bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural differences between the closely related RNA helicases, UAP56 and URH49, fashion distinct functional apo-complexes
Authors: Fujita Ken-ichi , Ito Misa , Irie Midori , Harada Kotaro , Fujiwara Naoko , Ikeda Yuya , Yoshioka Hanae , Yamazaki Tomohiro , Kojima Masaki , Mikami Bunzo , Mayeda Akila , Masuda Seiji 
Published: January 2024

AbstractmRNA export is an essential pathway for the regulation of gene expression. In humans, closely related RNA helicases, UAP56 and URH49, shape selective mRNA export pathways through the formation of distinct complexes, known as apo-TREX and apo-AREX complexes, and their subsequent remodeling into similar ATP-bound complexes. Therefore, defining the unidentified components of the apo-AREX complex and elucidating the molecular mechanisms underlying the formation of distinct apo-complexes is key to understanding their functional divergence. In this study, we identify additional apo-AREX components physically and functionally associated with URH49. Furthermore, by comparing the structures of UAP56 and URH49 and performing an integrated analysis of their chimeric mutants, we exhibit unique structural features that would contribute to the formation of their respective complexes. This study provides insights into the specific structural and functional diversification of these two helicases that diverged from the common ancestral gene Sub2.
A retrofit sensing strategy for soft fluidic robots
Authors: Zou Shibo , Picella Sergio , de Vries Jelle , Kortman Vera G. , Sakes Aimée , Overvelde Johannes T. B. 
Published: January 2024

AbstractSoft robots are intrinsically capable of adapting to different environments by changing their shape in response to interaction forces. However, sensory feedback is still required for higher level decisions. Most sensing technologies integrate separate sensing elements in soft actuators, which presents a considerable challenge for both the fabrication and robustness of soft robots. Here we present a versatile sensing strategy that can be retrofitted to existing soft fluidic devices without the need for design changes. We achieve this by measuring the fluidic input that is required to activate a soft actuator during interaction with the environment, and relating this input to its deformed state. We demonstrate the versatility of our strategy by tactile sensing of the size, shape, surface roughness and stiffness of objects. We furthermore retrofit sensing to a range of existing pneumatic soft actuators and grippers. Finally, we show the robustness of our fluidic sensing strategy in closed-loop control of a soft gripper for sorting, fruit picking and ripeness detection. We conclude that as long as the interaction of the actuator with the environment results in a shape change of the interval volume, soft fluidic actuators require no embedded sensors and design modifications to implement useful sensing.
Apoptosis-mediated ADAM10 activation removes a mucin barrier promoting T cell efferocytosis
Authors: Drexhage Linnea Z. , Zhang Shengpan , Dupont Maeva , Ragaller Franziska , Sjule Ellen , Cabezas-Caballero Jose , Deimel Lachlan P. , Robertson Helen , Russell Rebecca A. , Dushek Omer , Sezgin Erdinc , Karaji Niloofar , Sattentau Quentin J. 
Published: January 2024

AbstractEfferocytic clearance of apoptotic cells in general, and T cells in particular, is required for tissue and immune homeostasis. Transmembrane mucins are extended glycoproteins highly expressed in the cell glycocalyx that function as a barrier to phagocytosis. Whether and how mucins may be regulated during cell death to facilitate efferocytic corpse clearance is not well understood. Here we show that normal and transformed human T cells express a subset of mucins which are rapidly and selectively removed from the cell surface during apoptosis. This process is mediated by the ADAM10 sheddase, the activity of which is associated with XKR8-catalyzed flipping of phosphatidylserine to the outer leaflet of the plasma membrane. Mucin clearance enhances uptake of apoptotic T cells by macrophages, confirming mucins as an enzymatically-modulatable barrier to efferocytosis. Together these findings demonstrate a glycocalyx regulatory pathway with implications for therapeutic intervention in the clearance of normal and transformed apoptotic T cells.
Haplotype-aware modeling of cis-regulatory effects highlights the gaps remaining in eQTL data
Authors: Ehsan Nava , Kotis Bence M. , Castel Stephane E. , Song Eric J. , Mancuso Nicholas , Mohammadi Pejman 
Published: January 2024

AbstractExpression Quantitative Trait Loci (eQTLs) are critical to understanding the mechanisms underlying disease-associated genomic loci. Nearly all protein-coding genes in the human genome have been associated with one or more eQTLs. Here we introduce a multi-variant generalization of allelic Fold Change (aFC), aFC-n, to enable quantification of the cis-regulatory effects in multi-eQTL genes under the assumption that all eQTLs are known and conditionally independent. Applying aFC-n to 458,465 eQTLs in the Genotype-Tissue Expression (GTEx) project data, we demonstrate significant improvements in accuracy over the original model in estimating the eQTL effect sizes and in predicting genetically regulated gene expression over the current tools. We characterize some of the empirical properties of the eQTL data and use this framework to assess the current state of eQTL data in terms of characterizing cis-regulatory landscape in individual genomes. Notably, we show that 77.4% of the genes with an allelic imbalance in a sample show 0.5 log2 fold or more of residual imbalance after accounting for the eQTL data underlining the remaining gap in characterizing regulatory landscape in individual genomes. We further contrast this gap across tissue types, and ancestry backgrounds to identify its correlates and guide future studies.
Nanoscale silicate melt textures determine volcanic ash surface chemistry
Authors: Hornby Adrian J. , Ayris Paul M. , Damby David E. , Diplas Spyridon , Eychenne Julia , Kendrick Jackie E. , Cimarelli Corrado , Kueppers Ulrich , Scheu Bettina , Utley James E. P. , Dingwell Donald B. 
Published: January 2024

AbstractExplosive volcanic eruptions produce vast quantities of silicate ash, whose surfaces are subsequently altered during atmospheric transit. These altered surfaces mediate environmental interactions, including atmospheric ice nucleation, and toxic effects in biota. A lack of knowledge of the initial, pre-altered ash surface has required previous studies to assume that the ash surface composition created during magmatic fragmentation is equivalent to the bulk particle assemblage. Here we examine ash particles generated by controlled fragmentation of andesite and find that fragmentation generates ash particles with substantial differences in surface chemistry. We attribute this disparity to observations of nanoscale melt heterogeneities, in which Fe-rich nanophases in the magmatic melt deflect and blunt fractures, thereby focusing fracture propagation within aureoles of single-phase melt formed during diffusion-limited growth of crystals. In this manner, we argue that commonly observed pre-eruptive microtextures caused by disequilibrium crystallisation and/or melt unmixing can modify fracture propagation and generate primary discrepancies in ash surface chemistry, an essential consideration for understanding the cascading consequences of reactive ash surfaces in various environments.
A dicarbonate solvent electrolyte for high performance 5 V-Class Lithium-based batteries
Authors: Zhang Xiaozhe , Xu Pan , Duan Jianing , Lin Xiaodong , Sun Juanjuan , Shi Wenjie , Xu Hewei , Dou Wenjie , Zheng Qingyi , Yuan Ruming , Wang Jiande , Zhang Yan , Yu Shanshan , Chen Zehan , Zheng Mingsen , Gohy Jean-François , Dong Quanfeng , Vlad Alexandru 
Published: January 2024

AbstractRechargeable lithium batteries using 5 V positive electrode materials can deliver considerably higher energy density as compared to state-of-the-art lithium-ion batteries. However, their development remains plagued by the lack of electrolytes with concurrent anodic stability and Li metal compatibility. Here we report a new electrolyte based on dimethyl 2,5-dioxahexanedioate solvent for 5 V-class batteries. Benefiting from the particular chemical structure, weak interaction with lithium cation and resultant peculiar solvation structure, the resulting electrolyte not only enables stable, dendrite-free lithium plating-stripping, but also displays anodic stability up to 5.2 V (vs. Li/Li+), in additive or co-solvent-free formulation, and at low salt concentration of 1 M. Consequently, the Li | |LiNi0.5Mn1.5O4 cells using the 1 M LiPF6 in 2,5-dioxahexanedioate based electrolyte retain >97% of the initial capacity after 250 cycles, outperforming the conventional carbonate-based electrolyte formulations, making this, and potentially other dicarbonate solvents promising for future Lithium-based battery practical explorations.
Cyto-molecular characterization of rDNA and chromatin composition in the NOR-associated satellite in Chestnut (Castanea spp.)
Authors: Islam-Faridi Nurul , Hodnett George L. , Zhebentyayeva Tetyana , Georgi Laura L. , Sisco Paul H. , Hebard Frederick V. , Nelson C. Dana 
Published: January 2024

AbstractThe American chestnut (Castanea dentata, 2n = 2x = 24), once known as the “King of the Appalachian Forest”, was decimated by chestnut blight during the first half of the twentieth century by an invasive fungus (Cryphonectria parasitica). The Chinese chestnut (C. mollissima,2n = 2x = 24), in contrast to American chestnut, is resistant to this blight. Efforts are being made to transfer this resistance to American chestnut through backcross breeding and genetic engineering. Both chestnut genomes have been genetically mapped and recently sequenced to facilitate gene discovery efforts aimed at assisting molecular breeding and genetic engineering. To complement and extend this genomic work, we analyzed the distribution and organization of their ribosomal DNAs (35S and 5S rDNA), and the chromatin composition of the nucleolus organizing region (NOR)-associated satellites. Using fluorescent in situ hybridization (FISH), we have identified two 35S (one major and one minor) and one 5S rDNA sites. The major 35S rDNA sites are terminal and sub-terminal in American and Chinese chestnuts, respectively, originating at the end of the short arm of the chromosome, extending through the secondary constriction and into the satellites. An additional 5S locus was identified in certain Chinese chestnut accessions, and it was linked distally to the major 35S site. The NOR-associated satellite in Chinese chestnut was found to comprise a proximal region packed with 35S rDNA and a distinct distal heterochromatic region. In contrast, the American chestnut satellite was relatively small and devoid of the distal heterochromatic region.
Quantum discriminator for binary classification
Authors: Date Prasanna , Smith Wyatt 
Published: January 2024

AbstractQuantum computers have the unique ability to operate relatively quickly in high-dimensional spaces—this is sought to give them a competitive advantage over classical computers. In this work, we propose a novel quantum machine learning model called the Quantum Discriminator, which leverages the ability of quantum computers to operate in the high-dimensional spaces. The quantum discriminator is trained using a quantum-classical hybrid algorithm in $$\mathcal {O}(N\log N)$$

O
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time, and inferencing is performed on a universal quantum computer in $$\mathcal {O}(N)$$

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time. The quantum discriminator takes as input the binary features extracted from a given datum along with a prediction qubit, and outputs the predicted label. We analyze its performance on the Iris and Bars and Stripes data sets, and show that it can attain 99% accuracy in simulation.
A CIC-related-epigenetic factors-based model associated with prediction, the tumor microenvironment and drug sensitivity in osteosarcoma
Authors: Yu Bin , Geng Chengkui , Wu Zhongxiong , Zhang Zhongzi , Zhang Aili , Yang Ze , Huang Jiazheng , Xiong Ying , Yang Huiqin , Chen Zhuoyuan 
Published: January 2024

AbstractOsteosarcoma is generally considered a cold tumor and is characterized by epigenetic alterations. Although tumor cells are surrounded by many immune cells such as macrophages, T cells may be suppressed, be inactivated, or not be presented due to various mechanisms, which usually results in poor prognosis and insensitivity to immunotherapy. Immunotherapy is considered a promising anti-cancer therapy in osteosarcoma but requires more research, but osteosarcoma does not currently respond well to this therapy. The cancer immunity cycle (CIC) is essential for anti-tumor immunity, and is epigenetically regulated. Therefore, it is possible to modulate the immune microenvironment of osteosarcoma by targeting epigenetic factors. In this study, we explored the correlation between epigenetic modulation and CIC in osteosarcoma through bioinformatic methods. Based on the RNA data from TARGET and GSE21257 cohorts, we identified epigenetic related subtypes by NMF clustering and constructed a clinical prognostic model by the LASSO algorithm. ESTIMATE, Cibersort, and xCell algorithms were applied to analyze the tumor microenvironment. Based on eight epigenetic biomarkers (SFMBT2, SP140, CBX5, HMGN2, SMARCA4, PSIP1, ACTR6, and CHD2), two subtypes were identified, and they are mainly distinguished by immune response and cell cycle regulation. After excluding ACTR6 by LASSO regression, the prognostic model was established and it exhibited good predictive efficacy. The risk score showed a strong correlation with the tumor microenvironment, drug sensitivity and many immune checkpoints. In summary, our study sheds a new light on the CIC-related epigenetic modulation mechanism of osteosarcoma and helps search for potential drugs for osteosarcoma treatment.
Biologically informed deep learning for explainable epigenetic clocks
Authors: Prosz Aurel , Pipek Orsolya , Börcsök Judit , Palla Gergely , Szallasi Zoltan , Spisak Sandor , Csabai István 
Published: January 2024

AbstractAgeing is often characterised by progressive accumulation of damage, and it is one of the most important risk factors for chronic disease development. Epigenetic mechanisms including DNA methylation could functionally contribute to organismal aging, however the key functions and biological processes may govern ageing are still not understood. Although age predictors called epigenetic clocks can accurately estimate the biological age of an individual based on cellular DNA methylation, their models have limited ability to explain the prediction algorithm behind and underlying key biological processes controlling ageing. Here we present XAI-AGE, a biologically informed, explainable deep neural network model for accurate biological age prediction across multiple tissue types. We show that XAI-AGE outperforms the first-generation age predictors and achieves similar results to deep learning-based models, while opening up the possibility to infer biologically meaningful insights of the activity of pathways and other abstract biological processes directly from the model.
Arterial and venous peripheral vascular assessment using wearable electro-resistive morphic sensors
Authors: Varaki Elham Shabani , Gargiulo Gaetano D. , Malone Matthew , Breen Paul P. 
Published: January 2024

AbstractPeripheral vascular diseases (PVDs) represent a significant burden on global human health and healthcare systems. With continued growth in obesity and diabetes, it is likely that the incidence of these conditions will increase. As many PVDs remain undiagnosed, low-cost and easy to use diagnostic methods are required. This work uses newly developed wearable electro-resistive morphic sensors to assess venous and arterial competence in the lower limbs of 36 healthy subjects. Comparison of this HeMo device was made to currently available benchtop light reflection rheography and photoplethymography devices. Results indicate that HeMo can detect the physiological signals of interest for both chronic venous insufficiency and peripheral arterial disease and all subjects were interpreted as healthy by each system. However, measurement repeatability of HeMo was highlighted as an issue that requires further system development. Furthermore, as HeMo captures changes in a section of limb circumference due to changes in underlying blood movement, rather than at a single point, the recorded signal is typically damped by comparison. This factor should be considered in any future developments.
Efficacy of endophytic bacteria as promising inducers for enhancing the immune responses in tomato plants and managing Rhizoctonia root-rot disease
Authors: Abbas Mona M. , Ismael Walaa H. , Mahfouz Amira Y. , Daigham Ghadir E. , Attia Mohamed S. 
Published: January 2024

AbstractAround the world, a variety of crops, including tomatoes, suffer serious economic losses due to the Rhizoctonia root-rot disease. Herein, Bacillus velezensis, Bacillus megaterium, and Herpaspirillum huttiense isolated from strawberry (Fragaria chiloensis var. ananassa) plants were pragmatic as plant growth promotors for battling the Rhizoctonia root rot disease and bringing about defense mechanisms as well as growth promotional strategies in tomato plants. These endophytic bacteria demonstrated potent antifungal activity against R. solani in vitro along in vivo. Data explained that the isolated endophytic bacteria could produce Indole acetic acid, Gibberellic acid GA, and siderophore as well as solubilize phosphate in the soil. The consortium of (Bacillus velezensis, Bacillus megaterium, and Herpaspirillum huttiense) increased the protection % against Rhizoctonia infection by (79.4%), followed by B. velezensis by (73.52%), H. huttiense by (70.5%), and B. megaterium by (67.64%), respectively. There was an increase in soluble proteins and carbohydrates in infected plants treated with a consortium of endophytic bacteria by 30.7% and 100.2% over untreated infected plants, respectively. Applying endophytic bacteria either alone or in combination lowered the level of malondialdehyde MDA and hydrogen peroxide H2O2 and improved the activities of antioxidant enzymes in both infected and uninfected plants. Also, bacterial endophytes have distinctive reactions regarding the number and concentrations of isozymes in both infected and uninfected plants. It could be recommended the commercial usage of a mixture of targeted bacterial endophyte strains as therapeutic nutrients against Rhizoctonia root-rot disease as well as plant growth inducer.
Understanding the exposure risk of aerosolized Coccidioides in a Valley fever endemic metropolis
Authors: Porter W. Tanner , Gade Lalitha , Montfort Parker , Mihaljevic Joseph R. , Bowers Jolene R. , Willman Andrew , Klimowski Brian A. , LaFleur Bonnie J. , Sunenshine Rebecca H. , Collins Jennifer , Adame Guillermo , Brady Shane , Komatsu Kenneth K. , Williams Samantha , Toda Mitsuru , Chiller Tom , Litvintseva Anastasia P. , Engelthaler David M. 
Published: January 2024

AbstractCoccidioides is the fungal causative agent of Valley fever, a primarily pulmonary disease caused by inhalation of fungal arthroconidia, or spores. Although Coccidioides has been an established pathogen for 120 years and is responsible for hundreds of thousands of infections per year, little is known about when and where infectious Coccidioides arthroconidia are present within the ambient air in endemic regions. Long-term air sampling programs provide a means to investigate these characteristics across space and time. Here we present data from > 18 months of collections from 11 air sampling sites across the Phoenix, Arizona, metropolitan area. Overall, prevalence was highly variable across space and time with no obvious spatial or temporal correlations. Several high prevalence periods were identified at select sites, with no obvious spatial or temporal associations. Comparing these data with weather and environmental factor data, wind gusts and temperature were positively associated with Coccidioides detection, while soil moisture was negatively associated with Coccidioides detection. These results provide critical insights into the frequency and distribution of airborne arthroconidia and the associated risk of inhalation and potential disease that is present across space and time in a highly endemic locale.
Imaging built-in electric fields and light matter by Fourier-precession TEM
Authors: Lorenzen Tizian , März Benjamin , Xue Tianhao , Beyer Andreas , Volz Kerstin , Bein Thomas , Müller-Caspary Knut 
Published: January 2024

AbstractWe report the precise measurement of electric fields in nanostructures, and high-contrast imaging of soft matter at ultralow electron doses by transmission electron microscopy (TEM). In particular, a versatile method based on the theorem of reciprocity is introduced to enable differential phase contrast imaging and ptychography in conventional, plane-wave illumination TEM. This is realised by a series of TEM images acquired under different tilts, thereby introducing the sampling rate in reciprocal space as a tuneable parameter, in contrast to momentum-resolved scanning techniques. First, the electric field of a p–n junction in GaAs is imaged. Second, low-dose, in-focus ptychographic and DPC characterisation of Kagome pores in weakly scattering covalent organic frameworks is demonstrated by using a precessing electron beam in combination with a direct electron detector. The approach offers utmost flexibility to record relevant spatial frequencies selectively, while acquisition times and dose requirements are significantly reduced compared to the 4D-STEM counterpart.
Analysis of the effects of importin α1 on the nuclear translocation of IL-1α in HeLa cells
Authors: Yamada Akiko , Wake Kiyotaka , Imaoka Saya , Motoyoshi Mitsuru , Yamamoto Takenori , Asano Masatake 
Published: January 2024

AbstractInterleukin-1α (IL-1α), a cytokine released by necrotic cells, causes sterile inflammation. On the other hand, IL-1α is present in the nucleus and also regulates the expression of many proteins. A protein substrate containing a classical nuclear localization signal (cNLS) typically forms a substrate/importin α/β complex, which is subsequently transported to the nucleus. To the best of our knowledge, no study has directly investigated whether IL-1α—which includes cNLS—is imported into the nucleus in an importin α/β-dependent manner. In this study, we noted that all detected importin α subtypes interacted with IL-1α. In HeLa cells, importin α1-mediated nuclear translocation of IL-1α occurred at steady state and was independent of importin β1. Importin α1 not only was engaged in IL-1α nuclear transport but also concurrently functioned as a molecule that regulated IL-1α protein level in the cell. Furthermore, we discussed the underlying mechanism of IL-1α nuclear translocation by importin α1 based on our findings.