bluuebunny/crossref_metadata_2025_split huggingface dataset:
Constraints on axion-like dark matter from a SERF comagnetometer
Authors: Bloch Itay M. , Shaham Roy , Hochberg Yonit , Kuflik Eric , Volansky Tomer , Katz Or 
Published: September 2023

AbstractUltralight axion-like particles are well-motivated relics that might compose the cosmological dark matter and source anomalous time-dependent magnetic fields. We report on terrestrial bounds from the Noble And Alkali Spin Detectors for Ultralight Coherent darK matter (NASDUCK) collaboration on the coupling of axion-like particles to neutrons and protons. The detector uses nuclei of noble-gas and alkali-metal atoms and operates in the Spin-Exchange Relaxation-Free (SERF) regime, achieving high sensitivity to axion-like dark matter fields. Conducting a month-long search, we cover the mass range of 1.4 × 10−12 eV/c2 to 2 × 10−10 eV/c2 and provide limits which supersede robust astrophysical bounds, and improve upon previous terrestrial constraints by over two orders of magnitude for many masses within this range for protons, and up to two orders of magnitude for neutrons. These are the sole reliable terrestrial bounds reported on the coupling of protons with axion-like dark matter, covering an unexplored terrain in its parameter space.
Host heparan sulfate promotes ACE2 super-cluster assembly and enhances SARS-CoV-2-associated syncytium formation
Authors: Zhang Qi , Tang Weichun , Stancanelli Eduardo , Jung Eunkyung , Syed Zulfeqhar , Pagadala Vijayakanth , Saidi Layla , Chen Catherine Z. , Gao Peng , Xu Miao , Pavlinov Ivan , Li Bing , Huang Wenwei , Chen Liqiang , Liu Jian , Xie Hang , Zheng Wei , Ye Yihong 
Published: September 2023

AbstractSARS-CoV-2 infection causes spike-dependent fusion of infected cells with ACE2 positive neighboring cells, generating multi-nuclear syncytia that are often associated with severe COVID. To better elucidate the mechanism of spike-induced syncytium formation, we combine chemical genetics with 4D confocal imaging to establish the cell surface heparan sulfate (HS) as a critical stimulator for spike-induced cell-cell fusion. We show that HS binds spike and promotes spike-induced ACE2 clustering, forming synapse-like cell-cell contacts that facilitate fusion pore formation between ACE2-expresing and spike-transfected human cells. Chemical or genetic inhibition of HS mitigates ACE2 clustering, and thus, syncytium formation, whereas in a cell-free system comprising purified HS and lipid-anchored ACE2, HS stimulates ACE2 clustering directly in the presence of spike. Furthermore, HS-stimulated syncytium formation and receptor clustering require a conserved ACE2 linker distal from the spike-binding site. Importantly, the cell fusion-boosting function of HS can be targeted by an investigational HS-binding drug, which reduces syncytium formation in vitro and viral infection in mice. Thus, HS, as a host factor exploited by SARS-CoV-2 to facilitate receptor clustering and a stimulator of infection-associated syncytium formation, may be a promising therapeutic target for severe COVID.
Metabolic Reprogramming via ACOD1 depletion enhances function of human induced pluripotent stem cell-derived CAR-macrophages in solid tumors
Authors: Wang Xudong , Su Siyu , Zhu Yuqing , Cheng Xiaolong , Cheng Chen , Chen Leilei , Lei Anhua , Zhang Li , Xu Yuyan , Ye Dan , Zhang Yi , Li Wei , Zhang Jin 
Published: September 2023

AbstractThe pro-inflammatory state of macrophages, underpinned by their metabolic condition, is essentially affecting their capacity of combating tumor cells. Here we find, via a pooled metabolic gene knockout CRISPR screen that KEAP1 and ACOD1 are strong regulators of the pro-inflammatory state in macrophages. We show that ACOD1 knockout macrophages, generated in our induced pluripotent stem cell-derived CAR-macrophage (CAR-iMAC) platform, are strongly and persistently polarized toward the pro-inflammatory state, which manifests in increased reactive oxygen species (ROS) production, more potent phagocytosis and enhanced cytotoxic functions against cancer cells in vitro. In ovarian or pancreatic cancer mouse models, ACOD1-depleted CAR-iMACs exhibit enhanced capacity in repressing tumors, leading to increased survival. In addition, combining ACOD1-depleted CAR-iMACs with immune checkpoint inhibitors (ICI), such as anti-CD47 or anti-PD1 antibodies, result in even stronger tumor suppressing effect. Mechanistically, the depletion of ACOD1 reduces levels of the immuno-metabolite itaconate, allowing KEAP1 to prevent NRF2 from entering the nucleus to activate an anti-inflammatory program. This study thus lays down the proof of principle for targeting ACOD1 in myeloid cells for cancer immunotherapy and introduces metabolically engineered human iPSC-derived CAR-iMACs cells with enhanced polarization and anti-tumor functions in adoptive cell transfer therapies.
Cross-national analyses require additional controls to account for the non-independence of nations
Authors: Claessens Scott , Kyritsis Thanos , Atkinson Quentin D. 
Published: September 2023

AbstractCross-national analyses test hypotheses about the drivers of variation in national outcomes. However, since nations are connected in various ways, such as via spatial proximity and shared cultural ancestry, cross-national analyses often violate assumptions of non-independence, inflating false positive rates. Here, we show that, despite being recognised as an important statistical pitfall for over 200 years, cross-national research in economics and psychology still does not sufficiently account for non-independence. In a review of the 100 highest-cited cross-national studies of economic development and values, we find that controls for non-independence are rare. When studies do control for non-independence, our simulations suggest that most commonly used methods are insufficient for reducing false positives in non-independent data. In reanalyses of twelve previous cross-national correlations, half of the estimates are compatible with no association after controlling for non-independence using global proximity matrices. We urge social scientists to sufficiently control for non-independence in cross-national research.
The role of intra-guild indirect interactions in assembling plant-pollinator networks
Authors: Dritz Sabine , Nelson Rebecca A. , Valdovinos Fernanda S. 
Published: September 2023

AbstractUnderstanding the assembly of plant-pollinator communities has become critical to their conservation given the rise of species invasions, extirpations, and species’ range shifts. Over the course of assembly, colonizer establishment produces core interaction patterns, called motifs, which shape the trajectory of assembling network structure. Dynamic assembly models can advance our understanding of this process by linking the transient dynamics of colonizer establishment to long-term network development. In this study, we investigate the role of intra-guild indirect interactions and adaptive foraging in shaping the structure of assembling plant-pollinator networks by developing: 1) an assembly model that includes population dynamics and adaptive foraging, and 2) a motif analysis tracking the intra-guild indirect interactions of colonizing species throughout their establishment. We find that while colonizers leverage indirect competition for shared mutualistic resources to establish, adaptive foraging maintains the persistence of inferior competitors. This produces core motifs in which specialist and generalist species coexist on shared mutualistic resources which leads to the emergence of nested networks. Further, the persistence of specialists develops richer and less connected networks which is consistent with empirical data. Our work contributes new understanding and methods to study the effects of species’ intra-guild indirect interactions on community assembly.
Efficient intervention for pulmonary fibrosis via mitochondrial transfer promoted by mitochondrial biogenesis
Authors: Huang Ting , Lin Ruyi , Su Yuanqin , Sun Hao , Zheng Xixi , Zhang Jinsong , Lu Xiaoyan , Zhao Baiqin , Jiang Xinchi , Huang Lingling , Li Ni , Shi Jing , Fan Xiaohui , Xu Donghang , Zhang Tianyuan , Gao Jianqing 
Published: September 2023

AbstractThe use of exogenous mitochondria to replenish damaged mitochondria has been proposed as a strategy for the treatment of pulmonary fibrosis. However, the success of this strategy is partially restricted by the difficulty of supplying sufficient mitochondria to diseased cells. Herein, we report the generation of high-powered mesenchymal stem cells with promoted mitochondrial biogenesis and facilitated mitochondrial transfer to injured lung cells by the sequential treatment of pioglitazone and iron oxide nanoparticles. This highly efficient mitochondrial transfer is shown to not only restore mitochondrial homeostasis but also reactivate inhibited mitophagy, consequently recovering impaired cellular functions. We perform studies in mouse to show that these high-powered mesenchymal stem cells successfully mitigate fibrotic progression in a progressive fibrosis model, which was further verified in a humanized multicellular lung spheroid model. The present findings provide a potential strategy to overcome the current limitations in mitochondrial replenishment therapy, thereby promoting therapeutic applications for fibrotic intervention.
Discovery of the major 15–30 nt mammalian small RNAs, their biogenesis and function
Authors: Lai Hejin , Feng Ning , Zhai Qiwei 
Published: September 2023

AbstractSmall RNAs (sRNAs) within 15-30 nt such as miRNA, tsRNA, srRNA with 3’-OH have been identified. However, whether these sRNAs are the major 15-30 nt sRNAs is still unknown. Here we show about 90% mammalian sRNAs within 15-30 nt end with 2’,3’-cyclic phosphate (3’-cP). TANT-seq was developed to simultaneously profile sRNAs with 3’-cP (sRNA-cPs) and sRNA-OHs, and huge amount of sRNA-cPs were detected. Surprisingly, sRNA-cPs and sRNA-OHs usually have distinct sequences. The data from TANT-seq were validated by a novel method termed TE-qPCR, and Northern blot. Furthermore, we found that Angiogenin and RNase 4 contribute to the biogenesis of sRNA-cPs. Moreover, much more sRNA-cPs than sRNA-OHs bind to Ago2, and can regulate gene expression. Particularly, snR-2-cP regulates Bcl2 by targeting to its 3’UTR dependent on Ago2, and subsequently regulates apoptosis. In addition, sRNA-cPs can guide the cleavage of target RNAs in Ago2 complex as miRNAs without the requirement of 3’-cP. Our discovery greatly expands the repertoire of mammalian sRNAs, and provides strategies and powerful tools towards further investigation of sRNA-cPs.
Elementary school teachers’ perspectives about learning during the COVID-19 pandemic
Authors: Alvarez-Rivero Aymee , Odgers Candice , Ansari Daniel 
Published: September 2023

AbstractHow did school closures affect student access to education and learning rates during the COVID-19 pandemic? How did teachers adapt to the new instructional contexts? To answer these questions, we distributed an online survey to Elementary School teachers (N = 911) in the United States and Canada at the end of the 2020–2021 school year. Around 85.8% of participants engaged in remote instruction, and nearly half had no previous experience teaching online. Overall, this transition was challenging for most teachers and more than 50% considered they were not as effective in the classroom during remote instruction and reported not being able to deliver all the curriculum expected for their grade. Despite the widespread access to digital technologies in our sample, nearly 65% of teachers observed a drop in class attendance. More than 50% of participants observed a decline in students’ academic performance, a growth in the gaps between low and high-performing students, and predicted long-term adverse effects. We also observed consistent effects of SES in teachers’ reports. The proportion of teachers reporting a drop in performance increases from 40% in classrooms with high-income students, to more than 70% in classrooms with low-income students. Students in lower-income households were almost twice less likely to have teachers with previous experience teaching online and almost twice less likely to receive support from adults with homeschooling. Overall, our data suggest the effects of the pandemic were not equally distributed.
Understanding the recent increase in multiyear La Niñas
Authors: Wang Bin , Sun Weiyi , Jin Chunhan , Luo Xiao , Yang Young-Min , Li Tim , Xiang Baoqiang , McPhaden Michael J. , Cane Mark A. , Jin Feifei , Liu Fei , Liu Jian 
Published: September 2023

AbstractFive out of six La Niña events since 1998 have lasted two to three years. Why so many long-lasting multiyear La Niña events have emerged recently and whether they will become more common remains unknown. Here we show that ten multiyear La Niña events over the past century had an accelerated trend, with eight of these occurring after 1970. The two types of multiyear La Niña events over this time period followed either a super El Niño or a central Pacific El Niño. We find that multiyear La Niña events differ from single-year La Niñas by a prominent onset rate, which is rooted in the western Pacific warming-enhanced zonal advective feedback for the central Pacific multiyear La Niña events type and thermocline feedback for the super El Niño multiyear La Niña events type. The results from large ensemble climate simulations support the observed multiyear La Niña events–western Pacific warming link. More multiyear La Niña events will exacerbate adverse socioeconomic impacts if the western Pacific continues to warm relative to the central Pacific.
Longitudinal genomic surveillance of carriage and transmission of Clostridioides difficile in an intensive care unit
Authors: Miles-Jay Arianna , Snitkin Evan S. , Lin Michael Y. , Shimasaki Teppei , Schoeny Michael , Fukuda Christine , Dangana Thelma , Moore Nicholas , Sansom Sarah E. , Yelin Rachel D. , Bell Pamela , Rao Krishna , Keidan Micah , Standke Alexandra , Bassis Christine , Hayden Mary K. , Young Vincent B. 
Published: September 2023

AbstractDespite enhanced infection prevention efforts, Clostridioides difficile remains the leading cause of healthcare-associated infections in the United States. Current prevention strategies are limited by their failure to account for patients who carry C. difficile asymptomatically, who may act as hidden reservoirs transmitting infections to other patients. To improve the understanding of asymptomatic carriers’ contribution to C. difficile spread, we conducted admission and daily longitudinal culture-based screening for C. difficile in a US-based intensive care unit over nine months and performed whole-genome sequencing on all recovered isolates. Despite a high burden of carriage, with 9.3% of admissions having toxigenic C. difficile detected in at least one sample, only 1% of patients culturing negative on admission to the unit acquired C. difficile via cross-transmission. While patients who carried toxigenic C. difficile on admission posed minimal risk to others, they themselves had a 24-times greater risk for developing a healthcare-onset C. difficile infection than noncarriers. Together, these findings suggest that current infection prevention practices can be effective in preventing nosocomial cross-transmission of C. difficile, and that decreasing C. difficile infections in hospitals further will require interventions targeting the transition from asymptomatic carriage to infection.
Correlative montage parallel array cryo-tomography for in situ structural cell biology
Authors: Yang Jie E. , Larson Matthew R. , Sibert Bryan S. , Kim Joseph Y. , Parrell Daniel , Sanchez Juan C. , Pappas Victoria , Kumar Anil , Cai Kai , Thompson Keith , Wright Elizabeth R. 
Published: September 2023

AbstractImaging large fields of view while preserving high-resolution structural information remains a challenge in low-dose cryo-electron tomography. Here we present robust tools for montage parallel array cryo-tomography (MPACT) tailored for vitrified specimens. The combination of correlative cryo-fluorescence microscopy, focused-ion-beam milling, substrate micropatterning, and MPACT supports studies that contextually define the three-dimensional architecture of cells. To further extend the flexibility of MPACT, tilt series may be processed in their entirety or as individual tiles suitable for sub-tomogram averaging, enabling efficient data processing and analysis.
Mate-choice for close kin is associated with improved offspring survival in Lodoicea maldivica, the largest-seeded plant in the world
Authors: Morgan Emma J. , Kaiser-Bunbury Christopher N. , Edwards Peter J. , Fleischer-Dogley Frauke , Kettle Chris J. 
Published: September 2023

AbstractWe studied spatial patterns of kinship in the offspring of the endangered Lodoicea maldivica, a dioecious palm that produces the largest seed of any plant. Previous research has suggested that restricted seed and pollen dispersal in populations resulted in strong spatial genetic structure. We used microsatellites to genotype young plants and their potential parents at four sites across the species’ entire natural range. We determined the most likely parents of each young plant based on the spatial separation of each parent pair, their genetic relatedness, and the level of correlated paternity. We identified both parents (43 female, 54 male) for 139 of 493 young plants. Mean distance between parental pairs was 26.8 m. Correlated paternity was low (0.168), indicating that mother trees were often pollinated by several fathers. Parental pairs were more closely related than expected by chance, suggesting outbreeding depression. Our results highlight the apparent strong mate choice for close kin in parent pairs of surviving offspring. We discuss the alternative biological processes that could lead to this, including the potential for break-up of favourable allelic combinations necessary for the development of the palm’s very large seed. Management implications include germinating seeds where they naturally fall, using a diverse range of male plants as pollen donors for hand pollination, and protecting the native community of gecko pollinators.
The role of interpersonal synchrony in forming impressions of autistic and non-autistic adults
Authors: Plank I. S. , Traiger L. S. , Nelson A. M. , Koehler J. C. , Lang S. F. , Tepest R. , Vogeley K. , Georgescu A. L. , Falter-Wagner C. M. 
Published: September 2023

AbstractWhen people meet, they almost instantaneously form an impression of each other. First impressions of character traits and rapport are less favourable when people with autism spectrum condition (ASC) are judged compared to non-autistic people. Little is known about the behavioural differences that drive these altered impressions. In the present study, we investigated the influence of interpersonal synchrony on impression formation of autistic and non-autistic people. Specifically, we used lagged cross-correlations to assess how much each interactant’s motion energy, a measure which can be determined from video recordings, influenced the other interactant’s motion energy. In short, silent clips of dyadic conversations, we asked non-autistic participants to rate their impression of one of the two interactants, which was solely based on the outlines of both interactants. We expected that the amount of leading of the target interactant, their diagnostic status as well as the interaction of these factors would influence impression formation. We found that while the amount of leading had a positive effect on the impressions of non-autistic interactants, this was not true for interactants with ASC. This suggests that interpersonal synchrony of motion energy is one driver of less favourable impressions of autistic compared to non-autistic people.
Association analysis of agronomic traits and construction of genetic networks by resequencing of 306 sugar beet (Beta vulgaris L.) lines
Authors: Wang Liang , Zhang Ziqiang , Han Pingan , Liang Yahui , Zhang Huizhong , Fu Zengjuan , Zhao Shangmin , E Yuanyuan , Zhang Hui , Wu Xinrong , Zhang Bizhou , Chang Yue , Tang Kuangang , Zheng Wenzhe , Chen Li , Wang Ronghua , Gao Weishi , Hasi Agula , Li Xiaodong , Bai Chen 
Published: September 2023

AbstractDue to the relatively brief domestication history of sugar beet (Beta vulgaris ssp. vulgaris), our understanding of the genomic diversity and functional genes in its cultivars is limited, resulting in slow breeding progress. To address this issue, a total of 306 germplasm materials of major cultivars and breeding lines from China, the USA, and Europe were selected for genome resequencing. We investigated population structure and genetic diversity and performed selective scanning of genomic regions, identifying six novel genes associated with important agronomic traits: the candidate genes DFAX2 and P5CS for skin roughness; the candidate genes FRO5, GL24, and PPR91 for root yield and sugar yield, and the pleiotropic candidate gene POLX for flourishing growth vigour, plant height, crown size, flesh coarseness, and sugar yield. In addition, we constructed a protein–protein interaction network map and a phenotype-gene network map, which provide valuable information for identifying and characterizing functional genes affecting agronomic traits in sugar beet. Overall, our study sheds light on the future improvement of sugar beet agronomic traits at the molecular level.
Predicting unplanned readmissions in the intensive care unit: a multimodality evaluation
Authors: Sheetrit Eitam , Brief Menachem , Elisha Oren 
Published: September 2023

AbstractA hospital readmission is when a patient who was discharged from the hospital is admitted again for the same or related care within a certain period. Hospital readmissions are a significant problem in the healthcare domain, as they lead to increased hospitalization costs, decreased patient satisfaction, and increased risk of adverse outcomes such as infections, medication errors, and even death. The problem of hospital readmissions is particularly acute in intensive care units (ICUs), due to the severity of the patients’ conditions, and the substantial risk of complications. Predicting Unplanned Readmissions in ICUs is a challenging task, as it involves analyzing different data modalities, such as static data, unstructured free text, sequences of diagnoses and procedures, and multivariate time-series. Here, we investigate the effectiveness of each data modality separately, then alongside with others, using state-of-the-art machine learning approaches in time-series analysis and natural language processing. Using our evaluation process, we are able to determine the contribution of each data modality, and for the first time in the context of readmission, establish a hierarchy of their predictive value. Additionally, we demonstrate the impact of Temporal Abstractions in enhancing the performance of time-series approaches to readmission prediction. Due to conflicting definitions in the literature, we also provide a clear definition of the term Unplanned Readmission to enhance reproducibility and consistency of future research and to prevent any potential misunderstandings that could result from diverse interpretations of the term. Our experimental results on a large benchmark clinical data set show that Discharge Notes written by physicians, have better capabilities for readmission prediction than all other modalities.