bluuebunny/crossref_metadata_2025_split huggingface dataset:
One-year breakthrough SARS-CoV-2 infection and correlates of protection in fully vaccinated hematological patients
Authors: Piñana José Luis , Vazquez Lourdes , Calabuig Marisa , López-Corral Lucia , Martin-Martin Gabriel , Villalon Lucia , Sanz-Linares Gabriela , Conesa-Garcia Venancio , Sanchez-Salinas Andrés , Gago Beatriz , Facal Ana , Risco-Gálvez Irene , Olave María T. , Espigado Ildefonso , Lopez-Jimenez Javier , Hernández-Rivas José Ángel , Avendaño-Pita Alejandro , Arroyo Ignacio , Ferrer Elena , García-Cadenas Irene , González-Santillana Clara , Roldán-Pérez Alicia , Ferrer Blanca , Guerreiro Manuel , Suarez-Lledó María , Camara Angela , Campos-Beltrán Diana , Navarro David , Cedillo Ángel , Sureda Anna , Solano Carlos ,   Spanish Hematopoietic Stem Cell Transplantation and Cell Therapy Group (GETH-TC), Martino Rodrigo 
Published: January 2023

AbstractThe long-term clinical efficacy of SARS-CoV-2 vaccines according to antibody response in immunosuppressed patients such as hematological patients has been little explored. A prospective multicenter registry-based cohort study conducted from December 2020 to July 2022 by the Spanish Transplant and Cell Therapy group, was used to analyze the relationship of antibody response over time after full vaccination (at 3–6 weeks, 3, 6 and 12 months) (2 doses) and of booster doses with breakthrough SARS-CoV-2 infection in 1551 patients with hematological disorders. At a median follow-up of 388 days after complete immunization, 266 out of 1551 (17%) developed breakthrough SARS-CoV-2 infection at median of 86 days (range 7–391) after full vaccination. The cumulative incidence was 18% [95% confidence interval (C.I.), 16–20%]. Multivariate analysis identified higher incidence in chronic lymphocytic leukemia patients (29%) and with the use of corticosteroids (24.5%), whereas female sex (15.5%) and more than 1 year after last therapy (14%) were associated with a lower incidence (p < 0.05 for all comparisons). Median antibody titers at different time points were significantly lower in breakthrough cases than in non-cases. A serological titer cut-off of 250 BAU/mL was predictive of breakthrough infection and its severity. SARS-CoV-2 infection-related mortality was encouragingly low (1.9%) in our series. Our study describes the incidence of and risk factors for COVID-19 breakthrough infections during the initial vaccination and booster doses in the 2021 to mid-2022 period. The level of antibody titers at any time after 2-dose vaccination is strongly linked with protection against both breakthrough infection and severe disease, even with the Omicron SARS-CoV-2 variant.
Hallmarks of peripheral nerve function in bone regeneration
Authors: Tao Ranyang , Mi Bobin , Hu Yiqiang , Lin Sien , Xiong Yuan , Lu Xuan , Panayi Adriana C. , Li Gang , Liu Guohui 
Published: January 2023

AbstractSkeletal tissue is highly innervated. Although different types of nerves have been recently identified in the bone, the crosstalk between bone and nerves remains unclear. In this review, we outline the role of the peripheral nervous system (PNS) in bone regeneration following injury. We first introduce the conserved role of nerves in tissue regeneration in species ranging from amphibians to mammals. We then present the distribution of the PNS in the skeletal system under physiological conditions, fractures, or regeneration. Furthermore, we summarize the ways in which the PNS communicates with bone-lineage cells, the vasculature, and immune cells in the bone microenvironment. Based on this comprehensive and timely review, we conclude that the PNS regulates bone regeneration through neuropeptides or neurotransmitters and cells in the peripheral nerves. An in-depth understanding of the roles of peripheral nerves in bone regeneration will inform the development of new strategies based on bone-nerve crosstalk in promoting bone repair and regeneration.
Intrastriatal injection of Parkinson’s disease intestine and vagus lysates initiates α-synucleinopathy in rat brain
Authors: Yang Zhaofei , Wang Ying , Wei Min , Li Song , Jia Congcong , Cheng Cheng , Al-Nusaif Murad , Zhang Jun , Liu Cong , Le Weidong 
Published: January 2023

AbstractParkinson’s disease (PD) is characterized by the selective loss of dopaminergic neurons in the midbrain and the pathological accumulation of misfolded α-synuclein (α-syn) in the brain. A growing body of evidence suggests that the formation of misfolded α-syn and aggregation may begin in the peripheral nervous system, specifically the enteric nervous system, and then propagate to the central nervous system via the vagus nerve. However, the PD-like neuropathology induced by the intestine and vagus nerve extracts is rarely investigated. In this work, we injected lysates of the intestine and vagus obtained from a diagnosed PD patient, which contained abnormal α-syn aggregates, into the rat striatum unilaterally. Strikingly, such an injection induced dopaminergic neurodegeneration and α-syn depositions in the striatum, substantia nigra, and other brain regions, including the frontal cortex, somatosensory cortex, hypothalamus, brain stem, and cerebellum. Moreover, significant activation of microglia and the development of astrogliosis were observed in the substantia nigra pars compacta of the injected rats. These findings provide essential information for our understanding of PD pathogenesis, as we established for the first time that the α-syn aggregates in the intestine and vagus of a PD patient were sufficient to induce prion-like propagation of endogenous α-syn pathology in wild-type rats.
Adipose tissue is a source of regenerative cells that augment the repair of skeletal muscle after injury
Authors: Sastourné-Arrey Quentin , Mathieu Maxime , Contreras Xavier , Monferran Sylvie , Bourlier Virginie , Gil-Ortega Marta , Murphy Enda , Laurens Claire , Varin Audrey , Guissard Christophe , Barreau Corinne , André Mireille , Juin Noémie , Marquès Marie , Chaput Benoit , Moro Cédric , O’Gorman Donal , Casteilla Louis , Girousse Amandine , Sengenès Coralie 
Published: January 2023

AbstractFibro-adipogenic progenitors (FAPs) play a crucial role in skeletal muscle regeneration, as they generate a favorable niche that allows satellite cells to perform efficient muscle regeneration. After muscle injury, FAP content increases rapidly within the injured muscle, the origin of which has been attributed to their proliferation within the muscle itself. However, recent single-cell RNAseq approaches have revealed phenotype and functional heterogeneity in FAPs, raising the question of how this differentiation of regenerative subtypes occurs. Here we report that FAP-like cells residing in subcutaneous adipose tissue (ScAT), the adipose stromal cells (ASCs), are rapidly released from ScAT in response to muscle injury. Additionally, we find that released ASCs infiltrate the damaged muscle, via a platelet-dependent mechanism and thus contribute to the FAP heterogeneity. Moreover, we show that either blocking ASCs infiltration or removing ASCs tissue source impair muscle regeneration. Collectively, our data reveal that ScAT is an unsuspected physiological reservoir of regenerative cells that support skeletal muscle regeneration, underlining a beneficial relationship between muscle and fat.
Constructing robust heterostructured interface for anode-free zinc batteries with ultrahigh capacities
Authors: Zheng Xinhua , Liu Zaichun , Sun Jifei , Luo Ruihao , Xu Kui , Si Mingyu , Kang Ju , Yuan Yuan , Liu Shuang , Ahmad Touqeer , Jiang Taoli , Chen Na , Wang Mingming , Xu Yan , Chuai Mingyan , Zhu Zhengxin , Peng Qia , Meng Yahan , Zhang Kai , Wang Weiping , Chen Wei 
Published: January 2023

AbstractThe development of Zn-free anodes to inhibit Zn dendrite formation and modulate high-capacity Zn batteries is highly applauded yet very challenging. Here, we design a robust two-dimensional antimony/antimony-zinc alloy heterostructured interface to regulate Zn plating. Benefiting from the stronger adsorption and homogeneous electric field distribution of the Sb/Sb2Zn3-heterostructured interface in Zn plating, the Zn anode enables an ultrahigh areal capacity of 200 mAh cm−2with an overpotential of 112 mV and a Coulombic efficiency of 98.5%. An anode-free Zn-Br2battery using the Sb/Sb2Zn3-heterostructured interface@Cu anode shows an attractive energy density of 274 Wh kg−1 with a practical pouch cell energy density of 62 Wh kg−1. The scaled-up Zn-Br2battery in a capacity of 500 mAh exhibits over 400 stable cycles. Further, the Zn-Br2battery module in an energy of 9 Wh (6 V, 1.5 Ah) is integrated with a photovoltaic panel to demonstrate the practical renewable energy storage capabilities. Our superior anode-free Zn batteries enabled by the heterostructured interface enlighten an arena towards large-scale energy storage applications.
Improving cassava bacterial blight resistance by editing the epigenome
Authors: Veley Kira M. , Elliott Kiona , Jensen Greg , Zhong Zhenhui , Feng Suhua , Yoder Marisa , Gilbert Kerrigan B. , Berry Jeffrey C. , Lin Zuh-Jyh Daniel , Ghoshal Basudev , Gallego-Bartolomé Javier , Norton Joanna , Motomura-Wages Sharon , Carrington James C. , Jacobsen Steven E. , Bart Rebecca S. 
Published: January 2023

AbstractPathogens rely on expression of host susceptibility (S) genes to promote infection and disease. As DNA methylation is an epigenetic modification that affects gene expression, blocking access to S genes through targeted methylation could increase disease resistance. Xanthomonas phaseoli pv. manihotis, the causal agent of cassava bacterial blight (CBB), uses transcription activator-like20 (TAL20) to induce expression of the S gene MeSWEET10a. In this work, we direct methylation to the TAL20 effector binding element within the MeSWEET10a promoter using a synthetic zinc-finger DNA binding domain fused to a component of the RNA-directed DNA methylation pathway. We demonstrate that this methylation prevents TAL20 binding, blocks transcriptional activation of MeSWEET10a in vivo and that these plants display decreased CBB symptoms while maintaining normal growth and development. This work therefore presents an epigenome editing approach useful for crop improvement.
Photonic machine learning with on-chip diffractive optics
Authors: Fu Tingzhao , Zang Yubin , Huang Yuyao , Du Zhenmin , Huang Honghao , Hu Chengyang , Chen Minghua , Yang Sigang , Chen Hongwei 
Published: January 2023

AbstractMachine learning technologies have been extensively applied in high-performance information-processing fields. However, the computation rate of existing hardware is severely circumscribed by conventional Von Neumann architecture. Photonic approaches have demonstrated extraordinary potential for executing deep learning processes that involve complex calculations. In this work, an on-chip diffractive optical neural network (DONN) based on a silicon-on-insulator platform is proposed to perform machine learning tasks with high integration and low power consumption characteristics. To validate the proposed DONN, we fabricated 1-hidden-layer and 3-hidden-layer on-chip DONNs with footprints of 0.15 mm2 and 0.3 mm2 and experimentally verified their performance on the classification task of the Iris plants dataset, yielding accuracies of 86.7% and 90%, respectively. Furthermore, a 3-hidden-layer on-chip DONN is fabricated to classify the Modified National Institute of Standards and Technology handwritten digit images. The proposed passive on-chip DONN provides a potential solution for accelerating future artificial intelligence hardware with enhanced performance.
Systematic review and meta-analysis of prevalence, trajectories, and clinical outcomes for frailty in COPD
Authors: Hanlon Peter , Guo Xuetong , McGhee Eveline , Lewsey Jim , McAllister David , Mair Frances S. 
Published: January 2023

AbstractThis systematic review synthesised measurement and prevalence of frailty in COPD and associations between frailty and adverse health outcomes. We searched Medline, Embase and Web of Science (1 January 2001–8 September 2021) for observational studies in adults with COPD assessing frailty prevalence, trajectories, or association with health-related outcomes. We performed narrative synthesis and random-effects meta-analyses. We found 53 eligible studies using 11 different frailty measures. Most common were frailty phenotype (n = 32), frailty index (n = 5) and Kihon checklist (n = 4). Prevalence estimates varied by frailty definitions, setting, and age (2.6–80.9%). Frailty was associated with mortality (5/7 studies), COPD exacerbation (7/11), hospitalisation (3/4), airflow obstruction (11/14), dyspnoea (15/16), COPD severity (10/12), poorer quality of life (3/4) and disability (1/1). In conclusion, frailty is a common among people with COPD and associated with increased risk of adverse outcomes. Proactive identification of frailty may aid risk stratification and identify candidates for targeted intervention.
Interaction-free, single-pixel quantum imaging with undetected photons
Authors: Yang Yiquan , Liang Hong , Xu Xiaze , Zhang Lijian , Zhu Shining , Ma Xiao-song 
Published: January 2023

AbstractA typical imaging scenario requires three basic ingredients: (1) a light source that emits light, which in turn interacts and scatters off the object of interest; (2) detection of the light being scattered from the object and (3) a detector with spatial resolution. These indispensable ingredients in typical imaging scenarios may limit their applicability in the imaging of biological or other sensitive specimens due to unavailable photon-starved detection capabilities and inevitable damage induced by interaction. Here, we propose and experimentally realize a quantum imaging protocol that alleviates all three requirements. By embedding a single-photon Michelson interferometer into a nonlinear interferometer based on induced coherence and harnessing single-pixel imaging technique, we demonstrate interaction-free, single-pixel quantum imaging of a structured object with undetected photons. Thereby, we push the capability of quantum imaging to the extreme point in which no interaction is required between object and photons and the detection requirement is greatly reduced. Our work paves the path for applications in characterizing delicate samples with single-pixel imaging at silicon-detectable wavelengths.
Teleconnections among tipping elements in the Earth system
Authors: Liu Teng , Chen Dean , Yang Lan , Meng Jun , Wang Zanchenling , Ludescher Josef , Fan Jingfang , Yang Saini , Chen Deliang , Kurths Jürgen , Chen Xiaosong , Havlin Shlomo , Schellnhuber Hans Joachim 
Published: January 2023

AbstractTipping elements are components of the Earth system that may shift abruptly and irreversibly from one state to another at specific thresholds. It is not well understood to what degree tipping of one system can influence other regions or tipping elements. Here, we propose a climate network approach to analyse the global impacts of a prominent tipping element, the Amazon Rainforest Area (ARA). We find that the ARA exhibits strong correlations with regions such as the Tibetan Plateau (TP) and West Antarctic ice sheet. Models show that the identified teleconnection propagation path between the ARA and the TP is robust under climate change. In addition, we detect that TP snow cover extent has been losing stability since 2008. We further uncover that various climate extremes between the ARA and the TP are synchronized under climate change. Our framework highlights that tipping elements can be linked and also the potential predictability of cascading tipping dynamics.
Prediction of effector protein structures from fungal phytopathogens enables evolutionary analyses
Authors: Seong Kyungyong , Krasileva Ksenia V. 
Published: January 2023

AbstractElucidating the similarity and diversity of pathogen effectors is critical to understand their evolution across fungal phytopathogens. However, rapid divergence that diminishes sequence similarities between putatively homologous effectors has largely concealed the roots of effector evolution. Here we modelled the structures of 26,653 secreted proteins from 14 agriculturally important fungal phytopathogens, six non-pathogenic fungi and one oomycete with AlphaFold 2. With 18,000 successfully predicted folds, we performed structure-guided comparative analyses on two aspects of effector evolution: uniquely expanded sequence-unrelated structurally similar (SUSS) effector families and common folds present across the fungal species. Extreme expansion of lineage-specific SUSS effector families was found only in several obligate biotrophs,Blumeria graminisandPuccinia graminis. The highly expanded effector families were the source of conserved sequence motifs, such as the Y/F/WxC motif. We identified new classes of SUSS effector families that include known virulence factors, such as AvrSr35, AvrSr50 and Tin2. Structural comparisons revealed that the expanded structural folds further diversify through domain duplications and fusion with disordered stretches. Putatively sub- and neo-functionalized SUSS effectors could reconverge on regulation, expanding the functional pools of effectors in the pathogen infection cycle. We also found evidence that many effector families could have originated from ancestral folds conserved across fungi. Collectively, our study highlights diverse effector evolution mechanisms and supports divergent evolution as a major force in driving SUSS effector evolution from ancestral proteins.
Structure, sequon recognition and mechanism of tryptophan C-mannosyltransferase
Authors: Bloch Joël S. , John Alan , Mao Runyu , Mukherjee Somnath , Boilevin Jérémy , Irobalieva Rossitza N. , Darbre Tamis , Scott Nichollas E. , Reymond Jean-Louis , Kossiakoff Anthony A. , Goddard-Borger Ethan D. , Locher Kaspar P. 
Published: January 2023

AbstractC-linked glycosylation is essential for the trafficking, folding and function of secretory and transmembrane proteins involved in cellular communication processes. The tryptophan C-mannosyltransferase (CMT) enzymes that install the modification attach a mannose to the first tryptophan of WxxW/C sequons in nascent polypeptide chains by an unknown mechanism. Here, we report cryogenic-electron microscopy structures of Caenorhabditiselegans CMT in four key states: apo, acceptor peptide-bound, donor-substrate analog-bound and as a trapped ternary complex with both peptide and a donor-substrate mimic bound. The structures indicate how the C-mannosylation sequon is recognized by this CMT and its paralogs, and how sequon binding triggers conformational activation of the donor substrate: a process relevant to all glycosyltransferase C superfamily enzymes. Our structural data further indicate that the CMTs adopt an unprecedented electrophilic aromatic substitution mechanism to enable the C-glycosylation of proteins. These results afford opportunities for understanding human disease and therapeutic targeting of specific CMT paralogs.
Human DNA-dependent protein kinase activation mechanism
Authors: Liang Shikang , Blundell Tom L. 
Published: January 2023

AbstractDNA-dependent protein kinase (DNA-PK), a multicomponent complex including the DNA-PK catalytic subunit and Ku70/80 heterodimer together with DNA, is central to human DNA damage response and repair. Using a DNA-PK-selective inhibitor (M3814), we identified from one dataset two cryo-EM structures of the human DNA-PK complex in different states, the intermediate state and the active state. Here we show that activation of the kinase is regulated through conformational changes caused by the binding ligand and the string region (residues 802–846) of the DNA-PK catalytic subunit, particularly the helix-hairpin-helix motif (residues 816–836) that interacts with DNA. These observations demonstrate the regulatory role of the ligand and explain why DNA-PK is DNA dependent. Cooperation and coordination among binding partners, disordered flexible regions and mechanically flexible HEAT repeats modulate the activation of the kinase. Together with previous findings, these results provide a better molecular understanding of DNA-PK catalysis.
Functional group analyses of herpetofauna in South Korea using a large dataset
Authors: Jeon Jong Yoon , Lee Dong Kun , Kim Jae Hyun 
Published: January 2023

AbstractFunctional traits are characteristics of species that affect their fitness and ecosystem, and they greatly influence ecological niches. Thus, biodiversity assessment based on functional groups rather than species per se can more realistically reflect the ecological niche space. As essential players of ecosystem functions, herpetofauna are appropriate subjects of functional trait-based analyses. In this study, using a nationwide dataset and applying trait information and ecological niche modeling, the richness within each functional group, and the taxonomic and functional diversity indices of South Korean herpetofauna were visualized to identify and compare the geographic distributions. The results revealed that the reptile community seemed more locally diverse with more overlapping randomized patterns among groups than amphibians, while amphibians showed wider distributions and a higher within-grid occurrence ratio. Functional diversity indices of reptiles also showed more randomized geographic patterns with higher levels at Jejudo Island than amphibians. The findings of this study may help to identify biodiversity hot spots and understand its ecosystem health. Increasing survey data and trait information will improve the assessment.
Circulating microparticle proteins predict pregnancies complicated by placenta accreta spectrum
Authors: Yu Hope Y. , Gumusoglu Serena B. , Cantonwine David E. , Carusi Daniela A. , Gurnani Prem , Schickling Brandon , Doss Robert C. , Santillan Mark K. , Rosenblatt Kevin P. , McElrath Thomas F. 
Published: January 2023

AbstractPlacenta accreta spectrum (PAS) is characterized by abnormal attachment of the placenta to the uterus, and attempts at placental delivery can lead to catastrophic maternal hemorrhage and death. Multidisciplinary delivery planning can significantly improve outcomes; however, current diagnostics are lacking as approximately half of pregnancies with PAS are undiagnosed prior to delivery. This is a nested case–control study of 35 cases and 70 controls with the primary objective of identifying circulating microparticle (CMP) protein panels that identify pregnancies complicated by PAS. Size exclusion chromatography and liquid chromatography with tandem mass spectrometry were used for CMP protein isolation and identification, respectively. A two-step iterative workflow was used to establish putative panels. Using plasma sampled at a median of 26 weeks’ gestation, five CMP proteins distinguished PAS from controls with a mean area under the curve (AUC) of 0.83. For a separate sample taken at a median of 35 weeks’ gestation, the mean AUC was 0.78. In the second trimester, canonical pathway analyses demonstrate over-representation of processes related to iron homeostasis and erythropoietin signaling. In the third trimester, these analyses revealed abnormal immune function. CMP proteins classify PAS well prior to delivery and have potential to significantly reduce maternal morbidity and mortality.