bluuebunny/crossref_metadata_2025 huggingface dataset:
Northern Hemisphere Stratosphere‐Troposphere Circulation Change in CMIP6 Models: 2. Mechanisms and Sources of the Spread
Authors: Karpechko Alexey Yu. , Wu Zheng , Simpson Isla R. , Kretschmer Marlene , Afargan‐Gerstman Hilla , Butler Amy H. , Domeisen Daniela I.V. , Garny Hella , Lawrence Zachary , Manzini Elisa , Sigmond Michael
Published: July 2024

We analyze the sources for spread in the response of the Northern Hemisphere wintertime stratospheric polar vortex (SPV) to global warming in Climate Model Intercomparison Project Phase 5 (CMIP5) and Phase 6 (CMIP6) model projections. About half of the intermodel spread in SPV projections by CMIP6 models, but less than a third in CMIP5 models, can be attributed to the intermodel spread in stationary planetary wave driving. In CMIP6, SPV weakening is mostly driven by increased upward wave flux from the troposphere, while SPV strengthening is associated with increased equatorward wave propagation away from the polar stratosphere. We test hypothesized factors contributing to changes in the upward and equatorward planetary wave fluxes and show that an across‐model regression using projected global warming rates, strengthening of the subtropical jet and basic state lower stratospheric wind biases as predictors can explain nearly the same fraction in the CMIP6 SPV spread as the planetary wave driving (r = 0.67). The dependence of the SPV spread on the model biases in the basic state winds offers a possible emergent constraint; however, a large uncertainty prevents a substantial reduction of the projected SPV spread. The lack of this dependence in CMIP5 further calls for better understanding of underlying causes. Our results improve understanding of projected SPV uncertainty; however, further narrowing of the uncertainty remains challenging.
Sea Surface Wind Speed Estimation From the Combination of Satellite Scatterometer and Radiometer Parameters
Authors: Xiang Kunsheng , Zhou Wu , Bao Qingliu
Published: July 2024

Satellite research on global sea surface winds is crucial for understanding and monitoring the dynamics of earth's oceans, providing valuable insights into weather patterns, climate changes, and oceanographic processes. This study investigates the fusion of active (microwave scatterometer) and passive (microwave radiometer) satellite data using Machine learning (ML) for sea surface wind speed estimation. Employing Random Forest Regression (RF), Convolutional Neural Network Regression (CNN), and Multiple Linear Regression (MLR). Evaluation against reference data sets (Advanced Scatterometer, ERA5, Cross‐Calibrated Multi‐Platform (CCMP), buoy wind speeds) highlights the robustness of the proposed models. The research findings indicate that both RF and CNN exhibit superior accuracy in the active, passive, and joint active‐passive models compared to the simplistic MLR model. The joint models of the three regression methods outperform the individual active or passive models. The root mean square deviation (RMSD) accuracy of RF and CNN joint models, when compared with ASCAT, is in the order of 0.7 m/s, and when compared with buoys, the RMSD accuracy is around 1.1 m/s. The ML models, especially RF and CNN, demonstrate superior performance, providing accurate and reliable estimations crucial for meteorological and oceanographic applications. These findings underscore the potential operational use of ML techniques in enhancing remote sensing applications.
Oceanography of the Eastern Equatorial Pacific Ocean Across the Oligocene‐Miocene Transition
Authors: Liebrand Diederik , Wade Bridget S. , Beddow Helen M. , King David J. , Harrison Alexander D. , Johnstone Heather J. H. , Drury Anna Joy , Pälike Heiko , Sluijs Appy , Lourens Lucas J.
Published: July 2024

The functioning of the Pacific Ocean—the world's largest ocean—during a warmer‐than‐present paleoclimate state remains underexplored. We present planktonic and benthic foraminiferal stable oxygen (δ18O) and carbon (δ13C) isotope records from Integrated Ocean Drilling Program (IODP) Site U1334 that span the Oligocene‐Miocene Transition (OMT) interval, from 24.15 to 21.95 million years ago (Ma). We reconstruct (sub‐)surface and deep‐water conditions and provide better constraints on the physical and chemical oceanography of the eastern equatorial Pacific Ocean (EEP). Positive trends in planktonic and benthic foraminiferal δ18O values, mark a largely uniform imprint of increased land‐ice volume/global cooling on surface‐ and deep‐waters. We document a delayed planktonic foraminiferal δ18O increase across the OMT as well as an increase in the amplitude variability of planktonic foraminiferal δ18O values on eccentricity timescales during the early Miocene. We interpret this as an enhanced glacioeustatic sea‐level control on Atlantic‐Pacific salinity exchange through the Central American Seaway (CAS) or as the onset of more variable surface currents and oceanic fronts in the EEP. Positive trends in planktonic and benthic foraminiferal δ13C values characterize the whole‐ocean depletion in 12C linked to organic carbon burial during the Oligocene‐Miocene carbon maximum (CM‐OM). However, this depletion is more pronounced in the planktonic foraminiferal δ13C record, especially during ∼400 Kyr eccentricity minima, reflecting an increase in nutrient upwelling and the efficacy of the biological carbon pump (BCP) when global temperatures decreased across the OMT and during the early Miocene. Our study highlights the dynamic behavior of the EEP in a warmer‐than‐present unipolar icehouse state.
Advocating for the inclusion of kidney health outcomes in neonatal research: best practice recommendations by the Neonatal Kidney Collaborative
Authors: Reidy Kimberly J. , Guillet Ronnie , Selewski David T. , Defreitas Marissa , Stone Sadie , Starr Michelle C. , Harer Matthew W. , Todurkar Namrata , Vuong Kim T. , Gogcu Semsa , Askenazi David , Tipple Trent E. , Charlton Jennifer R.
Published: July 2024

Acute kidney injury (AKI) occurs in nearly 30% of sick neonates. Chronic kidney disease (CKD) can be detected in certain populations of sick neonates as early as 2 years. AKI is often part of a multisystem syndrome that negatively impacts developing organs resulting in short- and long-term pulmonary, neurodevelopmental, and cardiovascular morbidities. It is critical to incorporate kidney-related data into neonatal clinical trials in a uniform manner to better understand how neonatal AKI or CKD could affect an outcome of interest. Here, we provide expert opinion recommendations and rationales to support the inclusion of short- and long-term neonatal kidney outcomes using a tiered approach based on study design: (1) observational studies (prospective or retrospective) limited to data available within a center’s standard practice, (2) observational studies involving prospective data collection where prespecified kidney outcomes are included in the design, (3) interventional studies with non-nephrotoxic agents, and (4) interventional studies with known nephrotoxic agents. We also provide recommendations for biospecimen collection to facilitate ancillary kidney specific research initiatives. This approach balances the costs of AKI and CKD ascertainment with knowledge gained. We advocate that kidney outcomes be included routinely in neonatal clinical study design. Consistent incorporation of kidney outcomes across studies will increase our knowledge of neonatal morbidity.
Metabolic adaptations in prostate cancer
Authors: Pujana-Vaquerizo Mikel , Bozal-Basterra Laura , Carracedo Arkaitz
Published: July 2024

Prostate cancer is one of the most commonly diagnosed cancers in men and is a major cause of cancer-related deaths worldwide. Among the molecular processes that contribute to this disease, the weight of metabolism has been placed under the limelight in recent years. Tumours exhibit metabolic adaptations to comply with their biosynthetic needs. However, metabolites also play an important role in supporting cell survival in challenging environments or remodelling the tumour microenvironment, thus being recognized as a hallmark in cancer. Prostate cancer is uniquely driven by androgen receptor signalling, and this knowledge has also influenced the paths of cancer metabolism research. This review provides a comprehensive perspective on the metabolic adaptations that support prostate cancer progression beyond androgen signalling, with a particular focus on tumour cell intrinsic and extrinsic pathways.
Zero-shot prediction of mutation effects with multimodal deep representation learning guides protein engineering
Authors: Cheng Peng , Mao Cong , Tang Jin , Yang Sen , Cheng Yu , Wang Wuke , Gu Qiuxi , Han Wei , Chen Hao , Li Sihan , Chen Yaofeng , Zhou Jianglin , Li Wuju , Pan Aimin , Zhao Suwen , Huang Xingxu , Zhu Shiqiang , Zhang Jun , Shu Wenjie , Wang Shengqi
Published: July 2024

Mutations in amino acid sequences can provoke changes in protein function. Accurate and unsupervised prediction of mutation effects is critical in biotechnology and biomedicine, but remains a fundamental challenge. To resolve this challenge, here we present Protein Mutational Effect Predictor (ProMEP), a general and multiple sequence alignment-free method that enables zero-shot prediction of mutation effects. A multimodal deep representation learning model embedded in ProMEP was developed to comprehensively learn both sequence and structure contexts from ~160 million proteins. ProMEP achieves state-of-the-art performance in mutational effect prediction and accomplishes a tremendous improvement in speed, enabling efficient and intelligent protein engineering. Specifically, ProMEP accurately forecasts mutational consequences on the gene-editing enzymes TnpB and TadA, and successfully guides the development of high-performance gene-editing tools with their engineered variants. The gene-editing efficiency of a 5-site mutant of TnpB reaches up to 74.04% (vs 24.66% for the wild type); and the base editing tool developed on the basis of a TadA 15-site mutant (in addition to the A106V/D108N double mutation that renders deoxyadenosine deaminase activity to TadA) exhibits an A-to-G conversion frequency of up to 77.27% (vs 69.80% for ABE8e, a previous TadA-based adenine base editor) with significantly reduced bystander and off-target effects compared to ABE8e. ProMEP not only showcases superior performance in predicting mutational effects on proteins but also demonstrates a great capability to guide protein engineering. Therefore, ProMEP enables efficient exploration of the gigantic protein space and facilitates practical design of proteins, thereby advancing studies in biomedicine and synthetic biology.
Functional multi-organelle units control inflammatory lipid metabolism of macrophages
Authors: Zimmermann Julia A. , Lucht Kerstin , Stecher Manuel , Badhan Chahat , Glaser Katharina M. , Epple Maximilian W. , Koch Lena R. , Deboutte Ward , Manke Thomas , Ebnet Klaus , Brinkmann Frauke , Fehler Olesja , Vogl Thomas , Schuster Ev-Marie , Bremser Anna , Buescher Joerg M. , Rambold Angelika S.
Published: July 2024

Eukaryotic cells contain several membrane-separated organelles to compartmentalize distinct metabolic reactions. However, it has remained unclear how these organelle systems are coordinated when cells adapt metabolic pathways to support their development, survival or effector functions. Here we present OrgaPlexing, a multi-spectral organelle imaging approach for the comprehensive mapping of six key metabolic organelles and their interactions. We use this analysis on macrophages, immune cells that undergo rapid metabolic switches upon sensing bacterial and inflammatory stimuli. Our results identify lipid droplets (LDs) as primary inflammatory responder organelle, which forms three- and four-way interactions with other organelles. While clusters with endoplasmic reticulum (ER) and mitochondria (mitochondria–ER–LD unit) help supply fatty acids for LD growth, the additional recruitment of peroxisomes (mitochondria–ER–peroxisome–LD unit) supports fatty acid efflux from LDs. Interference with individual components of these units has direct functional consequences for inflammatory lipid mediator synthesis. Together, we show that macrophages form functional multi-organellar units to support metabolic adaptation and provide an experimental strategy to identify organelle-metabolic signalling hubs.
Algal methylated compounds shorten the lag phase of Phaeobacter inhibens bacteria
Authors: Sperfeld Martin , Narváez-Barragán Delia A. , Malitsky Sergey , Frydman Veronica , Yuda Lilach , Rocha Jorge , Segev Einat
Published: July 2024

The lag phase is key in resuming bacterial growth, but it remains underexplored particularly in environmental bacteria. Here we use transcriptomics and 13C-labelled metabolomics to show that the lag phase of the model marine bacterium Phaeobacter inhibens is shortened by methylated compounds produced by the microalgal partner, Emiliania huxleyi. Methylated compounds are abundantly produced and released by microalgae, and we show that their methyl groups can be collected by bacteria and assimilated through the methionine cycle. Our findings underscore the significance of methyl groups as a limiting factor during the lag phase and highlight the adjustability of this growth phase. In addition, we show that methylated compounds, typical of photosynthetic organisms, prompt diverse reductions in lag times in bacteria associated with algae and plants, potentially favouring early growth in some bacteria. These findings suggest ways to accelerate bacterial growth and underscore the significance of studying bacteria within an environmental context.
Saturation genome editing of BAP1 functionally classifies somatic and germline variants
Authors: Waters Andrew J. , Brendler-Spaeth Timothy , Smith Danielle , Offord Victoria , Tan Hong Kee , Zhao Yajie , Obolenski Sofia , Nielsen Maartje , van Doorn Remco , Murphy Jo-Ellen , Gupta Prashant , Rowlands Charlie F. , Hanson Helen , Delage Erwan , Thomas Mark , Radford Elizabeth J. , Gerety Sebastian S. , Turnbull Clare , Perry John R. B. , Hurles Matthew E. , Adams David J.
Published: July 2024

Many variants that we inherit from our parents or acquire de novo or somatically are rare, limiting the precision with which we can associate them with disease. We performed exhaustive saturation genome editing (SGE) of BAP1, the disruption of which is linked to tumorigenesis and altered neurodevelopment. We experimentally characterized 18,108 unique variants, of which 6,196 were found to have abnormal functions, and then used these data to evaluate phenotypic associations in the UK Biobank. We also characterized variants in a large population-ascertained tumor collection, in cancer pedigrees and ClinVar, and explored the behavior of cancer-associated variants compared to that of variants linked to neurodevelopmental phenotypes. Our analyses demonstrated that disruptive germline BAP1 variants were significantly associated with higher circulating levels of the mitogen IGF-1, suggesting a possible pathological mechanism and therapeutic target. Furthermore, we built a variant classifier with >98% sensitivity and specificity and quantify evidence strengths to aid precision variant interpretation.
Saturation genome editing maps the functional spectrum of pathogenic VHL alleles
Authors: Buckley Megan , Terwagne Chloé , Ganner Athina , Cubitt Laura , Brewer Reid , Kim Dong-Kyu , Kajba Christina M. , Forrester Nicole , Dace Phoebe , De Jonghe Joachim , Shepherd Scott T. C. , Sawyer Chelsea , McEwen Mairead , Diederichs Sven , Neumann-Haefelin Elke , Turajlic Samra , Ivakine Evgueni A. , Findlay Gregory M.
Published: July 2024

To maximize the impact of precision medicine approaches, it is critical to identify genetic variants underlying disease and to accurately quantify their functional effects. A gene exemplifying the challenge of variant interpretation is the von Hippel–Lindautumor suppressor (VHL). VHL encodes an E3 ubiquitin ligase that regulates the cellular response to hypoxia. Germline pathogenic variants in VHL predispose patients to tumors including clear cell renal cell carcinoma (ccRCC) and pheochromocytoma, and somatic VHL mutations are frequently observed in sporadic renal cancer. Here we optimize and apply saturation genome editing to assay nearly all possible single-nucleotide variants (SNVs) across VHL’s coding sequence. To delineate mechanisms, we quantify mRNA dosage effects and compare functional effects in isogenic cell lines. Function scores for 2,268 VHL SNVs identify a core set of pathogenic alleles driving ccRCC with perfect accuracy, inform differential risk across tumor types and reveal new mechanisms by which variants impact function. These results have immediate utility for classifying VHL variants encountered clinically and illustrate how precise functional measurements can resolve pleiotropic and dosage-dependent genotype–phenotype relationships across complete genes.
Improvement of sand-washing performance and internal flow field analysis of a novel downhole sand removal device
Authors: Wang Zhiliang , Fang Zhigang , Wang Zhensong , Zhang Manlai , Liao Ruiquan
Published: July 2024

With the progression of many shale gas wells in the Sichuan-Chongqing region of China into the middle and late stages of exploitation, the problem of sand production in these wells is a primary factor influencing production. Failure to implement measures to remove sand from the gas wells will lead to a sharp decline in production after a certain period of exploitation. Moreover, As the amount of sand produced in the well increases, the production layer will be potentially buried by sand. To boost the production of shale gas wells in the Sichuan-Chongqing region and improve production efficiency, a novel downhole jet sand-washing device has been developed. Upon analyzing the device's overall structure, it is revealed that the device adopts a structural design integrating a jet pump with an efficient sand- washing nozzle, providing dual capabilities for jet sand- washing and sand conveying via negative pressure. To enhance the sand- washing and unblocking performance of the device, various sand- washing fluids and the structures of different sand- washing nozzles are compared for selection, aiming to elevate the device's sand- washing and unblocking performance from a macro perspective. Subsequently, drawing on simulation and internal flow field analysis of the device's sand- washing and unblocking process through CFD and the control variable method, it is ultimately found that the length diameter ratio of the cylindrical segment of the nozzle outlet, the outlet diameter, and the contraction angle of the nozzle greatly influence the device's sand- washing and unblocking performance. And the optimum ranges for the length-diameter ratio of the cylindrical segment of the nozzle outlet, the outlet diameter, the contraction angle of the nozzle, and the inlet diameter are 2 to 4, 6 mm to 10 mm, 12° to 16°, and 18 mm and 22 mm, respectively. The findings of the research not only provide new insights into existing sand removal processes but also offer a novel structure for current downhole sand removal devices and a specific range for the optimal size of the nozzle.
Paramixta manurensis gen. nov., sp. nov., a novel member of the family Erwiniaceae producing indole-3-acetic acid isolated from mushroom compost
Authors: Kim Jueun , Yun Hyosuk , Tahmasebi Aminallah , Nam Jiyoung , Pham Ha , Kim Yong-Hak , Min Hye Jung , Lee Chul Won
Published: July 2024

There are numerous species in the Erwiniaceae family that are important for agricultural and clinical purposes. Here we described the Erwiniaceae bacterium PD-1 isolated from mushroom (Pleurotus eryngii) compost. Comparative genomic and phylogenetic analyses showed that the strain PD-1 was assigned to a new genus and species, Paramixta manurensis gen. nov., sp. nov. in the family Erwiniaceae. From the average amino acid index, we identified the five AroBEKAC proteins in the shikimate pathway as a minimal set of molecular markers to reconstruct the phylogenetic tree of the Erwiniaceae species. The strain PD-1 containing annotated genes for ubiquinone and menaquinone produced a higher level of ubiquinone (Q8) than demethylmenaquinone (DMK8) and menaquinone (MK8) in anaerobic condition compared to aerobic condition, as similarly did the reference strains from the genera Mixta and Erwinia. Results from fatty acid methyl ester and numerical analyses of strain PD-1 showed a similarity to species of the genera Mixta and Winslowiella. This study revealed that the strain’s ability to utilize polyols, such as glycerol, erythritol, and d-arabitol, distinguished the strain PD-1 from the nearest relative and other type strains. The analyzed genetic markers and biochemical properties of the strain PD-1 suggest its potential role in the process of mushroom compost through the degradation of carbohydrates and polysaccharides derived from fungi and plants. Additionally, it can produce a high concentration of indole-3-acetic acid as a plant growth-promoting agent.
Identification and validation of potential common biomarkers for papillary thyroid carcinoma and Hashimoto’s thyroiditis through bioinformatics analysis and machine learning
Authors: Jiang Hui , He Yanbin , Lan Xiaofeng , Xie Xiang
Published: July 2024

There is a growing body of evidence suggesting that Hashimoto’s thyroiditis (HT) may contribute to an increased risk of papillary thyroid carcinoma (PTC). However, the exact relationship between HT and PTC is still not fully understood. The objective of this study was to identify potential common biomarkers that may be associated with both PTC and HT. Three microarray datasets from the GEO database and RNA-seq dataset from TCGA database were collected to identify shared differentially expressed genes (DEGs) between HT and PTC. A total of 101 genes was identified as common DEGs, primarily enriched inflammation- and immune-related pathways through GO and KEGG analysis. We performed protein–protein interaction analysis and identified six significant modules comprising a total of 29 genes. Subsequently, tree hub genes (CD53, FCER1G, TYROBP) were selected using random forest (RF) algorithms for the development of three diagnostic models. The artificial neural network (ANN) model demonstrates superior performance. Notably, CD53 exerted the greatest influence on the ANN model output. We analyzed the protein expressions of the three genes using the Human Protein Atlas database. Moreover, we observed various dysregulated immune cells that were significantly associated with the hub genes through immune infiltration analysis. Immunofluorescence staining confirmed the differential expression of CD53, FCER1G, and TYROBP, as well as the results of immune infiltration analysis. Lastly, we hypothesise that benzylpenicilloyl polylysine and aspirinmay be effective in the treatment of HT and PTC and may prevent HT carcinogenesis. This study indicates that CD53, FCER1G, and TYROBP play a role in the development of HT and PTC, and may contribute to the progression of HT to PTC. These hub genes could potentially serve as diagnostic markers and therapeutic targets for PTC and HT.
Exploring the efficacy of GRU model in classifying the signal to noise ratio of microgrid model
Authors: Alsulami Abdulaziz A. , Abu Al-Haija Qasem , Alturki Badraddin , Alqahtani Ali , Binzagr Faisal , Alghamdi Bandar , Alsemmeari Rayan A.
Published: July 2024

Microgrids are small-scale energy system that supplies power to homes, businesses, and industries. Microgrids can be considered as a trending technology in energy fields due to their power to supply reliable and sustainable energy. Microgrids have a mode called the island, in this mode, microgrids are disconnected from the major grid and keep providing energy in the situation of an energy outage. Therefore, they help the main grid during peak energy demand times. The microgrids can be connected to the network, which is called networked microgrids. It is possible to have flexible energy resources by using their enhanced energy management systems. However, connection microgrid systems to the communication network introduces various challenges, including increased in systems complicity and noise interference. Integrating network communication into a microgrid system causes the system to be susceptible to noise, potentially disrupting the critical control signals that ensure smooth operation. Therefore, there is a need for predicting noise caused by communication network to ensure the operation stability of microgrids. In addition, there is a need for a simulation model that includes communication network and can generate noise to simulate real scenarios. This paper proposes a classifying model named Noise Classification Simulation Model (NCSM) that exploits the potential of deep learning to predict noise levels by classifying the values of signal-to-noise ratio (SNR) in real-time network traffic of microgrid system. This is accomplished by initially applying Gaussian white noise into the data that is generated by microgrid model. Then, the data has noise and data without noise is transmitted through serial communication to simulate real world scenario. At the end, a Gated Recurrent Unit (GRU) model is implemented to predict SNR values for the network traffic data. Our findings show that the proposed model produced promising results in predicting noise. In addition, the classification performance of the proposed model is compared with well-known machine learning models and according to the experimental results, our proposed model has noticeable performance, which achieved 99.96% classification accuracy.
Quadrotor with wheels: design and experimental evaluation
Authors: Aizelman Ilan , Magazinnik Dan , Feldman Dan , Klein Itzik
Published: July 2024

Quadrotors have found widespread use in indoor applications, including tracking and mapping. In general, to carry out such tasks effectively, a navigation solution should provide both accuracy and battery efficiency. To achieve both, we propose a cost-effective and lightweight wheeled quadrotor that combines both driving and flying capabilities. Our design allows the quadrotor to perform both functions seamlessly. We provide a detailed description of the design and construction process, highlighting its advantages. Our focus was on the Tello quadrotor, which weighs 80 grams. Our design allowed driving capability with an increased weight of only fifteen grams, resulting in less than 20% of the added weight. Furthermore, we evaluate the quadrotor’s pure inertial navigation performance and corresponding battery consumption by employing various flying and driving patterns. Our results show that when only driving the battery consumption was the lowest with 10% and some flying scenarios improve the positioning error by more than 70%.
An effective video inpainting technique using morphological Haar wavelet transform with krill herd based criminisi algorithm
Authors: Srinivasan M. Nuthal , Chinnadurai M. , Senthilkumar S. , Dinesh E.
Published: July 2024

In recent times, video inpainting techniques have intended to fill the missing areas or gaps in a video by utilizing known pixels. The variety in brightness or difference of the patches causes the state-of-the-art video inpainting techniques to exhibit high computation complexity and create seams in the target areas. To resolve these issues, this paper introduces a novel video inpainting technique that employs the Morphological Haar Wavelet Transform combined with the Krill Herd based Criminisi algorithm (MHWT-KHCA) to address the challenges of high computational demand and visible seam artifacts in current inpainting practices. The proposed MHWT-KHCA algorithm strategically reduces computation times and enhances the seamlessness of the inpainting process in videos. Through a series of experiments, the technique is validated against standard metrics such as peak signal-to-noise ratio (PSNR) and structural similarity index (SSIM), where it demonstrates superior performance compared to existing methods. Additionally, the paper outlines potential real-world applications ranging from video restoration to real-time surveillance enhancement, highlighting the technique’s versatility and effectiveness. Future research directions include optimizing the algorithm for diverse video formats and integrating machine learning models to advance its capabilities further.
Nuclear ATP-citrate lyase regulates chromatin-dependent activation and maintenance of the myofibroblast gene program
Authors: Lazaropoulos Michael P. , Gibb Andrew A. , Chapski Douglas J. , Nair Abheya A. , Reiter Allison N. , Roy Rajika , Eaton Deborah M. , Bedi Kenneth C. , Margulies Kenneth B. , Wellen Kathryn E. , Estarás Conchi , Vondriska Thomas M. , Elrod John W.
Published: July 2024

Differentiation of cardiac fibroblasts to myofibroblasts is necessary for matrix remodeling and fibrosis in heart failure. We previously reported that mitochondrial calcium signaling drives α-ketoglutarate-dependent histone demethylation, promoting myofibroblast formation. Here we investigate the role of ATP-citrate lyase (ACLY), a key enzyme for acetyl-CoA biosynthesis, in histone acetylation regulating myofibroblast fate and persistence in cardiac fibrosis. We show that inactivation of ACLY prevents myofibroblast differentiation and reverses myofibroblasts towards quiescence. Genetic deletion of Acly in post-activated myofibroblasts prevents fibrosis and preserves cardiac function in pressure-overload heart failure. TGFβ stimulation enhances ACLY nuclear localization and ACLY–SMAD2/3 interaction, and increases H3K27ac at fibrotic gene loci. Pharmacological inhibition of ACLY or forced nuclear expression of a dominant-negative ACLY mutant prevents myofibroblast formation and H3K27ac. Our data indicate that nuclear ACLY activity is necessary for myofibroblast differentiation and persistence by maintaining histone acetylation at TGFβ-induced myofibroblast genes. These findings provide targets to prevent and reverse pathological fibrosis.
Operability-economics trade-offs in adsorption-based CO2 capture processes
Authors: Sachio Steven , Ward Adam , Pini Ronny , Papathanasiou Maria M.
Published: July 2024

Dispatchable low-carbon power underpins the transition to a sustainable energy system, providing balancing load for the integration of intermittent renewable power. In such load-following operation, the post-combustion carbon capture process must be capable of highly transient operation. Here we have developed a computational framework that integrates process design, operability and techno-economic assessment of a pressure-vacuum swing adsorption process for CO2 capture. We demonstrate that the cost-optimal design has limited process flexibility, challenging reactiveness to disturbances in the flue gas conditions. Flexibility can be introduced by relaxing the CO2 recovery constraint on the operation, albeit at the expense of the capture efficiency of the process. We discover that adsorption-based processes can be designed to enhance flexibility, while improving performance with respect to the operational constraints on CO2 recovery and purity. The results herein demonstrate a trade-off between process economics and process operability, which must be rationalised to integrate CO2 capture units in low-carbon energy systems.
The septin cytoskeleton is required for plasma membrane repair
Authors: Prislusky M Isabella , Lam Jonathan G T , Contreras Viviana Ruiz , Ng Marilynn , Chamberlain Madeline , Pathak-Sharma Sarika , Fields Madalyn , Zhang Xiaoli , Amer Amal O , Seveau Stephanie
Published: July 2024

Plasma membrane repair is a fundamental homeostatic process of eukaryotic cells. Here, we report a new function for the conserved cytoskeletal proteins known as septins in the repair of cells perforated by pore-forming toxins or mechanical disruption. Using a silencing RNA screen, we identified known repair factors (e.g. annexin A2, ANXA2) and novel factors such as septin 7 (SEPT7) that is essential for septin assembly. Upon plasma membrane injury, the septin cytoskeleton is extensively redistributed to form submembranous domains arranged as knob and loop structures containing F-actin, myosin IIA, S100A11, and ANXA2. Formation of these domains is Ca2+-dependent and correlates with plasma membrane repair efficiency. Super-resolution microscopy revealed that septins and F-actin form intertwined filaments associated with ANXA2. Depletion of SEPT7 prevented ANXA2 recruitment and formation of submembranous actomyosin domains. However, ANXA2 depletion had no effect on domain formation. Collectively, our data support a novel septin-based mechanism for resealing damaged cells, in which the septin cytoskeleton plays a key structural role in remodeling the plasma membrane by promoting the formation of SEPT/F-actin/myosin IIA/ANXA2/S100A11 repair domains.
One-pot chemo- and photo-enzymatic linear cascade processes
Authors: Carceller J. M. , Arias K. S. , Climent M. J. , Iborra S. , Corma A.
Published: July 2024

This review explores linear cascade reactions by combining chemo-, photo- and biocatalysts for organic synthesis and strategies to overcome incompatibility issues.
Application of S-transform-based nonlinear processing for accurate LIBS quantitative analysis of iron ore slurry
Authors: Chen Tong , Sun Lanxiang , Yu Haibin , Qi Lifeng , Zhang Peng , Dong Haiyan
Published: July 2024

A nonlinear analysis process integrates a feature selection unit based on the spectral distance variable selection method (SDVS), a nonlinear processing unit based on the S-transform (ST), and a partial least squares regression model (PLS).
Synthesis of macrocyclic thiolactone peptides via photochemical intramolecular radical acyl thiol–ene ligation
Authors: Benny Alby , Scanlan Eoin M.
Published: July 2024

Rapid (15 min) photochemical peptide macrothiolactonisation. Fully unprotected peptides. Fmoc SPPS synthesis of required linear peptide. Compatible with aqueous conditions.
A fluorinated metal–organic framework-based quasi-solid electrolyte for stabilizing Li metal anodes
Authors: Wang Xiang , Bai Mengxi , Li Qiufen , Li Jiashuai , Li Dongze , Lin Xiaoyan , Shao Siyuan , Wang Ziqi
Published: July 2024

A fluorinated MOF-based quasi-solid electrolyte (QSE) is proposed. The triflyl groups inside the QSE not only favor Li+ transport but also contribute to a LiF-rich SEI, which effectively promotes the reversibility and reaction kinetics of Li anodes.
Three-component cascade carbopalladation/Heck cyclization/borylation: facile access to boryl-functionalized indenes
Authors: Sun Fei , Zheng Yiyi , Wu Mingxia , Ji Hongsen , Jiang Zhongyao , Liu Chenglin , Wu Xin-Xing
Published: July 2024

A mild Pd-catalyzed three-component cascade cyclization functionalization of o-iodostyrenes, internal alkynes and boron reagents for versatile boryl-functionalized indenes is presented.
Click assembly through selective azaylide formation
Authors: Hamada Mayo , Orimoto Gaku , Yoshida Suguru
Published: July 2024

The selective azaylide formation of tetrafluorophenyl azides was achieved leaving dichlorophenyl azides untouched. Based on the selectivity, an efficient triple-click assembly was realized.
Two water-rich amphiphilic and hydrophilic coordination polymers: syntheses, structures and proton conduction behaviors in Nafion composite membranes
Authors: Huan Zhipeng , Zou Huiqi , Wang Na , Lu Jing , Liu Houting , Wang Suna , Li Yunwu
Published: July 2024

Two amphiphilic and hydrophilic coordination compounds were obtained, which can be doped into Nafion membranes with different optimal amounts and improve the proton conductivity of Nafion composite membranes to different degrees.
Using eugenol scaffold to explore the explosive sensing properties of Cd(ii)-based coordination polymers: experimental studies and real sample analysis
Authors: Malik Suvamoy , Mondal Udayan , Jana Narayan Ch. , Banerjee Priyabrata , Saha Amrita
Published: July 2024

Two luminescent CPs: [Cd2(L)2(NCS)2]n and [Cd2(L)2(N(CN)2)2]n (HL: eugenol-based chelating ligand) for nitroaromatics (NACs) sensing via a combinatorial RET-IFE-PET-π⋯π interactions and collisional quenching pathway.
Terminal {Ni(ii)-SH} complex promoted anaerobic catalytic sulfur atom transfer reaction: implication to the sulfide oxidase function of Cu/Zn-superoxide dismutase
Authors: Bag Jayanta , Das Surajit , Pal Kuntal
Published: July 2024

The catalytic activity of the sulfur atom transfer reaction from the terminal Ni(ii)-SH group to free PPh3 was proposed as a functional model system of excess sulfide oxidation function of Cu/Zn-containing superoxide dismutase.
Rational design of biomass-derived electrocatalysts for hydrogen/oxygen evolution reactions: a synthetic strategy for multiple components and their corresponding properties
Authors: Zhuang Xiuzheng , Liang Huiyi , Hu Xiaohong , Li Song , Zhang Xinghua , Zhang Qi , Ma Longlong
Published: July 2024

H2 produced via water electrolysis is a promising alternative to traditional energy, with electrodes playing a dominant role in the production process.
2-Aryl-1-hydroxyimidazoles possessing antiviral activity against a wide range of orthopoxviruses, including the variola virus
Authors: Basanova Elizaveta I. , Kulikova Ekaterina A. , Bormotov Nikolai I. , Serova Olga A. , Shishkina Larisa N. , Ovchinnikova Alyona S. , Odnoshevskiy Dmitry A. , Pyankov Oleg V. , Agafonov Alexander P. , Yarovaya Olga I. , Borisevich Sophia S. , Ilyina Margarita G. , Kolybalov Dmitry S. , Arkhipov Sergey G. , Bogdanov Nikita E. , Pavlova Marina A. , Salakhutdinov Nariman F. , Perevalov Valery P. , Nikitina Polina A.
Published: July 2024

Newly synthesized 2-aryl-1-hydroxyimidazoles display promising antiviral activity against orthopoxviruses, including the variola virus.
Controlled synthesis, properties, and applications of ultralong carbon nanotubes
Authors: Wang Kangkang , Wang Fei , Jiang Qinyuan , Zhu Ping , Leu Khaixien , Zhang Rufan
Published: July 2024

Growth mechanism, controlled synthesis, and excellent properties of ultralong CNTs.
Effect of the extended π-surface and N-butyl substituents of imidazoles on their reactivity, electrochemical behaviours and biological interactions of corresponding Pt(ii)-CNC carbene complexes: exploring DFT and docking interactions
Authors: Bellam Rajesh , Onunga Daniel O. , Jaganyi Deogratius , Robinson Ross , Mambanda Allen
Published: July 2024

The extended π surface and the N-butyl arms on the bis(3-methylimidazolium-1-yl)pyridine ligand cause prominent σ-inductive effect and steric influences on the complexes which stabilises the metal centres which leads to damping in their reactivity.
Copper(ii) complexes derived from naphthalene-based halogenated Schiff bases: synthesis, structural analysis, DFT computational studies and in vitro biological activities
Authors: Oladipo Segun D. , Luckay Robert C.
Published: July 2024

Copper(ii) complexes were synthesized and their structures solved. DFT studies complements their structures. Anti-diabetes, antioxidant and antibacterial potential was evaluated which shows very promising results compared to standard compounds.
Ultrasensitive and reusable Cu2O/Ag composite SERS substrates for trace thiram detection
Authors: Qin Shaoxiong , Wu Haoran , Ding Hualin , Li Zixiu , Zhang Yang , Pan Jiaqi , Cao Jun , Li Chaorong , Wang Jingjing
Published: July 2024

Cu2O/Ag composite substrates synthesized by electrodeposition and magnetron sputtering could serve as photocatalytic reusable SERS platforms for the detection of thiram in soil.
Low-dose alcohol exacerbates hyperdynamic circulation and shunting in non-alcoholic cirrhotic rats
Authors: Pun Chon Kit , Huang Hui-Chun , Chang Ching-Chih , Hsu Shao-Jung , Chuang Chiao-Lin , Huang Yi-Hsiang , Hou Ming-Chih , Lee Fa-Yauh
Published: July 2024

Background: Portal hypertension affects hepatic, splanchnic and portosystemic collateral systems. Although alcohol is a well-known risk factor for liver cirrhosis, it also affects vascular contractility. However, the relevant effects on portal hypertension have not been evaluated in non-alcoholic cirrhosis. The present study aimed to investigate the impacts of low-dose alcohol on portal hypertension-related derangements in non-alcoholic cirrhotic rats.

Methods: Sprague-Dawley rats received bile duct ligation to induce cirrhosis or sham operation as controls. The chronic or acute effects of low-dose alcohol (2.4 g/kg/day, oral gavage, approximately 1.3 drinks/day in humans) were evaluated.

Results: The chronic administration of low-dose alcohol did not precipitate liver fibrosis in the sham or cirrhotic rats; however, it significantly increased splanchnic blood inflow (P=0.034) and portosystemic collaterals (P=0.001). Mesenteric angiogenesis and pro-angiogenic proteins were up-regulated in the alcohol-treated cirrhotic rats, and poorer collateral vasoresponsiveness to vasoconstrictors (P<0.001) was noted. Consistently, acute alcohol administration reduced splenorenal shunt resistance. Collateral vasoresponsiveness to vasoconstrictors also significantly decreased (P=0.003).

Conclusions: In non-alcoholic cirrhosis rats, a single dose of alcohol adversely affected portosystemic collateral vessels due to vasodilatation. Long-term alcohol use precipitated splanchnic hyperdynamic circulation, in which mesenteric angiogenesis played a role. Further studies are warranted to evaluate the benefits of avoiding low-dose alcohol consumption in patients with non-alcoholic cirrhosis.
Extinction and AGN over host galaxy contrast effects on the optical spectroscopic classification of AGN
Authors: Barquín-González L. , Mateos S. , Carrera F. J. , Ordovás-Pascual I. , Alonso-Herrero A. , Caccianiga A. , Cardiel N. , Corral A. , Domínguez R. M. , García-Bernete I. , Mountrichas G. , Severgnini P.
Published: July 2024

The optical spectroscopic classification of active galactic nuclei (AGN) into type 1 and type 2 can be understood in the frame of the AGN unification models. However, it remains unclear which physical properties are driving the classification into intermediate sub-types (1.0, 1.2, 1.5, 1.8, 1.9). To shed light on this issue, we present an analysis of the effect of extinction and AGN and host galaxy luminosities on sub-type determination for a sample of 159 X-ray selected AGN with a complete and robust optical spectroscopic classification. The sample spans a rest-frame 2–10 keV X-ray luminosity range of 1042–1046 erg s−1 and redshifts between 0.05 and 0.75. From the fitting of their ultraviolet-to-mid-infrared spectral energy distributions, we extracted the observed AGN over total AGN+galaxy contrast, optical/ultraviolet line-of-sight extinction, as well as host galaxy and AGN luminosities. The observed contrast exhibits a clear decline with sub-type, distinguishing two main groups: 1.0–5 and 1.8–2. This difference is partly driven by an increase in extinction following the same trend. Nevertheless, 50% of 1.9s and 2s lack sufficient extinction to explain the lack of detection of broad emission lines, unveiling the necessity of an additional effect. Our findings show that 1.8–2s preferentially live in host galaxies with higher luminosities while displaying similar intrinsic AGN luminosities to 1.0–5s. Consequently, the AGN to host galaxy luminosity ratio diminishes, hindering the detection of the emission of the broad emission lines, resulting in the 1.8–2 classification of those with insufficient extinction. Thus, the combination of increasing extinction and decreasing AGN over galaxy luminosity ratio, mainly driven by an increasing host galaxy luminosity, constitutes the main reasons behind the sub-type classification into 1.0–5 and 1.8–2.
First resolved stellar halo kinematics of a Milky Way-mass galaxy outside the Local Group: The flat counter-rotating halo in NGC 4945
Authors: Beltrand Camila , Monachesi Antonela , D’Souza Richard , Bell Eric F. , de Jong Roelof S. , Gomez Facundo A. , Bailin Jeremy , Jang In Sung , Smercina Adam
Published: July 2024

The stellar halos of galaxies, primarily formed through the accretion and merger of smaller objects, are an important tool for understanding the hierarchical mass assembly of galaxies. However, the inner regions of stellar halos in disk galaxies are predicted to have an in situ component that is expected to be prominent along the major axis. Kinematic information is crucial to disentangle the contribution of the in situ component from the accreted stellar halos. The low surface brightness of stellar halos makes it inaccessible with traditional integrated light spectroscopy. In this work, we used a novel technique to study the kinematics of the stellar halo of the edge-on galaxy NGC 4945. We couple new deep Multi Unit Spectroscopic Explorer spectroscopic observations with existing Hubble Space Telescope imaging data to spectroscopically measure the line-of-sight (LOS) heliocentric velocity and velocity dispersion in two fields at a galactocentric distance of 12.2 kpc (outer disk field) and 34.6 kpc (stellar halo field) along the NGC 4945 major axis, by stacking individual spectra of red giant branch and asymptotic giant branch stars. We obtained a LOS velocity and dispersion of 673 ± 11 km s−1 and 73 ± 14 km s−1, respectively, for the outer disk field. This is consistent with the mean HI velocity of the disk at that distance. For the halo field, we obtained a LOS velocity and dispersion of 519 ± 12 km s−1 and 42 ± 22 km s−1. The halo fields’ velocity measurement is within ∼40 km s−1 from the systemic LOS velocity of NGC 4945, which is 563 km s−1, suggesting that its stellar halo at 34.6 kpc along the major axis is counter-rotating and its origins are likely to be the result of accretion. This provides the first-ever kinematic measurement of the stellar halo of a Milky Way-mass galaxy outside the Local Group from its resolved stellar population. Thus, we have established a powerful technique for measuring the velocity field for the stellar halos of nearby galaxies.
TDCOSMO
Authors: Wong Kenneth C. , Dux Frédéric , Shajib Anowar J. , Suyu Sherry H. , Millon Martin , Mozumdar Pritom , Wells Patrick R. , Agnello Adriano , Birrer Simon , Buckley-Geer Elizabeth J. , Courbin Frédéric , Fassnacht Christopher D. , Frieman Joshua , Galan Aymeric , Lin Huan , Marshall Philip J. , Poh Jason , Schuldt Stefan , Sluse Dominique , Treu Tommaso
Published: July 2024

Time-delay cosmography is a powerful technique to constrain cosmological parameters, particularly the Hubble constant (H0). The TDCOSMO Collaboration is performing an ongoing analysis of lensed quasars to constrain cosmology using this method. In this work, we obtain constraints from the lensed quasar WGD 2038−4008 using new time-delay measurements and previous mass models by TDCOSMO. This is the first TDCOSMO lens to incorporate multiple lens modeling codes and the full time-delay covariance matrix into the cosmological inference. The models are fixed before the time delay is measured, and the analysis is performed blinded with respect to the cosmological parameters to prevent unconscious experimenter bias. We obtain DΔ t = 1.68−0.38+0.40 Gpc using two families of mass models, a power-law describing the total mass distribution, and a composite model of baryons and dark matter, although the composite model is disfavored due to kinematics constraints. In a flat ΛCDM cosmology, we constrain the Hubble constant to be H0 = 65−14+23 km s−1 Mpc−1. The dominant source of uncertainty comes from the time delays, due to the low variability of the quasar. Future long-term monitoring, especially in the era of the Vera C. Rubin Observatory’s Legacy Survey of Space and Time, could catch stronger quasar variability and further reduce the uncertainties. This system will be incorporated into an upcoming hierarchical analysis of the entire TDCOSMO sample, and improved time delays and spatially-resolved stellar kinematics could strengthen the constraints from this system in the future.