bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomic-scale regulation of anionic and cationic migration in alkali metal batteries
Authors: Xiong Pan , Zhang Fan , Zhang Xiuyun , Liu Yifan , Wu Yunyan , Wang Shijian , Safaei Javad , Sun Bing , Ma Renzhi , Liu Zongwen , Bando Yoshio , Sasaki Takayoshi , Wang Xin , Zhu Junwu , Wang Guoxiu 
Published: July 2021

AbstractThe regulation of anions and cations at the atomic scale is of great significance in membrane-based separation technologies. Ionic transport regulation techniques could also play a crucial role in developing high-performance alkali metal batteries such as alkali metal-sulfur and alkali metal-selenium batteries, which suffer from the non-uniform transport of alkali metal ions (e.g., Li+ or Na+) and detrimental shuttling effect of polysulfide/polyselenide anions. These drawbacks could cause unfavourable growth of alkali metal depositions at the metal electrode and irreversible consumption of cathode active materials, leading to capacity decay and short cycling life. Herein, we propose the use of a polypropylene separator coated with negatively charged Ti0.87O2 nanosheets with Ti atomic vacancies to tackle these issues. In particular, we demonstrate that the electrostatic interactions between the negatively charged Ti0.87O2 nanosheets and polysulfide/polyselenide anions reduce the shuttling effect. Moreover, the Ti0.87O2-coated separator regulates the migration of alkali ions ensuring a homogeneous ion flux and the Ti vacancies, acting as sub-nanometric pores, promote fast alkali-ion diffusion.
The role of membrane destabilisation and protein dynamics in BAM catalysed OMP folding
Authors: White Paul , Haysom Samuel F. , Iadanza Matthew G. , Higgins Anna J. , Machin Jonathan M. , Whitehouse James M. , Horne Jim E. , Schiffrin Bob , Carpenter-Platt Charlotte , Calabrese Antonio N. , Storek Kelly M. , Rutherford Steven T. , Brockwell David J. , Ranson Neil A. , Radford Sheena E. 
Published: July 2021

AbstractThe folding of β-barrel outer membrane proteins (OMPs) in Gram-negative bacteria is catalysed by the β-barrel assembly machinery (BAM). How lateral opening in the β-barrel of the major subunit BamA assists in OMP folding, and the contribution of membrane disruption to BAM catalysis remain unresolved. Here, we use an anti-BamA monoclonal antibody fragment (Fab1) and two disulphide-crosslinked BAM variants (lid-locked (LL), and POTRA-5-locked (P5L)) to dissect these roles. Despite being lethal in vivo, we show that all complexes catalyse folding in vitro, albeit less efficiently than wild-type BAM. CryoEM reveals that while Fab1 and BAM-P5L trap an open-barrel state, BAM-LL contains a mixture of closed and contorted, partially-open structures. Finally, all three complexes globally destabilise the lipid bilayer, while BamA does not, revealing that the BAM lipoproteins are required for this function. Together the results provide insights into the role of BAM structure and lipid dynamics in OMP folding.
Mapping mutations to the SARS-CoV-2 RBD that escape binding by different classes of antibodies
Authors: Greaney Allison J. , Starr Tyler N. , Barnes Christopher O. , Weisblum Yiska , Schmidt Fabian , Caskey Marina , Gaebler Christian , Cho Alice , Agudelo Marianna , Finkin Shlomo , Wang Zijun , Poston Daniel , Muecksch Frauke , Hatziioannou Theodora , Bieniasz Paul D. , Robbiani Davide F. , Nussenzweig Michel C. , Bjorkman Pamela J. , Bloom Jesse D. 
Published: July 2021

AbstractMonoclonal antibodies targeting a variety of epitopes have been isolated from individuals previously infected with SARS-CoV-2, but the relative contributions of these different antibody classes to the polyclonal response remains unclear. Here we use a yeast-display system to map all mutations to the viral spike receptor-binding domain (RBD) that escape binding by representatives of three potently neutralizing classes of anti-RBD antibodies with high-resolution structures. We compare the antibody-escape maps to similar maps for convalescent polyclonal plasmas, including plasmas from individuals from whom some of the antibodies were isolated. While the binding of polyclonal plasma antibodies are affected by mutations across multiple RBD epitopes, the plasma-escape maps most resemble those of a single class of antibodies that target an epitope on the RBD that includes site E484. Therefore, although the human immune system can produce antibodies that target diverse RBD epitopes, in practice the polyclonal response to infection is skewed towards a single class of antibodies targeting an epitope that is already undergoing rapid evolution.
Chaperone-like protein DAY plays critical roles in photomorphogenesis
Authors: Lee Ho-Seok , Choi Ilyeong , Jeon Young , Ahn Hee-Kyung , Cho Huikyong , Kim JiWoo , Kim Jae-Hee , Lee Jung-Min , Lee SungHee , Bünting Julian , Seo Dong Hye , Lee Tak , Lee Du-Hwa , Lee Insuk , Oh Man-Ho , Kim Tae-Wuk , Belkhadir Youssef , Pai Hyun-Sook 
Published: July 2021

AbstractPhotomorphogenesis, light-mediated development, is an essential feature of all terrestrial plants. While chloroplast development and brassinosteroid (BR) signaling are known players in photomorphogenesis, proteins that regulate both pathways have yet to be identified. Here we report that DE-ETIOLATION IN THE DARKANDYELLOWING IN THE LIGHT (DAY), a membrane protein containing DnaJ-like domain, plays a dual-role in photomorphogenesis by stabilizing the BR receptor, BRI1, as well as a key enzyme in chlorophyll biosynthesis, POR. DAY localizes to both the endomembrane and chloroplasts via its first transmembrane domain and chloroplast transit peptide, respectively, and interacts with BRI1 and POR in their respective subcellular compartments. Using genetic analysis, we show that DAY acts independently on BR signaling and chlorophyll biogenesis. Collectively, this work uncovers DAY as a factor that simultaneously regulates BR signaling and chloroplast development, revealing a key regulator of photomorphogenesis that acts across cell compartments.
A genomic surveillance framework and genotyping tool for Klebsiella pneumoniae and its related species complex
Authors: Lam Margaret M. C. , Wick Ryan R. , Watts Stephen C. , Cerdeira Louise T. , Wyres Kelly L. , Holt Kathryn E. 
Published: July 2021

AbstractKlebsiella pneumoniae is a leading cause of antimicrobial-resistant (AMR) healthcare-associated infections, neonatal sepsis and community-acquired liver abscess, and is associated with chronic intestinal diseases. Its diversity and complex population structure pose challenges for analysis and interpretation of K. pneumoniae genome data. Here we introduce Kleborate, a tool for analysing genomes of K. pneumoniae and its associated species complex, which consolidates interrogation of key features of proven clinical importance. Kleborate provides a framework to support genomic surveillance and epidemiology in research, clinical and public health settings. To demonstrate its utility we apply Kleborate to analyse publicly available Klebsiella genomes, including clinical isolates from a pan-European study of carbapenemase-producing Klebsiella, highlighting global trends in AMR and virulence as examples of what could be achieved by applying this genomic framework within more systematic genomic surveillance efforts. We also demonstrate the application of Kleborate to detect and type K. pneumoniae from gut metagenomes.
Fractional response analysis reveals logarithmic cytokine responses in cellular populations
Authors: Nienałtowski Karol , Rigby Rachel E. , Walczak Jarosław , Zakrzewska Karolina E. , Głów Edyta , Rehwinkel Jan , Komorowski Michał 
Published: July 2021

AbstractAlthough we can now measure single-cell signaling responses with multivariate, high-throughput techniques our ability to interpret such measurements is still limited. Even interpretation of dose–response based on single-cell data is not straightforward: signaling responses can differ significantly between cells, encompass multiple signaling effectors, and have dynamic character. Here, we use probabilistic modeling and information-theory to introduce fractional response analysis (FRA), which quantifies changes in fractions of cells with given response levels. FRA can be universally performed for heterogeneous, multivariate, and dynamic measurements and, as we demonstrate, quantifies otherwise hidden patterns in single-cell data. In particular, we show that fractional responses to type I interferon in human peripheral blood mononuclear cells are very similar across different cell types, despite significant differences in mean or median responses and degrees of cell-to-cell heterogeneity. Further, we demonstrate that fractional responses to cytokines scale linearly with the log of the cytokine dose, which uncovers that heterogeneous cellular populations are sensitive to fold-changes in the dose, as opposed to additive changes.
Sensitive detection of tumor mutations from blood and its application to immunotherapy prognosis
Authors: Li Shuo , Noor Zorawar S. , Zeng Weihua , Stackpole Mary L. , Ni Xiaohui , Zhou Yonggang , Yuan Zuyang , Wong Wing Hung , Agopian Vatche G. , Dubinett Steven M. , Alber Frank , Li Wenyuan , Garon Edward B. , Zhou Xianghong Jasmine 
Published: July 2021

AbstractCell-free DNA (cfDNA) is attractive for many applications, including detecting cancer, identifying the tissue of origin, and monitoring. A fundamental task underlying these applications is SNV calling from cfDNA, which is hindered by the very low tumor content. Thus sensitive and accurate detection of low-frequency mutations (<5%) remains challenging for existing SNV callers. Here we present cfSNV, a method incorporating multi-layer error suppression and hierarchical mutation calling, to address this challenge. Furthermore, by leveraging cfDNA’s comprehensive coverage of tumor clonal landscape, cfSNV can profile mutations in subclones. In both simulated and real patient data, cfSNV outperforms existing tools in sensitivity while maintaining high precision. cfSNV enhances the clinical utilities of cfDNA by improving mutation detection performance in medium-depth sequencing data, therefore making Whole-Exome Sequencing a viable option. As an example, we demonstrate that the tumor mutation profile from cfDNA WES data can provide an effective biomarker to predict immunotherapy outcomes.
Improved genetic prediction of complex traits from individual-level data or summary statistics
Authors: Zhang Qianqian , Privé Florian , Vilhjálmsson Bjarni , Speed Doug 
Published: July 2021

AbstractMost existing tools for constructing genetic prediction models begin with the assumption that all genetic variants contribute equally towards the phenotype. However, this represents a suboptimal model for how heritability is distributed across the genome. Therefore, we develop prediction tools that allow the user to specify the heritability model. We compare individual-level data prediction tools using 14 UK Biobank phenotypes; our new tool LDAK-Bolt-Predict outperforms the existing tools Lasso, BLUP, Bolt-LMM and BayesR for all 14 phenotypes. We compare summary statistic prediction tools using 225 UK Biobank phenotypes; our new tool LDAK-BayesR-SS outperforms the existing tools lassosum, sBLUP, LDpred and SBayesR for 223 of the 225 phenotypes. When we improve the heritability model, the proportion of phenotypic variance explained increases by on average 14%, which is equivalent to increasing the sample size by a quarter.
GapClust is a light-weight approach distinguishing rare cells from voluminous single cell expression profiles
Authors: Fa Botao , Wei Ting , Zhou Yuan , Johnston Luke , Yuan Xin , Ma Yanran , Zhang Yue , Yu Zhangsheng 
Published: July 2021

AbstractSingle cell RNA sequencing (scRNA-seq) is a powerful tool in detailing the cellular landscape within complex tissues. Large-scale single cell transcriptomics provide both opportunities and challenges for identifying rare cells playing crucial roles in development and disease. Here, we develop GapClust, a light-weight algorithm to detect rare cell types from ultra-large scRNA-seq datasets with state-of-the-art speed and memory efficiency. Benchmarking on diverse experimental datasets demonstrates the superior performance of GapClust compared to other recently proposed methods. When applying our algorithm to an intestine and 68 k PBMC datasets, GapClust identifies the tuft cells and a previously unrecognised subtype of monocyte, respectively.
Engineering phase and polarization singularity sheets
Authors: Lim Soon Wei Daniel , Park Joon-Suh , Meretska Maryna L. , Dorrah Ahmed H. , Capasso Federico 
Published: July 2021

AbstractOptical phase singularities are zeros of a scalar light field. The most systematically studied class of singular fields is vortices: beams with helical wavefronts and a linear (1D) singularity along the optical axis. Beyond these common and stable 1D topologies, we show that a broader family of zero-dimensional (point) and two-dimensional (sheet) singularities can be engineered. We realize sheet singularities by maximizing the field phase gradient at the desired positions. These sheets, owning to their precise alignment requirements, would otherwise only be observed in rare scenarios with high symmetry. Furthermore, by applying an analogous procedure to the full vectorial electric field, we can engineer paraxial transverse polarization singularity sheets. As validation, we experimentally realize phase and polarization singularity sheets with heart-shaped cross-sections using metasurfaces. Singularity engineering of the dark enables new degrees of freedom for light-matter interaction and can inspire similar field topologies beyond optics, from electron beams to acoustics.
Translocation of vaginal microbiota is involved in impairment and protection of uterine health
Authors: Wang Jinfeng , Li Zhanzhan , Ma Xiuling , Du Lifeng , Jia Zhen , Cui Xue , Yu Liqun , Yang Jing , Xiao Liwen , Zhang Bing , Fan Huimin , Zhao Fangqing 
Published: July 2021

AbstractThe vaginal and uterine microbiota play important roles in the health of the female reproductive system. However, the interactions among the microbes in these two niches and their effects on uterine health remain unclear. Here we profile the vaginal and uterine microbial samples of 145 women, and combine with deep mining of public data and animal experiments to characterize the microbial translocation in the female reproductive tract and its role in modulating uterine health. Synchronous variation and increasing convergence of the uterine and vaginal microbiome with advancing age are shown. We also find that transplanting certain strains of vaginal bacteria into the vagina of rats induces or reduces endometritis-like symptoms, and verify the damaging or protective effects of certain vaginal bacteria on endometrium. This study clarifies the interdependent relationship of vaginal bacterial translocation with uterine microecology and endometrial health, which will undoubtedly increase our understanding of female reproductive health.
Energy-saving hydrogen production by chlorine-free hybrid seawater splitting coupling hydrazine degradation
Authors: Sun Fu , Qin Jingshan , Wang Zhiyu , Yu Mengzhou , Wu Xianhong , Sun Xiaoming , Qiu Jieshan 
Published: July 2021

AbstractSeawater electrolysis represents a potential solution to grid-scale production of carbon-neutral hydrogen energy without reliance on freshwater. However, it is challenged by high energy costs and detrimental chlorine chemistry in complex chemical environments. Here we demonstrate chlorine-free hydrogen production by hybrid seawater splitting coupling hydrazine degradation. It yields hydrogen at a rate of 9.2 mol h–1 gcat–1 on NiCo/MXene-based electrodes with a low electricity expense of 2.75 kWh per m3 H2 at 500 mA cm–2 and 48% lower energy equivalent input relative to commercial alkaline water electrolysis. Chlorine electrochemistry is avoided by low cell voltages without anode protection regardless Cl– crossover. This electrolyzer meanwhile enables fast hydrazine degradation to ~3 ppb residual. Self-powered hybrid seawater electrolysis is realized by integrating low-voltage direct hydrazine fuel cells or solar cells. These findings enable further opportunities for efficient conversion of ocean resources to hydrogen fuel while removing harmful pollutants.
Quantum random number cloud platform
Authors: Huang Leilei , Zhou Hongyi , Feng Kai , Xie Chongjin 
Published: July 2021

AbstractRandomness lays the foundation for information security. Quantum random number generation based on various quantum principles has been proposed to provide true randomness in the last two decades. We integrate four different types of quantum random number generators on the Alibaba Cloud servers to enhance cybersecurity. Post-processing modules are integrated into the quantum platform to extract true random numbers. We employ improved authentication protocols where original pseudo-random numbers are replaced with quantum ones. Users from the Alibaba Cloud, such as Ant Financial and Smart Access Gateway, request random numbers from the quantum platform for various cryptographic tasks. For cloud services demanding the highest security, such as Alipay at Ant Financial, we combine the random numbers from four quantum devices by XOR the outputs to enhance practical security. The quantum platform has been continuously run for more than a year.
Optimization of catalytic wet oxidating fulvic acid with zero-valent copper chitosan activated carbon ball as the catalyst
Authors: Song Chaofei , Lv Yue , Qin Xia , Guo Chengrui , Cui Jiaxin , Kaghembega Wendkuuni Steve-Harold 
Published: July 2021

AbstractThe degradation efficiency of fulvic acid (FA) was investigated in the catalytic wet oxidation process (CWPO) by zero-valent copper chitosan activated carbon ball (ZVC/CTS-ACB). Characterization of ZVC/CTS-ACB shows that zero-valent copper was loaded successfully on the chitosan activated carbon. Plackett–Buiman (PB) design and response surface methodology (RSM) were employed to determine the influence factors and the optimum processing parameters. The model was well fitted to the actual data and the correlation coefficients of R2 and R2-adj were 0.9359 and 0.9039, respectively. Under the obtained optimum conditions for FA degradation: temperature = 94 °C and pH 3.8, the average FA removal by three replicate experiments was 93.02%, which has a high consistency to the RSM optimal target response of 93.86%. The comparison of catalytic performance showed that the addition of catalyst ZVC/CTS-ACS could increase the removal rate of FA, color number (CN) and TOC by 93.6%, 83.5% and 81.9% respectively. The high TOC removal rate indicated the good performance of the catalyst to FA mineralization. Additionally, the ICP analysis of copper ion leaching was only 0.08 mg/l after 5 repeated recycles of the catalyst, demonstrating the high stability of ZVC/CTS-ACB that is beneficial for the actual application.
Genomic epidemiology of SARS-CoV-2 in the UAE reveals novel virus mutation, patterns of co-infection and tissue specific host immune response
Authors: Liu Rong , Wu Pei , Ogrodzki Pauline , Mahmoud Sally , Liang Ke , Liu Pengjuan , Francis Stephen S. , Khalak Hanif , Liu Denghui , Li Junhua , Ma Tao , Chen Fang , Liu Weibin , Huang Xinyu , He Wenjun , Yuan Zhaorong , Qiao Nan , Meng Xin , Alqarni Budoor , Quilez Javier , Kusuma Vinay , Lin Long , Jin Xin , Yang Chongguang , Anton Xavier , Koshy Ashish , Yang Huanming , Xu Xun , Wang Jian , Xiao Peng , Al Kaabi Nawal , Fasihuddin Mohammed Saifuddin , Selvaraj Francis Amirtharaj , Weber Stefan , Al Hosani Farida Ismail , Liu Siyang , Zaher Walid Abbas 
Published: July 2021

AbstractTo unravel the source of SARS-CoV-2 introduction and the pattern of its spreading and evolution in the United Arab Emirates, we conducted meta-transcriptome sequencing of 1067 nasopharyngeal swab samples collected between May 9th and Jun 29th, 2020 during the first peak of the local COVID-19 epidemic. We identified global clade distribution and eleven novel genetic variants that were almost absent in the rest of the world and that defined five subclades specific to the UAE viral population. Cross-settlement human-to-human transmission was related to the local business activity. Perhaps surprisingly, at least 5% of the population were co-infected by SARS-CoV-2 of multiple clades within the same host. We also discovered an enrichment of cytosine-to-uracil mutation among the viral population collected from the nasopharynx, that is different from the adenosine-to-inosine change previously reported in the bronchoalveolar lavage fluid samples and a previously unidentified upregulation of APOBEC4 expression in nasopharynx among infected patients, indicating the innate immune host response mediated by ADAR and APOBEC gene families could be tissue-specific. The genomic epidemiological and molecular biological knowledge reported here provides new insights for the SARS-CoV-2 evolution and transmission and points out future direction on host–pathogen interaction investigation.
Label-free two-photon imaging of mitochondrial activity in murine macrophages stimulated with bacterial and viral ligands
Authors: Allen Christian Harry , Ahmed Duale , Raiche-Tanner Olivia , Chauhan Vinita , Mostaço-Guidolin Leila , Cassol Edana , Murugkar Sangeeta 
Published: July 2021

AbstractMitochondria are the metabolic hub of the cell, playing a central role in regulating immune responses. Dysfunction of mitochondrial reprogramming can occur during bacterial and viral infections compromising hosts’ immune signaling. Comparative evaluation of these alterations in response to bacterial and viral ligands can provide insights into a cell’s ability to mount pathogen-specific responses. In this study, we used two-photon excitation fluorescence (TPEF) imaging to quantify reduced nicotinamide adenine dinucleotide phosphate (NAD(P)H) and flavin adenine dinucleotide (FAD) levels in the cell and to calculate the optical redox ratio (ORR), an indicator of mitochondrial dysfunction. Analyses were performed on RAW264.7 cells and murine bone marrow derived macrophages (BMM) stimulated with bacterial (LPS) and viral (Poly(I:C)) ligands. Responses were cell type dependent, with primary cells having significantly higher levels of FAD and higher oxygen consumption rates suggesting BMM may be more dependent on mitochondrial metabolism. Our findings also suggest that FAD-TPEF intensity may be a better predictor of mitochondrial activity and localization since it demonstrates unique mitochondrial clustering patterns in LPS vs. Poly(I:C) stimulated macrophages. Collectively, we demonstrate that TPEF imaging is a powerful label-free approach for quantifying changes in mitochondrial function and organization in macrophages following bacterial and viral stimuli.