bluuebunny/crossref_metadata_2025_split huggingface dataset:
Assessing Outcomes in Stratospheric Aerosol Injection Scenarios Shortly After Deployment
Authors: Hueholt Daniel M. , Barnes Elizabeth A. , Hurrell James W. , Richter Jadwiga H. , Sun Lantao 
Published: May 2023

AbstractStratospheric aerosol injection (SAI) is a proposed form of climate intervention that would release reflective particles into the stratosphere, thereby reducing solar insolation and cooling the planet. The climate response to SAI is not well understood, particularly on short‐term time horizons frequently used by decision‐makers and planning practitioners to assess climate information. We demonstrate two framings to explore the climate response in the decade after SAI deployment in modeling experiments with parallel SAI and no‐SAI simulations. The first framing, which we call a snapshot around deployment, displays change over time within the SAI scenarios and applies to the question “What happens before and after SAI is deployed in the model?” The second framing, the intervention impact, displays the difference between the SAI and no‐SAI simulations, corresponding to the question “What is the impact of a given intervention relative to climate change with no intervention?” We apply these framings to annual mean 2 m temperature, precipitation, and a precipitation extreme during the 10 yr after deployment in two large ensembles of Earth system model simulations that comprehensively represent both the SAI injection process and climate response, and connect these results to implications for other climate variables. We show that SAI deployment robustly reduces changes in many high‐impact climate variables even on these short timescales where the forced response is relatively small, but that details of the climate response depend on the model version, greenhouse gas emissions scenario, and other aspects of the experimental design.
Thermospheric Temperature and ΣO/N2 Variations as Observed by GOLD and Compared to MSIS and WACCM‐X Simulations During 2019–2020 at Deep Solar Minimum
Authors: Liu Guiping , Rowland Douglas E. , Gan Quan , Liu Han‐Li , Klenzing Jeffrey H. , England Scott L. , Eastes Richard W. 
Published: May 2023

AbstractThe ultraviolet‐imaging spectrograph that comprises Global‐scale Observations of the Limb and Disk (GOLD) mission in geostationary orbit at 47.5°W longitude has taken full disk images at high cadence throughout the deep solar minimum period of 2019–2020. Synoptic (i.e., concurrent and spatially unified and resolved) observations of thermospheric temperature and composition at ∼150 km altitude are made for the first time, allowing GOLD to disambiguate temporal and spatial variations. Here we analyze the daytime effective temperature and column integrated O and N2 density ratio (ΣO/N2) data simultaneously observed by GOLD over 120°W–20°E longitude and 60°S–60°N latitude from 13 October 2019 to 12 October 2020. Daily zonal mean values are calculated for each latitude and compared with NRLMSIS 2.0 and simulations from the Whole Atmosphere Community Climate Model with thermosphere and ionosphere extension (WACCM‐X). On average, the GOLD observations show higher temperatures than Mass Spectrometer Incoherent Scatter radar (MSIS) and WACCM‐X by ∼20–60 K (5%–10%) and 80–120 K (12%–18%), respectively. The ΣO/N2 ratios observed by GOLD are larger than the MSIS results by ∼0.4 (40%) but smaller than the WACCM‐X simulations by ∼0.3 (30%). The observed and modeled results are correlated at most latitudes (r = 0.4–0.8), and GOLD, MSIS, and WACCM‐X all display a similar seasonal variation and change with latitude. WACCM‐X simulates a larger annual variation in ΣO/N2, suggesting that the thermospheric circulation is overestimated and atmospheric waves and turbulence transport are not properly represented in the model.
Macrophages in immunoregulation and therapeutics
Authors: Chen Shanze , Saeed Abdullah F.U.H. , Liu Quan , Jiang Qiong , Xu Haizhao , Xiao Gary Guishan , Rao Lang , Duo Yanhong 
Published: May 2023

AbstractMacrophages exist in various tissues, several body cavities, and around mucosal surfaces and are a vital part of the innate immune system for host defense against many pathogens and cancers. Macrophages possess binary M1/M2 macrophage polarization settings, which perform a central role in an array of immune tasks via intrinsic signal cascades and, therefore, must be precisely regulated. Many crucial questions about macrophage signaling and immune modulation are yet to be uncovered. In addition, the clinical importance of tumor-associated macrophages is becoming more widely recognized as significant progress has been made in understanding their biology. Moreover, they are an integral part of the tumor microenvironment, playing a part in the regulation of a wide variety of processes including angiogenesis, extracellular matrix transformation, cancer cell proliferation, metastasis, immunosuppression, and resistance to chemotherapeutic and checkpoint blockade immunotherapies. Herein, we discuss immune regulation in macrophage polarization and signaling, mechanical stresses and modulation, metabolic signaling pathways, mitochondrial and transcriptional, and epigenetic regulation. Furthermore, we have broadly extended the understanding of macrophages in extracellular traps and the essential roles of autophagy and aging in regulating macrophage functions. Moreover, we discussed recent advances in macrophages-mediated immune regulation of autoimmune diseases and tumorigenesis. Lastly, we discussed targeted macrophage therapy to portray prospective targets for therapeutic strategies in health and diseases.
Accelerated aging in articular cartilage by ZMPSTE24 deficiency leads to osteoarthritis with impaired metabolic signaling and epigenetic regulation
Authors: Suo Jinlong , Shao Rui , Yang Ruici , Wang Jinghui , Zhang Zhong , Wang Duo , Niu Ningning , Zheng Xianyou , Zou Weiguo 
Published: May 2023

AbstractOsteoarthritis (OA) is an age-related degenerative disease without disease-modifying therapy. The lack of aging-induced osteoarthritis models makes the discovery of therapeutic drugs more challenging. The deficiency of ZMPSTE24 could induce Hutchinson–Gilford progeria syndrome (HGPS), a genetic disorder of rapid aging. However, the relationship between HGPS and OA remains unclear. Our results found that the expression of Zmpste24 was decreased in the articular cartilage during the aging process. Zmpste24 knockout mice, Prx1-Cre; Zmpste24fl/fl mice and Col2-CreERT2; Zmpste24fl/fl mice displayed OA phenotype. Loss of Zmpste24 in articular cartilage could exacerbate the occurrence and development of osteoarthritis. Transcriptome sequencing revealed that deletion of Zmpste24 or accumulation of progerin affects chondrocyte metabolism, inhibits cell proliferation and promotes cell senescence. Using this animal model, we elucidate the upregulation of H3K27me3 during chondrocyte senescence and discover the molecular mechanism by which lamin A mutant stabilizes EZH2 expression. The construction of aging-induced osteoarthritis models and the elucidation of the signaling pathways and molecular mechanisms of articular chondrocyte senescence would benefit the discovery and development of new drugs for OA.
The deleted in oral cancer (DOC1 aka CDK2AP1) tumor suppressor gene is downregulated in oral squamous cell carcinoma by multiple microRNAs
Authors: Stabile Roberto , Cabezas Mario Román , Verhagen Mathijs P. , Tucci Francesco A. , van den Bosch Thierry P. P. , De Herdt Maria J. , van der Steen Berdine , Nigg Alex L. , Chen Meng , Ivan Cristina , Shimizu Masayoshi , Koljenović Senada , Hardillo Jose A. , Verrijzer C. Peter , Baatenburg de Jong Robert J. , Calin George A. , Fodde Riccardo 
Published: May 2023

AbstractCyclin-dependent kinase 2-associated protein 1 (CDK2AP1; also known as deleted in oral cancer or DOC1) is a tumor suppressor gene known to play functional roles in both cell cycle regulation and in the epigenetic control of embryonic stem cell differentiation, the latter as a core subunit of the nucleosome remodeling and histone deacetylation (NuRD) complex. In the vast majority of oral squamous cell carcinomas (OSCC), expression of the CDK2AP1 protein is reduced or lost. Notwithstanding the latter (and the DOC1 acronym), mutations or deletions in its coding sequence are extremely rare. Accordingly, CDK2AP1 protein-deficient oral cancer cell lines express as much CDK2AP1 mRNA as proficient cell lines. Here, by combining in silico and in vitro approaches, and by taking advantage of patient-derived data and tumor material in the analysis of loss of CDK2AP1 expression, we identified a set of microRNAs, namely miR-21-5p, miR-23b-3p, miR-26b-5p, miR-93-5p, and miR-155-5p, which inhibit its translation in both cell lines and patient-derived OSCCs. Of note, no synergistic effects were observed of the different miRs on the CDK2AP1–3-UTR common target. We also developed a novel approach to the combined ISH/IF tissue microarray analysis to study the expression patterns of miRs and their target genes in the context of tumor architecture. Last, we show that CDK2AP1 loss, as the result of miRNA expression, correlates with overall survival, thus highlighting the clinical relevance of these processes for carcinomas of the oral cavity.
Clinical diagnosis of genetic disorders at both single-nucleotide and chromosomal levels based on BGISEQ-500 platform
Authors: Liu Yanqiu , Mao Liangwei , Huang Hui , Li Wei , Man Jianfen , Zhang Wenqian , Wang Lina , Li Long , Sun Yan , Zhai Teng , Guo Xueqin , Du Lique , Huang Jin , Li Hao , Wan Yang , Wei Xiaoming 
Published: May 2023

AbstractMost variations in the human genome refer to single-nucleotide variation (SNV), small fragment insertions and deletions, and genomic copy number variation (CNV). Many human diseases including genetic disorders are associated with variations in the genome. These disorders are often difficult to be diagnosed because of their complex clinical conditions, therefore, an effective detection method is needed to facilitate clinical diagnosis and prevent birth defects. With the development of high-throughput sequencing technology, the method of targeted sequence capture chip has been extensively used owing to its high throughput, high accuracy, fast speed, and low cost. In this study, we designed a chip that potentially captured the coding region of 3043 genes associated with 4013 monogenic diseases, with an addition of 148 chromosomal abnormalities that can be identified by targeting specific regions. To assess the efficiency, a strategy of combining the BGISEQ500 sequencing platform with the designed chip was utilized to screen variants in 63 patients. Eventually, 67 disease-associated variants were found, 31 of which were novel. The results of the evaluation test also show that this combined strategy complies with the requirements of clinical testing and has proper clinical application value.
Accuracy of cuff blood pressure and systolic blood pressure amplification
Authors: Bui Tan V. , Picone Dean S. , Schultz Martin G. , Peng Xiaoqing , Black J. Andrew , Dwyer Nathan , Roberts-Thomson Philip , Adams Heath , Chen Chen-Huan , Cheng Hao-min , Pucci Giacomo , Wang Jiguang , Goupil Remi , Sharman James E. 
Published: May 2023

AbstractAutomated cuff measured blood pressure (BP) is the global standard used for diagnosing hypertension, but there are concerns regarding the accuracy of the method. Individual variability in systolic BP (SBP) amplification from central (aorta) to peripheral (brachial) arteries could be related to the accuracy of cuff BP, but this has never been determined and was the aim of this study. Automated cuff BP and invasive brachial BP were recorded in 795 participants (74% male, aged 64 ± 11 years) receiving coronary angiography at five independent research sites (using seven different automated cuff BP devices). SBP amplification was recorded invasively by catheter and defined as brachial SBP minus aortic SBP. Compared with invasive brachial SBP, cuff SBP was significantly underestimated (130 ± 18 mmHg vs. 138 ± 22 mmHg, p < 0.001). The level of SBP amplification varied significantly among individuals (mean ± SD, 7.3 ± 9.1 mmHg) and was similar to level of difference between cuff and invasive brachial SBP (mean difference –7.6 ± 11.9 mmHg). SBP amplification explained most of the variance in accuracy of cuff SBP (R2 = 19%). The accuracy of cuff SBP was greatest among participants with the lowest SBP amplification (ptrend < 0.001). After cuff BP values were corrected for SBP amplification, there was a significant improvement in the mean difference from the intra-arterial standard (p < 0.0001) and in the accuracy of hypertension classification according to 2017 ACC/AHA guideline thresholds (p = 0.005). The level of SBP amplification is a critical factor associated with the accuracy of conventional automated cuff measured BP.
Neural-network decoders for measurement induced phase transitions
Authors: Dehghani Hossein , Lavasani Ali , Hafezi Mohammad , Gullans Michael J. 
Published: May 2023

AbstractOpen quantum systems have been shown to host a plethora of exotic dynamical phases. Measurement-induced entanglement phase transitions in monitored quantum systems are a striking example of this phenomena. However, naive realizations of such phase transitions requires an exponential number of repetitions of the experiment which is practically unfeasible on large systems. Recently, it has been proposed that these phase transitions can be probed locally via entangling reference qubits and studying their purification dynamics. In this work, we leverage modern machine learning tools to devise a neural network decoder to determine the state of the reference qubits conditioned on the measurement outcomes. We show that the entanglement phase transition manifests itself as a stark change in the learnability of the decoder function. We study the complexity and scalability of this approach in both Clifford and Haar random circuits and discuss how it can be utilized to detect entanglement phase transitions in generic experiments.
Reference-free assembly of long-read transcriptome sequencing data with RNA-Bloom2
Authors: Nip Ka Ming , Hafezqorani Saber , Gagalova Kristina K. , Chiu Readman , Yang Chen , Warren René L. , Birol Inanc 
Published: May 2023

AbstractLong-read sequencing technologies have improved significantly since their emergence. Their read lengths, potentially spanning entire transcripts, is advantageous for reconstructing transcriptomes. Existing long-read transcriptome assembly methods are primarily reference-based and to date, there is little focus on reference-free transcriptome assembly. We introduce “RNA-Bloom2 [https://github.com/bcgsc/RNA-Bloom]”, a reference-free assembly method for long-read transcriptome sequencing data. Using simulated datasets and spike-in control data, we show that the transcriptome assembly quality of RNA-Bloom2 is competitive to those of reference-based methods. Furthermore, we find that RNA-Bloom2 requires 27.0 to 80.6% of the peak memory and 3.6 to 10.8% of the total wall-clock runtime of a competing reference-free method. Finally, we showcase RNA-Bloom2 in assembling a transcriptome sample of Picea sitchensis (Sitka spruce). Since our method does not rely on a reference, it further sets the groundwork for large-scale comparative transcriptomics where high-quality draft genome assemblies are not readily available.
Decentralized federated learning through proxy model sharing
Authors: Kalra Shivam , Wen Junfeng , Cresswell Jesse C. , Volkovs Maksims , Tizhoosh H. R. 
Published: May 2023

AbstractInstitutions in highly regulated domains such as finance and healthcare often have restrictive rules around data sharing. Federated learning is a distributed learning framework that enables multi-institutional collaborations on decentralized data with improved protection for each collaborator’s data privacy. In this paper, we propose a communication-efficient scheme for decentralized federated learning called ProxyFL, or proxy-based federated learning. Each participant in ProxyFL maintains two models, a private model, and a publicly shared proxy model designed to protect the participant’s privacy. Proxy models allow efficient information exchange among participants without the need of a centralized server. The proposed method eliminates a significant limitation of canonical federated learning by allowing model heterogeneity; each participant can have a private model with any architecture. Furthermore, our protocol for communication by proxy leads to stronger privacy guarantees using differential privacy analysis. Experiments on popular image datasets, and a cancer diagnostic problem using high-quality gigapixel histology whole slide images, show that ProxyFL can outperform existing alternatives with much less communication overhead and stronger privacy.
Upregulation of breathing rate during running exercise by central locomotor circuits in mice
Authors: Hérent Coralie , Diem Séverine , Usseglio Giovanni , Fortin Gilles , Bouvier Julien 
Published: May 2023

AbstractWhile respiratory adaptation to exercise is compulsory to cope with the increased metabolic demand, the neural signals at stake remain poorly identified. Using neural circuit tracing and activity interference strategies in mice, we uncover here two systems by which the central locomotor network can enable respiratory augmentation in relation to running activity. One originates in the mesencephalic locomotor region (MLR), a conserved locomotor controller. Through direct projections onto the neurons of the preBötzinger complex that generate the inspiratory rhythm, the MLR can trigger a moderate increase of respiratory frequency, prior to, or even in the absence of, locomotion. The other is the lumbar enlargement of the spinal cord containing the hindlimb motor circuits. When activated, and through projections onto the retrotrapezoid nucleus (RTN), it also potently upregulates breathing rate. On top of identifying critical underpinnings for respiratory hyperpnea, these data also expand the functional implication of cell types and pathways that are typically regarded as “locomotor” or “respiratory” related.
Spectroscopic signature of obstructed surface states in SrIn2P2
Authors: Liu Xiang-Rui , Deng Hanbin , Liu Yuntian , Yin Zhouyi , Chen Congrun , Zhu Yu-Peng , Yang Yichen , Jiang Zhicheng , Liu Zhengtai , Ye Mao , Shen Dawei , Yin Jia-Xin , Wang Kedong , Liu Qihang , Zhao Yue , Liu Chang 
Published: May 2023

AbstractThe century-long development of surface sciences has witnessed the discoveries of a variety of quantum states. In the recently proposed “obstructed atomic insulators”, symmetric charges are pinned at virtual sites where no real atoms reside. The cleavage through these sites could lead to a set of obstructed surface states with partial electronic occupation. Here, utilizing scanning tunneling microscopy, angle-resolved photoemission spectroscopy and first-principles calculations, we observe spectroscopic signature of obstructed surface states in SrIn2P2. We find that a pair of surface states that are originated from the pristine obstructed surface states split in energy by a unique surface reconstruction. The upper branch is marked with a striking differential conductance peak followed by negative differential conductance, signaling its localized nature, while the lower branch is found to be highly dispersive. This pair of surface states is in consistency with our calculational results. Our finding not only demonstrates a surface quantum state induced by a new type of bulk-boundary correspondence, but also provides a platform for exploring efficient catalysts and related surface engineering.
Chemo-mechanical diffusion waves explain collective dynamics of immune cell podosomes
Authors: Gong Ze , van den Dries Koen , Migueles-Ramírez Rodrigo A. , Wiseman Paul W. , Cambi Alessandra , Shenoy Vivek B. 
Published: May 2023

AbstractImmune cells, such as macrophages and dendritic cells, can utilize podosomes, mechanosensitive actin-rich protrusions, to generate forces, migrate, and patrol for foreign antigens. Individual podosomes probe their microenvironment through periodic protrusion and retraction cycles (height oscillations), while oscillations of multiple podosomes in a cluster are coordinated in a wave-like fashion. However, the mechanisms governing both the individual oscillations and the collective wave-like dynamics remain unclear. Here, by integrating actin polymerization, myosin contractility, actin diffusion, and mechanosensitive signaling, we develop a chemo-mechanical model for podosome dynamics in clusters. Our model reveals that podosomes show oscillatory growth when actin polymerization-driven protrusion and signaling-associated myosin contraction occur at similar rates, while the diffusion of actin monomers drives wave-like coordination of podosome oscillations. Our theoretical predictions are validated by different pharmacological treatments and the impact of microenvironment stiffness on chemo-mechanical waves. Our proposed framework can shed light on the role of podosomes in immune cell mechanosensing within the context of wound healing and cancer immunotherapy.
Platelet-derived chemokines promote skeletal muscle regeneration by guiding neutrophil recruitment to injured muscles
Authors: Graca Flavia A. , Stephan Anna , Minden-Birkenmaier Benjamin A. , Shirinifard Abbas , Wang Yong-Dong , Demontis Fabio , Labelle Myriam 
Published: May 2023

AbstractSkeletal muscle regeneration involves coordinated interactions between different cell types. Injection of platelet-rich plasma is circumstantially considered an aid to muscle repair but whether platelets promote regeneration beyond their role in hemostasis remains unexplored. Here, we find that signaling via platelet-released chemokines is an early event necessary for muscle repair in mice. Platelet depletion reduces the levels of the platelet-secreted neutrophil chemoattractants CXCL5 and CXCL7/PPBP. Consequently, early-phase neutrophil infiltration to injured muscles is impaired whereas later inflammation is exacerbated. Consistent with this model, neutrophil infiltration to injured muscles is compromised in male mice with Cxcl7-knockout platelets. Moreover, neo-angiogenesis and the re-establishment of myofiber size and muscle strength occurs optimally in control mice post-injury but not in Cxcl7ko mice and in neutrophil-depleted mice. Altogether, these findings indicate that platelet-secreted CXCL7 promotes regeneration by recruiting neutrophils to injured muscles, and that this signaling axis could be utilized therapeutically to boost muscle regeneration.
Data-driven prediction of complex crystal structures of dense lithium
Authors: Wang Xiaoyang , Wang Zhenyu , Gao Pengyue , Zhang Chengqian , Lv Jian , Wang Han , Liu Haifeng , Wang Yanchao , Ma Yanming 
Published: May 2023

AbstractLithium (Li) is a prototypical simple metal at ambient conditions, but exhibits remarkable changes in structural and electronic properties under compression. There has been intense debate about the structure of dense Li, and recent experiments offered fresh evidence for yet undetermined crystalline phases near the enigmatic melting minimum region in the pressure-temperature phase diagram of Li. Here, we report on an extensive exploration of the energy landscape of Li using an advanced crystal structure search method combined with a machine-learning approach, which greatly expands the scale of structure search, leading to the prediction of four complex Li crystal structures containing up to 192 atoms in the unit cell that are energetically competitive with known Li structures. These findings provide a viable solution to the observed yet unidentified crystalline phases of Li, and showcase the predictive power of the global structure search method for discovering complex crystal structures in conjunction with accurate machine learning potentials.