bluuebunny/crossref_metadata_2025_split huggingface dataset:
Thunder-DDA-PASEF enables high-coverage immunopeptidomics and is boosted by MS2Rescore with MS2PIP timsTOF fragmentation prediction model
Authors: Gomez-Zepeda David , Arnold-Schild Danielle , Beyrle Julian , Declercq Arthur , Gabriels Ralf , Kumm Elena , Preikschat Annica , Łącki Mateusz Krzysztof , Hirschler Aurélie , Rijal Jeewan Babu , Carapito Christine , Martens Lennart , Distler Ute , Schild Hansjörg , Tenzer Stefan 
Published: March 2024

AbstractHuman leukocyte antigen (HLA) class I peptide ligands (HLAIps) are key targets for developing vaccines and immunotherapies against infectious pathogens or cancer cells. Identifying HLAIps is challenging due to their high diversity, low abundance, and patient individuality. Here, we develop a highly sensitive method for identifying HLAIps using liquid chromatography-ion mobility-tandem mass spectrometry (LC-IMS-MS/MS). In addition, we train a timsTOF-specific peak intensity MS2PIP model for tryptic and non-tryptic peptides and implement it in MS2Rescore (v3) together with the CCS predictor from ionmob. The optimized method, Thunder-DDA-PASEF, semi-selectively fragments singly and multiply charged HLAIps based on their IMS and m/z. Moreover, the method employs the high sensitivity mode and extended IMS resolution with fewer MS/MS frames (300 ms TIMS ramp, 3 MS/MS frames), doubling the coverage of immunopeptidomics analyses, compared to the proteomics-tailored DDA-PASEF (100 ms TIMS ramp, 10 MS/MS frames). Additionally, rescoring boosts the HLAIps identification by 41.7% to 33%, resulting in 5738 HLAIps from as little as one million JY cell equivalents, and 14,516 HLAIps from 20 million. This enables in-depth profiling of HLAIps from diverse human cell lines and human plasma. Finally, profiling JY and Raji cells transfected to express the SARS-CoV-2 spike protein results in 16 spike HLAIps, thirteen of which have been reported to elicit immune responses in human patients.
Understanding of complex spin up-conversion processes in charge-transfer-type organic molecules
Authors: Kim Hyung Suk , Lee Sang Hoon , Yoo Seunghyup , Adachi Chihaya 
Published: March 2024

AbstractDespite significant progress made over the past decade in thermally activated delayed fluorescence (TADF) molecules as a material paradigm for enhancing the performance of organic light-emitting diodes, the underlying spin-flip mechanism in these charge-transfer (CT)-type molecular systems remains an enigma, even since its initial report in 2012. While the initial and final electronic states involved in spin-flip between the lowest singlet and lowest triplet excited states are well understood, the exact dynamic processes and the role of intermediate high-lying triplet (T) states are still not fully comprehended. In this context, we propose a comprehensive model to describe the spin-flip processes applicable for a typical CT-type molecule, revealing the origin of the high-lying T state in a partial molecular framework in CT-type molecules. This work provides experimental and theoretical insights into the understanding of intersystem crossing for CT-type molecules, facilitating more precise control over spin-flip rates and thus advancing toward developing the next-generation platform for purely organic luminescent candidates.
A transposon insertion in the promoter of OsUBC12 enhances cold tolerance during japonica rice germination
Authors: Zhang Chuanzhong , Wang Hongru , Tian Xiaojie , Lin Xinyan , Han Yunfei , Han Zhongmin , Sha Hanjing , Liu Jia , Liu Jianfeng , Zhang Jian , Bu Qingyun , Fang Jun 
Published: March 2024

AbstractLow-temperature germination (LTG) is an important agronomic trait for rice (Oryza sativa). Japonica rice generally has greater capacity for germination at low temperatures than the indica subpopulation. However, the genetic basis and molecular mechanisms underlying this complex trait are poorly understood. Here, we report that OsUBC12, encoding an E2 ubiquitin-conjugating enzyme, increases low-temperature germinability in japonica, owing to a transposon insertion in its promoter enhancing its expression. Natural variation analysis reveals that transposon insertion in the OsUBC12 promoter mainly occurs in the japonica lineage. The variation detected in eight representative two-line male sterile lines suggests the existence of this allele introgression by indica-japonica hybridization breeding, and varieties carrying the japonica OsUBC12 locus (transposon insertion) have higher low-temperature germinability than varieties without the locus. Further molecular analysis shows that OsUBC12 negatively regulate ABA signaling. OsUBC12-regulated seed germination and ABA signaling mainly depend on a conserved active site required for ubiquitin-conjugating enzyme activity. Furthermore, OsUBC12 directly associates with rice SUCROSE NON-FERMENTING 1-RELATED PROTEIN KINASE 1.1 (OsSnRK1.1), promoting its degradation. OsSnRK1.1 inhibits LTG by enhancing ABA signaling and acts downstream of OsUBC12. These findings shed light on the underlying mechanisms of UBC12 regulating LTG and provide genetic reference points for improving LTG in indica rice.
A solid-state lithium-ion battery with micron-sized silicon anode operating free from external pressure
Authors: Pan Hui , Wang Lei , Shi Yu , Sheng Chuanchao , Yang Sixie , He Ping , Zhou Haoshen 
Published: March 2024

AbstractApplying high stack pressure (often up to tens of megapascals) to solid-state Li-ion batteries is primarily done to address the issues of internal voids formation and subsequent Li-ion transport blockage within the solid electrode due to volume changes. Whereas, redundant pressurizing devices lower the energy density of batteries and raise the cost. Herein, a mechanical optimization strategy involving elastic electrolyte is proposed for SSBs operating without external pressurizing, but relying solely on the built-in pressure of cells. We combine soft-rigid dual monomer copolymer with deep eutectic mixture to design an elastic solid electrolyte, which exhibits not only high stretchability and deformation recovery capability but also high room-temperature Li-ion conductivity of 2×10−3 S cm−1 and nonflammability. The micron-sized Si anode without additional stack pressure, paired with the elastic electrolyte, exhibits exceptional stability for 300 cycles with 90.8% capacity retention. Furthermore, the solid Li/elastic electrolyte/LiFePO4 battery delivers 143.3 mAh g−1 after 400 cycles. Finally, the micron-sized Si/elastic electrolyte/LiFePO4 full cell operates stably for 100 cycles in the absence of any additional pressure, maintaining a capacity retention rate of 98.3%. This significantly advances the practical applications of solid-state batteries.
Distinct evolution of SARS-CoV-2 Omicron XBB and BA.2.86/JN.1 lineages combining increased fitness and antibody evasion
Authors: Planas Delphine , Staropoli Isabelle , Michel Vincent , Lemoine Frederic , Donati Flora , Prot Matthieu , Porrot Francoise , Guivel-Benhassine Florence , Jeyarajah Banujaa , Brisebarre Angela , Dehan Océane , Avon Léa , Bolland William Henry , Hubert Mathieu , Buchrieser Julian , Vanhoucke Thibault , Rosenbaum Pierre , Veyer David , Péré Hélène , Lina Bruno , Trouillet-Assant Sophie , Hocqueloux Laurent , Prazuck Thierry , Simon-Loriere Etienne , Schwartz Olivier 
Published: March 2024

AbstractThe unceasing circulation of SARS-CoV-2 leads to the continuous emergence of novel viral sublineages. Here, we isolate and characterize XBB.1, XBB.1.5, XBB.1.9.1, XBB.1.16.1, EG.5.1.1, EG.5.1.3, XBF, BA.2.86.1 and JN.1 variants, representing >80% of circulating variants in January 2024. The XBB subvariants carry few but recurrent mutations in the spike, whereas BA.2.86.1 and JN.1 harbor >30 additional changes. These variants replicate in IGROV-1 but no longer in Vero E6 and are not markedly fusogenic. They potently infect nasal epithelial cells, with EG.5.1.3 exhibiting the highest fitness. Antivirals remain active. Neutralizing antibody (NAb) responses from vaccinees and BA.1/BA.2-infected individuals are markedly lower compared to BA.1, without major differences between variants. An XBB breakthrough infection enhances NAb responses against both XBB and BA.2.86 variants. JN.1 displays lower affinity to ACE2 and higher immune evasion properties compared to BA.2.86.1. Thus, while distinct, the evolutionary trajectory of these variants combines increased fitness and antibody evasion.
Intranational synergies and trade-offs reveal common and differentiated priorities of sustainable development goals in China
Authors: Xing Qiang , Wu Chaoyang , Chen Fang , Liu Jianguo , Pradhan Prajal , Bryan Brett A. , Schaubroeck Thomas , Carrasco L. Roman , Gonsamo Alemu , Li Yunkai , Chen Xiuzhi , Deng Xiangzheng , Albanese Andrea , Li Yingjie , Xu Zhenci 
Published: March 2024

AbstractAccelerating efforts for the Sustainable Development Goals requires understanding their synergies and trade-offs at the national and sub-national levels, which will help identify the key hurdles and opportunities to prioritize them in an indivisible manner for a country. Here, we present the importance of the 17 goals through synergy and trade-off networks. Our results reveal that 19 provinces show the highest trade-offs in SDG13 (Combating Climate Change) or SDG5 (Gender Equality) consistent with the national level, with other 12 provinces varying. 24 provinces show the highest synergies in SDG1 (No Poverty) or SDG6 (Clean Water and Sanitation) consistent with the national level, with the remaining 7 provinces varying. These common but differentiated SDG priorities reflect that to ensure a coordinated national response, China should pay more attention to the provincial situation, so that provincial governments can formulate more targeted policies in line with their own priorities towards accelerating sustainable development.
Toll/interleukin-1 receptor (TIR) domain-containing proteins have NAD-RNA decapping activity
Authors: Wang Xufeng , Yu Dongli , Yu Jiancheng , Hu Hao , Hang Runlai , Amador Zachary , Chen Qi , Chai Jijie , Chen Xuemei 
Published: March 2024

AbstractThe occurrence of NAD+ as a non-canonical RNA cap has been demonstrated in diverse organisms. TIR domain-containing proteins present in all kingdoms of life act in defense responses and can have NADase activity that hydrolyzes NAD+. Here, we show that TIR domain-containing proteins from several bacterial and one archaeal species can remove the NAM moiety from NAD-capped RNAs (NAD-RNAs). We demonstrate that the deNAMing activity of AbTir (from Acinetobacter baumannii) on NAD-RNA specifically produces a cyclic ADPR-RNA, which can be further decapped in vitro by known decapping enzymes. Heterologous expression of the wild-type but not a catalytic mutant AbTir in E. coli suppressed cell propagation and reduced the levels of NAD-RNAs from a subset of genes before cellular NAD+ levels are impacted. Collectively, the in vitro and in vivo analyses demonstrate that TIR domain-containing proteins can function as a deNAMing enzyme of NAD-RNAs, raising the possibility of TIR domain proteins acting in gene expression regulation.
Time-of-flight detection of terahertz phonon-polariton
Authors: Luo Tianchuang , Ilyas Batyr , Hoegen A. von , Lee Youjin , Park Jaena , Park Je-Geun , Gedik Nuh 
Published: March 2024

AbstractA polariton is a fundamental quasiparticle that arises from strong light-matter interaction and as such has attracted wide scientific and practical interest. When light is strongly coupled to the crystal lattice, it gives rise to phonon-polaritons (PPs), which have been proven useful in the dynamical manipulation of quantum materials and the advancement of terahertz technologies. Yet, current detection and characterization methods of polaritons are still limited. Traditional techniques such as Raman or transient grating either rely on fine-tuning of external parameters or complex phase extraction techniques. To overcome these inherent limitations, we propose and demonstrate a technique based on a time-of-flight measurement of PPs. We resonantly launch broadband PPs with intense terahertz fields and measure the time-of-flight of each spectral component with time-resolved second harmonic generation. The time-of-flight information, combined with the PP attenuation, enables us to resolve the real and imaginary parts of the PP dispersion relation. We demonstrate this technique in the van der Waals magnets NiI2 and MnPS3 and reveal a hidden magnon-phonon interaction. We believe that this approach will unlock new opportunities for studying polaritons across diverse material systems and enhance our understanding of strong light-matter interaction.
Characterization of elusive rhamnosyl dioxanium ions and their application in complex oligosaccharide synthesis
Authors: Moons Peter H. , ter Braak Floor , de Kleijne Frank F. J. , Bijleveld Bart , Corver Sybren J. R. , Houthuijs Kas J. , Almizori Hero R. , Berden Giel , Martens Jonathan , Oomens Jos , White Paul B. , Boltje Thomas J. 
Published: March 2024

AbstractAttaining complete anomeric control is still one of the biggest challenges in carbohydrate chemistry. Glycosyl cations such as oxocarbenium and dioxanium ions are key intermediates of glycosylation reactions. Characterizing these highly-reactive intermediates and understanding their glycosylation mechanisms are essential to the stereoselective synthesis of complex carbohydrates. Although C-2 acyl neighbouring-group participation has been well-studied, the reactive intermediates in more remote participation remain elusive and are challenging to study. Herein, we report a workflow that is utilized to characterize rhamnosyl 1,3-bridged dioxanium ions derived from C-3 p-anisoyl esterified donors. First, we use a combination of quantum-chemical calculations and infrared ion spectroscopy to determine the structure of the cationic glycosylation intermediate in the gas-phase. In addition, we establish the structure and exchange kinetics of highly-reactive, low-abundance species in the solution-phase using chemical exchange saturation transfer, exchange spectroscopy, correlation spectroscopy, heteronuclear single-quantum correlation, and heteronuclear multiple-bond correlation nuclear magnetic resonance spectroscopy. Finally, we apply C-3 acyl neighbouring-group participation to the synthesis of complex bacterial oligosaccharides. This combined approach of finding answers to fundamental physical-chemical questions and their application in organic synthesis provides a robust basis for elucidating highly-reactive intermediates in glycosylation reactions.
Spatial engineering of single-atom Fe adjacent to Cu-assisted nanozymes for biomimetic O2 activation
Authors: Wang Ying , Paidi Vinod K. , Wang Weizhen , Wang Yong , Jia Guangri , Yan Tingyu , Cui Xiaoqiang , Cai Songhua , Zhao Jingxiang , Lee Kug-Seung , Lee Lawrence Yoon Suk , Wong Kwok-Yin 
Published: March 2024

AbstractThe precise design of single-atom nanozymes (SAzymes) and understanding of their biocatalytic mechanisms hold great promise for developing ideal bio-enzyme substitutes. While considerable efforts have been directed towards mimicking partial bio-inspired structures, the integration of heterogeneous SAzymes configurations and homogeneous enzyme-like mechanism remains an enormous challenge. Here, we show a spatial engineering strategy to fabricate dual-sites SAzymes with atomic Fe active center and adjacent Cu sites. Compared to planar Fe–Cu dual-atomic sites, vertically stacked Fe–Cu geometry in FePc@2D-Cu–N–C possesses highly optimized scaffolds, favorable substrate affinity, and fast electron transfer. These characteristics of FePc@2D-Cu–N–C SAzyme induces biomimetic O2 activation through homogenous enzymatic pathway, resembling functional and mechanistic similarity to natural cytochrome c oxidase. Furthermore, it presents an appealing alternative of cytochrome P450 3A4 for drug metabolism and drug–drug interaction. These findings are expected to deepen the fundamental understanding of atomic-level design in next-generation bio-inspired nanozymes.
Inter-species gene flow drives ongoing evolution of Streptococcus pyogenes and Streptococcus dysgalactiae subsp. equisimilis
Authors: Xie Ouli , Morris Jacqueline M. , Hayes Andrew J. , Towers Rebecca J. , Jespersen Magnus G. , Lees John A. , Ben Zakour Nouri L. , Berking Olga , Baines Sarah L. , Carter Glen P. , Tonkin-Hill Gerry , Schrieber Layla , McIntyre Liam , Lacey Jake A. , James Taylah B. , Sriprakash Kadaba S. , Beatson Scott A. , Hasegawa Tadao , Giffard Phil , Steer Andrew C. , Batzloff Michael R. , Beall Bernard W. , Pinho Marcos D. , Ramirez Mario , Bessen Debra E. , Dougan Gordon , Bentley Stephen D. , Walker Mark J. , Currie Bart J. , Tong Steven Y. C. , McMillan David J. , Davies Mark R. 
Published: March 2024

AbstractStreptococcus dysgalactiae subsp. equisimilis (SDSE) is an emerging cause of human infection with invasive disease incidence and clinical manifestations comparable to the closely related species, Streptococcus pyogenes. Through systematic genomic analyses of 501 disseminated SDSE strains, we demonstrate extensive overlap between the genomes of SDSE and S. pyogenes. More than 75% of core genes are shared between the two species with one third demonstrating evidence of cross-species recombination. Twenty-five percent of mobile genetic element (MGE) clusters and 16 of 55 SDSE MGE insertion regions were shared across species. Assessing potential cross-protection from leading S. pyogenes vaccine candidates on SDSE, 12/34 preclinical vaccine antigen genes were shown to be present in >99% of isolates of both species. Relevant to possible vaccine evasion, six vaccine candidate genes demonstrated evidence of inter-species recombination. These findings demonstrate previously unappreciated levels of genomic overlap between these closely related pathogens with implications for streptococcal pathobiology, disease surveillance and prevention.
Complete separation of benzene-cyclohexene-cyclohexane mixtures via temperature-dependent molecular sieving by a flexible chain-like coordination polymer
Authors: Xie Feng , Chen Lihang , Cedeño Morales Eder Moisés , Ullah Saif , Fu Yiwen , Thonhauser Timo , Tan Kui , Bao Zongbi , Li Jing 
Published: March 2024

AbstractThe separation and purification of C6 cyclic hydrocarbons (benzene, cyclohexene, cyclohexane) represent a critically important but energy intensive process. Developing adsorptive separation technique to replace thermally driven distillation processes holds great promise to significantly reduce energy consumption. Here we report a flexible one-dimensional coordination polymer as an efficient adsorbent to discriminate ternary C6 cyclic hydrocarbons via an ideal molecular sieving mechanism. The compound undergoes fully reversible structural transformation associated with removal/re-coordination of water molecules and between activated and hydrocarbon-loaded forms. It exhibits distinct temperature- and adsorbate-dependent adsorption behavior which facilitates the complete separation of benzene, cyclohexene and cyclohexane from their binary and ternary mixtures, with the record-high uptake ratios for C6H6/C6H12 and C6H10/C6H12 in vapor phase and highest binary and ternary selectivities in liquid phase. In situ infrared spectroscopic analysis and ab initio calculations provide insight into the host-guest interactions and their effect on the preferential adsorption and structural transformation.
HLA-class II restricted TCR targeting human papillomavirus type 18 E7 induces solid tumor remission in mice
Authors: Long Jianting , Chen Xihe , He Mian , Ou Shudan , Zhao Yunhe , Yan Qingjia , Ma Minjun , Chen Jingyu , Qin Xuping , Zhou Xiangjun , Chu Junjun , Han Yanyan 
Published: March 2024

AbstractT cell receptor (TCR)-engineered T cell therapy is a promising potential treatment for solid tumors, with preliminary efficacy demonstrated in clinical trials. However, obtaining clinically effective TCR molecules remains a major challenge. We have developed a strategy for cloning tumor-specific TCRs from long-term surviving patients who have responded to immunotherapy. Here, we report the identification of a TCR (10F04), which is human leukocyte antigen (HLA)-DRA/DRB1*09:01 restricted and human papillomavirus type 18 (HPV18) E784-98 specific, from a multiple antigens stimulating cellular therapy (MASCT) benefited metastatic cervical cancer patient. Upon transduction into human T cells, the 10F04 TCR demonstrated robust antitumor activity in both in vitro and in vivo models. Notably, the TCR effectively redirected both CD4+ and CD8+ T cells to specifically recognize tumor cells and induced multiple cytokine secretion along with durable antitumor activity and outstanding safety profiles. As a result, this TCR is currently being investigated in a phase I clinical trial for treating HPV18-positive cancers. This study provides an approach for developing safe and effective TCR-T therapies, while underscoring the potential of HLA class II-restricted TCR-T therapy as a cancer treatment.
Double charge flips of polyamide membrane by ionic liquid-decoupled bulk and interfacial diffusion for on-demand nanofiltration
Authors: Guo Bian-Bian , Liu Chang , Zhu Cheng-Ye , Xin Jia-Hui , Zhang Chao , Yang Hao-Cheng , Xu Zhi-Kang 
Published: March 2024

AbstractFine design of surface charge properties of polyamide membranes is crucial for selective ionic and molecular sieving. Traditional membranes face limitations due to their inherent negative charge and limited charge modification range. Herein, we report a facile ionic liquid-decoupled bulk/interfacial diffusion strategy to elaborate the double charge flips of polyamide membranes, enabling on-demand transformation from inherently negative to highly positive and near-neutral charges. The key to these flips lies in the meticulous utilization of ionic liquid that decouples intertwined bulk/interfacial diffusion, enhancing interfacial while inhibiting bulk diffusion. These charge-tunable polyamide membranes can be customized for impressive separation performance, for example, profound Cl−/SO42− selectivity above 470 in sulfate recovery, ultrahigh Li+/Mg2+ selectivity up to 68 in lithium extraction, and effective divalent ion removal in pharmaceutical purification, surpassing many reported polyamide nanofiltration membranes. This advancement adds a new dimension to in the design of advanced polymer membranes via interfacial polymerization.
An exposome atlas of serum reveals the risk of chronic diseases in the Chinese population
Authors: You Lei , Kou Jing , Wang Mengdie , Ji Guoqin , Li Xiang , Su Chang , Zheng Fujian , Zhang Mingye , Wang Yuting , Chen Tiantian , Li Ting , Zhou Lina , Shi Xianzhe , Zhao Chunxia , Liu Xinyu , Mei Surong , Xu Guowang 
Published: March 2024

AbstractAlthough adverse environmental exposures are considered a major cause of chronic diseases, current studies provide limited information on real-world chemical exposures and related risks. For this study, we collected serum samples from 5696 healthy people and patients, including those with 12 chronic diseases, in China and completed serum biomonitoring including 267 chemicals via gas and liquid chromatography-tandem mass spectrometry. Seventy-four highly frequently detected exposures were used for exposure characterization and risk analysis. The results show that region is the most critical factor influencing human exposure levels, followed by age. Organochlorine pesticides and perfluoroalkyl substances are associated with multiple chronic diseases, and some of them exceed safe ranges. Multi-exposure models reveal significant risk effects of exposure on hyperlipidemia, metabolic syndrome and hyperuricemia. Overall, this study provides a comprehensive human serum exposome atlas and disease risk information, which can guide subsequent in-depth cause-and-effect studies between environmental exposures and human health.