bluuebunny/crossref_metadata_2025_split huggingface dataset:
NERNST: a genetically-encoded ratiometric non-destructive sensing tool to estimate NADP(H) redox status in bacterial, plant and animal systems
Authors: Molinari Pamela E. , Krapp Adriana R. , Weiner Andrea , Beyer Hannes M. , Kondadi Arun Kumar , Blomeier Tim , López Melina , Bustos-Sanmamed Pilar , Tevere Evelyn , Weber Wilfried , Reichert Andreas S. , Calcaterra Nora B. , Beller Mathias , Carrillo Nestor , Zurbriggen Matias D. 
Published: June 2023

AbstractNADP(H) is a central metabolic hub providing reducing equivalents to multiple biosynthetic, regulatory and antioxidative pathways in all living organisms. While biosensors are available to determine NADP+ or NADPH levels in vivo, no probe exists to estimate the NADP(H) redox status, a determinant of the cell energy availability. We describe herein the design and characterization of a genetically-encoded ratiometric biosensor, termed NERNST, able to interact with NADP(H) and estimate ENADP(H). NERNST consists of a redox-sensitive green fluorescent protein (roGFP2) fused to an NADPH-thioredoxin reductase C module which selectively monitors NADP(H) redox states via oxido-reduction of the roGFP2 moiety. NERNST is functional in bacterial, plant and animal cells, and organelles such as chloroplasts and mitochondria. Using NERNST, we monitor NADP(H) dynamics during bacterial growth, environmental stresses in plants, metabolic challenges to mammalian cells, and wounding in zebrafish. NERNST estimates the NADP(H) redox poise in living organisms, with various potential applications in biochemical, biotechnological and biomedical research.
Whistler-mode chorus waves at Mars
Authors: Teng Shangchun , Wu Yifan , Harada Yuki , Bortnik Jacob , Zonca Fulvio , Chen Liu , Tao Xin 
Published: June 2023

AbstractChorus waves are naturally occurring electromagnetic emissions in space and are known to produce highly energetic electrons in the hazardous radiation belt. The characteristic feature of chorus is its fast frequency chirping, whose mechanism remains a long-standing problem. While many theories agree on its nonlinear nature, they differ on whether or how the background magnetic field inhomogeneity plays a key role. Here, using observations of chorus at Mars and Earth, we report direct evidence showing that the chorus chirping rate is consistently related to the background magnetic field inhomogeneity, despite orders of magnitude difference in a key parameter quantifying the inhomogeneity at the two planets. Our results show an extreme test of a recently proposed chorus generation model and confirm the connection between the chirping rate and magnetic field inhomogeneity, opening the door to controlled plasma wave excitation in the laboratory and space.
LIS1 RNA-binding orchestrates the mechanosensitive properties of embryonic stem cells in AGO2-dependent and independent ways
Authors: Kshirsagar Aditya , Doroshev Svetlana Maslov , Gorelik Anna , Olender Tsviya , Sapir Tamar , Tsuboi Daisuke , Rosenhek-Goldian Irit , Malitsky Sergey , Itkin Maxim , Argoetti Amir , Mandel-Gutfreund Yael , Cohen Sidney R. , Hanna Jacob H. , Ulitsky Igor , Kaibuchi Kozo , Reiner Orly 
Published: June 2023

AbstractLissencephaly-1 (LIS1) is associated with neurodevelopmental diseases and is known to regulate the molecular motor cytoplasmic dynein activity. Here we show that LIS1 is essential for the viability of mouse embryonic stem cells (mESCs), and it governs the physical properties of these cells. LIS1 dosage substantially affects gene expression, and we uncovered an unexpected interaction of LIS1 with RNA and RNA-binding proteins, most prominently the Argonaute complex. We demonstrate that LIS1 overexpression partially rescued the extracellular matrix (ECM) expression and mechanosensitive genes conferring stiffness to Argonaute null mESCs. Collectively, our data transforms the current perspective on the roles of LIS1 in post-transcriptional regulation underlying development and mechanosensitive processes.
Revealing CO2 dissociation pathways at vicinal copper (997) interfaces
Authors: Kim Jeongjin , Yu Youngseok , Go Tae Won , Gallet Jean-Jacques , Bournel Fabrice , Mun Bongjin Simon , Park Jeong Young 
Published: June 2023

AbstractSize- and shape-tailored copper (Cu) nanocrystals can offer vicinal planes for facile carbon dioxide (CO2) activation. Despite extensive reactivity benchmarks, a correlation between CO2 conversion and morphology structure has not yet been established at vicinal Cu interfaces. Herein, ambient pressure scanning tunneling microscopy reveals step-broken Cu nanocluster evolutions on the Cu(997) surface under 1 mbar CO2(g). The CO2 dissociation reaction produces carbon monoxide (CO) adsorbate and atomic oxygen (O) at Cu step-edges, inducing complicated restructuring of the Cu atoms to compensate for increased surface chemical potential energy at ambient pressure. The CO molecules bound at under-coordinated Cu atoms contribute to the reversible Cu clustering with the pressure gap effect, whereas the dissociated oxygen leads to irreversible Cu faceting geometries. Synchrotron-based ambient pressure X-ray photoelectron spectroscopy identifies the chemical binding energy changes in CO-Cu complexes, which proves the characterized real-space evidence for the step-broken Cu nanoclusters under CO(g) environments. Our in situ surface observations provide a more realistic insight into Cu nanocatalyst designs for efficient CO2 conversion to renewable energy sources during C1 chemical reactions.
Neoantigen-specific CD8 T cells with high structural avidity preferentially reside in and eliminate tumors
Authors: Schmidt Julien , Chiffelle Johanna , Perez Marta A. S. , Magnin Morgane , Bobisse Sara , Arnaud Marion , Genolet Raphael , Cesbron Julien , Barras David , Navarro Rodrigo Blanca , Benedetti Fabrizio , Michel Alexandra , Queiroz Lise , Baumgaertner Petra , Guillaume Philippe , Hebeisen Michael , Michielin Olivier , Nguyen-Ngoc Tu , Huber Florian , Irving Melita , Tissot-Renaud Stéphanie , Stevenson Brian J. , Rusakiewicz Sylvie , Dangaj Laniti Denarda , Bassani-Sternberg Michal , Rufer Nathalie , Gfeller David , Kandalaft Lana E. , Speiser Daniel E. , Zoete Vincent , Coukos George , Harari Alexandre 
Published: June 2023

AbstractThe success of cancer immunotherapy depends in part on the strength of antigen recognition by T cells. Here, we characterize the T cell receptor (TCR) functional (antigen sensitivity) and structural (monomeric pMHC-TCR off-rates) avidities of 371 CD8 T cell clones specific for neoantigens, tumor-associated antigens (TAAs) or viral antigens isolated from tumors or blood of patients and healthy donors. T cells from tumors exhibit stronger functional and structural avidity than their blood counterparts. Relative to TAA, neoantigen-specific T cells are of higher structural avidity and, consistently, are preferentially detected in tumors. Effective tumor infiltration in mice models is associated with high structural avidity and CXCR3 expression. Based on TCR biophysicochemical properties, we derive and apply an in silico model predicting TCR structural avidity and validate the enrichment in high avidity T cells in patients’ tumors. These observations indicate a direct relationship between neoantigen recognition, T cell functionality and tumor infiltration. These results delineate a rational approach to identify potent T cells for personalized cancer immunotherapy.
Rare phenomena of central rhythm and pattern generation in a case of complete spinal cord injury
Authors: Minassian Karen , Bayart Aymeric , Lackner Peter , Binder Heinrich , Freundl Brigitta , Hofstoetter Ursula S. 
Published: June 2023

AbstractLumbar central pattern generators (CPGs) control the basic rhythm and coordinate muscle activation underlying hindlimb locomotion in quadrupedal mammals. The existence and function of CPGs in humans have remained controversial. Here, we investigated a case of a male individual with complete thoracic spinal cord injury who presented with a rare form of self-sustained rhythmic spinal myoclonus in the legs and rhythmic activities induced by epidural electrical stimulation (EES). Analysis of muscle activation patterns suggested that the myoclonus tapped into spinal circuits that generate muscle spasms, rather than reflecting locomotor CPG activity as previously thought. The EES-induced patterns were fundamentally different in that they included flexor-extensor and left-right alternations, hallmarks of locomotor CPGs, and showed spontaneous errors in rhythmicity. These motor deletions, with preserved cycle frequency and period when rhythmic activity resumed, were previously reported only in animal studies and suggest a separation between rhythm generation and pattern formation. Spinal myoclonus and the EES-induced activity demonstrate that the human lumbar spinal cord contains distinct mechanisms for generating rhythmic multi-muscle patterns.
PIE-seq: identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing
Authors: Ruan Xiangbin , Hu Kaining , Zhang Xiaochang 
Published: June 2023

AbstractRNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. Here we present PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. We benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.
Estimating the impact of COVID-19 vaccine inequities: a modeling study
Authors: Gozzi Nicolò , Chinazzi Matteo , Dean Natalie E. , Longini Jr Ira M. , Halloran M. Elizabeth , Perra Nicola , Vespignani Alessandro 
Published: June 2023

AbstractAccess to COVID-19 vaccines on the global scale has been drastically hindered by structural socio-economic disparities. Here, we develop a data-driven, age-stratified epidemic model to evaluate the effects of COVID-19 vaccine inequities in twenty lower middle and low income countries (LMIC) selected from all WHO regions. We investigate and quantify the potential effects of higher or earlier doses availability. In doing so, we focus on the crucial initial months of vaccine distribution and administration, exploring counterfactual scenarios where we assume the same per capita daily vaccination rate reported in selected high income countries. We estimate that more than 50% of deaths (min-max range: [54−94%]) that occurred in the analyzed countries could have been averted. We further consider scenarios where LMIC had similarly early access to vaccine doses as high income countries. Even without increasing the number of doses, we estimate an important fraction of deaths (min-max range: [6−50%]) could have been averted. In the absence of the availability of high-income countries, the model suggests that additional non-pharmaceutical interventions inducing a considerable relative decrease of transmissibility (min-max range: [15−70%]) would have been required to offset the lack of vaccines. Overall, our results quantify the negative impacts of vaccine inequities and underscore the need for intensified global efforts devoted to provide faster access to vaccine programs in low and lower-middle-income countries.
Coherent dynamics of strongly interacting electronic spin defects in hexagonal boron nitride
Authors: Gong Ruotian , He Guanghui , Gao Xingyu , Ju Peng , Liu Zhongyuan , Ye Bingtian , Henriksen Erik A. , Li Tongcang , Zu Chong 
Published: June 2023

AbstractOptically active spin defects in van der Waals materials are promising platforms for modern quantum technologies. Here we investigate the coherent dynamics of strongly interacting ensembles of negatively charged boron-vacancy ($${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$VB−) centers in hexagonal boron nitride (hBN) with varying defect density. By employing advanced dynamical decoupling sequences to selectively isolate different dephasing sources, we observe more than 5-fold improvement in the measured coherence times across all hBN samples. Crucially, we identify that the many-body interaction within the$${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$VB−ensemble plays a substantial role in the coherent dynamics, which is then used to directly estimate the concentration of$${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$VB−. We find that at high ion implantation dosage, only a small portion of the created boron vacancy defects are in the desired negatively charged state. Finally, we investigate the spin response of$${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$VB−to the local charged defects induced electric field signals, and estimate its ground state transverse electric field susceptibility. Our results provide new insights on the spin and charge properties of$${{{{{{{{\rm{V}}}}}}}}}_{{{{{{{{\rm{B}}}}}}}}}^{-}$$VB−, which are important for future use of defects in hBN as quantum sensors and simulators.
Limosilactobacillus mucosae-derived extracellular vesicles modulates macrophage phenotype and orchestrates gut homeostasis in a diarrheal piglet model
Authors: Li Jingjing , Feng Shuaifei , Wang Zhenyu , He Jinhui , Zhang Zeyue , Zou Huicong , Wu Zhifeng , Liu Xiangdong , Wei Hong , Tao Shiyu 
Published: June 2023

AbstractThe diarrheal disease causes high mortality, especially in children and young animals. The gut microbiome is strongly associated with diarrheal disease, and some specific strains of bacteria have demonstrated antidiarrheal effects. However, the antidiarrheal mechanisms of probiotic strains have not been elucidated. Here, we used neonatal piglets as a translational model and found that gut microbiota dysbiosis observed in diarrheal piglets was mainly characterized by a deficiency of Lactobacillus, an abundance of Escherichia coli, and enriched lipopolysaccharide biosynthesis. Limosilactobacillus mucosae and Limosilactobacillus reuteri were a signature bacterium that differentiated healthy and diarrheal piglets. Germ-free (GF) mice transplanted with fecal microbiota from diarrheal piglets reproduced diarrheal disease symptoms. Administration of Limosilactobacillus mucosae but not Limosilactobacillus reuteri alleviated diarrheal disease symptoms induced by fecal microbiota of diarrheal piglets and by ETEC K88 challenge. Notably, Limosilactobacillus mucosae-derived extracellular vesicles alleviated diarrheal disease symptoms caused by ETEC K88 by regulating macrophage phenotypes. Macrophage elimination experiments demonstrated that the extracellular vesicles alleviated diarrheal disease symptoms in a macrophage-dependent manner. Our findings provide insights into the pathogenesis of diarrheal disease from the perspective of intestinal microbiota and the development of probiotic-based antidiarrheal therapeutic strategies.
Realizing all-to-all couplings among detachable quantum modules using a microwave quantum state router
Authors: Zhou Chao , Lu Pinlei , Praquin Matthieu , Chien Tzu-Chiao , Kaufman Ryan , Cao Xi , Xia Mingkang , Mong Roger S. K. , Pfaff Wolfgang , Pekker David , Hatridge Michael 
Published: June 2023

AbstractOne of the primary challenges in realizing large-scale quantum processors is the realization of qubit couplings that balance interaction strength, connectivity, and mode confinement. Moreover, it is very desirable for the device elements to be detachable, allowing components to be built, tested, and replaced independently. In this work, we present a microwave quantum state router, centered on parametrically driven, Josephson-junction based three-wave mixing, that realizes all-to-all couplings among four detachable quantum modules. We demonstrate coherent exchange among all four communication modes, with an average full-iSWAP time of 764 ns and average inferred inter-module exchange fidelity of 0.969, limited by mode coherence. We also demonstrate photon transfer and pairwise entanglement between module qubits, and parallel operation of simultaneousiSWAP exchange across the router. Our router-module architecture serves as a prototype of modular quantum computer that has great potential for enabling flexible, demountable, large-scale quantum networks of superconducting qubits and cavities.
Computational modeling of DLBCL predicts response to BH3-mimetics
Authors: Cloete Ielyaas , Smith Victoria M. , Jackson Ross A. , Pepper Andrea , Pepper Chris , Vogler Meike , Dyer Martin J. S. , Mitchell Simon 
Published: June 2023

AbstractIn healthy cells, pro- and anti-apoptotic BCL2 family and BH3-only proteins are expressed in a delicate equilibrium. In contrast, this homeostasis is frequently perturbed in cancer cells due to the overexpression of anti-apoptotic BCL2 family proteins. Variability in the expression and sequestration of these proteins in Diffuse Large B cell Lymphoma (DLBCL) likely contributes to variability in response to BH3-mimetics. Successful deployment of BH3-mimetics in DLBCL requires reliable predictions of which lymphoma cells will respond. Here we show that a computational systems biology approach enables accurate prediction of the sensitivity of DLBCL cells to BH3-mimetics. We found that fractional killing of DLBCL, can be explained by cell-to-cell variability in the molecular abundances of signaling proteins. Importantly, by combining protein interaction data with a knowledge of genetic lesions in DLBCL cells, our in silico models accurately predict in vitro response to BH3-mimetics. Furthermore, through virtual DLBCL cells we predict synergistic combinations of BH3-mimetics, which we then experimentally validated. These results show that computational systems biology models of apoptotic signaling, when constrained by experimental data, can facilitate the rational assignment of efficacious targeted inhibitors in B cell malignancies, paving the way for development of more personalized approaches to treatment.
Meta-analysis of single-cell and single-nucleus transcriptomics reveals kidney cell type consensus signatures
Authors: Quatredeniers Marceau , Serafin Alice S. , Benmerah Alexandre , Rausell Antonio , Saunier Sophie , Viau Amandine 
Published: June 2023

AbstractWhile the amount of studies involving single-cell or single-nucleus RNA-sequencing technologies grows exponentially within the biomedical research area, the kidney field requires reference transcriptomic signatures to allocate each cluster its matching cell type. The present meta-analysis of 39 previously published datasets, from 7 independent studies, involving healthy human adult kidney samples, offers a set of 24 distinct consensus kidney cell type signatures. The use of these signatures may help to assure the reliability of cell type identification in future studies involving single-cell and single-nucleus transcriptomics while improving the reproducibility in cell type allocation.
ICESat-2 river surface slope (IRIS): A global reach-scale water surface slope dataset
Authors: Scherer Daniel , Schwatke Christian , Dettmering Denise , Seitz Florian 
Published: June 2023

AbstractThe global reach-scale “ICESat-2 River Surface Slope” (IRIS) dataset comprises average and extreme water surface slopes (WSS) derived from ICESat-2 observations between October 2018 and August 2022 as a supplement to 121,583 reaches from the “SWOT Mission River Database” (SWORD). To gain full advantage of ICESat-2’s unique measurement geometry with six parallel lidar beams, the WSS is determined across pairs of beams or along individual beams, depending on the intersection angle of spacecraft orbit and river centerline. Combining both approaches maximizes spatial and temporal coverage. IRIS can be used to research river dynamics, estimate river discharge, and correct water level time series from satellite altimetry for shifting ground tracks. Additionally, by referencing SWORD as a common database, IRIS may be used in combination with observations from the recently launched SWOT mission.
Gap-free genome assembly of anadromous Coilia nasus
Authors: Ma Fengjiao , Wang Yinping , Su Bixiu , Zhao Chenxi , Yin Denghua , Chen Chunhai , Yang Yanping , Wang Chenhe , Luo Bei , Wang Hongqi , Deng Yanmin , Xu Pao , Yin Guojun , Jian Jianbo , Liu Kai 
Published: June 2023

AbstractThe Chinese tapertail anchovy,Coilia nasus, is a socioeconomically important anadromous fish that migrates from near ocean waters to freshwater to spawn every spring. The analysis of genomic architecture and information ofC. nasuswere hindered by the previously released versions of reference genomes with gaps. Here, we report the assembly of a chromosome-level gap-free genome ofC. nasusby incorporating high-coverage and accurate long-read sequence data with multiple assembly strategies. All 24 chromosomes were assembled without gaps, representing the highest completeness and assembly quality. We assembled the genome with a size of 851.67 Mb and used BUSCO to estimate the completeness of the assembly as 92.5%. Using a combination ofde novoprediction, protein homology and RNA-seq annotation, 21,900 genes were functionally annotated, representing 99.68% of the total predicted protein-coding genes. The availability of gap-free reference genomes forC. nasuswill provide the opportunity for understanding genome structure and function, and will also lay a solid foundation for further management and conservation of this important species.
Face mask is an efficient tool to fight the Covid-19 pandemic and some factors increase the probability of its adoption
Authors: Damette Olivier , Huynh Toan Luu Duc 
Published: June 2023

AbstractThis study examines the dynamic impact of face mask use on both infected cases and fatalities at a global scale by using a rich set of panel data econometrics. An increase of 100% of the proportion of people declaring wearing a mask (multiply by two) over the studied period lead to a reduction of around 12 and 13.5% of the number of Covid-19 infected cases (per capita) after 7 and 14 days respectively. The delay of action varies from around 7 days to 28 days concerning infected cases but is more longer concerning fatalities. Our results hold when using the rigorous controlling approach. We also document the increasing adoption of mask use over time and the drivers of mask adoption. In addition, population density and pollution levels are significant determinants of heterogeneity regarding mask adoption across countries, while altruism, trust in government and demographics are not. However, individualism index is negatively correlated with mask adoption. Finally, strict government policies against Covid-19 have a strong significant effect on mask use.