bluuebunny/crossref_metadata_2025_split huggingface dataset:
Phytohormone profiling in an evolutionary framework
Authors: Schmidt Vojtěch , Skokan Roman , Depaepe Thomas , Kurtović Katarina , Haluška Samuel , Vosolsobě Stanislav , Vaculíková Roberta , Pil Anthony , Dobrev Petre Ivanov , Motyka Václav , Van Der Straeten Dominique , Petrášek Jan 
Published: May 2024

AbstractThe genomes of charophyte green algae, close relatives of land plants, typically do not show signs of developmental regulation by phytohormones. However, scattered reports of endogenous phytohormone production in these organisms exist. We performed a comprehensive analysis of multiple phytohormones in Viridiplantae, focusing mainly on charophytes. We show that auxin, salicylic acid, ethylene and tRNA-derived cytokinins including cis-zeatin are found ubiquitously in Viridiplantae. By contrast, land plants but not green algae contain the trans-zeatin type cytokinins as well as auxin and cytokinin conjugates. Charophytes occasionally produce jasmonates and abscisic acid, whereas the latter is detected consistently in land plants. Several phytohormones are excreted into the culture medium, including auxin by charophytes and cytokinins and salicylic acid by Viridiplantae in general. We note that the conservation of phytohormone biosynthesis and signaling pathways known from angiosperms does not match the capacity for phytohormone biosynthesis in Viridiplantae. Our phylogenetically guided analysis of established algal cultures provides an important insight into phytohormone biosynthesis and metabolism across Streptophyta.
Cellulose nanofiber-mediated manifold dynamic synergy enabling adhesive and photo-detachable hydrogel for self-powered E-skin
Authors: Zhang Lei , Chen Lu , Wang Siheng , Wang Shanshan , Wang Dan , Yu Le , Xu Xu , Liu He , Chen Chaoji 
Published: May 2024

AbstractSelf-powered skin attachable and detachable electronics are under intense development to enable the internet of everything and everyone in new and useful ways. Existing on-demand separation strategies rely on complicated pretreatments and physical properties of the adherends, achieving detachable-on-demand in a facile, rapid, and universal way remains challenging. To overcome this challenge, an ingenious cellulose nanofiber-mediated manifold dynamic synergy strategy is developed to construct a supramolecular hydrogel with both reversible tough adhesion and easy photodetachment. The cellulose nanofiber-reinforced network and the coordination between Fe ions and polymer chains endow the dynamic reconfiguration of supramolecular networks and the adhesion behavior of the hydrogel. This strategy enables the simple and rapid fabrication of strong yet reversible hydrogels with tunable toughness ((Valuemax-Valuemin)/Valuemax of up to 86%), on-demand adhesion energy ((Valuemax-Valuemin)/Valuemax of up to 93%), and stable conductivity up to 12 mS cm−1. We further extend this strategy to fabricate different cellulose nanofiber/Fe3+-based hydrogels from various biomacromolecules and petroleum polymers, and shed light on exploration of fundamental dynamic supramolecular network reconfiguration. Simultaneously, we prepare an adhesive-detachable triboelectric nanogenerator as a human-machine interface for a self-powered wireless monitoring system based on this strategy, which can acquire the real-time, self-powered monitoring, and wireless whole-body movement signal, opening up possibilities for diversifying potential applications in electronic skins and intelligent devices.
Precise immunofluorescence canceling for highly multiplexed imaging to capture specific cell states
Authors: Tomimatsu Kosuke , Fujii Takeru , Bise Ryoma , Hosoda Kazufumi , Taniguchi Yosuke , Ochiai Hiroshi , Ohishi Hiroaki , Ando Kanta , Minami Ryoma , Tanaka Kaori , Tachibana Taro , Mori Seiichi , Harada Akihito , Maehara Kazumitsu , Nagasaki Masao , Uchida Seiichi , Kimura Hiroshi , Narita Masashi , Ohkawa Yasuyuki 
Published: May 2024

AbstractCell states are regulated by the response of signaling pathways to receptor ligand-binding and intercellular interactions. High-resolution imaging has been attempted to explore the dynamics of these processes and, recently, multiplexed imaging has profiled cell states by achieving a comprehensive acquisition of spatial protein information from cells. However, the specificity of antibodies is still compromised when visualizing activated signals. Here, we develop Precise Emission Canceling Antibodies (PECAbs) that have cleavable fluorescent labeling. PECAbs enable high-specificity sequential imaging using hundreds of antibodies, allowing for reconstruction of the spatiotemporal dynamics of signaling pathways. Additionally, combining this approach with seq-smFISH can effectively classify cells and identify their signal activation states in human tissue. Overall, the PECAb system can serve as a comprehensive platform for analyzing complex cell processes.
Revealing the three-dimensional arrangement of polar topology in nanoparticles
Authors: Jeong Chaehwa , Lee Juhyeok , Jo Hyesung , Oh Jaewhan , Baik Hionsuck , Go Kyoung-June , Son Junwoo , Choi Si-Young , Prosandeev Sergey , Bellaiche Laurent , Yang Yongsoo 
Published: May 2024

AbstractIn the early 2000s, low dimensional ferroelectric systems were predicted to have topologically nontrivial polar structures, such as vortices or skyrmions, depending on mechanical or electrical boundary conditions. A few variants of these structures have been experimentally observed in thin film model systems, where they are engineered by balancing electrostatic charge and elastic distortion energies. However, the measurement and classification of topological textures for general ferroelectric nanostructures have remained elusive, as it requires mapping the local polarization at the atomic scale in three dimensions. Here we unveil topological polar structures in ferroelectric BaTiO3 nanoparticles via atomic electron tomography, which enables us to reconstruct the full three-dimensional arrangement of cation atoms at an individual atom level. Our three-dimensional polarization maps reveal clear topological orderings, along with evidence of size-dependent topological transitions from a single vortex structure to multiple vortices, consistent with theoretical predictions. The discovery of the predicted topological polar ordering in nanoscale ferroelectrics, independent of epitaxial strain, widens the research perspective and offers potential for practical applications utilizing contact-free switchable toroidal moments.
Efficient recovery and recycling/upcycling of precious metals using hydrazide-functionalized star-shaped polymers
Authors: Shin Seung Su , Jung Youngkyun , Jeon Sungkwon , Park Sung-Joon , Yoon Su-Jin , Jung Kyung-Won , Choi Jae-Woo , Lee Jung-Hyun 
Published: May 2024

AbstractThere is a growing demand for adsorption technologies for recovering and recycling precious metals (PMs) in various industries. Unfortunately, amine-functionalized polymers widely used as metal adsorbents are ineffective at recovering PMs owing to their unsatisfactory PM adsorption performance. Herein, a star-shaped, hydrazide-functionalized polymer (S-PAcH) is proposed as a readily recoverable standalone adsorbent with high PM adsorption performance. The compact chain structure of S-PAcH containing numerous hydrazide groups with strong reducibility promotes PM adsorption by enhancing PM reduction while forming large, collectable precipitates. Compared with previously reported PM adsorbents, commercial amine polymers, and reducing agents, S-PAcH exhibited significantly higher adsorption capacity, selectivity, and kinetics toward three PMs (gold, palladium, and platinum) with model, simulated, and real-world feed solutions. The superior PM recovery performance of S-PAcH was attributed to its strong reduction capability combined with its chemisorption mechanism. Moreover, PM-adsorbed S-PAcH could be refined into high-purity PMs via calcination, directly utilized (upcycled) as catalysts for dye reduction, or regenerated for reuse, demonstrating its high practical feasibility. Our proposed PM adsorbents would have a tremendous impact on various industrial sectors from the perspectives of environmental protection and sustainable development.
A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem
Authors: Shi Bihai , Felipo-Benavent Amelia , Cerutti Guillaume , Galvan-Ampudia Carlos , Jilli Lucas , Brunoud Geraldine , Mutterer Jérome , Vallet Elody , Sakvarelidze-Achard Lali , Davière Jean-Michel , Navarro-Galiano Alejandro , Walia Ankit , Lazary Shani , Legrand Jonathan , Weinstain Roy , Jones Alexander M. , Prat Salomé , Achard Patrick , Vernoux Teva 
Published: May 2024

AbstractGrowth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signaling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signaling activity in the SAM. We show that high GA signaling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organization of internodes, thus contributing to internode specification in the SAM.
PD-1/CD80+ small extracellular vesicles from immunocytes induce cold tumours featured with enhanced adaptive immunosuppression
Authors: Zhang Lin-Zhou , Yang Jie-Gang , Chen Gai-Li , Xie Qi-Hui , Fu Qiu-Yun , Xia Hou-Fu , Li Yi-Cun , Huang Jue , Li Ye , Wu Min , Liu Hai-Ming , Wang Fu-Bing , Yi Ke-Zhen , Jiang Huan-Gang , Zhou Fu-Xiang , Wang Wei , Yu Zi-Li , Zhang Wei , Zhong Ya-Hua , Bian Zhuan , Yang Hong-Yu , Liu Bing , Chen Gang 
Published: May 2024

AbstractOnly a minority of cancer patients benefit from immune checkpoint blockade therapy. Sophisticated cross-talk among different immune checkpoint pathways as well as interaction pattern of immune checkpoint molecules carried on circulating small extracellular vesicles (sEV) might contribute to the low response rate. Here we demonstrate that PD-1 and CD80 carried on immunocyte-derived sEVs (I-sEV) induce an adaptive redistribution of PD-L1 in tumour cells. The resulting decreased cell membrane PD-L1 expression and increased sEV PD-L1 secretion into the circulation contribute to systemic immunosuppression. PD-1/CD80+ I-sEVs also induce downregulation of adhesion- and antigen presentation-related molecules on tumour cells and impaired immune cell infiltration, thereby converting tumours to an immunologically cold phenotype. Moreover, synchronous analysis of multiple checkpoint molecules, including PD-1, CD80 and PD-L1, on circulating sEVs distinguishes clinical responders from those patients who poorly respond to anti-PD-1 treatment. Altogether, our study shows that sEVs carry multiple inhibitory immune checkpoints proteins, which form a potentially targetable adaptive loop to suppress antitumour immunity.
Interplay of structural preorganization and conformational sampling in UDP-glucuronic acid 4-epimerase catalysis
Authors: Rapp Christian , Borg Annika , Nidetzky Bernd 
Published: May 2024

AbstractUnderstanding enzyme catalysis as connected to protein motions is a major challenge. Here, based on temperature kinetic studies combined with isotope effect measurements, we obtain energetic description of C-H activation in NAD-dependent UDP-glucuronic acid C4 epimerase. Approach from the ensemble-averaged ground state (GS) to the transition state-like reactive conformation (TSRC) involves, alongside uptake of heat ($${\Delta {{{{{\rm{H}}}}}}}^{{{\ddagger}} }$$

Δ
H

‡

= 54 kJ mol−1), significant loss in entropy ($$-T{\Delta {{{{{\rm{S}}}}}}}^{{{\ddagger}} }$$
−
T

Δ
S

‡

= 20 kJ mol−1; 298 K) and negative activation heat capacity ($${\Delta {{{{{\rm{C}}}}}}}_{{{{{{\rm{p}}}}}}}^{{{\ddagger}} }$$

Δ
C

p

‡

= −0.64 kJ mol−1 K−1). Thermodynamic changes suggest the requirement for restricting configurational freedom at the GS to populate the TSRC. Enzyme variants affecting the electrostatic GS preorganization reveal active-site interactions important for precise TSRC sampling and H-transfer. Collectively, our study captures thermodynamic effects associated with TSRC sampling and establishes rigid positioning for C-H activation in an enzyme active site that requires conformational flexibility in fulfillment of its natural epimerase function.
Measurement of the superfluid fraction of a supersolid by Josephson effect
Authors: Biagioni G. , Antolini N. , Donelli B. , Pezzè L. , Smerzi A. , Fattori M. , Fioretti A. , Gabbanini C. , Inguscio M. , Tanzi L. , Modugno G. 
Published: May 2024

AbstractA new class of superfluids and superconductors with spatially periodic modulation of the superfluid density is arising1–12. It might be related to the supersolid phase of matter, in which the spontaneous breaking of gauge and translational symmetries leads to a spatially modulated macroscopic wavefunction13–16. This relation was recognized only in some cases1,2,5–9 and there is the need for a universal property quantifying the differences between supersolids and ordinary matter, such as the superfluid fraction, which measures the reduction in superfluid stiffness resulting from the spatial modulation16–18. The superfluid fraction was introduced long ago16, but it has not yet been assessed experimentally. Here we demonstrate an innovative method to measure the superfluid fraction based on the Josephson effect, a ubiquitous phenomenon associated with the presence of a physical barrier between two superfluids or superconductors19, which might also be expected for supersolids20, owing to the spatial modulation. We demonstrate that individual cells of a supersolid can sustain Josephson oscillations and we show that, from the current–phase dynamics, we can derive directly the superfluid fraction. Our study of a cold-atom dipolar supersolid7 reveals a relatively large sub-unity superfluid fraction that makes realistic the study of previously unknown phenomena such as partially quantized vortices and supercurrents16–18. Our results open a new direction of research that may unify the description of all supersolid-like systems.
Genome-wide profiling of angiogenic cis-regulatory elements unravels cis-regulatory SNPs for vascular abnormality
Authors: Jin Lihui , Han Zhenyuan , Mao Xiaotong , Lu Jieru , Yan Bingqian , Lu Yiwen , Liang Lili , Wang Lin , Yu Yu , Sun Kun 
Published: May 2024

AbstractAngiogenesis is extensively involved in embryonic development and requires complex regulation networks, whose defects can cause a variety of vascular abnormalities. Cis-regulatory elements control gene expression at all developmental stages, but they have not been studied or profiled in angiogenesis yet. In this study, we exploited public DNase-seq and RNA-seq datasets from a VEGFA-stimulated in vitro angiogenic model, and carried out an integrated analysis of the transcriptome and chromatin accessibility across the entire process. Totally, we generated a bank of 47,125 angiogenic cis-regulatory elements with promoter (marker by H3K4me3) and/or enhancer (marker by H3K27ac) activities. Motif enrichment analysis revealed that these angiogenic cis-regulatory elements interacted preferentially with ETS family TFs. With this tool, we performed an association study using our WES data of TAPVC and identified rs199530718 as a cis-regulatory SNP associated with disease risk. Altogether, this study generated a genome-wide bank of angiogenic cis-regulatory elements and illustrated its utility in identifying novel cis-regulatory SNPs for TAPVC, expanding new horizons of angiogenesis as well as vascular abnormality genetics.
User factors affecting the use of digital services in five European regions and countries
Authors: Goodman-Deane Joy , Waller Sam , Bradley Mike , Clarkson P. John , Lazzarini Boris , Roca Bosch Elisabet , Gaggi Silvia 
Published: May 2024

AbstractDigitalisation has great potential to reduce costs, improve access and enhance user experience. However, it could also increase inequality, with some people struggling to access and use digital services. It is important to understand who is likely to be excluded in this way and why. This can help to identify groups at particular risk of digital exclusion, inform efforts to overcome the barriers, and develop more inclusive digital services. This paper introduces a set of five linked datasets examining a range of user factors affecting the use of digital services. The datasets focus on the use of digital mobility services, but the data is useful in understanding the use of other digital services as well. The user factors considered include technology access, use and competence and attitudes towards digital technology. The datasets were the results of surveys in five European regions and countries (Germany, Italy, Barcelona Metropolitan Area, Flanders and the Netherlands). Samples were taken of the adult (age 16+) population with a total of 3,454 participants.
Forecasting vaping health risks through neural network model prediction of flavour pyrolysis reactions
Authors: Kishimoto Akihiro , Wu Dan , O’Shea Donal F. 
Published: May 2024

AbstractVaping involves the heating of chemical solutions (e-liquids) to high temperatures prior to lung inhalation. A risk exists that these chemicals undergo thermal decomposition to new chemical entities, the composition and health implications of which are largely unknown. To address this concern, a graph-convolutional neural network (NN) model was used to predict pyrolysis reactivity of 180 e-liquid chemical flavours. The output of this supervised machine learning approach was a dataset of probability ranked pyrolysis transformations and their associated 7307 products. To refine this dataset, the molecular weight of each NN predicted product was automatically correlated with experimental mass spectrometry (MS) fragmentation data for each flavour chemical. This blending of deep learning methods with experimental MS data identified 1169 molecular weight matches that prioritized these compounds for further analysis. The average number of discrete matches per flavour between NN predictions and MS fragmentation was 6.4 with 92.8% of flavours having at least one match. Globally harmonized system classifications for NN/MS matches were extracted from PubChem, revealing that 127 acute toxic, 153 health hazard and 225 irritant classifications were predicted. This approach may reveal the longer-term health risks of vaping in advance of clinical diseases emerging in the general population.
Identification of domains in Plasmodium falciparum proteins of unknown function using DALI search on AlphaFold predictions
Authors: Behrens Hannah Michaela , Spielmann Tobias 
Published: May 2024

AbstractPlasmodium falciparum, the causative agent of malaria, poses a significant global health challenge, yet much of its biology remains elusive. A third of the genes in the P. falciparum genome lack annotations regarding their function, impeding our understanding of the parasite's biology. In this study, we employ structure predictions and the DALI search algorithm to analyse proteins encoded by uncharacterized genes in the reference strain 3D7 of P. falciparum. By comparing AlphaFold predictions to experimentally determined protein structures in the Protein Data Bank, we found similarities to known domains in 353 proteins of unknown function, shedding light on their potential functions. The lowest-scoring 5% of similarities were additionally validated using the size-independent TM-align algorithm, confirming the detected similarities in 88% of the cases. Notably, in over 70 P. falciparum proteins the presence of domains resembling heptatricopeptide repeats, which are typically involvement in RNA binding and processing, was detected. This suggests this family, which is important in transcription in mitochondria and apicoplasts, is much larger in Plasmodium parasites than previously thought. The results of this domain search provide a resource to the malaria research community that is expected to inform and enable experimental studies.
Joint association of overweight/obesity, high electronic screen time, and low physical activity time with early pubertal development in girls: a case–control study
Authors: Li Weiqin , Feng Lingyan , Song Panpan , Wang Leishen , Zhang Shuang , Li Wei , Zhu Dandan , Du Yuexin , Leng Junhong 
Published: May 2024

AbstractTo examine the joint association of electronic screen time (EST), moderate-to-vigorous physical activity time (MVPA) and overweight/obesity with early pubertal development (EPD) in girls. A case–control study of 177 EPD girls and 354 girls with normal pubertal development was conducted between October 2019 and August 2022. Overweight/obesity was defined as body mass index ≥ 85th percentiles for age and sex. We found a non-significant increase of EPD risk among girls with high EST alone [OR: 2.75 (0.65–11.58)] or low MVPA alone [OR: 2.54 (0.74–8.69)], but a significant increase of EPD risk among girls with overweight/obesity alone [OR: 4.91 (1.01–23.92)], compared to girls without any of the three risk factors (low MVPA, high EST and overweight/obesity). Girls with any two of the three risk factors faced increased risk of EPD, and girls with all three risk factors faced the highest risk of EPD [OR and 95% CI: 26.10 (6.40–106.45)]. Being overweight/obesity might be more important than having low MVPA or high EST as a correlate of EPD compared to girls without any of the three risk factors, but the co-presence of low MVPA, high EST and overweight/obesity would largely increase the risk of EPD in girls.