bluuebunny/crossref_metadata_2025_split huggingface dataset:
Three Flavors of Radiative Feedbacks and Their Implications for Estimating Equilibrium Climate Sensitivity
Authors: Rugenstein Maria A. A. , Armour Kyle C. 
Published: July 2021

AbstractThe realization that atmospheric radiative feedbacks depend on the underlying patterns of surface warming and global temperature, and thus, change over time has lead to a proliferation of feedback definitions and methods to estimate equilibrium climate sensitivity (ECS). We contrast three flavors of radiative feedbacks – equilibrium, effective, and differential feedback – and discuss their physical interpretations and applications. We show that their values at any given time can differ more than 1 and their implied equilibrium or effective climate sensitivity can differ several degrees. With ten (quasi) equilibrated climate models, we show that 400 years might be enough to estimate the true ECS within a 5% error using a simple regression method utilizing the differential feedback parameter. We argue that a community‐wide agreement on the interpretation of the different feedback definitions would advance the quest to narrow the estimate of climate sensitivity.
Impact of Mesoscale Eddies on Deep Chlorophyll Maxima
Authors: Cornec Marin , Laxenaire Rémi , Speich Sabrina , Claustre Hervé 
Published: July 2021

AbstractDeep Chlorophyll Maxima (DCM) are ubiquitous features in stratified oceanic systems. Their establishment and maintenance result from hydrographical stability favoring specific environmental conditions with respect to light and nutrient availability required for phytoplankton growth. This stability can potentially be challenged by mesoscale eddies impacting the water column's vertical structure and thus the environmental parameters that condition the subsistence of DCMs. Here, data from the global BGC‐Argo float network are collocated with mesoscale eddies to explore their impact on DCMs. We show that cyclonic eddies, by providing optimal light and nutrient conditions, increase the occurrence of DCMs characterized by Deep Biomass Maxima for phytoplankton. In contrast, DCMs in anticyclonic eddies seem to be driven by photoacclimation as they coincide with Deep Acclimation Maxima without biomass accumulation. These findings suggest that the two types of eddies potentially have different impacts on the role of DCMs in global primary production.
Quasi-phase-matching-division multiplexing holography in a three-dimensional nonlinear photonic crystal
Authors: Chen Pengcheng , Wang Chaowei , Wei Dunzhao , Hu Yanlei , Xu Xiaoyi , Li Jiawen , Wu Dong , Ma Jianan , Ji Shengyun , Zhang Leran , Xu Liqun , Wang Tianxin , Xu Chuan , Chu Jiaru , Zhu Shining , Xiao Min , Zhang Yong 
Published: July 2021

AbstractNonlinear holography has recently emerged as a novel tool to reconstruct the encoded information at a new wavelength, which has important applications in optical display and optical encryption. However, this scheme still struggles with low conversion efficiency and ineffective multiplexing. In this work, we demonstrate a quasi-phase-matching (QPM) -division multiplexing holography in a three-dimensional (3D) nonlinear photonic crystal (NPC). 3D NPC works as a nonlinear hologram, in which multiple images are distributed into different Ewald spheres in reciprocal space. The reciprocal vectors locating in a given Ewald sphere are capable of fulfilling the complete QPM conditions for the high-efficiency reconstruction of the target image at the second-harmonic (SH) wave. One can easily switch the reconstructed SH images by changing the QPM condition. The multiplexing capacity is scalable with the period number of 3D NPC. Our work provides a promising strategy to achieve highly efficient nonlinear multiplexing holography for high-security and high-density storage of optical information.
CD147 receptor is essential for TFF3-mediated signaling regulating colorectal cancer progression
Authors: Cui Hong-Yong , Wang Shi-Jie , Song Fei , Cheng Xu , Nan Gang , Zhao Yu , Qian Mei-Rui , Chen Xi , Li Jia-Yue , Liu Fen-Ling , Zhu Yu-Meng , Tian Ruo-Fei , Wang Bin , Wu Bin , Zhang Yang , Sun Xiu-Xuan , Guo Ting , Yang Xiang-Min , Zhang Hai , Li Ling , Xu Jing , Bian Hui-Jie , Jiang Jian-Li , Chen Zhi-Nan 
Published: July 2021

AbstractMajor gaps in understanding the molecular mechanisms of colorectal cancer (CRC) progression and intestinal mucosal repair have hampered therapeutic development for gastrointestinal disorders. Trefoil factor 3 (TFF3) has been reported to be involved in CRC progression and intestinal mucosal repair; however, how TFF3 drives tumors to become more aggressive or metastatic and how TFF3 promotes intestinal mucosal repair are still poorly understood. Here, we found that the upregulated TFF3 in CRC predicted a worse overall survival rate. TFF3 deficiency impaired mucosal restitution and adenocarcinogenesis. CD147, a membrane protein, was identified as a binding partner for TFF3. Via binding to CD147, TFF3 enhanced CD147-CD44s interaction, resulting in signal transducer and activator of transcription 3 (STAT3) activation and prostaglandin G/H synthase 2 (PTGS2) expression, which were indispensable for TFF3-induced migration, proliferation, and invasion. PTGS2-derived PGE2 bound to prostaglandin E2 receptor EP4 subtype (PTGER4) and contributed to TFF3-stimulated CRC progression. Solution NMR studies of the TFF3-CD147 interaction revealed the key residues critical for TFF3 binding and the induction of PTGS2 expression. The ability of TFF3 to enhance mucosal restitution was weakened by a PTGS2 inhibitor. Blockade of TFF3-CD147 signaling using competitive inhibitory antibodies or a PTGS2 inhibitor reduced CRC lung metastasis in mice. Our findings bring strong evidence that CD147 is a novel receptor for TFF3 and PTGS2 signaling is critical for TFF3-induced mucosal restitution and CRC progression, which widens and deepens the understanding of the molecular function of trefoil factors.
Safety and immunogenicity of a recombinant COVID-19 vaccine (Sf9 cells) in healthy population aged 18 years or older: two single-center, randomised, double-blind, placebo-controlled, phase 1 and phase 2 trials
Authors: Meng Fan-Yue , Gao Fan , Jia Si-Yue , Wu Xiang-Hong , Li Jing-Xin , Guo Xi-Ling , Zhang Jia-Lu , Cui Bo-Pei , Wu Zhi-Ming , Wei Ming-Wei , Ma Zhi-Long , Peng Hai-Lin , Pan Hong-Xing , Fan Lin , Zhang Jing , Wan Jiu-Qin , Zhu Zhong-Kui , Wang Xue-Wen , Zhu Feng-Cai 
Published: July 2021

AbstractCOVID-19 vaccines from multiple manufacturers are needed to cope with the problem of insufficient supply. We did two single-center, randomised, double-blind, placebo-controlled phase 1 and phase 2 trials to assess the safety, tolerability and immunogenicity of a recombinant COVID-19 vaccine (Sf9 cells) in healthy population aged 18 years or older in China. Eligible participants were enrolled, the ratio of candidate vaccine and placebo within each dose group was 3:1 (phase 1) or 5:1 (phase 2). From August 28, 2020, 168 participants were sequentially enrolled and randomly assigned to receive the low dose vaccine, high dose vaccine or placebo with the schedule of 0, 28 days or 0, 14, 28 days in phase 1 trial. From November 18, 2020, 960 participants were randomly assigned to receive the low dose vaccine, high dose vaccine or placebo with the schedule of 0, 21 days or 0, 14, 28 days in phase 2 trial. The most common solicited injection site adverse reaction within 7 days in both trials was pain. The most common solicited systematic adverse reactions within 7 days were fatigue, cough, sore throat, fever and headache. ELISA antibodies and neutralising antibodies increased at 14 days, and peaked at 28 days (phase 1) or 30 days (phase 2) after the last dose vaccination. The GMTs of neutralising antibody against live SARS-CoV-2 at 28 days or 30 days after the last dose vaccination were highest in the adult high dose group (0, 14, 28 days), with 102.9 (95% CI 61.9–171.2) and 102.6 (95% CI 75.2–140.1) in phase 1 and phase 2 trials, respectively. Specific T-cell response peaked at 14 days after the last dose vaccination in phase 1 trial. This vaccine is safe, and induced significant immune responses after three doses of vaccination.
The gut microbiome: what the oncologist ought to know
Authors: Lee K. A. , Luong M. K. , Shaw H. , Nathan P. , Bataille V. , Spector T. D. 
Published: July 2021

AbstractThe gut microbiome (GM) has been implicated in a vast number of human pathologies and has become a focus of oncology research over the past 5 years. The normal gut microbiota imparts specific function in host nutrient metabolism, xenobiotic and drug metabolism, maintenance of structural integrity of the gut mucosal barrier, immunomodulation and protection against pathogens. Strong evidence is emerging to support the effects of the GM on the development of some malignancies but also on responses to cancer therapies, most notably, immune checkpoint inhibition. Tools for manipulating the GM including dietary modification, probiotics and faecal microbiota transfer (FMT) are in development. Current understandings of the many complex interrelationships between the GM, cancer, the immune system, nutrition and medication are ultimately based on a combination of short‐term clinical trials and observational studies, paired with an ever-evolving understanding of cancer biology. The next generation of personalised cancer therapies focusses on molecular and phenotypic heterogeneity, tumour evolution and immune status; it is distinctly possible that the GM will become an increasingly central focus amongst them. The aim of this review is to provide clinicians with an overview of microbiome science and our current understanding of the role the GM plays in cancer.
Drice restrains Diap2-mediated inflammatory signalling and intestinal inflammation
Authors: Kietz Christa , Mohan Aravind K. , Pollari Vilma , Tuominen Ida-Emma , Ribeiro Paulo S. , Meier Pascal , Meinander Annika 
Published: July 2021

AbstractThe Drosophila IAP protein, Diap2, is a key mediator of NF-κB signalling and innate immune responses. Diap2 is required for both local immune activation, taking place in the epithelial cells of the gut and trachea, and for mounting systemic immune responses in the cells of the fat body. We have found that transgenic expression of Diap2 leads to a spontaneous induction of NF-κB target genes, inducing chronic inflammation in the Drosophila midgut, but not in the fat body. Drice is a Drosophila effector caspase known to interact and form a stable complex with Diap2. We have found that this complex formation induces its subsequent degradation, thereby regulating the amount of Diap2 driving NF-κB signalling in the intestine. Concordantly, loss of Drice activity leads to accumulation of Diap2 and to chronic intestinal inflammation. Interestingly, Drice does not interfere with pathogen-induced signalling, suggesting that it protects from immune responses induced by resident microbes. Accordingly, no inflammation was detected in transgenic Diap2 flies and Drice-mutant flies reared in axenic conditions. Hence, we show that Drice, by restraining Diap2, halts unwanted inflammatory signalling in the intestine.
Ocular benzalkonium chloride exposure: problems and solutions
Authors: Goldstein Michael H. , Silva Fabiana Q. , Blender Nysha , Tran Trung , Vantipalli Srilatha 
Published: July 2021

AbstractPreservatives in multidose formulations of topical ophthalmic medications are crucial for maintaining sterility but can be toxic to the ocular surface. Benzalkonium chloride (BAK)—used in approximately 70% of ophthalmic formulations—is well known to cause cytotoxic damage to conjunctival and corneal epithelial cells, resulting in signs and symptoms of ocular surface disease (OSD) including ocular surface staining, increased tear break-up time, and higher OSD symptom scores. These adverse effects are more problematic with chronic exposure, as in lifetime therapy for glaucoma, but can also manifest after exposure as brief as seven days. Multiple strategies are available to minimize or eliminate BAK exposure, among them alternative preservatives, preservative-free formulations including sustained release drug delivery platforms, and non-pharmacological therapies for common eye diseases and conditions. In this paper, we review the cytotoxic and clinical effects of BAK on the ocular surface and discuss existing and emerging options for ocular disease management that can minimize or eliminate BAK exposure.
Lanthanum(III) triggers AtrbohD- and jasmonic acid-dependent systemic endocytosis in plants
Authors: Cheng Mengzhu , Wang Lihong , Zhou Qing , Chao Daiyin , Nagawa Shingo , He Ding , Zhang Jiazhi , Li Hui , Tan Li , Gu Zhenhong , Huang Xiaohua , Yang Zhenbiao 
Published: July 2021

AbstractTrivalent rare earth elements (REEs) are widely used in agriculture. Aerially applied REEs enter leaf epidermal cells by endocytosis and act systemically to improve the growth of the whole plant. The mechanistic basis of their systemic activity is unclear. Here, we show that treatment of Arabidopsis leaves with trivalent lanthanum [La(III)], a representative of REEs, triggers systemic endocytosis from leaves to roots. La(III)-induced systemic endocytosis requires AtrbohD-mediated reactive oxygen species production and jasmonic acid. Systemic endocytosis impacts the accumulation of mineral elements and the development of roots consistent with the growth promoting effects induced by aerially applied REEs. These findings provide insights into the mechanistic basis of REE activity in plants.
Redefining the specificity of phosphoinositide-binding by human PH domain-containing proteins
Authors: Singh Nilmani , Reyes-Ordoñez Adriana , Compagnone Michael A. , Moreno Jesus F. , Leslie Benjamin J. , Ha Taekjip , Chen Jie 
Published: July 2021

AbstractPleckstrin homology (PH) domains are presumed to bind phosphoinositides (PIPs), but specific interaction with and regulation by PIPs for most PH domain-containing proteins are unclear. Here we employ a single-molecule pulldown assay to study interactions of lipid vesicles with full-length proteins in mammalian whole cell lysates. Of 67 human PH domain-containing proteins initially examined, 36 (54%) are found to have affinity for PIPs with various specificity, the majority of which have not been reported before. Further investigation of ARHGEF3 reveals distinct structural requirements for its binding to PI(4,5)P2 and PI(3,5)P2, and functional relevance of its PI(4,5)P2 binding. We generate a recursive-learning algorithm based on the assay results to analyze the sequences of 242 human PH domains, predicting that 49% of them bind PIPs. Twenty predicted binders and 11 predicted non-binders are assayed, yielding results highly consistent with the prediction. Taken together, our findings reveal unexpected lipid-binding specificity of PH domain-containing proteins.
Polarization-transparent silicon photonic add-drop multiplexer with wideband hitless tuneability
Authors: Morichetti Francesco , Milanizadeh Maziyar , Petrini Matteo , Zanetto Francesco , Ferrari Giorgio , de Aguiar Douglas Oliveira , Guglielmi Emanuele , Sampietro Marco , Melloni Andrea 
Published: July 2021

AbstractFlexible optical networks require reconfigurable devices with operation on a wavelength range of several tens of nanometers, hitless tuneability (i.e. transparency to other channels during reconfiguration), and polarization independence. All these requirements have not been achieved yet in a single photonic integrated device and this is the reason why the potential of integrated photonics is still largely unexploited in the nodes of optical communication networks. Here we report on a fully-reconfigurable add-drop silicon photonic filter, which can be tuned well beyond the extended C-band (almost 100 nm) in a complete hitless (>35 dB channel isolation) and polarization transparent (1.2 dB polarization dependent loss) way. This achievement is the result of blended strategies applied to the design, calibration, tuning and control of the device. Transmission quality assessment on dual polarization 100 Gbit/s (QPSK) and 200 Gbit/s (16-QAM) signals demonstrates the suitability for dynamic bandwidth allocation in core networks, backhaul networks, intra- and inter-datacenter interconnects.
Effective variant filtering and expected candidate variant yield in studies of rare human disease
Authors: Pedersen Brent S. , Brown Joe M. , Dashnow Harriet , Wallace Amelia D. , Velinder Matt , Tristani-Firouzi Martin , Schiffman Joshua D. , Tvrdik Tatiana , Mao Rong , Best D. Hunter , Bayrak-Toydemir Pinar , Quinlan Aaron R. 
Published: July 2021

AbstractIn studies of families with rare disease, it is common to screen for de novo mutations, as well as recessive or dominant variants that explain the phenotype. However, the filtering strategies and software used to prioritize high-confidence variants vary from study to study. In an effort to establish recommendations for rare disease research, we explore effective guidelines for variant (SNP and INDEL) filtering and report the expected number of candidates for de novo dominant, recessive, and autosomal dominant modes of inheritance. We derived these guidelines using two large family-based cohorts that underwent whole-genome sequencing, as well as two family cohorts with whole-exome sequencing. The filters are applied to common attributes, including genotype-quality, sequencing depth, allele balance, and population allele frequency. The resulting guidelines yield ~10 candidate SNP and INDEL variants per exome, and 18 per genome for recessive and de novo dominant modes of inheritance, with substantially more candidates for autosomal dominant inheritance. For family-based, whole-genome sequencing studies, this number includes an average of three de novo, ten compound heterozygous, one autosomal recessive, four X-linked variants, and roughly 100 candidate variants following autosomal dominant inheritance. The slivar software we developed to establish and rapidly apply these filters to VCF files is available at https://github.com/brentp/slivar under an MIT license, and includes documentation and recommendations for best practices for rare disease analysis.
Longitudinal evolution of non-motor symptoms in early Parkinson’s disease: a 3-year prospective cohort study
Authors: Ou Ruwei , Hou Yanbing , Wei Qianqian , Lin Junyu , Liu Kuncheng , Zhang Lingyu , Jiang Zheng , Cao Bei , Zhao Bi , Song Wei , Shang Huifang 
Published: July 2021

AbstractThe progression of global non-motor symptoms (NMS) in Chinese patients with Parkinson’s disease (PD) has not been explored. We aimed to examine the longitudinal evolution of overall NMS in a 3-year prospective Chinese cohort with early-stage PD. We included 224 patients with early PD who underwent annual evaluation of motor and non-motor symptoms. NMS was assessed using the non-motor symptoms scale (NMSS). We observed an increased number of NMS in the majority of the NMSS domains except mood/apathy and sexual dysfunctions. Significant deterioration was observed in the sleep/fatigue, perceptual problems/hallucinations, attention/memory, gastrointestinal, urinary, and miscellaneous domains during the follow-up (P < 0.05). Notably, the number and the score of sexual dysfunctions decreased with the progression of the disease. All NMSS domains showed a small effect size from baseline to 1-, 2-, and 3-year follow-ups (effect size < 0.5). The generalized estimating equations model indicated that the total number of NMS was significantly associated with age and the Unified Parkinson’s Disease Rating Scale (UPDRS) III score (P < 0.05). Multiple logistic regression indicated that a high number of NMS at baseline was associated with a 3-point, a 6-point, and a 9-point increase in the UPDRS III score from baseline to 1-year (odds ratio [OR] 1.074, P = 0.017), 2-year (OR 1.113, P = 0.001), and 3-year (OR 1.117, P < 0.001), respectively. Our study indicated that overall NMS evolution in early PD is mild and multidimensional; a high NMS burden in early PD predicts the faster motor progression of PD. Our study is helpful for understanding the longitudinal evolution of NMS in PD.
Selectively targeting haemagglutinin antigen to chicken CD83 receptor induces faster and stronger immunity against avian influenza
Authors: Shrestha Angita , Sadeyen Jean-Remy , Lukosaityte Deimante , Chang Pengxiang , Smith Adrian , Van Hulten Marielle , Iqbal Munir 
Published: July 2021

AbstractThe immunogenicity and protective efficacy of vaccines can be enhanced by the selective delivery of antigens to the antigen-presenting cells (APCs). In this study, H9N2 avian influenza virus haemagglutinin (HA) antigen, was targeted by fusing it to single-chain fragment variable (scFv) antibodies specific to CD83 receptor expressed on chicken APCs. We observed an increased level of IFNγ, IL6, IL1β, IL4, and CxCLi2 mRNA upon stimulation of chicken splenocytes ex vivo by CD83 scFv targeted H9HA. In addition, CD83 scFv targeted H9HA induced higher serum haemagglutinin inhibition activity and virus neutralising antibodies compared to untargeted H9HA, with induction of antibodies as early as day 6 post primary vaccination. Furthermore, chickens vaccinated with CD83 scFv targeted H9HA showed reduced H9N2 challenge virus shedding compared to untargeted H9HA. These results suggest that targeting antigens to CD83 receptors could improve the efficacy of poultry vaccines.
Structural and functional characterization of the intracellular filament-forming nitrite oxidoreductase multiprotein complex
Authors: Chicano Tadeo Moreno , Dietrich Lea , de Almeida Naomi M. , Akram Mohd. , Hartmann Elisabeth , Leidreiter Franziska , Leopoldus Daniel , Mueller Melanie , Sánchez Ricardo , Nuijten Guylaine H. L. , Reimann Joachim , Seifert Kerstin-Anikó , Schlichting Ilme , van Niftrik Laura , Jetten Mike S. M. , Dietl Andreas , Kartal Boran , Parey Kristian , Barends Thomas R. M. 
Published: July 2021

AbstractNitrate is an abundant nutrient and electron acceptor throughout Earth’s biosphere. Virtually all nitrate in nature is produced by the oxidation of nitrite by the nitrite oxidoreductase (NXR) multiprotein complex. NXR is a crucial enzyme in the global biological nitrogen cycle, and is found in nitrite-oxidizing bacteria (including comammox organisms), which generate the bulk of the nitrate in the environment, and in anaerobic ammonium-oxidizing (anammox) bacteria which produce half of the dinitrogen gas in our atmosphere. However, despite its central role in biology and decades of intense study, no structural information on NXR is available. Here, we present a structural and biochemical analysis of the NXR from the anammox bacterium Kuenenia stuttgartiensis, integrating X-ray crystallography, cryo-electron tomography, helical reconstruction cryo-electron microscopy, interaction and reconstitution studies and enzyme kinetics. We find that NXR catalyses both nitrite oxidation and nitrate reduction, and show that in the cell, NXR is arranged in tubules several hundred nanometres long. We reveal the tubule architecture and show that tubule formation is induced by a previously unidentified, haem-containing subunit, NXR-T. The results also reveal unexpected features in the active site of the enzyme, an unusual cofactor coordination in the protein’s electron transport chain, and elucidate the electron transfer pathways within the complex.