bluuebunny/crossref_metadata_2025_split huggingface dataset:
A2AR eGFP reporter mouse enables elucidation of A2AR expression dynamics during anti-tumor immune responses
Authors: Todd Kirsten L. , Lai Junyun , Sek Kevin , Huang Yu-Kuan , Newman Dane M. , Derrick Emily B. , Koay Hui-Fern , Nguyen Dat , Hoang Thang X. , Petley Emma V. , Chan Cheok Weng , Munoz Isabelle , House Imran G. , Lee Joel N. , Kim Joelle S. , Li Jasmine , Tong Junming , N. de Menezes Maria , Scheffler Christina M. , Yap Kah Min , Chen Amanda X. Y. , Dunbar Phoebe A. , Haugen Brandon , Parish Ian A. , Johnstone Ricky W. , Darcy Phillip K. , Beavis Paul A. 
Published: November 2023

AbstractThere is significant clinical interest in targeting adenosine-mediated immunosuppression, with several small molecule inhibitors having been developed for targeting the A2AR receptor. Understanding of the mechanism by which A2AR is regulated has been hindered by difficulty in identifying the cell types that express A2AR due to a lack of robust antibodies for these receptors. To overcome this limitation, here an A2AR eGFP reporter mouse is developed, enabling the expression of A2AR during ongoing anti-tumor immune responses to be assessed. This reveals that A2AR is highly expressed on all tumor-infiltrating lymphocyte subsets including Natural Killer (NK) cells, NKT cells, γδ T cells, conventional CD4+ and CD8+ T lymphocytes and on a MHCIIhiCD86hi subset of type 2 conventional dendritic cells. In response to PD-L1 blockade, the emergence of PD-1+A2AR- cells correlates with successful therapeutic responses, whilst IL-18 is identified as a cytokine that potently upregulates A2AR and synergizes with A2AR deficiency to improve anti-tumor immunity. These studies provide insight into the biology of A2AR in the context of anti-tumor immunity and reveals potential combination immunotherapy approaches.
Quantum storage of entangled photons at telecom wavelengths in a crystal
Authors: Jiang Ming-Hao , Xue Wenyi , He Qian , An Yu-Yang , Zheng Xiaodong , Xu Wen-Jie , Xie Yu-Bo , Lu Yanqing , Zhu Shining , Ma Xiao-Song 
Published: November 2023

AbstractQuantum storage and distribution of entanglement are the key ingredients for realizing a global quantum internet. Compatible with existing fiber networks, telecom-wavelength entangled photons and corresponding quantum memories are of central interest. Recently, 167Er3+ ions have been identified as a promising candidate for an efficient telecom quantum memory. However, to date, no storage of entangled photons, the crucial step of quantum memory using these promising ions, 167Er3+, has been reported. Here, we demonstrate the storage and retrieval of the entangled state of two telecom photons generated from an integrated photonic chip. Combining the natural narrow linewidth of the entangled photons and long storage time of 167Er3+ ions, we achieve storage time of 1.936 μs, more than 387 times longer than in previous works. Successful storage of entanglement in the crystal is certified using entanglement witness measurements. These results pave the way for realizing quantum networks based on solid-state devices.
Hepatocyte FBXW7-dependent activity of nutrient-sensing nuclear receptors controls systemic energy homeostasis and NASH progression in male mice
Authors: Xia Hui , Dufour Catherine R. , Medkour Younes , Scholtes Charlotte , Chen Yonghong , Guluzian Christina , B’chir Wafa , Giguère Vincent 
Published: November 2023

AbstractNonalcoholic steatohepatitis (NASH) is epidemiologically associated with obesity and diabetes and can lead to liver cirrhosis and hepatocellular carcinoma if left untreated. The intricate signaling pathways that orchestrate hepatocyte energy metabolism and cellular stress, intrahepatic cell crosstalk, as well as interplay between peripheral tissues remain elusive and are crucial for the development of anti-NASH therapies. Herein, we reveal E3 ligase FBXW7 as a key factor regulating hepatic catabolism, stress responses, systemic energy homeostasis, and NASH pathogenesis with attenuated FBXW7 expression as a feature of advanced NASH. Multiomics and pharmacological intervention showed that FBXW7 loss-of-function in hepatocytes disrupts a metabolic transcriptional axis conjointly controlled by the nutrient-sensing nuclear receptors ERRα and PPARα, resulting in suppression of fatty acid oxidation, elevated ER stress, apoptosis, immune infiltration, fibrogenesis, and ultimately NASH progression in male mice. These results provide the foundation for developing alternative strategies co-targeting ERRα and PPARα for the treatment of NASH.
The potential of CO2-based production cycles in biotechnology to fight the climate crisis
Authors: Bachleitner Simone , Ata Özge , Mattanovich Diethard 
Published: November 2023

AbstractRising CO2 emissions have pushed scientists to develop new technologies for a more sustainable bio-based economy. Microbial conversion of CO2 and CO2-derived carbon substrates into valuable compounds can contribute to carbon neutrality and sustainability. Here, we discuss the potential of C1 carbon sources as raw materials to produce energy, materials, and food and feed using microbial cell factories. We provide an overview of potential microbes, natural and synthetic C1 utilization pathways, and compare their metabolic driving forces. Finally, we sketch a future in which C1 substrates replace traditional feedstocks and we evaluate the costs associated with such an endeavor.
Kinetically matched C–N coupling toward efficient urea electrosynthesis enabled on copper single-atom alloy
Authors: Xu Mengqiu , Wu Fangfang , Zhang Ye , Yao Yuanhui , Zhu Genping , Li Xiaoyu , Chen Liang , Jia Gan , Wu Xiaohong , Huang Youju , Gao Peng , Ye Wei 
Published: November 2023

AbstractChemical C–N coupling from CO2 and NO3–, driven by renewable electricity, toward urea synthesis is an appealing alternative for Bosch–Meiser urea production. However, the unmatched kinetics in CO2 and NO3– reduction reactions and the complexity of C- and N-species involved in the co-reduction render the challenge of C–N coupling, leading to the low urea yield rate and Faradaic efficiency. Here, we report a single-atom copper-alloyed Pd catalyst (Pd4Cu1) that can achieve highly efficient C–N coupling toward urea electrosynthesis. The reduction kinetics of CO2 and NO3– is regulated and matched by steering Cu doping level and Pd4Cu1/FeNi(OH)2 interface. Charge-polarized Pdδ–-Cuδ+ dual-sites stabilize the key *CO and *NH2 intermediates to promote C–N coupling. The synthesized Pd4Cu1-FeNi(OH)2 composite catalyst achieves a urea yield rate of 436.9 mmol gcat.–1 h–1 and Faradaic efficiency of 66.4%, as well as a long cycling stability of 1000 h. In-situ spectroscopic results and theoretical calculation reveal that atomically dispersed Cu in Pd lattice promotes the deep reduction of NO3– to *NH2, and the Pd-Cu dual-sites lower the energy barrier of the pivotal C–N coupling between *NH2 and *CO.
Epigenetic regulation during cancer transitions across 11 tumour types
Authors: Terekhanova Nadezhda V. , Karpova Alla , Liang Wen-Wei , Strzalkowski Alexander , Chen Siqi , Li Yize , Southard-Smith Austin N. , Iglesia Michael D. , Wendl Michael C. , Jayasinghe Reyka G. , Liu Jingxian , Song Yizhe , Cao Song , Houston Andrew , Liu Xiuting , Wyczalkowski Matthew A. , Lu Rita Jui-Hsien , Caravan Wagma , Shinkle Andrew , Naser Al Deen Nataly , Herndon John M. , Mudd Jacqueline , Ma Cong , Sarkar Hirak , Sato Kazuhito , Ibrahim Omar M. , Mo Chia-Kuei , Chasnoff Sara E. , Porta-Pardo Eduard , Held Jason M. , Pachynski Russell , Schwarz Julie K. , Gillanders William E. , Kim Albert H. , Vij Ravi , DiPersio John F. , Puram Sidharth V. , Chheda Milan G. , Fuh Katherine C. , DeNardo David G. , Fields Ryan C. , Chen Feng , Raphael Benjamin J. , Ding Li 
Published: November 2023

AbstractChromatin accessibility is essential in regulating gene expression and cellular identity, and alterations in accessibility have been implicated in driving cancer initiation, progression and metastasis1–4. Although the genetic contributions to oncogenic transitions have been investigated, epigenetic drivers remain less understood. Here we constructed a pan-cancer epigenetic and transcriptomic atlas using single-nucleus chromatin accessibility data (using single-nucleus assay for transposase-accessible chromatin) from 225 samples and matched single-cell or single-nucleus RNA-sequencing expression data from 206 samples. With over 1 million cells from each platform analysed through the enrichment of accessible chromatin regions, transcription factor motifs and regulons, we identified epigenetic drivers associated with cancer transitions. Some epigenetic drivers appeared in multiple cancers (for example, regulatory regions of ABCC1 and VEGFA; GATA6 and FOX-family motifs), whereas others were cancer specific (for example, regulatory regions of FGF19, ASAP2 and EN1, and the PBX3 motif). Among epigenetically altered pathways, TP53, hypoxia and TNF signalling were linked to cancer initiation, whereas oestrogen response, epithelial–mesenchymal transition and apical junction were tied to metastatic transition. Furthermore, we revealed a marked correlation between enhancer accessibility and gene expression and uncovered cooperation between epigenetic and genetic drivers. This atlas provides a foundation for further investigation of epigenetic dynamics in cancer transitions.
Dropsonde observations during the Aerosol Cloud meTeorology Interactions oVer the western ATlantic Experiment
Authors: Vömel Holger , Sorooshian Armin , Robinson Claire , Shingler Taylor J. , Thornhill Kenneth Lee , Ziemba Luke D. 
Published: November 2023

AbstractThe Aerosol Cloud meTeorology Interactions oVer the western ATlantic Experiment (ACTIVATE) field campaign provides accurate data for aerosol characterization and trace gas profiles, and establishes knowledge of the relationships between aerosols and water. The dropsonde dataset provides an in situ characterization of the vertical thermodynamic structure of the atmosphere during 165 research flights by NASA Langley’s King Air research aircraft between February 2020 and June 2022 and four test flights between December 2019 and November 2021. The research flights covered the western North Atlantic region, off the coast of the Eastern United States and around Bermuda and covered all seasons. The dropsonde profiles provide observations of temperature, pressure, relative humidity, and horizontal and vertical winds between the surface and about 9 km. 801 dropsondes were released, of which 796 were processed and 788 provide complete profiles of all parameters between the flight level and the surface with normal parachute performance. Here, we describe the dataset, the processing of the measurements, general statistics, and applications of this rich dataset.
A chromosome-level genome assembly of the Asian giant softshell turtle Pelochelys cantorii
Authors: Hong Xiaoyou , Liu Haiyang , Wang Yakun , Li Mingzhi , Ji Liqin , Wang Kaikuo , Wei Chengqing , Li Wei , Chen Chen , Yu Lingyun , Zhu Xinping , Liu Xiaoli 
Published: November 2023

AbstractThe Asian giant softshell turtle Pelochelys cantorii is one of the largest aquatic turtles in China and has been designated a First Grade Protected Animal in China. To advance conservation research, a combination of Illumina short-read, PacBio long-read, and Hi-C scaffolding technologies was used to develop a high-quality chromosome-level genome assembly for P. cantorii. A total of 262.77 Gb of clean data were produced (121.6 × depth) and then the genome was assembled into 2.16 Gb with a contig N50 of 41.44 Mb and scaffold N50 length of 120.17 Mb, respectively. Moreover, about 99.98% assembly genome sequences were clustered and ordered onto 33 pseudochromosomes. Genome annotation revealed that 21,833 protein-coding genes were predicted, and 96.40% of them were annotated. This new chromosome-level assembly will be an enabling resource for genetic and genomic studies to support fundamental insight into P. cantorii biology.
Sequence optimized diagnostic assay for Ebola virus detection
Authors: Koehler Jeffrey W. , Stefan Christopher P. , Hall Adrienne T. , Delp Korey L. , O’Hearn Aileen E. , Taylor-Howell Cheryl L. , Wauquier Nadia , Schoepp Randal J. , Minogue Timothy D. 
Published: November 2023

AbstractRapid pathogen identification is a critical first step in patient isolation, treatment, and controlling an outbreak. Real-time PCR is a highly sensitive and specific approach commonly used for infectious disease diagnostics. However, mismatches in the primer or probe sequence and the target organism can cause decreased sensitivity, assay failure, and false negative results. Limited genomic sequences for rare pathogens such as Ebola virus (EBOV) can negatively impact assay performance due to undiscovered genetic diversity. We previously developed and validated several EBOV assays prior to the 2013–2016 EBOV outbreak in West Africa, and sequencing EBOV Makona identified sequence variants that could impact assay performance. Here, we assessed the impact sequence mismatches have on EBOV assay performance, finding one or two primer or probe mismatches resulted in a range of impact from minimal to almost two log sensitivity reduction. Redesigning this assay improved detection of all EBOV variants tested. Comparing the performance of the new assay with the previous assays across a panel of human EBOV samples confirmed increased assay sensitivity as reflected in decreased Cq values with detection of three positive that tested negative with the original assay.
Preclinical evaluation of [58mCo]Co-DOTA-PSMA-617 for Auger electron therapy of prostate cancer
Authors: Baun Christina , Dam Johan Hygum , Hildebrandt Malene Grubbe , Ewald Jesper Dupont , Kristensen Bjarne Winther , Gammelsrød Vigga Sand , Olsen Birgitte Brinkmann , Thisgaard Helge 
Published: November 2023

AbstractProstate-specific membrane antigen (PSMA), highly expressed in prostate cancer, is a promising target for radionuclide therapy. Auger electron-emitting radionuclides are well suited for targeted radionuclide therapy if they can be delivered close to the DNA of the targeted cells. This preclinical study evaluated the theranostic pair [55/58mCo]Co-DOTA-PSMA-617 for PET imaging and Auger electron therapy of prostate cancer. [58mCo]Co-DOTA-PSMA-617 was successfully prepared with > 99% radiochemical yield and purity. In vitro, uptake and subcellular distribution assays in PSMA-positive prostate cancer cells showed PSMA-specific uptake with high cell-associated activity in the nucleus. Incubation with [58mCo]Co-DOTA-PSMA-617 reduced cell viability and clonogenic survival in a significant dose-dependent manner (p < 0.05). Biodistribution of xenografted mice showed high specific tumor uptake of the cobalt-labeled PSMA ligand for all time points with rapid clearance from normal tissues, which PET imaging confirmed. In vivo, therapy with [58mCo]Co-DOTA-PSMA-617 in tumor-bearing mice demonstrated significantly increased median survival for treated mice compared to control animals (p = 0.0014). In conclusion, [55/58mCo]Co-DOTA-PSMA-617 displayed excellent in vitro and in vivo properties, offering significant survival benefits in mice with no observed toxicities.
The effectiveness of hot-air, infrared and hybrid drying techniques for lemongrass: appearance acceptability, essential oil yield, and volatile compound preservation
Authors: Setareh Roghayeh , Mohammadi-Ghermezgoli Khosro , Ghaffari-Setoubadi Hossein , Alizadeh-Salteh Saeideh 
Published: November 2023

AbstractLemongrass is a fragrant herb with lengthy, thin leaves that contains myrcene (an aromatic compound) as well as citral and geraniol (antimicrobial compounds). Therefore, identifying an appropriate drying method for this plant is crucial for maintaining aromatic and antimicrobial compounds and enhancing the shelf life of the product. This investigation seeks to assess the influence of various drying tactics involving hot air at temperatures of 40, 50, and 60 °C, infrared radiation at intensities of 0.5, 0.6, and 0.8 $$\mathrm{W}/{\mathrm{cm}}^{2}$$

W
/

cm

2

, sequential hot-air/infrared, as well as simultaneous hot air-infrared, on the drying mechanism, color, appearance, yield, and essential oil constituents of lemongrass leaves, with the objective of enhancing the marketability of the product. The essential oils of lemongrass were extracted through the process of hydro-distillation, and subsequently, the volatile compounds present were analyzed using Gas Chromatography—Mass Spectrometry (GC–MS). The findings indicated: (a) The most appropriate technique for preserving optimal color quality of lemongrass leaves was through the application of hot air drying solely at a temperature of 60 °C; (b) To optimize the retention and amplification of the essential oil content in lemongrass, our study recommends the employment of a simultaneous hybrid drying technique involving hot air drying at a temperature of 50 °C in conjunction with infrared drying set at a radiation intensity level of 0.6 $$\mathrm{W}/{\mathrm{cm}}^{2}$$

W
/

cm

2

; and (c) The data analysis demonstrated that in order to achieve elevated levels of volatile compounds, specifically neral and geranial, infrared drying with a radiation intensity of 0.6 and 0.8 $$\mathrm{W}/{\mathrm{cm}}^{2}$$

W
/

cm

2

, respectively, was found to be optimal.
Extended methods for spatial cell classification with DBSCAN-CellX
Authors: Küchenhoff Leonie , Lukas Pascal , Metz-Zumaran Camila , Rothhaar Paul , Ruggieri Alessia , Lohmann Volker , Höfer Thomas , Stanifer Megan L. , Boulant Steeve , Talemi Soheil Rastgou , Graw Frederik 
Published: November 2023

AbstractLocal cell densities and positioning within cellular monolayers and stratified epithelia have important implications for cell interactions and the functionality of various biological processes. To analyze the relationship between cell localization and tissue physiology, density-based clustering algorithms, such as DBSCAN, allow for a detailed characterization of the spatial distribution and positioning of individual cells. However, these methods rely on predefined parameters that influence the outcome of the analysis. With varying cell densities in cell cultures or tissues impacting cell sizes and, thus, cellular proximities, these parameters need to be carefully chosen. In addition, standard DBSCAN approaches generally come short in appropriately identifying individual cell positions. We therefore developed three extensions to the standard DBSCAN-algorithm that provide: (i) an automated parameter identification to reliably identify cell clusters, (ii) an improved identification of cluster edges; and (iii) an improved characterization of the relative positioning of cells within clusters. We apply our novel methods, which are provided as a user-friendly OpenSource-software package (DBSCAN-CellX), to cellular monolayers of different cell lines. Thereby, we show the importance of the developed extensions for the appropriate analysis of cell culture experiments to determine the relationship between cell localization and tissue physiology.
Association between serum 25-hydroxyvitamin D and fasting blood glucose in osteoporosis patients
Authors: Ye Yao-wei , Lu Ke , Yin Yi , Yang Xu-feng , Xu Si-ming , Xu Min-zhe , Shi Qin , Gong Ya-qin 
Published: November 2023

AbstractOsteoporosis (OP) is often associated with other complications, such as impaired glucose homeostasis. Vitamin D deficiency is common and has been linked to bone metabolism and the regulation of blood sugar levels. The aim of this study was to evaluate the independent relationship between serum 25-hydroxyvitamin D (25[OH]D) and fasting blood glucose levels (FBG) in a group of patients diagnosed with OP. This is a retrospective cross-sectional study from a prospectively collected database at our tertiary referral center. Consecutive 2084 OP patients who were hospitalization were finally analyzed in this study. FBG is the dependent variable, serum 25(OH)D level of OP patients is exposure variable of this study. There was a linear significantly negative association between serum 25(OH)D and FBG (β, − 0.02; 95% CI − 0.03 to − 0.01; P = 0.0011) in the fully adjusted models. Specifically, when serum 25(OH)D level was less than 23.39 ng/mL, FBG decreased by 0.04 mmol/L for every 1 ng/mL increase of serum 25(OH)D level. When serum 25(OH)D was greater than 23.39 ng/ mL, the negative association was insignificant (P = 0.9616). If the association is confirmed, the clinical management of blood glucose in OP patients with serum 25(OH)D deficiency has instructive implications.
Effect of He2+ ion irradiation on the mechanical properties of automated fibre placement (AFP) CF-PEEK thermoplastics composites
Authors: Oromiehie Ebrahim , Nair Vishnu , Short Ken , Wei Tao , Bhattacharyya Dhriti , Prusty B. Gangadhara 
Published: November 2023

AbstractCarbon fibre-reinforced polyetheretherketone (CF-PEEK) composites have gained significant usage across diverse industries like automotive and aerospace due to their desirable characteristics. These properties encompass recyclability, low density, high strength, wear resistance and thermal stability. The components made from CF-PEEK composites for space applications will be subjected to a high radiation environment due to the incoming cosmic rays, comprising protons, α particles, electrons, γ rays, etc., once they escape the Earth’s atmosphere. The ion irradiation of CF-PEEK is accompanied by radiation-induced effects, which drastically change the structure and properties of irradiated material. Since the resistance of CF-PEEK to radiation damage has not been studied extensively, this study aims to understand the effect of high-energy He2+ ions on the microstructure and properties of CF-PEEK composites manufactured using automated fibre placement (AFP) under different processing conditions. The samples have been radiated with 5 MeV He2+ ions using an energy degrader wheel to create a layer with relatively uniform damage. Then, were characterized using optical and scanning electron microscopy and their hardness was evaluated using nanoindentation. It was observed that, irradiation increases the hardness of the fibres in all cases. Also, fibre orientation affects the hardness in a statistically significant manner in both unirradiated and irradiated conditions.