bluuebunny/crossref_metadata_2025_split huggingface dataset:
Non-hermiticity in spintronics: oscillation death in coupled spintronic nano-oscillators through emerging exceptional points
Authors: Wittrock Steffen , Perna Salvatore , Lebrun Romain , Ho Katia , Dutra Roberta , Ferreira Ricardo , Bortolotti Paolo , Serpico Claudio , Cros Vincent 
Published: February 2024

AbstractThe emergence of exceptional points (EPs) in the parameter space of a non-hermitian (2D) eigenvalue problem has long been interest in mathematical physics, however, only in the last decade entered the scope of experiments. In coupled systems, EPs give rise to unique physical phenomena, and enable the development of highly sensitive sensors. Here, we demonstrate at room temperature the emergence of EPs in coupled spintronic nanoscale oscillators and exploit the system’s non-hermiticity. We observe amplitude death of self-oscillations and other complex dynamics, and develop a linearized non-hermitian model of the coupled spintronic system, which describes the main experimental features. The room temperature operation, and CMOS compatibility of our spintronic nanoscale oscillators means that they are ready to be employed in a variety of applications, such as field, current or rotation sensors, radiofrequeny and wireless devices, and in dedicated neuromorphic computing hardware. Furthermore, their unique and versatile properties, notably their large nonlinear behavior, open up unprecedented perspectives in experiments as well as in theory on the physics of exceptional points expanding to strongly nonlinear systems.
Multiplexed screening reveals how cancer-specific alternative polyadenylation shapes tumor growth in vivo
Authors: Gabel Austin M. , Belleville Andrea E. , Thomas James D. , McKellar Siegen A. , Nicholas Taylor R. , Banjo Toshihiro , Crosse Edie I. , Bradley Robert K. 
Published: February 2024

AbstractAlternative polyadenylation (APA) is strikingly dysregulated in many cancers. Although global APA dysregulation is frequently associated with poor prognosis, the importance of most individual APA events is controversial simply because few have been functionally studied. Here, we address this gap by developing a CRISPR-Cas9-based screen to manipulate endogenous polyadenylation and systematically quantify how APA events contribute to tumor growth in vivo. Our screen reveals individual APA events that control mouse melanoma growth in an immunocompetent host, with concordant associations in clinical human cancer. For example, forced Atg7 3′ UTR lengthening in mouse melanoma suppresses ATG7 protein levels, slows tumor growth, and improves host survival; similarly, in clinical human melanoma, a long ATG7 3′ UTR is associated with significantly prolonged patient survival. Overall, our study provides an easily adaptable means to functionally dissect APA in physiological systems and directly quantifies the contributions of recurrent APA events to tumorigenic phenotypes.
Hydrogel dressings with intrinsic antibiofilm and antioxidative dual functionalities accelerate infected diabetic wound healing
Authors: Pranantyo Dicky , Yeo Chun Kiat , Wu Yang , Fan Chen , Xu Xiaofei , Yip Yun Sheng , Vos Marcus Ivan Gerard , Mahadevegowda Surendra H. , Lim Priscilla Lay Keng , Yang Liang , Hammond Paula T. , Leavesley David Ian , Tan Nguan Soon , Chan-Park Mary B. 
Published: February 2024

AbstractChronic wounds are often infected with biofilm bacteria and characterized by high oxidative stress. Current dressings that promote chronic wound healing either require additional processes such as photothermal irradiation or leave behind gross amounts of undesirable residues. We report a dual-functionality hydrogel dressing with intrinsic antibiofilm and antioxidative properties that are synergistic and low-leaching. The hydrogel is a crosslinked network with tethered antibacterial cationic polyimidazolium and antioxidative N-acetylcysteine. In a murine diabetic wound model, the hydrogel accelerates the closure of wounds infected with methicillin-resistant Staphylococcus aureus or carbapenem-resistant Pseudomonas aeruginosa biofilm. Furthermore, a three-dimensional ex vivo human skin equivalent model shows that N-acetylcysteine promotes the keratinocyte differentiation and accelerates the re-epithelialization process. Our hydrogel dressing can be made into different formats for the healing of both flat and deep infected chronic wounds without contamination of the wound or needing other modalities such as photothermal irradiation.
Nuclear to cytoplasmic transport is a druggable dependency in MYC-driven hepatocellular carcinoma
Authors: Deutzmann Anja , Sullivan Delaney K. , Dhanasekaran Renumathy , Li Wei , Chen Xinyu , Tong Ling , Mahauad-Fernandez Wadie D. , Bell John , Mosley Adriane , Koehler Angela N. , Li Yulin , Felsher Dean W. 
Published: February 2024

AbstractThe MYC oncogene is often dysregulated in human cancer, including hepatocellular carcinoma (HCC). MYC is considered undruggable to date. Here, we comprehensively identify genes essential for survival of MYChigh but not MYClow cells by a CRISPR/Cas9 genome-wide screen in a MYC-conditional HCC model. Our screen uncovers novel MYC synthetic lethal (MYC-SL) interactions and identifies most MYC-SL genes described previously. In particular, the screen reveals nucleocytoplasmic transport to be a MYC-SL interaction. We show that the majority of MYC-SL nucleocytoplasmic transport genes are upregulated in MYChigh murine HCC and are associated with poor survival in HCC patients. Inhibiting Exportin-1 (XPO1) in vivo induces marked tumor regression in an autochthonous MYC-transgenic HCC model and inhibits tumor growth in HCC patient-derived xenografts. XPO1 expression is associated with poor prognosis only in HCC patients with high MYC activity. We infer that MYC may generally regulate and require altered expression of nucleocytoplasmic transport genes for tumorigenesis.
Mitochondrial protein C15ORF48 is a stress-independent inducer of autophagy that regulates oxidative stress and autoimmunity
Authors: Takakura Yuki , Machida Moeka , Terada Natsumi , Katsumi Yuka , Kawamura Seika , Horie Kenta , Miyauchi Maki , Ishikawa Tatsuya , Akiyama Nobuko , Seki Takao , Miyao Takahisa , Hayama Mio , Endo Rin , Ishii Hiroto , Maruyama Yuya , Hagiwara Naho , Kobayashi Tetsuya J. , Yamaguchi Naoto , Takano Hiroyuki , Akiyama Taishin , Yamaguchi Noritaka 
Published: February 2024

AbstractAutophagy is primarily activated by cellular stress, such as starvation or mitochondrial damage. However, stress-independent autophagy is activated by unclear mechanisms in several cell types, such as thymic epithelial cells (TECs). Here we report that the mitochondrial protein, C15ORF48, is a critical inducer of stress-independent autophagy. Mechanistically, C15ORF48 reduces the mitochondrial membrane potential and lowers intracellular ATP levels, thereby activating AMP-activated protein kinase and its downstream Unc-51-like kinase 1. Interestingly, C15ORF48-dependent induction of autophagy upregulates intracellular glutathione levels, promoting cell survival by reducing oxidative stress. Mice deficient in C15orf48 show a reduction in stress-independent autophagy in TECs, but not in typical starvation-induced autophagy in skeletal muscles. Moreover, C15orf48–/– mice develop autoimmunity, which is consistent with the fact that the stress-independent autophagy in TECs is crucial for the thymic self-tolerance. These results suggest that C15ORF48 induces stress-independent autophagy, thereby regulating oxidative stress and self-tolerance.
3D atomic structure from a single X-ray free electron laser pulse
Authors: Bortel Gábor , Tegze Miklós , Sikorski Marcin , Bean Richard , Bielecki Johan , Kim Chan , Koliyadu Jayanath C. P. , Koua Faisal H. M. , Ramilli Marco , Round Adam , Sato Tokushi , Zabelskii Dmitrii , Faigel Gyula 
Published: February 2024

AbstractX-ray Free Electron Lasers (XFEL) are cutting-edge pulsed x-ray sources, whose extraordinary pulse parameters promise to unlock unique applications. Several new methods have been developed at XFELs; however, no methods are known, which allow ab initio atomic level structure determination using only a single XFEL pulse. Here, we present experimental results, demonstrating the determination of the 3D atomic structure from data obtained during a single 25 fs XFEL pulse. Parallel measurement of hundreds of Bragg reflections was done by collecting Kossel line patterns of GaAs and GaP. To the best of our knowledge with these measurements, we reached the ultimate temporal limit of the x-ray structure solution possible today. These measurements open the way for obtaining crystalline structures during non-repeatable fast processes, such as structural transformations. For example, the atomic structure of matter at extremely non-ambient conditions or transient structures formed in irreversible physical, chemical, or biological processes may be captured in a single shot measurement during the transformation. It would also facilitate time resolved pump-probe structural studies making them significantly shorter than traditional serial crystallography.
Quantum storage of 1650 modes of single photons at telecom wavelength
Authors: Wei Shi-Hai , Jing Bo , Zhang Xue-Ying , Liao Jin-Yu , Li Hao , You Li-Xing , Wang Zhen , Wang You , Deng Guang-Wei , Song Hai-Zhi , Oblak Daniel , Guo Guang-Can , Zhou Qiang 
Published: February 2024

AbstractTo advance the full potential of quantum networks one should be able to distribute quantum resources over long distances at appreciable rates. As a consequence, all components in such networks need to have large multimode capacity to manipulate photonic quantum states. Towards this end, a photonic quantum memory with a large multimode capacity, especially one operating at telecom wavelength, remains an important challenge. Here we optimize the preparation of atomic frequency combs and demonstrate a spectro-temporally multiplexed quantum memory in a 10-m-long cryogenically cooled erbium doped silica fibre. Our multiplexing storage has five spectral channels - each 10 GHz wide with 5 GHz separation - with up to 330 temporal modes in each, thus resulting in a simultaneous storage of 1,650 modes of heralded single photons with a 1000-fold increasing in coincidence detection rate with respect to single mode storage. Our results could pave the way for high speed quantum networks compatible with the infrastructure of fibre optical communication.
Mapping microhabitats of lignocellulose decomposition by a microbial consortium
Authors: Veličković Marija , Wu Ruonan , Gao Yuqian , Thairu Margaret W. , Veličković Dušan , Munoz Nathalie , Clendinen Chaevien S. , Bilbao Aivett , Chu Rosalie K. , Lalli Priscila M. , Zemaitis Kevin , Nicora Carrie D. , Kyle Jennifer E. , Orton Daniel , Williams Sarai , Zhu Ying , Zhao Rui , Monroe Matthew E. , Moore Ronald J. , Webb-Robertson Bobbie-Jo M. , Bramer Lisa M. , Currie Cameron R. , Piehowski Paul D. , Burnum-Johnson Kristin E. 
Published: February 2024

AbstractThe leaf-cutter ant fungal garden ecosystem is a naturally evolved model system for efficient plant biomass degradation. Degradation processes mediated by the symbiotic fungus Leucoagaricus gongylophorus are difficult to characterize due to dynamic metabolisms and spatial complexity of the system. Herein, we performed microscale imaging across 12-µm-thick adjacent sections of Atta cephalotes fungal gardens and applied a metabolome-informed proteome imaging approach to map lignin degradation. This approach combines two spatial multiomics mass spectrometry modalities that enabled us to visualize colocalized metabolites and proteins across and through the fungal garden. Spatially profiled metabolites revealed an accumulation of lignin-related products, outlining morphologically unique lignin microhabitats. Metaproteomic analyses of these microhabitats revealed carbohydrate-degrading enzymes, indicating a prominent fungal role in lignocellulose decomposition. Integration of metabolome-informed proteome imaging data provides a comprehensive view of underlying biological pathways to inform our understanding of metabolic fungal pathways in plant matter degradation within the micrometer-scale environment.
Exonuclease-enhanced prime editors
Authors: Truong Dong-Jiunn Jeffery , Geilenkeuser Julian , Wendel Stephanie Victoria , Wilming Julius Clemens Heinrich , Armbrust Niklas , Binder Eva Maria Hildegard , Santl Tobias Heinrich , Siebenhaar Annika , Gruber Christoph , Phlairaharn Teeradon , Živanić Milica , Westmeyer Gil Gregor 
Published: February 2024

AbstractPrime editing (PE) is a powerful gene-editing technique based on targeted gRNA-templated reverse transcription and integration of the de novo synthesized single-stranded DNA. To circumvent one of the main bottlenecks of the method, the competition of the reverse-transcribed 3′ flap with the original 5′ flap DNA, we generated an enhanced fluorescence-activated cell sorting reporter cell line to develop an exonuclease-enhanced PE strategy (‘Exo-PE’) composed of an improved PE complex and an aptamer-recruited DNA-exonuclease to remove the 5′ original DNA flap. Exo-PE achieved better overall editing efficacy than the reference PE2 strategy for insertions ≥30 base pairs in several endogenous loci and cell lines while maintaining the high editing precision of PE2. By enabling the precise incorporation of larger insertions, Exo-PE complements the growing palette of different PE tools and spurs additional refinements of the PE machinery.
The shape function method of nonlinear thermal stress of granite fracture tips in a high-temperature environment
Authors: Wang Yang , Chen Wen-hua 
Published: February 2024

AbstractExposed rock masses in tunnel portals are susceptible to thermal deterioration in southern China, where temperatures are relatively high. The thermal stress field of rock masses is affected by fracture shape and distribution as fractures near the surface are channels for solar radiation energy to be converted into rock thermal energy. In this study, a function expression is developed for triangular heat sources of fractured rock masses in a tunnel portal in a high-temperature environment. By the function expression, the temperature field and thermal stress field are calculated, and the influence of fracture shape parameters and multi-fracture interaction is analyzed. The results are as follows: (1) the temperature field and thermal stress field of exposed rocks are redistributed by fractures. The internal temperature of the fractured rocks is higher than that of non-fractured rocks, and thermal stress near the fracture tip increases. (2) For triangular fractures of the same length, thermal stress increases as the apex angle increases. (3) When the spacing between parallel fractures or coplanar fractures is close, the superposition effect of thermal stress becomes significant. (4) In a high-temperature environment, temperature field and thermal stress field of a fractured rock are both nonlinear as temperature and thermal stress around fractures increase significantly. The results provide effective reference for stability evaluation of fractured rock masses in tunnel portals and offer theoretical foundation for thermal diseases analysis and protection measures of tunnel engineering in high-temperature environments of southern China.
Perfect single-photon sources
Authors: Khalid Sana , Laussy Fabrice P. 
Published: February 2024

AbstractWe introduce the gapped coherent state in the form of a single-photon source (SPS) that consists of uncorrelated photons as a background, except that we demand that no two photons can be closer in time than a time gap $$t_\text{G}$$

t
G

. While no obvious quantum mechanism is yet identified to produce exactly such a photon stream, a numerical simulation is easily achieved by first generating an uncorrelated (Poissonian) signal and then for each photon in the list, either adding such a time gap or removing all photons that are closer in time from each other than $$t_\text{G}$$

t
G

. We study the statistical properties of such a hypothetical signal, which exhibits counter-intuitive features. This provides a neat and natural connection between continuous-wave (stationary) and pulsed single-photon sources, with also a bearing on what it means for such sources to be perfect in terms of single-photon emission.
Point convolutional neural network algorithm for Ising model ground state research based on spring vibration
Authors: Jiang Zhelong , Chen Gang , Qiao Ruixiu , Feng Pengcheng , Chen Yihao , Su Junjia , Zhao Zhiyuan , Jin Min , Chen Xu , Li Zhigang , Lu Huaxiang 
Published: February 2024

AbstractThe ground state search of the Ising model can be used to solve many combinatorial optimization problems. Under the current computer architecture, an Ising ground state search algorithm suitable for hardware computing is necessary for solving practical problems. Inspired by the potential energy conversion of the springs, we propose the Spring-Ising Algorithm, a point convolutional neural network algorithm for ground state search based on the spring vibration model. Spring-Ising Algorithm regards the spin as a moving mass point connected to a spring and establishes the equation of motion for all spins. Spring-Ising Algorithm can be mapped on AI chips through the basic structure of the neural network for fast and efficient parallel computing. The algorithm has shown promising results in solving the Ising model and has been tested in the recognized test benchmark K2000. The optimal results of this algorithm after 10,000 steps of iteration are 2.9% of all results. The algorithm introduces the concept of dynamic equilibrium to achieve a more detailed local search by dynamically adjusting the weight of the Ising model in the spring oscillation model. Spring-Ising Algorithm offers the possibility to calculate the Ising model on a chip which focuses on accelerating neural network calculations.
The impact of microcrystalline and nanocrystalline cellulose on the antioxidant phenolic compounds level of the cultured Artemisia absinthium
Authors: Khosravi Faezeh , Mohammadi Samin , Kosari-Nasab Morteza , Asgharian Parina 
Published: February 2024

AbstractArtemisia absinthium has long been used traditionally as an anti-microbial and antioxidant agent. Various biologically active secondary metabolites, including phenolic compounds such as gallic acid and p-coumaric acid, have been reported from the species. In addition, growing the plants under in vitro conditions enriched with elicitors is a cost-effective approach to enhance secondary metabolite production. This paper examined microcrystalline cellulose (MCC) and nanocrystalline cellulose (NCC) effects on morphological characteristics, phenolic compounds, antioxidant activity, and volatile oil content of A. absinthium. The treated shoots with various concentrations of MCC and NCC were subjected to spectrophotometric, GC–MS, and LC–MS analysis. FESEM-EDX, TEM, XRD, and DLS methods were applied to characterize MCC and NCC properties. Morphological findings revealed that the stem length, dry, and fresh weights were improved significantly (P ≤ 0.05) under several MCC and NCC concentrations. Some treatments enhanced gallic and p-coumaric acid levels in the plant. Although 1.5 g/L of MCC treatment showed the highest antioxidant activity, all NCC treatments reduced the antioxidant effect. The findings suggest that both MCC and NCC, at optimized concentrations, could be exploited as elicitors to improve the secondary metabolite production and morphological properties.
A gene expression-based classifier for HER2-low breast cancer
Authors: Di Cosimo Serena , Pizzamiglio Sara , Ciniselli Chiara Maura , Duroni Valeria , Cappelletti Vera , De Cecco Loris , De Marco Cinzia , Silvestri Marco , De Santis Maria Carmen , Vingiani Andrea , Paolini Biagio , Orlandi Rosaria , Iorio Marilena Valeria , Pruneri Giancarlo , Verderio Paolo 
Published: February 2024

AbstractIn clinical trials evaluating antibody-conjugated drugs (ADCs), HER2-low breast cancer is defined through protein immunohistochemistry scoring (IHC) 1+ or 2+ without gene amplification. However, in daily practice, the accuracy of IHC is compromised by inter-observer variability. Herein, we aimed to identify HER2-low breast cancer primary tumors by leveraging gene expression profiling. A discovery approach was applied to gene expression profile of institutional INT1 (n = 125) and INT2 (n = 84) datasets. We identified differentially expressed genes (DEGs) in each specific HER2 IHC category 0, 1+, 2+ and 3+. Principal Component Analysis was used to generate a HER2-low signature whose performance was evaluated in the independent INT3 (n = 95), and in the publicly available TCGA and GSE81538 datasets. The association between the HER2-low signature and HER2 IHC categories was evaluated by Kruskal–Wallis test with post hoc pair-wise comparisons. The HER2-low signature discriminatory capability was assessed by estimating the area under the receiver operating characteristic curve (AUC). Gene Ontology and KEGG analyses were performed to evaluate the HER2-low signature genes functional enrichment. A HER2-low signature was computed based on HER2 IHC category-specific DEGs. The twenty genes included in the signature were significantly enriched with lipid and steroid metabolism pathways, peptidase regulation, and humoral immune response. The HER2-low signature values showed a bell-shaped distribution across IHC categories (low values in 0 and 3+; high values in 1+ and 2+), effectively distinguishing HER2-low from 0 (p < 0.001) to 3+ (p < 0.001). Notably, the signature values were higher in tumors scored with 1+ as compared to 0. The HER2-low signature association with IHC categories and its bell-shaped distribution was confirmed in the independent INT3, TCGA and GSE81538 datasets. In the combined INT1 and INT3 datasets, the HER2-low signature achieved an AUC value of 0.74 (95% confidence interval, CI 0.67–0.81) in distinguishing HER2-low vs. the other categories, outperforming the individual ERBB2 mRNA AUC value of 0.52 (95% CI 0.43–0.60). These results represent a proof-of-concept for an observer-independent gene-expression-based classifier of HER2-low status. The herein identified 20-gene signature shows promise in distinguishing between HER2 0 and HER2-low expressing tumors, including those scored as 1+ at IHC, and in developing a selection approach for ADCs candidates.
Optimized preparation pipeline for emergency phage therapy against Pseudomonas aeruginosa at Yale University
Authors: Würstle Silvia , Lee Alina , Kortright Kaitlyn E. , Winzig Franziska , An William , Stanley Gail L. , Rajagopalan Govindarajan , Harris Zach , Sun Ying , Hu Buqu , Blazanin Michael , Hajfathalian Maryam , Bollyky Paul L. , Turner Paul E. , Koff Jonathan L. , Chan Benjamin K. 
Published: February 2024

AbstractBacteriophage therapy is one potential strategy to treat antimicrobial resistant or persistent bacterial infections, and the year 2021 marked the centennial of Felix d’Hérelle’s first publication on the clinical applications of phages. At the Center for Phage Biology & Therapy at Yale University, a preparatory modular approach has been established to offer safe and potent phages for single-patient investigational new drug applications while recognizing the time constraints imposed by infection(s). This study provides a practical walkthrough of the pipeline with an Autographiviridae phage targeting Pseudomonas aeruginosa (phage vB_PaeA_SB, abbreviated to ΦSB). Notably, a thorough phage characterization and the evolutionary selection pressure exerted on bacteria by phages, analogous to antibiotics, are incorporated into the pipeline.