bluuebunny/crossref_metadata_2025_split huggingface dataset:
The arginase 1/ornithine decarboxylase pathway suppresses HDAC3 to ameliorate the myeloid cell inflammatory response: implications for retinal ischemic injury
Authors: Shosha Esraa , Shahror Rami A. , Morris Carol A. , Xu Zhimin , Lucas Rudolf , McGee-Lawrence Meghan E. , Rusch Nancy J. , Caldwell Ruth B. , Fouda Abdelrahman Y. 
Published: September 2023

AbstractThe enzyme arginase 1 (A1) hydrolyzes the amino acid arginine to form L-ornithine and urea. Ornithine is further converted to polyamines by the ornithine decarboxylase (ODC) enzyme. We previously reported that deletion of myeloid A1 in mice exacerbates retinal damage after ischemia/reperfusion (IR) injury. Furthermore, treatment with A1 protects against retinal IR injury in wild-type mice. PEG-A1 also mitigates the exaggerated inflammatory response of A1 knockout (KO) macrophages in vitro. Here, we sought to identify the anti-inflammatory pathway that confers macrophage A1-mediated protection against retinal IR injury. Acute elevation of intraocular pressure was used to induce retinal IR injury in mice. A multiplex cytokine assay revealed a marked increase in the inflammatory cytokines interleukin 1β (IL-1β) and tumor necrosis factor α (TNF-α) in the retina at day 5 after IR injury. In vitro, blocking the A1/ODC pathway augmented IL-1β and TNF-α production in stimulated macrophages. Furthermore, A1 treatment attenuated the stimulated macrophage metabolic switch to a pro-inflammatory glycolytic phenotype, whereas A1 deletion had the opposite effect. Screening for histone deacetylases (HDACs) which play a role in macrophage inflammatory response showed that A1 deletion or ODC inhibition increased the expression of HDAC3. We further showed the involvement of HDAC3 in the upregulation of TNF-α but not IL-1β in stimulated macrophages deficient in the A1/ODC pathway. Investigating HDAC3 KO macrophages showed a reduced inflammatory response and a less glycolytic phenotype upon stimulation. In vivo, HDAC3 co-localized with microglia/macrophages at day 2 after IR in WT retinas and was further increased in A1-deficient retinas. Collectively, our data provide initial evidence that A1 exerts its anti-inflammatory effect in macrophages via ODC-mediated suppression of HDAC3 and IL-1β. Collectively we propose that interventions that augment the A1/ODC pathway and inhibit HDAC3 may confer therapeutic benefits for the treatment of retinal ischemic diseases.
Creating speech zones with self-distributing acoustic swarms
Authors: Itani Malek , Chen Tuochao , Yoshioka Takuya , Gollakota Shyamnath 
Published: September 2023

AbstractImagine being in a crowded room with a cacophony of speakers and having the ability to focus on or remove speech from a specific 2D region. This would require understanding and manipulating an acoustic scene, isolating each speaker, and associating a 2D spatial context with each constituent speech. However, separating speech from a large number of concurrent speakers in a room into individual streams and identifying their precise 2D locations is challenging, even for the human brain. Here, we present the first acoustic swarm that demonstrates cooperative navigation with centimeter-resolution using sound, eliminating the need for cameras or external infrastructure. Our acoustic swarm forms a self-distributing wireless microphone array, which, along with our attention-based neural network framework, lets us separate and localize concurrent human speakers in the 2D space, enabling speech zones. Our evaluations showed that the acoustic swarm could localize and separate 3-5 concurrent speech sources in real-world unseen reverberant environments with median and 90-percentile 2D errors of 15 cm and 50 cm, respectively. Our system enables applications like mute zones (parts of the room where sounds are muted), active zones (regions where sounds are captured), multi-conversation separation and location-aware interaction.
The NCOR-HDAC3 co-repressive complex modulates the leukemogenic potential of the transcription factor ERG
Authors: Kugler Eitan , Madiwale Shreyas , Yong Darren , Thoms Julie A. I. , Birger Yehudit , Sykes David B. , Schmoellerl Johannes , Drakul Aneta , Priebe Valdemar , Yassin Muhammad , Aqaqe Nasma , Rein Avigail , Fishman Hila , Geron Ifat , Chen Chun-Wei , Raught Brian , Liu Qiao , Ogana Heather , Liedke Elisabeth , Bourquin Jean-Pierre , Zuber Johannes , Milyavsky Michael , Pimanda John , Privé Gilbert G. , Izraeli Shai 
Published: September 2023

AbstractThe ERG (ETS-related gene) transcription factor is linked to various types of cancer, including leukemia. However, the specific ERG domains and co-factors contributing to leukemogenesis are poorly understood. Drug targeting a transcription factor such as ERG is challenging. Our study reveals the critical role of a conserved amino acid, proline, at position 199, located at the 3’ end of the PNT (pointed) domain, in ERG’s ability to induce leukemia. P199 is necessary for ERG to promote self-renewal, prevent myeloid differentiation in hematopoietic progenitor cells, and initiate leukemia in mouse models. Here we show that P199 facilitates ERG’s interaction with the NCoR-HDAC3 co-repressor complex. Inhibiting HDAC3 reduces the growth of ERG-dependent leukemic and prostate cancer cells, indicating that the interaction between ERG and the NCoR-HDAC3 co-repressor complex is crucial for its oncogenic activity. Thus, targeting this interaction may offer a potential therapeutic intervention.
Reassessing chain tilt in the lamellar crystals of polyethylene
Authors: Kanomi Shusuke , Marubayashi Hironori , Miyata Tomohiro , Jinnai Hiroshi 
Published: September 2023

AbstractSemicrystalline polymers are extensively used in various forms, including fibres, films, and bottles. They exhibit remarkable properties, e.g., mechanical and thermal, that are governed by hierarchical structures comprising 10–20-nm-thick lamellar crystals. In 1957, Keller deduced that long polyethylene (PE) chains fold to form thin single lamellar crystals, with the molecular chains perpendicular to the flat faces of the crystals (the chain-folding model). Chains inclining to the perpendicular orientation in single crystals have since been reported, along with their effects on the physical properties of PE. For bulk specimens, the chain tilt angle (φ) has been investigated only for model samples with well-annealed internal structures. However, for briefly annealed specimens, the φ values of lamellae and their origins are controversial owing to the disordered lamellar morphology and orientation. Herein, we report the direct determination of molecular-chain orientations in the lamellar crystals of high-density PE using a state-of-the-art electron-diffraction-based imaging technique with nanometre-scale positional resolution and provide compelling evidence for the existence of lamellar crystals with different inner-chain orientations. Clarifying the nanoscale variation in lamellar crystals in PE can allow precise tuning of properties and expedite resource-saving material design.
Signal-noise metrics for RNA binding protein identification reveal broad spectrum protein-RNA interaction frequencies and dynamics
Authors: Kristofich JohnCarlo , Nicchitta Christopher V. 
Published: September 2023

AbstractRecent efforts towards the comprehensive identification of RNA-bound proteomes have revealed a large, surprisingly diverse family of candidate RNA-binding proteins (RBPs). Quantitative metrics for characterization and validation of protein-RNA interactions and their dynamic interactions have, however, proven analytically challenging and prone to error. Here we report a method termed LEAP-RBP (Liquid-Emulsion-Assisted-Purification of RNA-Bound Protein) for the selective, quantitative recovery of UV-crosslinked RNA-protein complexes. By virtue of its high specificity and yield, LEAP-RBP distinguishes RNA-bound and RNA-free protein levels and reveals common sources of experimental noise in RNA-centric RBP enrichment methods. We introduce strategies for accurate RBP identification and signal-based metrics for quantifying protein-RNA complex enrichment, relative RNA occupancy, and method specificity. In this work, the utility of our approach is validated by comprehensive identification of RBPs whose association with mRNA is modulated in response to global mRNA translation state changes and through in-depth benchmark comparisons with current methodologies.
Accelerated discovery of multi-elemental reverse water-gas shift catalysts using extrapolative machine learning approach
Authors: Wang Gang , Mine Shinya , Chen Duotian , Jing Yuan , Ting Kah Wei , Yamaguchi Taichi , Takao Motoshi , Maeno Zen , Takigawa Ichigaku , Matsushita Koichi , Shimizu Ken-ichi , Toyao Takashi 
Published: September 2023

AbstractDesigning novel catalysts is key to solving many energy and environmental challenges. Despite the promise that data science approaches, including machine learning (ML), can accelerate the development of catalysts, truly novel catalysts have rarely been discovered through ML approaches because of one of its most common limitations and criticisms—the assumed inability to extrapolate and identify extraordinary materials. Herein, we demonstrate an extrapolative ML approach to develop new multi-elemental reverse water-gas shift catalysts. Using 45 catalysts as the initial data points and performing 44 cycles of the closed loop discovery system (ML prediction + experiment), we experimentally tested a total of 300 catalysts and identified more than 100 catalysts with superior activity compared to those of the previously reported high-performance catalysts. The composition of the optimal catalyst discovered was Pt(3)/Rb(1)-Ba(1)-Mo(0.6)-Nb(0.2)/TiO2. Notably, niobium (Nb) was not included in the original dataset, and the catalyst composition identified was not predictable even by human experts.
mRNA vaccine quality analysis using RNA sequencing
Authors: Gunter Helen M. , Idrisoglu Senel , Singh Swati , Han Dae Jong , Ariens Emily , Peters Jonathan R. , Wong Ted , Cheetham Seth W. , Xu Jun , Rai Subash Kumar , Feldman Robert , Herbert Andy , Marcellin Esteban , Tropee Romain , Munro Trent , Mercer Tim R. 
Published: September 2023

AbstractThe success of mRNA vaccines has been realised, in part, by advances in manufacturing that enabled billions of doses to be produced at sufficient quality and safety. However, mRNA vaccines must be rigorously analysed to measure their integrity and detect contaminants that reduce their effectiveness and induce side-effects. Currently, mRNA vaccines and therapies are analysed using a range of time-consuming and costly methods. Here we describe a streamlined method to analyse mRNA vaccines and therapies using long-read nanopore sequencing. Compared to other industry-standard techniques, VAX-seq can comprehensively measure key mRNA vaccine quality attributes, including sequence, length, integrity, and purity. We also show how direct RNA sequencing can analyse mRNA chemistry, including the detection of nucleoside modifications. To support this approach, we provide supporting software to automatically report on mRNA and plasmid template quality and integrity. Given these advantages, we anticipate that RNA sequencing methods, such as VAX-seq, will become central to the development and manufacture of mRNA drugs.
Strained few-layer MoS2 with atomic copper and selectively exposed in-plane sulfur vacancies for CO2 hydrogenation to methanol
Authors: Zhou Shenghui , Ma Wenrui , Anjum Uzma , Kosari Mohammadreza , Xi Shibo , Kozlov Sergey M. , Zeng Hua Chun 
Published: September 2023

AbstractIn-plane sulfur vacancies (Sv) in molybdenum disulfide (MoS2) were newly unveiled for CO2 hydrogenation to methanol, whereas edge Sv were found to facilitate methane formation. Thus, selective exposure and activation of basal plane is crucial for methanol synthesis. Here, we report a mesoporous silica-encapsulated MoS2 catalysts with fullerene-like structure and atomic copper (Cu/MoS2@SiO2). The main approach is based on a physically constrained topologic conversion of molybdenum dioxide (MoO2) to MoS2 within silica. The spherical curvature enables the generation of strain and Sv in inert basal plane. More importantly, fullerene-like structure of few-layer MoS2 can selectively expose in-plane Sv and reduce the exposure of edge Sv. After promotion by atomic copper, the resultant Cu/MoS2@SiO2 exhibits stable specific methanol yield of 6.11 molMeOH molMo–1 h–1 with methanol selectivity of 72.5% at 260 °C, much superior to its counterparts lacking the fullerene-like structure and copper decoration. The reaction mechanism and promoting role of copper are investigated by in-situ DRIFTS and in-situ XAS. Theoretical calculations demonstrate that the compressive strain facilitates Sv formation and CO2 hydrogenation, while tensile strain accelerates the regeneration of active sites, rationalizing the critical role of strain.
Lola-I is a promoter pioneer factor that establishes de novo Pol II pausing during development
Authors: Ramalingam Vivekanandan , Yu Xinyang , Slaughter Brian D. , Unruh Jay R. , Brennan Kaelan J. , Onyshchenko Anastasiia , Lange Jeffrey J. , Natarajan Malini , Buck Michael , Zeitlinger Julia 
Published: September 2023

AbstractWhile the accessibility of enhancers is dynamically regulated during development, promoters tend to be constitutively accessible and poised for activation by paused Pol II. By studying Lola-I, a Drosophila zinc finger transcription factor, we show here that the promoter state can also be subject to developmental regulation independently of gene activation. Lola-I is ubiquitously expressed at the end of embryogenesis and causes its target promoters to become accessible and acquire paused Pol II throughout the embryo. This promoter transition is required but not sufficient for tissue-specific target gene activation. Lola-I mediates this function by depleting promoter nucleosomes, similar to the action of pioneer factors at enhancers. These results uncover a level of regulation for promoters that is normally found at enhancers and reveal a mechanism for the de novo establishment of paused Pol II at promoters.
Proof of crystal-field-perturbation-enhanced luminescence of lanthanide-doped nanocrystals through interstitial H+ doping
Authors: Li Guowei , Jiang Shihui , Liu Aijun , Ye Lixiang , Ke Jianxi , Liu Caiping , Chen Lian , Liu Yongsheng , Hong Maochun 
Published: September 2023

AbstractCrystal-field perturbation is theoretically the most direct and effective method of achieving highly efficient photoluminescence from trivalent lanthanide (Ln3+) ions through breaking the parity-forbidden nature of their 4f-transitions. However, exerting such crystal-field perturbation remains an arduous task even in well-developed Ln3+-doped luminescent nanocrystals (NCs). Herein, we report crystal-field perturbation through interstitial H+-doping in orthorhombic-phase NaMgF3:Ln3+ NCs and achieve a three-orders-of-magnitude emission amplification without a distinct lattice distortion. Mechanistic studies reveal that the interstitial H+ ions perturb the local charge density distribution, leading to anisotropic polarization of the F− ligand, which affects the highly symmetric Ln3+-substituted [MgF6]4− octahedral clusters. This effectively alleviates the parity-forbidden selective rule to enhance the 4f–4 f radiative transition rate of the Ln3+ emitter and is directly corroborated by the apparent shortening of the radiative recombination lifetime. The interstitially H+-doped NaMgF3:Yb/Er NCs are successfully used as bioimaging agents for real-time vascular imaging. These findings provide concrete evidence for crystal-field perturbation effects and promote the design of Ln3+-doped luminescent NCs with high brightness.
Self-organized and directed branching results in optimal coverage in developing dermal lymphatic networks
Authors: Uçar Mehmet Can , Hannezo Edouard , Tiilikainen Emmi , Liaqat Inam , Jakobsson Emma , Nurmi Harri , Vaahtomeri Kari 
Published: September 2023

AbstractBranching morphogenesis is a ubiquitous process that gives rise to high exchange surfaces in the vasculature and epithelial organs. Lymphatic capillaries form branched networks, which play a key role in the circulation of tissue fluid and immune cells. Although mouse models and correlative patient data indicate that the lymphatic capillary density directly correlates with functional output, i.e., tissue fluid drainage and trafficking efficiency of dendritic cells, the mechanisms ensuring efficient tissue coverage remain poorly understood. Here, we use the mouse ear pinna lymphatic vessel network as a model system and combine lineage-tracing, genetic perturbations, whole-organ reconstructions and theoretical modeling to show that the dermal lymphatic capillaries tile space in an optimal, space-filling manner. This coverage is achieved by two complementary mechanisms: initial tissue invasion provides a non-optimal global scaffold via self-organized branching morphogenesis, while VEGF-C dependent side-branching from existing capillaries rapidly optimizes local coverage by directionally targeting low-density regions. With these two ingredients, we show that a minimal biophysical model can reproduce quantitatively whole-network reconstructions, across development and perturbations. Our results show that lymphatic capillary networks can exploit local self-organizing mechanisms to achieve tissue-scale optimization.
Pick and place process for uniform shrinking of 3D printed micro- and nano-architected materials
Authors: Mori Tomohiro , Wang Hao , Zhang Wang , Ser Chern Chia , Arora Deepshikha , Pan Cheng-Feng , Li Hao , Niu Jiabin , Rahman M. A. , Mori Takeshi , Koishi Hideyuki , Yang Joel K. W. 
Published: September 2023

AbstractTwo-photon polymerization lithography is promising for producing three-dimensional structures with user-defined micro- and nanoscale features. Additionally, shrinkage by thermolysis can readily shorten the lattice constant of three-dimensional photonic crystals and enhance their resolution and mechanical properties; however, this technique suffers from non-uniform shrinkage owing to substrate pinning during heating. Here, we develop a simple method using poly(vinyl alcohol)-assisted uniform shrinking of three-dimensional printed structures. Microscopic three-dimensional printed objects are picked and placed onto a receiving substrate, followed by heating to induce shrinkage. We show the successful uniform heat-shrinking of three-dimensional prints with various shapes and sizes, without sacrificial support structures, and observe that the surface properties of the receiving substrate are important factors for uniform shrinking. Moreover, we print a three-dimensional mascot model that is then uniformly shrunk, producing vivid colors from colorless woodpile photonic crystals. The proposed method has significant potential for application in mechanics, optics, and photonics.
Nonlinear El Niño impacts on the global economy under climate change
Authors: Liu Yi , Cai Wenju , Lin Xiaopei , Li Ziguang , Zhang Ying 
Published: September 2023

AbstractThe El Niño-Southern Oscillation (ENSO) is a consequential climate phenomenon affecting global extreme weather events often with largescale socioeconomic impacts. To what extent the impact affects the macroeconomy, how long the impact lasts, and how the impact may change in a warming climate are important questions for the field. Using a smooth nonlinear climate-economy model fitted with historical data, here we find a damaging impact from an El Niño which increases for a further three years after initial shock, amounting to multi-trillion US dollars in economic loss; we attribute a loss of US$2.1 T and US$3.9 T globally to the 1997-98 and 2015-16 extreme El Niño events, far greater than that based on tangible losses. We find impacts from La Niña are asymmetric and weaker, and estimate a gain of only US$0.06 T from the 1998-99 extreme La Niña event. Under climate change, economic loss grows exponentially with increased ENSO variability. Under a high-emission scenario, increased ENSO variability causes an additional median loss of US$33 T to the global economy at a 3% discount rate aggregated over the remainder of the 21st century. Thus, exacerbated economic damage from changing ENSO in a warming climate should be considered in assessments of mitigation strategies.
Benchmarking universal quantum gates via channel spectrum
Authors: Gu Yanwu , Zhuang Wei-Feng , Chai Xudan , Liu Dong E. 
Published: September 2023

AbstractNoise remains the major obstacle to scalable quantum computation. Quantum benchmarking provides key information on noise properties and is an important step for developing more advanced quantum processors. However, current benchmarking methods are either limited to a specific subset of quantum gates or cannot directly describe the performance of the individual target gate. To overcome these limitations, we propose channel spectrum benchmarking (CSB), a method to infer the noise properties of the target gate, including process fidelity, stochastic fidelity, and some unitary parameters, from the eigenvalues of its noisy channel. Our CSB method is insensitive to state-preparation and measurement errors, and importantly, can benchmark universal gates and is scalable to many-qubit systems. Unlike standard randomized schemes, CSB can provide direct noise information for both target native gates and circuit fragments, allowing benchmarking and calibration of global entangling gates and frequently used modules in quantum algorithms like Trotterized Hamiltonian evolution operator in quantum simulation.
SRC and TKS5 mediated podosome formation in fibroblasts promotes extracellular matrix invasion and pulmonary fibrosis
Authors: Barbayianni Ilianna , Kanellopoulou Paraskevi , Fanidis Dionysios , Nastos Dimitris , Ntouskou Eleftheria-Dimitra , Galaris Apostolos , Harokopos Vaggelis , Hatzis Pantelis , Tsitoura Eliza , Homer Robert , Kaminski Naftali , Antoniou Katerina M. , Crestani Bruno , Tzouvelekis Argyrios , Aidinis Vassilis 
Published: September 2023

AbstractThe activation and accumulation of lung fibroblasts resulting in aberrant deposition of extracellular matrix components, is a pathogenic hallmark of Idiopathic Pulmonary Fibrosis, a lethal and incurable disease. In this report, increased expression of TKS5, a scaffold protein essential for the formation of podosomes, was detected in the lung tissue of Idiopathic Pulmonary Fibrosis patients and bleomycin-treated mice. Τhe profibrotic milieu is found to induceTKS5expression and the formation of prominent podosome rosettes in lung fibroblasts, that are retained ex vivo, culminating in increased extracellular matrix invasion.Tks5+/-mice are found resistant to bleomycin-induced pulmonary fibrosis, largely attributed to diminished podosome formation in fibroblasts and decreased extracellular matrix invasion. As computationally predicted, inhibition of src kinase is shown to potently attenuate podosome formation in lung fibroblasts and extracellular matrix invasion, and bleomycin-induced pulmonary fibrosis, suggesting pharmacological targeting of podosomes as a very promising therapeutic option in pulmonary fibrosis.