bluuebunny/crossref_metadata_2025_split huggingface dataset:
Synthetic five-wave mixing in an integrated microcavity for visible-telecom entanglement generation
Authors: Wang Jia-Qi , Yang Yuan-Hao , Li Ming , Zhou Haiqi , Xu Xin-Biao , Zhang Ji-Zhe , Dong Chun-Hua , Guo Guang-Can , Zou C.-L. 
Published: October 2022

AbstractNonlinear optics processes lie at the heart of photonics and quantum optics for their indispensable role in light sources and information processing. During the past decades, the three- and four-wave mixing (χ(2) and χ(3)) effects have been extensively studied, especially in the micro-/nano-structures by which the photon-photon interaction strength is greatly enhanced. So far, the high-order nonlinearity beyond the χ(3) has rarely been studied in dielectric materials due to their weak intrinsic nonlinear susceptibility, even in high-quality microcavities. Here, an effective five-wave mixing process (χ(4)) is synthesized by incorporating χ(2) and χ(3) processes in a single microcavity. The coherence of the synthetic χ(4) is verified by generating time-energy entangled visible-telecom photon pairs, which requires only one drive laser at the telecom waveband. The photon-pair generation rate from the synthetic process shows an estimated enhancement factor over 500 times upon intrinsic five-wave mixing. Our work demonstrates a universal approach of nonlinear synthesis via photonic structure engineering at the mesoscopic scale rather than material engineering, and thus opens a new avenue for realizing high-order optical nonlinearities and exploring functional photonic devices.
Cross-linking of the endolysosomal system reveals potential flotillin structures and cargo
Authors: Singh Jasjot , Elhabashy Hadeer , Muthukottiappan Pathma , Stepath Markus , Eisenacher Martin , Kohlbacher Oliver , Gieselmann Volkmar , Winter Dominic 
Published: October 2022

AbstractLysosomes are well-established as the main cellular organelles for the degradation of macromolecules and emerging as regulatory centers of metabolism. They are of crucial importance for cellular homeostasis, which is exemplified by a plethora of disorders related to alterations in lysosomal function. In this context, protein complexes play a decisive role, regulating not only metabolic lysosomal processes but also lysosome biogenesis, transport, and interaction with other organelles. Using cross-linking mass spectrometry, we analyze lysosomes and early endosomes. Based on the identification of 5376 cross-links, we investigate protein-protein interactions and structures of lysosome- and endosome-related proteins. In particular, we present evidence for a tetrameric assembly of the lysosomal hydrolase PPT1 and a heterodimeric structure of FLOT1/FLOT2 at lysosomes and early endosomes. For FLOT1-/FLOT2-positive early endosomes, we identify >300 putative cargo proteins and confirm eleven substrates for flotillin-dependent endocytosis, including the latrophilin family of adhesion G protein-coupled receptors.
Blood monocyte-derived CD169+ macrophages contribute to antitumor immunity against glioblastoma
Authors: Kim Hyun-Jin , Park Jang Hyun , Kim Hyeon Cheol , Kim Chae Won , Kang In , Lee Heung Kyu 
Published: October 2022

AbstractInfiltrating tumor-associated macrophages (TAM) are known to impede immunotherapy against glioblastoma (GBM), however, TAMs are heterogeneous, and there are no clear markers to distinguish immunosuppressive and potentially immune-activating populations. Here we identify a subset of CD169+ macrophages promoting an anti-tumoral microenvironment in GBM. Using single-cell transcriptome analysis, we find that CD169+ macrophages in human and mouse gliomas produce pro-inflammatory chemokines, leading to the accumulation of T cells and NK cells. CD169 expression on macrophages facilitates phagocytosis of apoptotic glioma cells and hence tumor-specific T cell responses. Depletion of CD169+ macrophages leads to functionally impaired antitumor lymphocytes and poorer survival of glioma-bearing mice. We show that NK-cell-derived IFN-γ is critical for the accumulation of blood monocyte-derived CD169+ macrophages in gliomas. Our work thus identifies a well-distinguished TAM subset promoting antitumor immunity against GBM, and identifies key factors that might shift the balance from immunosuppressive to anti-tumor TAM.
Large area polymer semiconductor sub-microwire arrays by coaxial focused electrohydrodynamic jet printing for high-performance OFETs
Authors: Wang Dazhi , Lu Liangkun , Zhao Zhiyuan , Zhao Kuipeng , Zhao Xiangyu , Pu Changchang , Li Yikang , Xu Pengfei , Chen Xiangji , Guo Yunlong , Suo Liujia , Liang Junsheng , Cui Yan , Liu Yunqi 
Published: October 2022

AbstractLarge area and highly aligned polymer semiconductor sub-microwires were fabricated using the coaxial focused electrohydrodynamic jet printing technology. As indicated by the results, the sub-microwire arrays have smooth morphology, well reproducibility and controllable with a width of ~110 nm. Analysis shows that the molecular chains inside the sub-microwires mainly exhibited edge-on arrangement and the π-stacking direction (010) of the majority of crystals is parallel to the long axis of the sub-microwires. Sub-microwires based organic field effect transistors showed high mobility with an average of 1.9 cm2 V−1 s−1, approximately 5 times higher than that of thin film based organic field effect transistors. In addition, the number of sub-microwires can be conveniently controlled by the printing technique, which can subsequently concisely control the performance of organic field effect transistors. This work demonstrates that sub-microwires fabricated by the coaxial focused electrohydrodynamic jet printing technology create an alternative path for the applications of high-performance organic flexible device.
RNA G-quadruplex structure contributes to cold adaptation in plants
Authors: Yang Xiaofei , Yu Haopeng , Duncan Susan , Zhang Yueying , Cheema Jitender , Liu Haifeng , Benjamin Miller J. , Zhang Jie , Kwok Chun Kit , Zhang Huakun , Ding Yiliang 
Published: October 2022

AbstractNucleotide composition is suggested to infer gene functionality and ecological adaptation of species to distinct environments. However, the underlying biological function of nucleotide composition dictating environmental adaptations is largely unknown. Here, we systematically analyze the nucleotide composition of transcriptomes across 1000 plants (1KP) and their corresponding habitats. Intriguingly, we find that plants growing in cold climates have guanine (G)-enriched transcriptomes, which are prone to forming RNA G-quadruplex structures. Both immunofluorescence detection and in vivo structure profiling reveal that RNA G-quadruplex formation in plants is globally enhanced in response to cold. Cold-responsive RNA G-quadruplexes strongly enhanced mRNA stability, rather than affecting translation. Disruption of individual RNA G-quadruplex promotes mRNA decay in the cold, leading to impaired plant cold response. Therefore, we propose that plants adopted RNA G-quadruplex structure as a molecular signature to facilitate their adaptation to the cold during evolution.
The salivary microbiome shows a high prevalence of core bacterial members yet variability across human populations
Authors: Ruan Xinwei , Luo Jiaqiang , Zhang Pangzhen , Howell Kate 
Published: October 2022

AbstractHuman saliva contains diverse bacterial communities, reflecting health status, dietary patterns and contributing to variability in the sensory perception of food. Many descriptions of the diversity of the salivary microbiome have focused on the changes induced by certain diseased states, but the commonalities and differences within healthy saliva have not been fully described. Here, we define and explore the core membership of the human salivary microbial community by collecting and re-analysing raw 16S rRNA amplicon sequencing data from 47 studies with 2206 saliva samples. We found 68 core bacterial taxa that were consistently detected. Differences induced by various host intrinsic and behaviour factors, including gender, age, geographic location, tobacco usage and alcohol consumption were evident. The core of the salivary microbiome was verified by collecting and analysing saliva in an independent study. These results suggest that the methods used can effectively define a core microbial community in human saliva. The core salivary microbiome demonstrated both stability and variability among populations. Geographic location was identified as the host factor that is most associated with the structure of salivary microbiota. The independent analysis confirmed the prevalence of the 68 core OTUs we defined from the global data and provides information about how bacterial taxa in saliva varies across human populations.
Biallelic variants in coenzyme Q10 biosynthesis pathway genes cause a retinitis pigmentosa phenotype
Authors: Jurkute Neringa , Cancellieri Francesca , Pohl Lisa , Li Catherina H. Z. , Heaton Robert A. , Reurink Janine , Bellingham James , Quinodoz Mathieu , Yioti Georgia , Stefaniotou Maria , Weener Marianna , Zuleger Theresia , Haack Tobias B. , Stingl Katarina ,   Genomics England Research Consortium, Ambrose J. C. , Arumugam P. , Bevers R. , Bleda M. , Boardman-Pretty F. , Boustred C. R. , Brittain H. , Brown M. A. , Caulfield M. J. , Chan G. C. , Giess A. , Griffin J. N. , Hamblin A. , Henderson S. , Hubbard T. J. P. , Jackson R. , Jones L. J. , Kasperaviciute D. , Kayikci M. , Kousathanas A. , Lahnstein L. , Lakey A. , Leigh S. E. A. , Leong I. U. S. , Lopez F. J. , Maleady-Crowe F. , McEntagart M. , Minneci F. , Mitchell J. , Moutsianas L. , Mueller M. , Murugaesu N. , Need A. C. , O‘Donovan P. , Odhams C. A. , Patch C. , Perez-Gil D. , Pereira M. B. , Pullinger J. , Rahim T. , Rendon A. , Rogers T. , Savage K. , Sawant K. , Scott R. H. , Siddiq A. , Sieghart A. , Smith S. C. , Sosinsky A. , Stuckey A. , Tanguy M. , Taylor Tavares A. L. , Thomas E. R. A. , Thompson S. R. , Tucci A. , Welland M. J. , Williams E. , Witkowska K. , Wood S. M. , Zarowiecki M. , Hoyng Carel B. , Mahroo Omar A. , Hargreaves Iain , Raymond F. Lucy , Michaelides Michel , Rivolta Carlo , Kohl Susanne , Roosing Susanne , Webster Andrew R. , Arno Gavin 
Published: October 2022

AbstractThe aim of this study was to investigate coenzyme Q10 (CoQ10) biosynthesis pathway defects in inherited retinal dystrophy. Individuals affected by inherited retinal dystrophy (IRD) underwent exome or genome sequencing for molecular diagnosis of their condition. Following negative IRD gene panel analysis, patients carrying biallelic variants in CoQ10 biosynthesis pathway genes were identified. Clinical data were collected from the medical records. Haplotypes harbouring the same missense variant were characterised from family genome sequencing (GS) data and direct Sanger sequencing. Candidate splice variants were characterised using Oxford Nanopore Technologies single molecule sequencing. The CoQ10 status of the human plasma was determined in some of the study patients. 13 individuals from 12 unrelated families harboured candidate pathogenic genotypes in the genes: PDSS1, COQ2, COQ4 and COQ5. The PDSS1 variant c.589 A > G was identified in three affected individuals from three unrelated families on a possible ancestral haplotype. Three variants (PDSS1 c.468-25 A > G, PDSS1 c.722-2 A > G, COQ5 c.682-7 T > G) were shown to lead to cryptic splicing. 6 affected individuals were diagnosed with non-syndromic retinitis pigmentosa and 7 had additional clinical findings. This study provides evidence of CoQ10 biosynthesis pathway gene defects leading to non-syndromic retinitis pigmentosa in some cases. Intronic variants outside of the canonical splice-sites represent an important cause of disease. RT-PCR nanopore sequencing is effective in characterising these splice defects.
Diverse MarR bacterial regulators of auxin catabolism in the plant microbiome
Authors: Conway Jonathan M. , Walton William G. , Salas-González Isai , Law Theresa F. , Lindberg Chloe A. , Crook Laura E. , Kosina Suzanne M. , Fitzpatrick Connor R. , Lietzan Adam D. , Northen Trent R. , Jones Corbin D. , Finkel Omri M. , Redinbo Matthew R. , Dangl Jeffery L. 
Published: October 2022

AbstractChemical signalling in the plant microbiome can have drastic effects on microbial community structure, and on host growth and development. Previously, we demonstrated that the auxin metabolic signal interference performed by the bacterial genus Variovorax via an auxin degradation locus was essential for maintaining stereotypic root development in an ecologically relevant bacterial synthetic community. Here, we dissect the Variovorax auxin degradation locus to define the genes iadDE as necessary and sufficient for indole-3-acetic acid (IAA) degradation and signal interference. We determine the crystal structures and binding properties of the operon’s MarR-family repressor with IAA and other auxins. Auxin degradation operons were identified across the bacterial tree of life and we define two distinct types on the basis of gene content and metabolic products: iac-like and iad-like. The structures of MarRs from representatives of each auxin degradation operon type establish that each has distinct IAA-binding pockets. Comparison of representative IAA-degrading strains from diverse bacterial genera colonizing Arabidopsis plants show that while all degrade IAA, only strains containing iad-like auxin-degrading operons interfere with auxin signalling in a complex synthetic community context. This suggests that iad-like operon-containing bacterial strains, including Variovorax species, play a key ecological role in modulating auxins in the plant microbiome.
Improved AlphaFold modeling with implicit experimental information
Authors: Terwilliger Thomas C. , Poon Billy K. , Afonine Pavel V. , Schlicksup Christopher J. , Croll Tristan I. , Millán Claudia , Richardson Jane. S. , Read Randy J. , Adams Paul D. 
Published: October 2022

AbstractMachine-learning prediction algorithms such as AlphaFold and RoseTTAFold can create remarkably accurate protein models, but these models usually have some regions that are predicted with low confidence or poor accuracy. We hypothesized that by implicitly including new experimental information such as a density map, a greater portion of a model could be predicted accurately, and that this might synergistically improve parts of the model that were not fully addressed by either machine learning or experiment alone. An iterative procedure was developed in which AlphaFold models are automatically rebuilt on the basis of experimental density maps and the rebuilt models are used as templates in new AlphaFold predictions. We show that including experimental information improves prediction beyond the improvement obtained with simple rebuilding guided by the experimental data. This procedure for AlphaFold modeling with density has been incorporated into an automated procedure for interpretation of crystallographic and electron cryo-microscopy maps.
The Immune Signatures data resource, a compendium of systems vaccinology datasets
Authors: Diray-Arce Joann , Miller Helen E. R. , Henrich Evan , Gerritsen Bram , Mulè Matthew P. , Fourati Slim , Gygi Jeremy , Hagan Thomas , Tomalin Lewis , Rychkov Dmitry , Kazmin Dmitri , Chawla Daniel G. , Meng Hailong , Dunn Patrick , Campbell John ,   The Human Immunology Project Consortium (HIPC), Deckhut-Augustine Alison , Gottardo Raphael , Haddad Elias K. , Hafler David A. , Harris Eva , Farber Donna , Levy Ofer , McElrath Julie , Montgomery Ruth R. , Peters Bjoern , Rahman Adeeb , Reed Elaine F. , Rouphael Nadine , Fernandez-Sesma Ana , Sette Alessandro , Stuart Ken , Togias Alkis , Tsang John S. , Sarwal Minnie , Tsang John S. , Levy Ofer , Pulendran Bali , Sekaly Rafick , Floratos Aris , Gottardo Raphael , Kleinstein Steven H. , Suárez-Fariñas Mayte 
Published: October 2022

AbstractVaccines are among the most cost-effective public health interventions for preventing infection-induced morbidity and mortality, yet much remains to be learned regarding the mechanisms by which vaccines protect. Systems immunology combines traditional immunology with modern ‘omic profiling techniques and computational modeling to promote rapid and transformative advances in vaccinology and vaccine discovery. The NIH/NIAID Human Immunology Project Consortium (HIPC) has leveraged systems immunology approaches to identify molecular signatures associated with the immunogenicity of many vaccines. However, comparative analyses have been limited by the distributed nature of some data, potential batch effects across studies, and the absence of multiple relevant studies from non-HIPC groups in ImmPort. To support comparative analyses across different vaccines, we have created the Immune Signatures Data Resource, a compendium of standardized systems vaccinology datasets. This data resource is available through ImmuneSpace, along with code to reproduce the processing and batch normalization starting from the underlying study data in ImmPort and the Gene Expression Omnibus (GEO). The current release comprises 1405 participants from 53 cohorts profiling the response to 24 different vaccines. This novel systems vaccinology data release represents a valuable resource for comparative and meta-analyses that will accelerate our understanding of mechanisms underlying vaccine responses.
Novel metallomic profiling and non-carcinogenic risk assessment of botanical ingredients for use in herbal, phytopharmaceutical and dietary products using HR-ICP-SFMS
Authors: Kenny Ciara-Ruth , Ring Gavin , Sheehan Aisling , Mc Auliffe Michael A. P. , Lucey Brigid , Furey Ambrose 
Published: October 2022

AbstractKnowledge of element concentrations in botanical extracts is relevant to assure consumer protection given the increased interest in plant-based ingredients. This study demonstrates successful multi-element investigations in order to address the lack of comprehensive profiling data for botanical extracts, while reporting for the first time the metallomic profile(s) of arnica, bush vetch, sweet cicely, yellow rattle, bogbean, rock-tea and tufted catchfly. Key element compositions were quantified using a validated HR-ICP-SFMS method (µg kg−1) and were found highly variable between the different plants: Lithium (18–3964); Beryllium (3–121); Molybdenum (75–4505); Cadmium (5–325); Tin (6–165); Barium (747–4646); Platinum (2–33); Mercury (5–30); Thallium (3–91); Lead (12–4248); Bismuth (2–30); Titanium (131–5827); Vanadium (15–1758); Chromium (100–4534); Cobalt (21–652); Nickel (230–6060) and Copper (1910–6340). Compendial permissible limits were not exceeded. Overall, no evidence of a health risk to consumers could be determined from consumption of the investigated plants at reasonable intake rates. Mathematical risk modelling (EDI, CDI, HQ, HI) estimated levels above safe oral thresholds only for Cd (16%) and Pb (8%) from higher intakes of the respective plant-derived material. Following high consumption of certain plants, 42% of the samples were categorised as potentially unsafe due to cumulative exposure to Cu, Cd, Hg and Pb. PCA suggested a potential influence of post-harvest processing on Cr, Ti and V levels in commercially-acquired plant material compared to wild-collected and farm-grown plants. Moreover, a strong correlation was observed between Pb-Bi, Be-V, Bi-Sn, and Tl-Mo occurrence. This study may support future research by providing both robust methodology and accompanying reference profile(s) suitable for the quality evaluation of essential elements and/or metal contaminants in botanical ingredients.
Abstract and concrete concepts in conversation
Authors: Villani Caterina , Orsoni Matteo , Lugli Luisa , Benassi Mariagrazia , Borghi Anna M. 
Published: October 2022

AbstractConcepts allow us to make sense of the world. Most evidence on their acquisition and representation comes from studies of single decontextualized words and focuses on the opposition between concrete and abstract concepts (e.g., “bottle” vs. “truth”). A significant step forward in research on concepts consists in investigating them in online interaction during their use. Our study examines linguistic exchanges analyzing the differences between sub-kinds of concepts. Participants were submitted to an online task in which they had to simulate a conversational exchange by responding to sentences involving sub-kinds of concrete (tools, animals, food) and abstract concepts (PS, philosophical-spiritual; EMSS, emotional-social, PSTQ, physical-spatio-temporal-quantitative). We found differences in content: foods evoked interoception; tools and animals elicited materials, spatial, auditive features, confirming their sensorimotor grounding. PS and EMSS yielded inner experiences (e.g., emotions, cognitive states, introspections) and opposed PSTQ, tied to visual properties and concrete agency. More crucially, the various concepts elicited different interactional dynamics: more abstract concepts generated higher uncertainty and more interactive exchanges than concrete ones. Investigating concepts in situated interactions opens new possibilities for studying conceptual knowledge and its pragmatic and social aspects.
Remnant cholesterol levels are associated with severity and death in COVID-19 patients
Authors: Fabre Bibiana , Fernandez Machulsky Nahuel , Olano Carolina , Jacobsen Darío , Gómez María Eugenia , Perazzi Beatriz , Zago Valeria , Zopatti Damián , Ferrero Andrés , Schreier Laura , Berg Gabriela 
Published: October 2022

AbstractCoronavirus disease-19 (COVID-19) patients with severe complications present comorbidities like cardiovascular-disease, hypertension and type-2 diabetes mellitus (DM), sharing metabolic alterations like insulin resistance (IR) and dyslipidemia. Our objective was to evaluate the association among different components of the lipid-lipoprotein profile, such as remnant lipoprotein (RLP)-cholesterol, in patients with COVID-19, and to analyze their associations with the severity of the disease and death. We studied 193 patients (68 (29–96) years; 49.7% male) hospitalized for COVID-19 and 200 controls (46 (18–79) years; 52.5% male). Lipoprotein profile, glucose and procalcitonin were assessed. Patients presented higher glucose, TG, TG/HDL-cholesterol and RLP-cholesterol levels, but lower total, LDL, HDL and no-HDL-cholesterol levels (p < 0.001). When a binary logistic regression was performed, age, non-HDL-cholesterol, and RLP-cholesterol were associated with death (p = 0.005). As the COVID-19 condition worsened, according to procalcitonin tertiles, a decrease in all the cholesterol fractions (p < 0.03) was observed with no differences in TG, while levels of RLP-cholesterol and TG/HDL-cholesterol increased (p < 0.001). Lower levels of all the cholesterol fractions were related with the presence and severity of COVID-19, except for RLP-cholesterol levels and TG/HDL-cholesterol index. These alterations indicate a lipid metabolic disorder, characteristic of IR states in COVID-19 patients. RLP-cholesterol levels predicted severity and death in these patients.