bluuebunny/crossref_metadata_2025_split huggingface dataset:
Atomically dispersed asymmetric cobalt electrocatalyst for efficient hydrogen peroxide production in neutral media
Authors: Liu Longxiang , Kang Liqun , Feng Jianrui , Hopkinson David G. , Allen Christopher S. , Tan Yeshu , Gu Hao , Mikulska Iuliia , Celorrio Veronica , Gianolio Diego , Wang Tianlei , Zhang Liquan , Li Kaiqi , Zhang Jichao , Zhu Jiexin , Held Georg , Ferrer Pilar , Grinter David , Callison June , Wilding Martin , Chen Sining , Parkin Ivan , He Guanjie 
Published: May 2024

AbstractElectrochemical hydrogen peroxide (H2O2) production (EHPP) via a two-electron oxygen reduction reaction (2e- ORR) provides a promising alternative to replace the energy-intensive anthraquinone process. M-N-C electrocatalysts, which consist of atomically dispersed transition metals and nitrogen-doped carbon, have demonstrated considerable EHPP efficiency. However, their full potential, particularly regarding the correlation between structural configurations and performances in neutral media, remains underexplored. Herein, a series of ultralow metal-loading M-N-C electrocatalysts are synthesized and investigated for the EHPP process in the neutral electrolyte. CoNCB material with the asymmetric Co-C/N/O configuration exhibits the highest EHPP activity and selectivity among various as-prepared M-N-C electrocatalyst, with an outstanding mass activity (6.1 × 105 A gCo−1 at 0.5 V vs. RHE), and a high practical H2O2 production rate (4.72 mol gcatalyst−1 h−1 cm−2). Compared with the popularly recognized square-planar symmetric Co-N4 configuration, the superiority of asymmetric Co-C/N/O configurations is elucidated by X-ray absorption fine structure spectroscopy analysis and computational studies.
Double-negative B cells and DNASE1L3 colocalise with microbiota in gut-associated lymphoid tissue
Authors: Montorsi Lucia , Pitcher Michael J. , Zhao Yuan , Dionisi Chiara , Demonti Alicia , Tull Thomas J. , Dhami Pawan , Ellis Richard J. , Bishop Cynthia , Sanderson Jeremy D. , Jain Sahil , D’Cruz David , Gibbons Deena L. , Winkler Thomas H. , Bemark Mats , Ciccarelli Francesca D. , Spencer Jo 
Published: May 2024

AbstractIntestinal homeostasis is maintained by the response of gut-associated lymphoid tissue to bacteria transported across the follicle associated epithelium into the subepithelial dome. The initial response to antigens and how bacteria are handled is incompletely understood. By iterative application of spatial transcriptomics and multiplexed single-cell technologies, we identify that the double negative 2 subset of B cells, previously associated with autoimmune diseases, is present in the subepithelial dome in health. We show that in this location double negative 2 B cells interact with dendritic cells co-expressing the lupus autoantigens DNASE1L3 and C1q and microbicides. We observe that in humans, but not in mice, dendritic cells expressing DNASE1L3 are associated with sampled bacteria but not DNA derived from apoptotic cells. We propose that fundamental features of autoimmune diseases are microbiota-associated, interacting components of normal intestinal immunity.
A HIMU-like component in Mariana Convergent Margin magma sources during initial arc rifting revealed by melt inclusions
Authors: Li Xiaohui , Ishizuka Osamu , Stern Robert J. , Li Sanzhong , Lai Zhiqing , Somerville Ian , Suo Yanhui , Chen Long , Yu Hongxia 
Published: May 2024

AbstractCompositions of island arc and back-arc basin basalts are often used to trace the recycling of subducted materials. However, the contribution of subducted components to the mantle source during initial arc rifting before back-arc basin spreading is not yet well constrained. The northernmost Mariana arc is ideal for studying this because the transition from rifting to back-arc spreading is happening here. Here we report major and trace element and Pb isotopic compositions of olivine-hosted melt inclusions from lavas erupted during initial rifting at 24°N (NSP-24) and compare them with those in active arc front at 21°N and mature back-arc basin at 18°N. NSP-24 high-K melt inclusions have highly radiogenic Pb compositions and are close to those of the HIMU end-member, suggesting the presence of this component in the magma source. The HIMU-like component may be stored in the over-riding plate and released into arc magma with rifting. HIMU-type seamounts may be subducted elsewhere beneath the Mariana arc, but obvious HIMU-type components appear only in the initial stages of arc rifting due to the low melting degree and being consumed during the process of back-arc spreading.
Systematic dissection of tumor-normal single-cell ecosystems across a thousand tumors of 30 cancer types
Authors: Kang Junho , Lee Jun Hyeong , Cha Hongui , An Jinhyeon , Kwon Joonha , Lee Seongwoo , Kim Seongryong , Baykan Mert Yakup , Kim So Yeon , An Dohyeon , Kwon Ah-Young , An Hee Jung , Lee Se-Hoon , Choi Jung Kyoon , Park Jong-Eun 
Published: May 2024

AbstractThe complexity of the tumor microenvironment poses significant challenges in cancer therapy. Here, to comprehensively investigate the tumor-normal ecosystems, we perform an integrative analysis of 4.9 million single-cell transcriptomes from 1070 tumor and 493 normal samples in combination with pan-cancer 137 spatial transcriptomics, 8887 TCGA, and 1261 checkpoint inhibitor-treated bulk tumors. We define a myriad of cell states constituting the tumor-normal ecosystems and also identify hallmark gene signatures across different cell types and organs. Our atlas characterizes distinctions between inflammatory fibroblasts marked by AKR1C1 or WNT5A in terms of cellular interactions and spatial co-localization patterns. Co-occurrence analysis reveals interferon-enriched community states including tertiary lymphoid structure (TLS) components, which exhibit differential rewiring between tumor, adjacent normal, and healthy normal tissues. The favorable response of interferon-enriched community states to immunotherapy is validated using immunotherapy-treated cancers (n = 1261) including our lung cancer cohort (n = 497). Deconvolution of spatial transcriptomes discriminates TLS-enriched from non-enriched cell types among immunotherapy-favorable components. Our systematic dissection of tumor-normal ecosystems provides a deeper understanding of inter- and intra-tumoral heterogeneity.
Electric-field tunable Type-I to Type-II band alignment transition in MoSe2/WS2 heterobilayers
Authors: Kistner-Morris Jed , Shi Ao , Liu Erfu , Arp Trevor , Farahmand Farima , Taniguchi Takashi , Watanabe Kenji , Aji Vivek , Lui Chun Hung , Gabor Nathaniel 
Published: May 2024

AbstractSemiconductor heterojunctions are ubiquitous components of modern electronics. Their properties depend crucially on the band alignment at the interface, which may exhibit straddling gap (type-I), staggered gap (type-II) or broken gap (type-III). The distinct characteristics and applications associated with each alignment make it highly desirable to switch between them within a single material. Here we demonstrate an electrically tunable transition between type-I and type-II band alignments in MoSe2/WS2 heterobilayers by investigating their luminescence and photocurrent characteristics. In their intrinsic state, these heterobilayers exhibit a type-I band alignment, resulting in the dominant intralayer exciton luminescence from MoSe2. However, the application of a strong interlayer electric field induces a transition to a type-II band alignment, leading to pronounced interlayer exciton luminescence. Furthermore, the formation of the interlayer exciton state traps free carriers at the interface, leading to the suppression of interlayer photocurrent and highly nonlinear photocurrent-voltage characteristics. This breakthrough in electrical band alignment control, interlayer exciton manipulation, and carrier trapping heralds a new era of versatile optical and (opto)electronic devices composed of van der Waals heterostructures.
Ammonium-derived nitrous oxide is a global source in streams
Authors: Wang Shanyun , Lan Bangrui , Yu Longbin , Xiao Manyi , Jiang Liping , Qin Yu , Jin Yucheng , Zhou Yuting , Armanbek Gawhar , Ma Jingchen , Wang Manting , Jetten Mike S. M. , Tian Hanqin , Zhu Guibing , Zhu Yong-Guan 
Published: May 2024

AbstractGlobal riverine nitrous oxide (N2O) emissions have increased more than 4-fold in the last century. It has been estimated that the hyporheic zones in small streams alone may contribute approximately 85% of these N2O emissions. However, the mechanisms and pathways controlling hyporheic N2O production in stream ecosystems remain unknown. Here, we report that ammonia-derived pathways, rather than the nitrate-derived pathways, are the dominant hyporheic N2O sources (69.6 ± 2.1%) in agricultural streams around the world. The N2O fluxes are mainly in positive correlation with ammonia. The potential N2O metabolic pathways of metagenome-assembled genomes (MAGs) provides evidence that nitrifying bacteria contain greater abundances of N2O production-related genes than denitrifying bacteria. Taken together, this study highlights the importance of mitigating agriculturally derived ammonium in low-order agricultural streams in controlling N2O emissions. Global models of riverine ecosystems need to better represent ammonia-derived pathways for accurately estimating and predicting riverine N2O emissions.
mTORC1 regulates cell survival under glucose starvation through 4EBP1/2-mediated translational reprogramming of fatty acid metabolism
Authors: Levy Tal , Voeltzke Kai , Hruby Laura , Alasad Khawla , Bas Zuelal , Snaebjörnsson Marteinn , Marciano Ran , Scharov Katerina , Planque Mélanie , Vriens Kim , Christen Stefan , Funk Cornelius M. , Hassiepen Christina , Kahler Alisa , Heider Beate , Picard Daniel , Lim Jonathan K. M. , Stefanski Anja , Bendrin Katja , Vargas-Toscano Andres , Kahlert Ulf D. , Stühler Kai , Remke Marc , Elkabets Moshe , Grünewald Thomas G. P. , Reichert Andreas S. , Fendt Sarah-Maria , Schulze Almut , Reifenberger Guido , Rotblat Barak , Leprivier Gabriel 
Published: May 2024

AbstractEnergetic stress compels cells to evolve adaptive mechanisms to adjust their metabolism. Inhibition of mTOR kinase complex 1 (mTORC1) is essential for cell survival during glucose starvation. How mTORC1 controls cell viability during glucose starvation is not well understood. Here we show that the mTORC1 effectors eukaryotic initiation factor 4E binding proteins 1/2 (4EBP1/2) confer protection to mammalian cells and budding yeast under glucose starvation. Mechanistically, 4EBP1/2 promote NADPH homeostasis by preventing NADPH-consuming fatty acid synthesis via translational repression of Acetyl-CoA Carboxylase 1 (ACC1), thereby mitigating oxidative stress. This has important relevance for cancer, as oncogene-transformed cells and glioma cells exploit the 4EBP1/2 regulation of ACC1 expression and redox balance to combat energetic stress, thereby supporting transformation and tumorigenicity in vitro and in vivo. Clinically, high EIF4EBP1 expression is associated with poor outcomes in several cancer types. Our data reveal that the mTORC1-4EBP1/2 axis provokes a metabolic switch essential for survival during glucose starvation which is exploited by transformed and tumor cells.
Enzyme-assisted high throughput sequencing of an expanded genetic alphabet at single base resolution
Authors: Wang Bang , Bradley Kevin M. , Kim Myong-Jung , Laos Roberto , Chen Cen , Gerloff Dietlind L. , Manfio Luran , Yang Zunyi , Benner Steven A. 
Published: May 2024

AbstractWith just four building blocks, low sequence information density, few functional groups, poor control over folding, and difficulties in forming compact folds, natural DNA and RNA have been disappointing platforms from which to evolve receptors, ligands, and catalysts. Accordingly, synthetic biology has created “artificially expanded genetic information systems” (AEGIS) to add nucleotides, functionality, and information density. With the expected improvements seen in AegisBodies and AegisZymes, the task for synthetic biologists shifts to developing for expanded DNA the same analytical tools available to natural DNA. Here we report one of these, an enzyme-assisted sequencing of expanded genetic alphabet (ESEGA) method to sequence six-letter AEGIS DNA. We show how ESEGA analyses this DNA at single base resolution, and applies it to optimized conditions for six-nucleotide PCR, assessing the fidelity of various DNA polymerases, and extending this to AEGIS components with functional groups. This supports the renewed exploitation of expanded DNA alphabets in biotechnology.
Spin-orbit torque manipulation of sub-terahertz magnons in antiferromagnetic α-Fe2O3
Authors: Yang Dongsheng , Kim Taeheon , Lee Kyusup , Xu Chang , Liu Yakun , Wang Fei , Zhao Shishun , Kumar Dushyant , Yang Hyunsoo 
Published: May 2024

AbstractThe ability to electrically manipulate antiferromagnetic magnons, essential for extending the operating speed of spintronic devices into the terahertz regime, remains a major challenge. This is because antiferromagnetic magnetism is challenging to perturb using traditional methods such as magnetic fields. Recent developments in spin-orbit torques have opened a possibility of accessing antiferromagnetic magnetic order parameters and controlling terahertz magnons, which has not been experimentally realised yet. Here, we demonstrate the electrical manipulation of sub-terahertz magnons in the α-Fe2O3/Pt antiferromagnetic heterostructure. By applying the spin-orbit torques in the heterostructure, we can modify the magnon dispersion and decrease the magnon frequency in α-Fe2O3, as detected by time-resolved magneto-optical techniques. We have found that optimal tuning occurs when the Néel vector is perpendicular to the injected spin polarisation. Our results represent a significant step towards the development of electrically tunable terahertz spintronic devices.
Transcription stress at telomeres leads to cytosolic DNA release and paracrine senescence
Authors: Siametis Athanasios , Stratigi Kalliopi , Giamaki Despoina , Chatzinikolaou Georgia , Akalestou-Clocher Alexia , Goulielmaki Evi , Luke Brian , Schumacher Björn , Garinis George A. 
Published: May 2024

AbstractTranscription stress has been linked to DNA damage -driven aging, yet the underlying mechanism remains unclear. Here, we demonstrate that Tcea1−/− cells, which harbor a TFIIS defect in transcription elongation, exhibit RNAPII stalling at oxidative DNA damage sites, impaired transcription, accumulation of R-loops, telomere uncapping, chromatin bridges, and genome instability, ultimately resulting in cellular senescence. We found that R-loops at telomeres causally contribute to the release of telomeric DNA fragments in the cytoplasm of Tcea1−/− cells and primary cells derived from naturally aged animals triggering a viral-like immune response. TFIIS-defective cells release extracellular vesicles laden with telomeric DNA fragments that target neighboring cells, which consequently undergo cellular senescence. Thus, transcription stress elicits paracrine signals leading to cellular senescence, promoting aging.
Proteome partitioning constraints in long-term laboratory evolution
Authors: Mori Matteo , Patsalo Vadim , Euler Christian , Williamson James R. , Scott Matthew 
Published: May 2024

AbstractAdaptive laboratory evolution experiments provide a controlled context in which the dynamics of selection and adaptation can be followed in real-time at the single-nucleotide level. And yet this precision introduces hundreds of degrees-of-freedom as genetic changes accrue in parallel lineages over generations. On short timescales, physiological constraints have been leveraged to provide a coarse-grained view of bacterial gene expression characterized by a small set of phenomenological parameters. Here, we ask whether this same framework, operating at a level between genotype and fitness, informs physiological changes that occur on evolutionary timescales. Using a strain adapted to growth in glucose minimal medium, we find that the proteome is substantially remodeled over 40 000 generations. The most striking change is an apparent increase in enzyme efficiency, particularly in the enzymes of lower-glycolysis. We propose that deletion of metabolic flux-sensing regulation early in the adaptation results in increased enzyme saturation and can account for the observed proteome remodeling.
Targeted protein degradation in mycobacteria uncovers antibacterial effects and potentiates antibiotic efficacy
Authors: Won Harim I. , Zinga Samuel , Kandror Olga , Akopian Tatos , Wolf Ian D. , Schweber Jessica T. P. , Schmid Ernst W. , Chao Michael C. , Waldor Maya , Rubin Eric J. , Zhu Junhao 
Published: May 2024

AbstractProteolysis-targeting chimeras (PROTACs) represent a new therapeutic modality involving selectively directing disease-causing proteins for degradation through proteolytic systems. Our ability to exploit targeted protein degradation (TPD) for antibiotic development remains nascent due to our limited understanding of which bacterial proteins are amenable to a TPD strategy. Here, we use a genetic system to model chemically-induced proximity and degradation to screen essential proteins in Mycobacterium smegmatis (Msm), a model for the human pathogen M. tuberculosis (Mtb). By integrating experimental screening of 72 protein candidates and machine learning, we find that drug-induced proximity to the bacterial ClpC1P1P2 proteolytic complex leads to the degradation of many endogenous proteins, especially those with disordered termini. Additionally, TPD of essential Msm proteins inhibits bacterial growth and potentiates the effects of existing antimicrobial compounds. Together, our results provide biological principles to select and evaluate attractive targets for future Mtb PROTAC development, as both standalone antibiotics and potentiators of existing antibiotic efficacy.
Deep learning with plasma plume image sequences for anomaly detection and prediction of growth kinetics during pulsed laser deposition
Authors: Harris Sumner B. , Rouleau Christopher M. , Xiao Kai , Vasudevan Rama K. 
Published: May 2024

AbstractMaterials synthesis platforms that are designed for autonomous experimentation are capable of collecting multimodal diagnostic data that can be utilized for feedback to optimize material properties. Pulsed laser deposition (PLD) is emerging as a viable autonomous synthesis tool, and so the need arises to develop machine learning (ML) techniques that are capable of extracting information from in situ diagnostics. Here, we demonstrate that intensified-CCD image sequences of the plasma plume generated during PLD can be used for anomaly detection and the prediction of thin film growth kinetics. We develop multi-output (2 + 1)D convolutional neural network regression models that extract deep features from plume dynamics that not only correlate with the measured chamber pressure and incident laser energy, but more importantly, predict parameters of an auto-catalytic film growth model derived from in situ laser reflectivity experiments. Our results demonstrate how ML with in situ plume diagnostics data in PLD can be utilized to maintain deposition conditions in an optimal regime. Further, the predictive capabilities of plume dynamics on the kinetics of film growth or other film properties prior to deposition provides a means for rapid pre-screening of growth conditions for the non-expert, which promises to accelerate materials optimization with PLD.
Accelerated MRI reconstructions via variational network and feature domain learning
Authors: Giannakopoulos Ilias I. , Muckley Matthew J. , Kim Jesi , Breen Matthew , Johnson Patricia M. , Lui Yvonne W. , Lattanzi Riccardo 
Published: May 2024

AbstractWe introduce three architecture modifications to enhance the performance of the end-to-end (E2E) variational network (VarNet) for undersampled MRI reconstructions. We first implemented the Feature VarNet, which propagates information throughout the cascades of the network in an N-channel feature-space instead of a 2-channel feature-space. Then, we add an attention layer that utilizes the spatial locations of Cartesian undersampling artifacts to further improve performance. Lastly, we combined the Feature and E2E VarNets into the Feature-Image (FI) VarNet, to facilitate cross-domain learning and boost accuracy. Reconstructions were evaluated on the fastMRI dataset using standard metrics and clinical scoring by three neuroradiologists. Feature and FI VarNets outperformed the E2E VarNet for 4$$\times$$
×
, 5$$\times$$
×
and 8$$\times$$
×
Cartesian undersampling in all studied metrics. FI VarNet secured second place in the public fastMRI leaderboard for 4$$\times$$
×
Cartesian undersampling, outperforming all open-source models in the leaderboard. Radiologists rated FI VarNet brain reconstructions with higher quality and sharpness than the E2E VarNet reconstructions. FI VarNet excelled in preserving anatomical details, including blood vessels, whereas E2E VarNet discarded or blurred them in some cases. The proposed FI VarNet enhances the reconstruction quality of undersampled MRI and could enable clinically acceptable reconstructions at higher acceleration factors than currently possible.
Stem cells derived exosomes as biological nano carriers for VCR sulfate for treating breast cancer stem cells
Authors: Farouk Ahmed H. , Aref Ahmed , Fathy Belal A. , Abdallah Ahmed N. 
Published: May 2024

AbstractDue to vincristine sulfate’s (VCR sulfate) toxicity and non-specific targeting, which might adversely damage healthy cells, its clinical application is restricted. In this study, we loaded VCR sulfate on exosomes generated from mesenchymal stem cells (MSCs) to enhance its targeted distribution. Exosomes are able to deliver molecules to specific cells and tissues and have therapeutic potential. In this study, we isolated exosomes from MSCs, and using probe-sonication approach loaded them with VCR sulfate. Using SRB assay, the cytotoxicity of VCR sulfate-Exo was assessed in T47D breast cancer cells, and the results were contrasted with those of free VCR sulfate. Then We labeled markers (CD44+/CD24−) in the cell line to assess the targeting effectiveness of VCR sulfate-Exo using flow cytometry. Our results showed that the cytotoxicity of VCR sulfate-Exo was nearly the same as that of VCR sulfate. Flow cytometry analysis revealed that VRC sulfate-Exo was more effectively targeted to MSCs than free VCR sulfate. Our study shows that loading VCR sulfate to MSCs-derived exosomes can improve their targeted delivery and lessen their side effects. Additional research is required to determine VCR sulfate-Exo’s in vivo effectiveness and safety and improve the loading and delivery strategies.