bluuebunny/crossref_metadata_2025_split huggingface dataset:
Adjuvant-dependent impact of inactivated SARS-CoV-2 vaccines during heterologous infection by a SARS-related coronavirus
Authors: Dillard Jacob A. , Taft-Benz Sharon A. , Knight Audrey C. , Anderson Elizabeth J. , Pressey Katia D. , Parotti Breantié , Martinez Sabian A. , Diaz Jennifer L. , Sarkar Sanjay , Madden Emily A. , De la Cruz Gabriela , Adams Lily E. , Dinnon Kenneth H. , Leist Sarah R. , Martinez David R. , Schäfer Alexandra , Powers John M. , Yount Boyd L. , Castillo Izabella N. , Morales Noah L. , Burdick Jane , Evangelista Mia Katrina D. , Ralph Lauren M. , Pankow Nicholas C. , Linnertz Colton L. , Lakshmanane Premkumar , Montgomery Stephanie A. , Ferris Martin T. , Baric Ralph S. , Baxter Victoria K. , Heise Mark T. 
Published: May 2024

AbstractWhole virus-based inactivated SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide have been critical to the COVID-19 pandemic response. Although these vaccines are protective against homologous coronavirus infection, the emergence of novel variants and the presence of large zoonotic reservoirs harboring novel heterologous coronaviruses provide significant opportunities for vaccine breakthrough, which raises the risk of adverse outcomes like vaccine-associated enhanced respiratory disease. Here, we use a female mouse model of coronavirus disease to evaluate inactivated vaccine performance against either homologous challenge with SARS-CoV-2 or heterologous challenge with a bat-derived coronavirus that represents a potential emerging disease threat. We show that inactivated SARS-CoV-2 vaccines adjuvanted with aluminum hydroxide can cause enhanced respiratory disease during heterologous infection, while use of an alternative adjuvant does not drive disease and promotes heterologous viral clearance. In this work, we highlight the impact of adjuvant selection on inactivated vaccine safety and efficacy against heterologous coronavirus infection.
Discovery of immunotherapy targets for pediatric solid and brain tumors by exon-level expression
Authors: Shaw Timothy I. , Wagner Jessica , Tian Liqing , Wickman Elizabeth , Poudel Suresh , Wang Jian , Paul Robin , Koo Selene C. , Lu Meifen , Sheppard Heather , Fan Yiping , O’Neill Francis H. , Lau Ching C. , Zhou Xin , Zhang Jinghui , Gottschalk Stephen 
Published: May 2024

AbstractImmunotherapy with chimeric antigen receptor T cells for pediatric solid and brain tumors is constrained by available targetable antigens. Cancer-specific exons present a promising reservoir of targets; however, these have not been explored and validated systematically in a pan-cancer fashion. To identify cancer specific exon targets, here we analyze 1532 RNA-seq datasets from 16 types of pediatric solid and brain tumors for comparison with normal tissues using a newly developed workflow. We find 2933 exons in 157 genes encoding proteins of the surfaceome or matrisome with high cancer specificity either at the gene (n = 148) or the alternatively spliced isoform (n = 9) level. Expression of selected alternatively spliced targets, including the EDB domain of fibronectin 1, and gene targets, such as COL11A1, are validated in pediatric patient derived xenograft tumors. We generate T cells expressing chimeric antigen receptors specific for the EDB domain or COL11A1 and demonstrate that these have antitumor activity. The full target list, explorable via an interactive web portal (https://cseminer.stjude.org/), provides a rich resource for developing immunotherapy of pediatric solid and brain tumors using gene or AS targets with high expression specificity in cancer.
Bose-Einstein condensation of non-ground-state caesium atoms
Authors: Horvath Milena , Dhar Sudipta , Das Arpita , Frye Matthew D. , Guo Yanliang , Hutson Jeremy M. , Landini Manuele , Nägerl Hanns-Christoph 
Published: May 2024

AbstractBose-Einstein condensates of ultracold atoms serve as low-entropy sources for a multitude of quantum-science applications, ranging from quantum simulation and quantum many-body physics to proof-of-principle experiments in quantum metrology and quantum computing. For stability reasons, in the majority of cases the energetically lowest-lying atomic spin state is used. Here, we report the Bose-Einstein condensation of caesium atoms in the Zeeman-excited mf = 2 state, realizing a non-ground-state Bose-Einstein condensate with tunable interactions and tunable loss. We identify two regions of magnetic field in which the two-body relaxation rate is low enough that condensation is possible. We characterize the phase transition and quantify the loss processes, finding unusually high three-body losses in one of the two regions. Our results open up new possibilities for the mixing of quantum-degenerate gases, for polaron and impurity physics, and in particular for the study of impurity transport in strongly correlated one-dimensional quantum wires.
A human neural crest model reveals the developmental impact of neuroblastoma-associated chromosomal aberrations
Authors: Saldana-Guerrero Ingrid M. , Montano-Gutierrez Luis F. , Boswell Katy , Hafemeister Christoph , Poon Evon , Shaw Lisa E. , Stavish Dylan , Lea Rebecca A. , Wernig-Zorc Sara , Bozsaky Eva , Fetahu Irfete S. , Zoescher Peter , Pötschger Ulrike , Bernkopf Marie , Wenninger-Weinzierl Andrea , Sturtzel Caterina , Souilhol Celine , Tarelli Sophia , Shoeb Mohamed R. , Bozatzi Polyxeni , Rados Magdalena , Guarini Maria , Buri Michelle C. , Weninger Wolfgang , Putz Eva M. , Huang Miller , Ladenstein Ruth , Andrews Peter W. , Barbaric Ivana , Cresswell George D. , Bryant Helen E. , Distel Martin , Chesler Louis , Taschner-Mandl Sabine , Farlik Matthias , Tsakiridis Anestis , Halbritter Florian 
Published: May 2024

AbstractEarly childhood tumours arise from transformed embryonic cells, which often carry large copy number alterations (CNA). However, it remains unclear how CNAs contribute to embryonic tumourigenesis due to a lack of suitable models. Here we employ female human embryonic stem cell (hESC) differentiation and single-cell transcriptome and epigenome analysis to assess the effects of chromosome 17q/1q gains, which are prevalent in the embryonal tumour neuroblastoma (NB). We show that CNAs impair the specification of trunk neural crest (NC) cells and their sympathoadrenal derivatives, the putative cells-of-origin of NB. This effect is exacerbated upon overexpression of MYCN, whose amplification co-occurs with CNAs in NB. Moreover, CNAs potentiate the pro-tumourigenic effects of MYCN and mutant NC cells resemble NB cells in tumours. These changes correlate with a stepwise aberration of developmental transcription factor networks. Together, our results sketch a mechanistic framework for the CNA-driven initiation of embryonal tumours.
Polymer hetero-electrolyte enabled solid-state 2.4-V Zn/Li hybrid batteries
Authors: Chen Ze , Wang Tairan , Wu Zhuoxi , Hou Yue , Chen Ao , Wang Yanbo , Huang Zhaodong , Schmidt Oliver G. , Zhu Minshen , Fan Jun , Zhi Chunyi 
Published: May 2024

AbstractThe high redox potential of Zn0/2+ leads to low voltage of Zn batteries and therefore low energy density, plaguing deployment of Zn batteries in many energy-demanding applications. Though employing high-voltage cathode like spinel LiNi0.5Mn1.5O4 can increase the voltages of Zn batteries, Zn2+ ions will be immobilized in LiNi0.5Mn1.5O4 once intercalated, resulting in irreversibility. Here, we design a polymer hetero-electrolyte consisting of an anode layer with Zn2+ ions as charge carriers and a cathode layer that blocks the Zn2+ ion shuttle, which allows separated Zn and Li reversibility. As such, the Zn‖LNMO cell exhibits up to 2.4 V discharge voltage and 450 stable cycles with high reversible capacity, which are also attained in a scale-up pouch cell. The pouch cell shows a low self-discharge after resting for 28 days. The designed electrolyte paves the way to develop high-voltage Zn batteries based on reversible lithiated cathodes.
LncRNA-LncDACH1 mediated phenotypic switching of smooth muscle cells during neointimal hyperplasia in male arteriovenous fistulas
Authors: Li Zhaozheng , Zhao Yao , Pan Zhenwei , Cai Benzhi , Zhang Chengwei , Jiao Jundong 
Published: May 2024

AbstractArteriovenous fistulas (AVFs) are the most common vascular access points for hemodialysis (HD), but they have a high incidence of postoperative dysfunction, mainly due to excessive neointimal hyperplasia (NIH). Our previous studies have revealed a highly conserved LncRNA-LncDACH1 as an important regulator of cardiomyocyte and fibroblast proliferation. Herein, we find that LncDACH1 regulates NIH in AVF in male mice with conditional knockout of smooth muscle cell-specific LncDACH1 and in male mice model of AVF with LncDACH1 overexpression by adeno-associated virus. Mechanistically, silence of LncDACH1 activates p-AKT through promoting the expression of heat shock protein 90 (HSP90) and serine/arginine-rich splicing factor protein kinase 1 (SRPK1). Moreover, LncDACH1 is transcriptionally activated by transcription factor KLF9 that binds directly to the promoter region of the LncDACH1 gene. In this work, during AVF NIH, LncDACH1 is downregulated by KLF9 and promotes NIH through the HSP90/ SRPK1/ AKT signaling axis.
Synthetic BZLF1-targeted transcriptional activator for efficient lytic induction therapy against EBV-associated epithelial cancers
Authors: Wu Man , Hau Pok Man , Li Linxian , Tsang Chi Man , Yang Yike , Taghbalout Aziz , Chung Grace Tin-Yun , Hui Shin Yee , Tang Wing Chung , Jillette Nathaniel , Zhu Jacqueline Jufen , Lee Horace Hok Yeung , Kong Ee Ling , Chan Melissa Sue Ann , Chan Jason Ying Kuen , Ma Brigette Buig Yue , Chen Mei-Ru , Lee Charles , To Ka Fai , Cheng Albert Wu , Lo Kwok-Wai 
Published: May 2024

AbstractThe unique virus-cell interaction in Epstein-Barr virus (EBV)-associated malignancies implies targeting the viral latent-lytic switch is a promising therapeutic strategy. However, the lack of specific and efficient therapeutic agents to induce lytic cycle in these cancers is a major challenge facing clinical implementation. We develop a synthetic transcriptional activator that specifically activates endogenous BZLF1 and efficiently induces lytic reactivation in EBV-positive cancer cells. A lipid nanoparticle encapsulating nucleoside-modified mRNA which encodes a BZLF1-specific transcriptional activator (mTZ3-LNP) is synthesized for EBV-targeted therapy. Compared with conventional chemical inducers, mTZ3-LNP more efficiently activates EBV lytic gene expression in EBV-associated epithelial cancers. Here we show the potency and safety of treatment with mTZ3-LNP to suppress tumor growth in EBV-positive cancer models. The combination of mTZ3-LNP and ganciclovir yields highly selective cytotoxic effects of mRNA-based lytic induction therapy against EBV-positive tumor cells, indicating the potential of mRNA nanomedicine in the treatment of EBV-associated epithelial cancers.
In vivo genome editing via CRISPR/Cas9-mediated homology-independent targeted integration for Bietti crystalline corneoretinal dystrophy treatment
Authors: Meng Xiang , Jia Ruixuan , Zhao Xinping , Zhang Fan , Chen Shaohong , Yu Shicheng , Liu Xiaozhen , Dou Hongliang , Feng Xuefeng , Zhang Jinlu , Wang Ni , Xu Boling , Yang Liping 
Published: May 2024

AbstractBietti crystalline corneoretinal dystrophy (BCD) is an autosomal recessive chorioretinal degenerative disease without approved therapeutic drugs. It is caused by mutations in CYP4V2 gene, and about 80% of BCD patients carry mutations in exon 7 to 11. Here, we apply CRISPR/Cas9 mediated homology-independent targeted integration (HITI)-based gene editing therapy in HEK293T cells, BCD patient derived iPSCs, and humanized Cyp4v3 mouse model (h-Cyp4v3mut/mut) using two rAAV2/8 vectors via sub-retinal administration. We find that sgRNA-guided Cas9 generates double-strand cleavage on intron 6 of the CYP4V2 gene, and the HITI donor inserts the carried sequence, part of intron 6, exon 7-11, and a stop codon into the DNA break, achieving precise integration, effective transcription and translation both in vitro and in vivo. HITI-based editing restores the viability of iPSC-RPE cells from BCD patient, improves the morphology, number and metabolism of RPE and photoreceptors in h-Cyp4v3mut/mut mice. These results suggest that HITI-based editing could be a promising therapeutic strategy for those BCD patients carrying mutations in exon 7 to 11, and one injection will achieve lifelong effectiveness.
The DEAD-box RNA helicase PfDOZI imposes opposing actions on RNA metabolism in Plasmodium falciparum
Authors: Min Hui , Liang Xiaoying , Wang Chengqi , Qin Junling , Boonhok Rachasak , Muneer Azhar , Brashear Awtum M. , Li Xiaolian , Minns Allen M. , Adapa Swamy Rakesh , Jiang Rays H. Y. , Ning Gang , Cao Yaming , Lindner Scott E. , Miao Jun , Cui Liwang 
Published: May 2024

AbstractIn malaria parasites, the regulation of mRNA translation, storage and degradation during development and life-stage transitions remains largely unknown. Here, we functionally characterized the DEAD-box RNA helicase PfDOZI inP. falciparum. Disruption ofpfdozienhanced asexual proliferation but reduced sexual commitment and impaired gametocyte development. By quantitative transcriptomics, we show that PfDOZI is involved in the regulation of invasion-related genes and sexual stage-specific genes during different developmental stages. PfDOZI predominantly participates in processing body-like mRNPs in schizonts but germ cell granule-like mRNPs in gametocytes to impose opposing actions of degradation and protection on different mRNA targets. We further show the formation of stress granule-like mRNPs during nutritional deprivation, highlighting an essential role of PfDOZI-associated mRNPs in stress response. We demonstrate that PfDOZI participates in distinct mRNPs to maintain mRNA homeostasis in response to life-stage transition and environmental changes by differentially executing post-transcriptional regulation on the target mRNAs.
Observation of dichotomic field-tunable electronic structure in twisted monolayer-bilayer graphene
Authors: Zhang Hongyun , Li Qian , Park Youngju , Jia Yujin , Chen Wanying , Li Jiaheng , Liu Qinxin , Bao Changhua , Leconte Nicolas , Zhou Shaohua , Wang Yuan , Watanabe Kenji , Taniguchi Takashi , Avila Jose , Dudin Pavel , Yu Pu , Weng Hongming , Duan Wenhui , Wu Quansheng , Jung Jeil , Zhou Shuyun 
Published: May 2024

AbstractTwisted bilayer graphene (tBLG) provides a fascinating platform for engineering flat bands and inducing correlated phenomena. By designing the stacking architecture of graphene layers, twisted multilayer graphene can exhibit different symmetries with rich tunability. For example, in twisted monolayer-bilayer graphene (tMBG) which breaks the C2z symmetry, transport measurements reveal an asymmetric phase diagram under an out-of-plane electric field, exhibiting correlated insulating state and ferromagnetic state respectively when reversing the field direction. Revealing how the electronic structure evolves with electric field is critical for providing a better understanding of such asymmetric field-tunable properties. Here we report the experimental observation of field-tunable dichotomic electronic structure of tMBG by nanospot angle-resolved photoemission spectroscopy (NanoARPES) with operando gating. Interestingly, selective enhancement of the relative spectral weight contributions from monolayer and bilayer graphene is observed when switching the polarity of the bias voltage. Combining experimental results with theoretical calculations, the origin of such field-tunable electronic structure, resembling either tBLG or twisted double-bilayer graphene (tDBG), is attributed to the selectively enhanced contribution from different stacking graphene layers with a strong electron-hole asymmetry. Our work provides electronic structure insights for understanding the rich field-tunable physics of tMBG.
Low-index mesoscopic surface reconstructions of Au surfaces using Bayesian force fields
Authors: Owen Cameron J. , Xie Yu , Johansson Anders , Sun Lixin , Kozinsky Boris 
Published: May 2024

AbstractMetal surfaces have long been known to reconstruct, significantly influencing their structural and catalytic properties. Many key mechanistic aspects of these subtle transformations remain poorly understood due to limitations of previous simulation approaches. Using active learning of Bayesian machine-learned force fields trained from ab initio calculations, we enable large-scale molecular dynamics simulations to describe the thermodynamics and time evolution of the low-index mesoscopic surface reconstructions of Au (e.g., the Au(111)-‘Herringbone,’ Au(110)-(1 × 2)-‘Missing-Row,’ and Au(100)-‘Quasi-Hexagonal’ reconstructions). This capability yields direct atomistic understanding of the dynamic emergence of these surface states from their initial facets, providing previously inaccessible information such as nucleation kinetics and a complete mechanistic interpretation of reconstruction under the effects of strain and local deviations from the original stoichiometry. We successfully reproduce previous experimental observations of reconstructions on pristine surfaces and provide quantitative predictions of the emergence of spinodal decomposition and localized reconstruction in response to strain at non-ideal stoichiometries. A unified mechanistic explanation is presented of the kinetic and thermodynamic factors driving surface reconstruction. Furthermore, we study surface reconstructions on Au nanoparticles, where characteristic (111) and (100) reconstructions spontaneously appear on a variety of high-symmetry particle morphologies.
A fast-charging/discharging and long-term stable artificial electrode enabled by space charge storage mechanism
Authors: Zhao Linyi , Wang Tiansheng , Zuo Fengkai , Ju Zhengyu , Li Yuhao , Li Qiang , Zhu Yue , Li Hongsen , Yu Guihua 
Published: May 2024

AbstractLithium‐ion batteries with fast-charging/discharging properties are urgently needed for the mass adoption of electric vehicles. Here, we show that fast charging/discharging, long-term stable and high energy charge-storage properties can be realized in an artificial electrode made from a mixed electronic/ionic conductor material (Fe/LixM, where M = O, F, S, N) enabled by a space charge principle. Particularly, the Fe/Li2O electrode is able to be charged/discharged to 126 mAh g−1 in 6 s at a high current density of up to 50 A g−1, and it also shows stable cycling performance for 30,000 cycles at a current density of 10 A g−1, with a mass-loading of ~2.5 mg cm−2 of the electrode materials. This study demonstrates the critical role of the space charge storage mechanism in advancing electrochemical energy storage and provides an unconventional perspective for designing high-performance anode materials for lithium-ion batteries.
Active learning graph neural networks for partial charge prediction of metal-organic frameworks via dropout Monte Carlo
Authors: Thaler Stephan , Mayr Felix , Thomas Siby , Gagliardi Alessio , Zavadlav Julija 
Published: May 2024

AbstractMetal-organic frameworks (MOF) are an attractive class of porous materials due to their immense design space, allowing for application-tailored properties. Properties of interest, such as gas sorption, can be predicted in silico with molecular mechanics simulations. However, the accuracy is limited by the available empirical force field and partial charge estimation scheme. In this work, we train a graph neural network for partial charge prediction via active learning based on Dropout Monte Carlo. We show that active learning significantly reduces the required amount of labeled MOFs to reach a target accuracy. The obtained model generalizes well to different distributions of MOFs and Zeolites. In addition, the uncertainty predictions of Dropout Monte Carlo enable reliable estimation of the mean absolute error for unseen MOFs. This work paves the way towards accurate molecular modeling of MOFs via next-generation potentials with machine learning predicted partial charges, supporting in-silico material design.
Engineering holography with stabilizer graph codes
Authors: Anglès Munné Gerard , Kasper Valentin , Huber Felix 
Published: May 2024

AbstractThe discovery of holographic codes established a surprising connection between quantum error correction and the anti-de Sitter-conformal field theory correspondence. Recent technological progress in artificial quantum systems renders the experimental realization of such holographic codes now within reach. Formulating the hyperbolic pentagon code in terms of a stabilizer graph code, we give gate sequences that are tailored to systems with long-range interactions. We show how to obtain encoding and decoding circuits for the hyperbolic pentagon code, before focusing on a small instance of the holographic code on twelve qubits. Our approach allows to verify holographic properties by partial decoding operations, recovering bulk degrees of freedom from their nearby boundary.
Phonological awareness mediates the relationship between DCDC2 and reading performance with home environment
Authors: Li Miao , DeMille Mellissa M. C. , Lovett Maureen W. , Bosson-Heenan Joan , Frijters Jan C. , Gruen Jeffrey R. ,   the GRaD Study Consortium, Boada Richard , Gottwald Stephanie , Hill Dina , Jacobson Lisa A. , Willcutt Erik G. , Wolf Maryanne 
Published: May 2024

AbstractProficient reading requires critical phonological processing skill that interacts with both genetic and environmental factors. However, the precise nature of the relationships between phonological processing and genetic and environmental factors are poorly understood. We analyzed data from the Genes, Reading and Dyslexia (GRaD) Study on 1419 children ages 8–15 years from African-American and Hispanic-American family backgrounds living in North America. The analyses showed that phonological awareness mediated the relationship between DCDC2-READ1 and reading outcomes when parental education and socioeconomic status was low. The association between READ1 and reading performance is complex, whereby mediation by phonological awareness was significantly moderated by both parental education and socioeconomic status. These results show the importance of home environment and phonological skills when determining associations between READ1 and reading outcomes. This will be an important consideration in the development of genetic screening for risk of reading disability.
Decoding the principle of cell-fate determination for its reverse control
Authors: Lee Jonghoon , Kim Namhee , Cho Kwang-Hyun 
Published: May 2024

AbstractUnderstanding and manipulating cell fate determination is pivotal in biology. Cell fate is determined by intricate and nonlinear interactions among molecules, making mathematical model-based quantitative analysis indispensable for its elucidation. Nevertheless, obtaining the essential dynamic experimental data for model development has been a significant obstacle. However, recent advancements in large-scale omics data technology are providing the necessary foundation for developing such models. Based on accumulated experimental evidence, we can postulate that cell fate is governed by a limited number of core regulatory circuits. Following this concept, we present a conceptual control framework that leverages single-cell RNA-seq data for dynamic molecular regulatory network modeling, aiming to identify and manipulate core regulatory circuits and their master regulators to drive desired cellular state transitions. We illustrate the proposed framework by applying it to the reversion of lung cancer cell states, although it is more broadly applicable to understanding and controlling a wide range of cell-fate determination processes.