (P3) with average hydrodynamic diameter of 210, 245,1643 nm, separately. The former two fractions accounted for the major parts of dry matter in the vinegar. The P1-NPs fraction was composed of proteins, carbohydrates, and a high number of polyphenols (15 wt%), demonstrated potent antioxidant activity as determined by ABTS and ORAC assays. Moreover, they effectively quenched peroxyl free radicals in peritoneal macrophages and promoted cellular growth. The P2 fraction contained majority of organic acids, esters and mineral elements of the vinegar. It demonstrated the NPs are bioactive units of the rice vinegar, inspiring the development of novel functional nanomaterials with nutraceutical and pharmaceutical applications.
A computational method for predicting nucleocapsid protein in retroviruses
Authors: Guo Manyun , Ma Yucheng , Liu Wanyuan , Yuan Zuyi 
Published: January 2022

AbstractNucleocapsid protein (NC) in the group-specific antigen (gag) of retrovirus is essential in the interactions of most retroviral gag proteins with RNAs. Computational method to predict NCs would benefit subsequent structure analysis and functional study on them. However, no computational method to predict the exact locations of NCs in retroviruses has been proposed yet. The wide range of length variation of NCs also increases the difficulties. In this paper, a computational method to identify NCs in retroviruses is proposed. All available retrovirus sequences with NC annotations were collected from NCBI. Models based on random forest (RF) and weighted support vector machine (WSVM) were built to predict initiation and termination sites of NCs. Factor analysis scales of generalized amino acid information along with position weight matrix were utilized to generate the feature space. Homology based gene prediction methods were also compared and integrated to bring out better predicting performance. Candidate initiation and termination sites predicted were then combined and screened according to their intervals, decision values and alignment scores. All available gag sequences without NC annotations were scanned with the model to detect putative NCs. Geometric means of sensitivity and specificity generated from prediction of initiation and termination sites under fivefold cross-validation are 0.9900 and 0.9548 respectively. 90.91% of all the collected retrovirus sequences with NC annotations could be predicted totally correct by the model combining WSVM, RF and simple alignment. The composite model performs better than the simplex ones. 235 putative NCs in unannotated gags were detected by the model. Our prediction method performs well on NC recognition and could also be expanded to solve other gene prediction problems, especially those whose training samples have large length variations.
Evaluation of the characterization of acoustic emission of brittle rocks from the experiment to numerical simulation
Authors: Bu Fengchang , Xue Lei , Zhai Mengyang , Huang Xiaolin , Dong Jinyu , Liang Ning , Xu Chao 
Published: January 2022

AbstractAcoustic emission (AE) characterization is an effective technique to indirectly capture the failure process of quasi brittle rock. In previous studies, both experiments and numerical simulations were adopted to investigate the AE characteristics of rocks. However, as the most popular numerical model, the moment tensor model (MTM) cannot be constrained by the experimental result because there is a gap between MTM and experiments in principle, signal processing and energy analysis. In this paper, we developed a particle-velocity-based model (PVBM) that enabled direct monitoring and analysis of the particle velocity in the numerical model and had good robustness. The PVBM imitated the actual experiment and could fill in gaps between the experiment and MTM. AE experiments of marine shale under uniaxial compression were carried out, and the results were simulated by MTM. In general, the variation trend of the experimental result could be presented by MTM. Nevertheless, the magnitudes of AE parameters by MTM presented notable differences of more than several orders of magnitude compared with those by the experiment. We sequentially used PVBM as a proxy to analyse these discrepancies and systematically evaluate the AE characterization of rocks from the experiment to numerical simulation, considering the influence of wave reflection, energy geometrical diffusion, viscous attenuation, particle size and progressive deterioration of rock material. The combination of MTM and PVBM could reasonably and accurately acquire AE characteristics of the actual AE experiment of rocks by making full use of their respective advantages.
Changes in soybean cultivars released over the past 50 years in southern Brazil
Authors: Umburanas Renan Caldas , Kawakami Jackson , Ainsworth Elizabeth Anna , Favarin José Laércio , Anderle Leonardo Zabot , Dourado-Neto Durval , Reichardt Klaus 
Published: January 2022

AbstractOn-farm soybean yield has increased considerably in the last 50 years in southern Brazil, but there is still little information about how selection and breeding for yield increase has changed the agronomic attributes of cultivars. The objectives of this study were to evaluate the changes in soybean yield, seed oil and protein concentration, and changes in plant attributes that might be associated with yield improvement of 26 soybean cultivars released over the past 50 years in southern Brazil, sown simultaneously in a common field environment for two growing seasons. The average rate of yield gain was 45.9 kg ha−1 yr−1 (2.1% ha−1 yr−1), mainly due increased seed number per area and harvest index. Over year of cultivar release, cultivars became less susceptible to lodging, as well as plant mortality reduced. Meanwhile, the seed oil concentration increased, and seed protein concentration decreased, which could have negative consequences for soybeans use and requires further attention for breeding of future cultivars. Breeders have successfully contributed to the annual rate of soybean yield increase in southern Brazil. By our results, as well as the official on-farm production data, there is no evidence of soybean yield reaching a plateau in the near future in southern Brazil.
Impact of age at onset on symptom profiles, treatment characteristics and health-related quality of life in Parkinson’s disease
Authors: Raket Lars Lau , Oudin Åström Daniel , Norlin Jenny M. , Kellerborg Klas , Martinez-Martin Pablo , Odin Per 
Published: January 2022

AbstractParkinson’s disease (PD) is typically considered an age-related disease, but the age at disease onset can vary by decades between patients. Aging and aging-associated diseases can affect the movement system independently of PD, and advanced age has previously been proposed to be associated with a more severe PD phenotype with accelerated progression. In this work, we investigated how interactions between PD progression and aging affect a wide range of outcomes related to PD motor and nonmotor symptoms as well as Health Related Quality of Life (HRQoL) and treatment characteristics. This population-based cohort study is based on 1436 PD patients from southern Sweden followed longitudinally for up to approximately 7.5 years from enrollment (3470 visits covering 2285 patient years, average follow-up time 1.7 years). Higher age at onset was generally associated with faster progression of motor symptoms, with a notable exception of dyskinesia and other levodopa-associated motor fluctuations that had less severe trajectories for patients with higher age at onset. Mixed results were observed for emergence of non-motor symptoms, while higher age at onset was generally associated with worse HRQoL trajectories. Accounting for these identified age-associated differences in disease progression could positively impact patient management and drug development efforts.
Potential distribution of fall armyworm in Africa and beyond, considering climate change and irrigation patterns
Authors: Paudel Timilsena Bipana , Niassy Saliou , Kimathi Emily , Abdel-Rahman Elfatih M. , Seidl-Adams Irmgard , Wamalwa Mark , Tonnang Henri E. Z. , Ekesi Sunday , Hughes David P. , Rajotte Edwin G. , Subramanian Sevgan 
Published: January 2022

AbstractThe fall armyworm, Spodoptera frugiperda (FAW), first invaded Africa in 2016 and has since become established in many areas across the continent where it poses a serious threat to food and nutrition security. We re-parameterized the existing CLIMEX model to assess the FAW global invasion threat, emphasizing the risk of transient and permanent population establishment in Africa under current and projected future climates, considering irrigation patterns. FAW can establish itself in almost all countries in eastern and central Africa and a large part of western Africa under the current climate. Climatic barriers, such as heat and dry stresses, may limit the spread of FAW to North and South Africa. Future projections suggest that FAW invasive range will retract from both northern and southern regions towards the equator. However, a large area in eastern and central Africa is projected to have an optimal climate for FAW persistence. These areas will serve as FAW ‘hotspots’ from where it may migrate to the north and south during favorable seasons and then pose an economic threat. Our projections can be used to identify countries at risk for permanent and transient FAW-population establishment and inform timely integrated pest management interventions under present and future climate in Africa.
Learning self-driven collective dynamics with graph networks
Authors: Wang Rui , Fang Feiteng , Cui Jiamei , Zheng Wen 
Published: January 2022

AbstractDespite decades of theoretical research, the nature of the self-driven collective motion remains indigestible and controversial, while the phase transition process of its dynamic is a major research issue. Recent methods propose to infer the phase transition process from various artificially extracted features using machine learning. In this thesis, we propose a new order parameter by using machine learning to quantify the synchronization degree of the self-driven collective system from the perspective of the number of clusters. Furthermore, we construct a powerful model based on the graph network to determine the long-term evolution of the self-driven collective system from the initial position of the particles, without any manual features. Results show that this method has strong predictive power, and is suitable for various noises. Our method can provide reference for the research of other physical systems with local interactions.
Genome-wide identification and expression profiling analysis of Wnt family genes affecting adipocyte differentiation in cattle
Authors: Pan Cuili , Wang Shuzhe , Yang Chaoyun , Hu Chunli , Sheng Hui , Xue Xiaoshu , Hu Honghong , Lei Zhaoxiong , Yang Mengli , Ma Yun 
Published: January 2022

AbstractThe Wnt family features conserved glycoproteins that play roles in tissue regeneration, animal development and cell proliferation and differentiation. For its functional diversity and importance, this family has been studied in several species, but not in the Bovinae. Herein we identified 19 Wnt genes in cattle, and seven other species of Bovinae, and described their corresponding protein properties. Phylogenetic analysis clustered the 149 Wnt proteins in Bovinae, and 38 Wnt proteins from the human and mouse into 12 major clades. Wnt genes from the same subfamilies shared similar protein motif compositions and exon–intron patterns. Chromosomal distribution and collinearity analysis revealed that they were conservative in cattle and five species of Bovinae. RNA-seq data analysis indicated that Wnt genes exhibited tissue-specific expression in cattle. qPCR analysis revealed a unique expression pattern of each gene during bovine adipocytes differentiation. Finally, the comprehensive analysis indicated thatWnt2Bmay regulate adipose differentiation by activatingFZD5, which is worthy of further study. Our study presents the first genome-wide study of the Wnt gene family in Bovinae, and lays the foundation for further functional characterization of this family in bovine adipocytes differentiation.