bluuebunny/crossref_metadata_2025_split huggingface dataset:
Indoor air surveillance and factors associated with respiratory pathogen detection in community settings in Belgium
Authors: Raymenants Joren , Geenen Caspar , Budts Lore , Thibaut Jonathan , Thijssen Marijn , De Mulder Hannelore , Gorissen Sarah , Craessaerts Bastiaan , Laenen Lies , Beuselinck Kurt , Ombelet Sien , Keyaerts Els , André Emmanuel 
Published: March 2023

AbstractCurrently, the real-life impact of indoor climate, human behaviour, ventilation and air filtration on respiratory pathogen detection and concentration are poorly understood. This hinders the interpretability of bioaerosol quantification in indoor air to surveil respiratory pathogens and transmission risk. We tested 341 indoor air samples from 21 community settings in Belgium for 29 respiratory pathogens using qPCR. On average, 3.9 pathogens were positive per sample and 85.3% of samples tested positive for at least one. Pathogen detection and concentration varied significantly by pathogen, month, and age group in generalised linear (mixed) models and generalised estimating equations. High CO2 and low natural ventilation were independent risk factors for detection. The odds ratio for detection was 1.09 (95% CI 1.03–1.15) per 100 parts per million (ppm) increase in CO2, and 0.88 (95% CI 0.80–0.97) per stepwise increase in natural ventilation (on a Likert scale). CO2 concentration and portable air filtration were independently associated with pathogen concentration. Each 100ppm increase in CO2 was associated with a qPCR Ct value decrease of 0.08 (95% CI −0.12 to −0.04), and portable air filtration with a 0.58 (95% CI 0.25–0.91) increase. The effects of occupancy, sampling duration, mask wearing, vocalisation, temperature, humidity and mechanical ventilation were not significant. Our results support the importance of ventilation and air filtration to reduce transmission.
Pan-genome inversion index reveals evolutionary insights into the subpopulation structure of Asian rice
Authors: Zhou Yong , Yu Zhichao , Chebotarov Dmytro , Chougule Kapeel , Lu Zhenyuan , Rivera Luis F. , Kathiresan Nagarajan , Al-Bader Noor , Mohammed Nahed , Alsantely Aseel , Mussurova Saule , Santos João , Thimma Manjula , Troukhan Maxim , Fornasiero Alice , Green Carl D. , Copetti Dario , Kudrna David , Llaca Victor , Lorieux Mathias , Zuccolo Andrea , Ware Doreen , McNally Kenneth , Zhang Jianwei , Wing Rod A. 
Published: March 2023

AbstractUnderstanding and exploiting genetic diversity is a key factor for the productive and stable production of rice. Here, we utilize 73 high-quality genomes that encompass the subpopulation structure of Asian rice (Oryza sativa), plus the genomes of two wild relatives (O. rufipogonandO. punctata), to build a pan-genome inversion index of 1769 non-redundant inversions that span an average of ~29% of theO. sativacv. Nipponbare reference genome sequence. Using this index, we estimate an inversion rate of ~700 inversions per million years in Asian rice, which is 16 to 50 times higher than previously estimated for plants. Detailed analyses of these inversions show evidence of their effects on gene expression, recombination rate, and linkage disequilibrium. Our study uncovers the prevalence and scale of large inversions (≥100 bp) across the pan-genome of Asian rice and hints at their largely unexplored role in functional biology and crop performance.
Hybrid spin Hall nano-oscillators based on ferromagnetic metal/ferrimagnetic insulator heterostructures
Authors: Ren Haowen , Zheng Xin Yu , Channa Sanyum , Wu Guanzhong , O’Mahoney Daisy A. , Suzuki Yuri , Kent Andrew D. 
Published: March 2023

AbstractSpin-Hall nano-oscillators (SHNOs) are promising spintronic devices to realize current controlled GHz frequency signals in nanoscale devices for neuromorphic computing and creating Ising systems. However, traditional SHNOs devices based on transition metals have high auto-oscillation threshold currents as well as low quality factors and output powers. Here we demonstrate a new type of hybrid SHNO based on a permalloy (Py) ferromagnetic-metal nanowire and low-damping ferrimagnetic insulator, in the form of epitaxial lithium aluminum ferrite (LAFO) thin films. The superior characteristics of such SHNOs are associated with the excitation of larger spin-precession angles and volumes. We further find that the presence of the ferrimagnetic insulator enhances the auto-oscillation amplitude of spin-wave edge modes, consistent with our micromagnetic modeling. This hybrid SHNO expands spintronic applications, including providing new means of coupling multiple SHNOs for neuromorphic computing and advancing magnonics.
An in-solution snapshot of SARS-COV-2 main protease maturation process and inhibition
Authors: Noske Gabriela Dias , Song Yun , Fernandes Rafaela Sachetto , Chalk Rod , Elmassoudi Haitem , Koekemoer Lizbé , Owen C. David , El-Baba Tarick J. , Robinson Carol V. ,   The COVID Moonshot Consortium, Oliva Glaucius , Godoy Andre Schutzer 
Published: March 2023

AbstractThe main protease from SARS-CoV-2 (Mpro) is responsible for cleavage of the viral polyprotein. Mpro self-processing is called maturation, and it is crucial for enzyme dimerization and activity. Here we use C145S Mpro to study the structure and dynamics of N-terminal cleavage in solution. Native mass spectroscopy analysis shows that mixed oligomeric states are composed of cleaved and uncleaved particles, indicating that N-terminal processing is not critical for dimerization. A 3.5 Å cryo-EM structure provides details of Mpro N-terminal cleavage outside the constrains of crystal environment. We show that different classes of inhibitors shift the balance between oligomeric states. While non-covalent inhibitor MAT-POS-e194df51-1 prevents dimerization, the covalent inhibitor nirmatrelvir induces the conversion of monomers into dimers, even with intact N-termini. Our data indicates that the Mpro dimerization is triggered by induced fit due to covalent linkage during substrate processing rather than the N-terminal processing.
The Torreya grandis genome illuminates the origin and evolution of gymnosperm-specific sciadonic acid biosynthesis
Authors: Lou Heqiang , Song Lili , Li Xiaolong , Zi Hailing , Chen Weijie , Gao Yadi , Zheng Shan , Fei Zhangjun , Sun Xuepeng , Wu Jiasheng 
Published: March 2023

AbstractTorreya plants produce dry fruits with assorted functions. Here, we report the 19-Gb chromosome-level genome assembly of T. grandis. The genome is shaped by ancient whole-genome duplications and recurrent LTR retrotransposon bursts. Comparative genomic analyses reveal key genes involved in reproductive organ development, cell wall biosynthesis and seed storage. Two genes encoding a C18 Δ9-elongase and a C20 Δ5-desaturase are identified to be responsible for sciadonic acid biosynthesis and both are present in diverse plant lineages except angiosperms. We demonstrate that the histidine-rich boxes of the Δ5-desaturase are crucial for its catalytic activity. Methylome analysis reveals that methylation valleys of the T. grandis seed genome harbor genes associated with important seed activities, including cell wall and lipid biosynthesis. Moreover, seed development is accompanied by DNA methylation changes that possibly fuel energy production. This study provides important genomic resources and elucidates the evolutionary mechanism of sciadonic acid biosynthesis in land plants.
Association of SARS-CoV-2 BA.4/BA.5 Omicron lineages with immune escape and clinical outcome
Authors: Lewnard Joseph A. , Hong Vennis , Kim Jeniffer S. , Shaw Sally F. , Lewin Bruno , Takhar Harpreet , Tartof Sara Y. 
Published: March 2023

AbstractExpansion of the SARS-CoV-2 BA.4 and BA.5 Omicron subvariants in populations with prevalent immunity from prior infection and vaccination, and associated burden of severe COVID-19, has raised concerns about epidemiologic characteristics of these lineages including their association with immune escape or severe clinical outcomes. Here we show that BA.4/BA.5 cases in a large US healthcare system had at least 55% (95% confidence interval: 43–69%) higher adjusted odds of prior documented infection than time-matched BA.2 cases, as well as 15% (9–21%) and 38% (27–49%) higher adjusted odds of having received 3 and ≥4 COVID-19 vaccine doses, respectively. However, after adjusting for differences in epidemiologic characteristics among cases with each lineage, BA.4/BA.5 infection was not associated with differential risk of emergency department presentation, hospital admission, or intensive care unit admission following an initial outpatient diagnosis. This finding held in sensitivity analyses correcting for potential exposure misclassification resulting from unascertained prior infections. Our results demonstrate that the reduced severity associated with prior (BA.1 and BA.2) Omicron lineages, relative to the Delta variant, has persisted with BA.4/BA.5, despite the association of BA.4/BA.5 with increased risk of breakthrough infection among previously vaccinated or infected individuals.
PIP4K2B is mechanoresponsive and controls heterochromatin-driven nuclear softening through UHRF1
Authors: Poli Alessandro , Pennacchio Fabrizio A. , Ghisleni Andrea , di Gennaro Mariagrazia , Lecacheur Margaux , Nastały Paulina , Crestani Michele , Pramotton Francesca M. , Iannelli Fabio , Beznusenko Galina , Mironov Alexander A. , Panzetta Valeria , Fusco Sabato , Sheth Bhavwanti , Poulikakos Dimos , Ferrari Aldo , Gauthier Nils , Netti Paolo A. , Divecha Nullin , Maiuri Paolo 
Published: March 2023

AbstractPhosphatidylinositol-5-phosphate (PtdIns5P)−4-kinases (PIP4Ks) are stress-regulated phosphoinositide kinases able to phosphorylate PtdIns5P to PtdIns(4,5)P2. In cancer patients their expression is typically associated with bad prognosis. Among the three PIP4K isoforms expressed in mammalian cells, PIP4K2B is the one with more prominent nuclear localisation. Here, we unveil the role of PIP4K2B as a mechanoresponsive enzyme. PIP4K2B protein level strongly decreases in cells growing on soft substrates. Its direct silencing or pharmacological inhibition, mimicking cell response to softness, triggers a concomitant reduction of the epigenetic regulator UHRF1 and induces changes in nuclear polarity, nuclear envelope tension and chromatin compaction. This substantial rewiring of the nucleus mechanical state drives YAP cytoplasmic retention and impairment of its activity as transcriptional regulator, finally leading to defects in cell spreading and motility. Since YAP signalling is essential for initiation and growth of human malignancies, our data suggest that potential therapeutic approaches targeting PIP4K2B could be beneficial in the control of the altered mechanical properties of cancer cells.
Genesis of Hawaiian lavas by crystallization of picritic magma in the deep mantle
Authors: Yang Junlong , Wang Chao , Zhang Junfeng , Jin Zhenmin 
Published: March 2023

AbstractOlivine is the dominant phenocryst or xenocryst of Hawaiian tholeiitic basalts, and the general consensus is that lavas with MgO concentrations from 7.5 to about 15 weight percent were derived from their primary magmas, which contain ~18–20 weight percent MgO, by only olivine crystallization. However, the major element composition of estimated primary magmas through olivine crystallization correction is inconsistent with direct partial melting of either mantle peridotite or its hybrid with subducted oceanic crust. Our melting experiments on peridotite-derived melt composition show that this discrepancy can be resolved if the primary magmas experienced two other processes before abundant olivine fractionation. First, the primary magmas experienced crystallization of clinopyroxene and garnet in the chamber at the base of the lithosphere (approximately the depths of 90–100 km). Second, the evolved magmas re-equilibrated with harzburgite when passing through the lithospheric mantle (approximately the depths of 60–10 km). Different from the isotopic evidence, the major and rare earth element compositions of Hawaiian post-shield alkali basalts and shield tholeiites suggest that they form from the same source by assimilating different amounts of orthopyroxene.
RETRACTED ARTICLE: Polymerase θ inhibition activates the cGAS-STING pathway and cooperates with immune checkpoint blockade in models of BRCA-deficient cancer
Authors: Patterson-Fortin Jeffrey , Jadhav Heta , Pantelidou Constantia , Phan Tin , Grochala Carter , Mehta Anita K. , Guerriero Jennifer L. , Wulf Gerburg M. , Wolpin Brian M. , Stanger Ben Z. , Aguirre Andrew J. , Cleary James M. , D’Andrea Alan D. , Shapiro Geoffrey I. 
Published: March 2023

AbstractRecently developed inhibitors of polymerase theta (POLθ) have demonstrated synthetic lethality in BRCA-deficient tumor models. To examine the contribution of the immune microenvironment to antitumor efficacy, we characterized the effects of POLθ inhibition in immunocompetent models of BRCA1-deficient triple-negative breast cancer (TNBC) or BRCA2-deficient pancreatic ductal adenocarcinoma (PDAC). We demonstrate that genetic POLQ depletion or pharmacological POLθ inhibition induces both innate and adaptive immune responses in these models. POLθ inhibition resulted in increased micronuclei, cGAS/STING pathway activation, type I interferon gene expression, CD8+ T cell infiltration and activation, local paracrine activation of dendritic cells and upregulation of PD-L1 expression. Depletion of CD8+ T cells compromised the efficacy of POLθ inhibition, whereas antitumor effects were augmented in combination with anti-PD-1 immunotherapy. Collectively, our findings demonstrate that POLθ inhibition induces immune responses in a cGAS/STING-dependent manner and provide a rationale for combining POLθ inhibition with immune checkpoint blockade for the treatment of HR-deficient cancers.
Conformational transitions and allosteric modulation in a heteromeric glycine receptor
Authors: Gibbs Eric , Klemm Emily , Seiferth David , Kumar Arvind , Ilca Serban L. , Biggin Philip C. , Chakrapani Sudha 
Published: March 2023

AbstractGlycine Receptors (GlyRs) provide inhibitory neuronal input in the spinal cord and brainstem, which is critical for muscle coordination and sensory perception. Synaptic GlyRs are a heteromeric assembly of α and β subunits. Here we present cryo-EM structures of full-length zebrafish α1βBGlyR in the presence of an antagonist (strychnine), agonist (glycine), or agonist with a positive allosteric modulator (glycine/ivermectin). Each structure shows a distinct pore conformation with varying degrees of asymmetry. Molecular dynamic simulations found the structures were in a closed (strychnine) and desensitized states (glycine and glycine/ivermectin). Ivermectin binds at all five interfaces, but in a distinct binding pose at the β-α interface. Subunit-specific features were sufficient to solve structures without a fiduciary marker and to confirm the 4α:1β stoichiometry recently observed. We also report features of the extracellular and intracellular domains. Together, our results show distinct compositional and conformational properties of α1βGlyR and provide a framework for further study of this physiologically important channel.
High thermoelectric efficiency realized in SnSe crystals via structural modulation
Authors: Qin Bingchao , Wang Dongyang , Hong Tao , Wang Yuping , Liu Dongrui , Wang Ziyuan , Gao Xiang , Ge Zhen-Hua , Zhao Li-Dong 
Published: March 2023

AbstractCrystalline thermoelectrics have been developed to be potential candidates for power generation and electronic cooling, among which SnSe crystals are becoming the most representative. Herein, we realize high-performance SnSe crystals with promising efficiency through a structural modulation strategy. By alloying strontium at Sn sites, we modify the crystal structure and facilitate the multiband synglisis in p-type SnSe, favoring the optimization of interactive parameters μ and m*. Resultantly, we obtain a significantly enhanced PF ~85 μW cm−1 K−2, with an ultrahigh ZT ~1.4 at 300 K and ZTave ~2.0 among 300–673 K. Moreover, the excellent properties lead to single-leg device efficiency of ~8.9% under a temperature difference ΔT ~300 K, showing superiority among the current low- to mid-temperature thermoelectrics, with an enhanced cooling ΔTmax of ~50.4 K in the 7-pair thermoelectric device. Our study further advances p-type SnSe crystals for practical waste heat recovery and electronic cooling.
1,2,4,5-Tetrazine-tethered probes for fluorogenically imaging superoxide in live cells with ultrahigh specificity
Authors: Jiang Xuefeng , Li Min , Wang Yule , Wang Chao , Wang Yingchao , Shen Tianruo , Shen Lili , Liu Xiaogang , Wang Yi , Li Xin 
Published: March 2023

AbstractSuperoxide (O2·−) is the primary reactive oxygen species in mammal cells. Detecting superoxide is crucial for understanding redox signaling but remains challenging. Herein, we introduce a class of activity-based sensing probes. The probes utilize 1,2,4,5-tetrazine as a superoxide-responsive trigger, which can be modularly tethered to various fluorophores to tune probe sensitivity and emission color. These probes afford ultra-specific and ultra-fluorogenic responses towards superoxide, and enable multiplexed imaging of various cellular superoxide levels in an organelle-resolved way. Notably, the probes reveal the aberrant superoxide generation in the pathology of myocardial ischemia/reperfusion injury, and facilitate the establishment of a high-content screening pipeline for mediators of superoxide homeostasis. One such identified mediator, coprostanone, is shown to effectively ameliorating oxidative stress-induced injury in mice with myocardial ischemia/reperfusion injury. Collectively, these results showcase the potential of 1,2,4,5-tetrazine-tethered probes as versatile tools to monitor superoxide in a range of pathophysiological settings.
A male-killing gene encoded by a symbiotic virus of Drosophila
Authors: Kageyama Daisuke , Harumoto Toshiyuki , Nagamine Keisuke , Fujiwara Akiko , Sugimoto Takafumi N. , Jouraku Akiya , Tamura Masaru , Katoh Takehiro K. , Watada Masayoshi 
Published: March 2023

AbstractIn most eukaryotes, biparentally inherited nuclear genomes and maternally inherited cytoplasmic genomes have different evolutionary interests. Strongly female-biased sex ratios that are repeatedly observed in various arthropods often result from the male-specific lethality (male-killing) induced by maternally inherited symbiotic bacteria such as Spiroplasma and Wolbachia. However, despite some plausible case reports wherein viruses are raised as male-killers, it is not well understood how viruses, having much smaller genomes than bacteria, are capable of inducing male-killing. Here we show that a maternally inherited double-stranded RNA (dsRNA) virus belonging to the family Partitiviridae (designated DbMKPV1) induces male-killing in Drosophila. DbMKPV1 localizes in the cytoplasm and possesses only four genes, i.e., one gene in each of the four genomic segments (dsRNA1−dsRNA4), in contrast to ca. 1000 or more genes possessed by Spiroplasma or Wolbachia. We also show that a protein (designated PVMKp1; 330 amino acids in size), encoded by a gene on the dsRNA4 segment, is necessary and sufficient for inducing male-killing. Our results imply that male-killing genes can be easily acquired by symbiotic viruses through reassortment and that symbiotic viruses are hidden players in arthropod evolution. We anticipate that host-manipulating genes possessed by symbiotic viruses can be utilized for controlling arthropods.
A co-anchoring strategy for the synthesis of polar bimodal polyethylene
Authors: Zou Chen , Wang Quan , Si Guifu , Chen Changle 
Published: March 2023

AbstractSince polar groups can poison the metal centers in catalysts, the incorporation of polar comonomers usually comes at the expense of catalytic activity and polymer molecular weight. In this contribution, we demonstrate polar bimodal polyethylene as a potential solution to this trade-off. The more-polar/more-branched low-molecular-weight fraction provides polarity and processability, while the less-polar/less-branched high-molecular-weight fraction provides mechanical and melt properties. To achieve high miscibility between these two fractions, three synthetic routes are investigated: mixtures of homogeneous catalysts, separately supported heterogeneous catalysts, and a co-anchoring strategy (CAS) to heterogenize different homogeneous catalysts on one solid support. The CAS route is the only viable strategy for the synthesis of polar bimodal polyethylene with good molecular level entanglement and minimal phase separation. This produces polyolefin materials with excellent mechanical properties, surface/dyeing properties, gas barrier properties, as well as extrudability and 3D-printability.
Acute liver steatosis translationally controls the epigenetic regulator MIER1 to promote liver regeneration in a study with male mice
Authors: Chen Yanhao , Chen Lanlan , Wu Xiaoshan , Zhao Yongxu , Wang Yuchen , Jiang Dacheng , Liu Xiaojian , Zhou Tingting , Li Shuang , Wei Yuda , Liu Yan , Hu Cheng , Zhou Ben , Qin Jun , Ying Hao , Ding Qiurong 
Published: March 2023

AbstractThe early phase lipid accumulation is essential for liver regeneration. However, whether this acute lipid accumulation can serve as signals to direct liver regeneration rather than simply providing building blocks for cell proliferation remains unclear. Through in vivo CRISPR screening, we identify MIER1 (mesoderm induction early response 1) as a key epigenetic regulator that bridges the acute lipid accumulation and cell cycle gene expression during liver regeneration in male animals. Physiologically, liver acute lipid accumulation induces the phosphorylation of EIF2S1(eukaryotic translation initiation factor 2), which consequently attenuated Mier1 translation. MIER1 downregulation in turn promotes cell cycle gene expression and regeneration through chromatin remodeling. Importantly, the lipids-EIF2S1-MIER1 pathway is impaired in animals with chronic liver steatosis; whereas MIER1 depletion significantly improves regeneration in these animals. Taken together, our studies identify an epigenetic mechanism by which the early phase lipid redistribution from adipose tissue to liver during regeneration impacts hepatocyte proliferation, and suggest a potential strategy to boost liver regeneration.
High-resolution separation of bioisomers using ion cloud profiling
Authors: Zhou Xiaoyu , Wang Zhuofan , Fan Jingjin , Ouyang Zheng 
Published: March 2023

AbstractElucidation of complex structures of biomolecules plays a key role in the field of chemistry and life sciences. In the past decade, ion mobility, by coupling with mass spectrometry, has become a unique tool for distinguishing isomers and isoforms of biomolecules. In this study, we develop a concept for performing ion mobility analysis using an ion trap, which enables isomer separation under ultra-high fields to achieve super high resolutions over 10,000. The potential of this technology has been demonstrated for analysis of isomers for biomolecules including disaccharides, phospholipids, and peptides with post-translational modifications.