bluuebunny/crossref_metadata_2025_split huggingface dataset:
Why we thrive beneath a northern sky – genomic signals of selection in apple for adaptation to northern Sweden
Authors: Skytte af Sätra J. , Garkava-Gustavsson L. , Ingvarsson P. K. 
Published: June 2024

AbstractGood understanding of the genomic regions underlying adaptation of apple to boreal climates is needed to facilitate efficient breeding of locally adapted apple cultivars. Proper infrastructure for phenotyping and evaluation is essential for identification of traits responsible for adaptation, and dissection of their genetic composition. However, such infrastructure is costly and currently not available for the boreal zone of northern Sweden. Therefore, we used historical pomological data on climate adaptation of 59 apple cultivars and whole genome sequencing to identify genomic regions that have undergone historical selection among apple cultivars recommended for cultivation in northern Sweden. We found the apple collection to be composed of two ancestral groups that are largely concordant with the grouping into ‘hardy’ and ‘not hardy’ cultivars based on the pomological literature. Using a number of genome-wide scans for signals of selection, we obtained strong evidence of positive selection at a genomic region around 29 MbHFTH1 of chromosome 1 among apple cultivars in the ‘hardy’ group. Using phased genotypic data from the 20 K apple Infinium® SNP array, we identified haplotypes associated with the two cultivar groups and traced transmission of these haplotypes through the pedigrees of some apple cultivars. This demonstrates that historical data from pomological literature can be analyzed by population genomic approaches as a step towards revealing the genomic control of a key property for a horticultural niche market. Such knowledge is needed to facilitate efficient breeding strategies for development of locally adapted apple cultivars in the future. The current study illustrates the response to a very strong selective pressure imposed on tree crops by climatic factors, and the importance of genetic research on this topic and feasibility of breeding efforts in the light of the ongoing climate change.
Heterogeneous organophotocatalytic HBr oxidation coupled with oxygen reduction for boosting bromination of arenes
Authors: Wang Jie , Liang Jiahao , Hou Hao , Liu Wei , Wu Hongru , Sun Hongli , Ou Wei , Su Chenliang , Liu Bin 
Published: June 2024

AbstractDeveloping mild photocatalytic bromination strategies using sustainable bromo source has been attracting intense interests, but there is still much room for improvement. Full utilization of redox centers of photocatalysts for efficient generation of Br+ species is the key. Herein we report heterogenous organophotocatalytic HBr oxidation coupled with oxygen reduction to furnish Br2 and H2O2 for effective bromination of arenes over Al2O3 supported perylene-3,4,9,10-tetracarboxylic dianhydride (PTCDA). Mechanism studies suggest that O-vacancy in Al2O3 can provide Lewis-acid-type anchoring sites for O2, enabling unexpected dual-electron transfer from anchored photoexcited PTCDA to chemically bound O2 to produce H2O2. The in-situ generated H2O2 and Br2 over redox centers work together to generate HBrO for bromination of arenes. This work provides new insights that heterogenization of organophotocatalysts can not only help to improve their stability and recyclability, but also endow them with the ability to trigger unusual reaction mode via cooperative catalysis with supports.
Stretchable OLEDs based on a hidden active area for high fill factor and resolution compensation
Authors: Lee Donggyun , Kim Su-Bon , Kim Taehyun , Choi Dongho , Sim Jee Hoon , Lee Woochan , Cho Hyunsu , Yang Jong-Heon , Kim Junho , Hahn Sangin , Moon Hanul , Yoo Seunghyup 
Published: June 2024

AbstractStretchable organic light-emitting diodes (OLEDs) have emerged as promising optoelectronic devices with exceptional degree of freedom in form factors. However, stretching OLEDs often results in a reduction in the geometrical fill factor (FF), that is the ratio of an active area to the total area, thereby limiting their potential for a broad range of applications. To overcome these challenges, we propose a three-dimensional (3D) architecture adopting a hidden active area that serves a dual role as both an emitting area and an interconnector. For this purpose, an ultrathin OLED is first attached to a 3D rigid island array structure through quadaxial stretching for precise, deformation-free alignment. A portion of the ultrathin OLED is concealed by letting it ‘fold in’ between the adjacent islands in the initial, non-stretched condition and gradually surfaces to the top upon stretching. This design enables the proposed stretchable OLEDs to exhibit a relatively high FF not only in the initial state but also after substantial deformation corresponding to a 30% biaxial system strain. Moreover, passive-matrix OLED displays that utilize this architecture are shown to be configurable for compensation of post-stretch resolution loss, demonstrating the efficacy of the proposed approach in realizing the full potential of stretchable OLEDs.
Bacteriophage defends murine gut from Escherichia coli invasion via mucosal adherence
Authors: Wu Jiaoling , Fu Kailai , Hou Chenglin , Wang Yuxin , Ji Chengyuan , Xue Feng , Ren Jianluan , Dai Jianjun , Barr Jeremy J. , Tang Fang 
Published: June 2024

AbstractBacteriophage are sophisticated cellular parasites that can not only parasitize bacteria but are increasingly recognized for their direct interactions with mammalian hosts. Phage adherence to mucus is known to mediate enhanced antimicrobial effects in vitro. However, little is known about the therapeutic efficacy of mucus-adherent phages in vivo. Here, using a combination of in vitro gastrointestinal cell lines, a gut-on-a-chip microfluidic model, and an in vivo murine gut model, we demonstrated that a E. coli phage, øPNJ-6, provided enhanced gastrointestinal persistence and antimicrobial effects. øPNJ-6 bound fucose residues, of the gut secreted glycoprotein MUC2, through domain 1 of its Hoc protein, which led to increased intestinal mucus production that was suggestive of a positive feedback loop mediated by the mucus-adherent phage. These findings extend the Bacteriophage Adherence to Mucus model into phage therapy, demonstrating that øPNJ-6 displays enhanced persistence within the murine gut, leading to targeted depletion of intestinal pathogenic bacteria.
Higher-order correlations reveal complex memory in temporal hypergraphs
Authors: Gallo Luca , Lacasa Lucas , Latora Vito , Battiston Federico 
Published: June 2024

AbstractMany real-world complex systems are characterized by interactions in groups that change in time. Current temporal network approaches, however, are unable to describe group dynamics, as they are based on pairwise interactions only. Here, we use time-varying hypergraphs to describe such systems, and we introduce a framework based on higher-order correlations to characterize their temporal organization. The analysis of human interaction data reveals the existence of coherent and interdependent mesoscopic structures, thus capturing aggregation, fragmentation and nucleation processes in social systems. We introduce a model of temporal hypergraphs with non-Markovian group interactions, which reveals complex memory as a fundamental mechanism underlying the emerging pattern in the data.
Systematic evaluation of fMRI data-processing pipelines for consistent functional connectomics
Authors: Luppi Andrea I. , Gellersen Helena M. , Liu Zhen-Qi , Peattie Alexander R. D. , Manktelow Anne E. , Adapa Ram , Owen Adrian M. , Naci Lorina , Menon David K. , Dimitriadis Stavros I. , Stamatakis Emmanuel A. 
Published: June 2024

AbstractFunctional interactions between brain regions can be viewed as a network, enabling neuroscientists to investigate brain function through network science. Here, we systematically evaluate 768 data-processing pipelines for network reconstruction from resting-state functional MRI, evaluating the effect of brain parcellation, connectivity definition, and global signal regression. Our criteria seek pipelines that minimise motion confounds and spurious test-retest discrepancies of network topology, while being sensitive to both inter-subject differences and experimental effects of interest. We reveal vast and systematic variability across pipelines’ suitability for functional connectomics. Inappropriate choice of data-processing pipeline can produce results that are not only misleading, but systematically so, with the majority of pipelines failing at least one criterion. However, a set of optimal pipelines consistently satisfy all criteria across different datasets, spanning minutes, weeks, and months. We provide a full breakdown of each pipeline’s performance across criteria and datasets, to inform future best practices in functional connectomics.
Burkholderia pseudomallei BipD modulates host mitophagy to evade killing
Authors: Nan Dongqi , Rao Chenglong , Tang Zhiheng , Yang Wenbo , Wu Pan , Chen Jiangao , Xia Yupei , Yan Jingmin , Liu Wenzheng , Zhang Ziyuan , Hu Zhiqiang , Chen Hai , Liao Yaling , Mao Xuhu , Liu Xiaoyun , Zou Quanming , Li Qian 
Published: June 2024

AbstractMitophagy is critical for mitochondrial quality control and function to clear damaged mitochondria. Here, we found that Burkholderia pseudomallei maneuvered host mitophagy for its intracellular survival through the type III secretion system needle tip protein BipD. We identified BipD, interacting with BTB-containing proteins KLHL9 and KLHL13 by binding to the Back and Kelch domains, recruited NEDD8 family RING E3 ligase CUL3 in response to B. pseudomallei infection. Although evidently not involved in regulation of infectious diseases, KLHL9/KLHL13/CUL3 E3 ligase complex was essential for BipD-dependent ubiquitination of mitochondria in mouse macrophages. Mechanistically, we discovered the inner mitochondrial membrane IMMT via host ubiquitome profiling as a substrate of KLHL9/KLHL13/CUL3 complex. Notably, K63-linked ubiquitination of IMMT K211 was required for initiating host mitophagy, thereby reducing mitochondrial ROS production. Here, we show a unique mechanism used by bacterial pathogens that hijacks host mitophagy for their survival.
Bio-inspired multimodal learning with organic neuromorphic electronics for behavioral conditioning in robotics
Authors: Krauhausen Imke , Griggs Sophie , McCulloch Iain , den Toonder Jaap M. J. , Gkoupidenis Paschalis , van de Burgt Yoeri 
Published: June 2024

AbstractBiological systems interact directly with the environment and learn by receiving multimodal feedback via sensory stimuli that shape the formation of internal neuronal representations. Drawing inspiration from biological concepts such as exploration and sensory processing that eventually lead to behavioral conditioning, we present a robotic system handling objects through multimodal learning. A small-scale organic neuromorphic circuit locally integrates and adaptively processes multimodal sensory stimuli, enabling the robot to interact intelligently with its surroundings. The real-time handling of sensory stimuli via low-voltage organic neuromorphic devices with synaptic functionality forms multimodal associative connections that lead to behavioral conditioning, and thus the robot learns to avoid potentially dangerous objects. This work demonstrates that adaptive neuro-inspired circuitry with multifunctional organic materials, can accommodate locally efficient bio-inspired learning for advancing intelligent robotics.
Highly reversible transition metal migration in superstructure-free Li-rich oxide boosting voltage stability and redox symmetry
Authors: Cui Tianwei , Xu Jialiang , Wang Xin , Liu Longxiang , Xiang Yuxuan , Zhu Hong , Li Xiang , Fu Yongzhu 
Published: June 2024

AbstractThe further practical applications of Li-rich layered oxides are impeded by voltage decay and redox asymmetry, which are closely related to the structural degradation involving irreversible transition metal migration. It has been demonstrated that the superstructure ordering in O2-type materials can effectively suppress voltage decay and redox asymmetry. Herein, we elucidate that the absence of this superstructure ordering arrangement in a Ru-based O2-type oxide can still facilitate the highly reversible transition metal migration. We certify that Ru in superstructure-free O2-type structure can unlock a quite different migration path from Mn in mostly studied cases. The highly reversible migration of Ru helps the cathode maintain the structural robustness, thus realizing terrific capacity retention with neglectable voltage decay and inhibited oxygen redox asymmetry. We untie the knot that the absence of superstructure ordering fails to enable a high-performance Li-rich layered oxide cathode material with suppressed voltage decay and redox asymmetry.
Orthogonal proteogenomic analysis identifies the druggable PA2G4-MYC axis in 3q26 AML
Authors: Marchesini Matteo , Gherli Andrea , Simoncini Elisa , Tor Lucas Moron Dalla , Montanaro Anna , Thongon Natthakan , Vento Federica , Liverani Chiara , Cerretani Elisa , D’Antuono Anna , Pagliaro Luca , Zamponi Raffaella , Spadazzi Chiara , Follini Elena , Cambò Benedetta , Giaimo Mariateresa , Falco Angela , Sammarelli Gabriella , Todaro Giannalisa , Bonomini Sabrina , Adami Valentina , Piazza Silvano , Corbo Claudia , Lorusso Bruno , Mezzasoma Federica , Lagrasta Costanza Anna Maria , Martelli Maria Paola , La Starza Roberta , Cuneo Antonio , Aversa Franco , Mecucci Cristina , Quaini Federico , Colla Simona , Roti Giovanni 
Published: June 2024

AbstractThe overexpression of the ecotropic viral integration site-1 gene (EVI1/MECOM) marks the most lethal acute myeloid leukemia (AML) subgroup carrying chromosome 3q26 abnormalities. By taking advantage of the intersectionality of high-throughput cell-based and gene expression screens selective and pan-histone deacetylase inhibitors (HDACis) emerge as potent repressors of EVI1. To understand the mechanism driving on-target anti-leukemia activity of this compound class, here we dissect the expression dynamics of the bone marrow leukemia cells of patients treated with HDACi and reconstitute the EVI1 chromatin-associated co-transcriptional complex merging on the role of proliferation-associated 2G4 (PA2G4) protein. PA2G4 overexpression rescues AML cells from the inhibitory effects of HDACis, while genetic and small molecule inhibition of PA2G4 abrogates EVI1 in 3q26 AML cells, including in patient-derived leukemia xenografts. This study positions PA2G4 at the crosstalk of the EVI1 leukemogenic signal for developing new therapeutics and urges the use of HDACis-based combination therapies in patients with 3q26 AML.
One-step formation of polymorphous sperm-like microswimmers by vortex turbulence-assisted microfluidics
Authors: Tan Rong , Yang Xiong , Lu Haojian , Shen Yajing 
Published: June 2024

AbstractMicroswimmers are considered promising candidates for active cargo delivery to benefit a wide spectrum of biomedical applications. Yet, big challenges still remain in designing the microswimmers with effective propelling, desirable loading and adaptive releasing abilities all in one. Inspired by the morphology and biofunction of spermatozoa, we report a one-step formation strategy of polymorphous sperm-like magnetic microswimmers (PSMs) by developing a vortex turbulence-assisted microfluidics (VTAM) platform. The fabricated PSM is biodegradable with a core-shell head and flexible tail, and their morphology can be adjusted by vortex flow rotation speed and calcium chloride solution concentration. Benefiting from the sperm-like design, our PSM exhibits both effective motion ability under remote mag/netic actuation and protective encapsulation ability for material loading. Further, it can also realize the stable sustain release after alginate-chitosan-alginate (ACA) layer coating modification. This research proposes and verifies a new strategy for the sperm-like microswimmer construction, offering an alternative solution for the target delivery of diverse drugs and biologics for future biomedical treatment. Moreover, the proposed VTAM could also be a general method for other sophisticated polymorphous structures fabrication that isn’t achievable by conventional laminar flow.
Structure and mechanism of the K+/H+ exchanger KefC
Authors: Gulati Ashutosh , Kokane Surabhi , Perez-Boerema Annemarie , Alleva Claudia , Meier Pascal F. , Matsuoka Rei , Drew David 
Published: June 2024

AbstractIntracellular potassium (K+) homeostasis is fundamental to cell viability. In addition to channels, K+ levels are maintained by various ion transporters. One major family is the proton-driven K+ efflux transporters, which in gram-negative bacteria is important for detoxification and in plants is critical for efficient photosynthesis and growth. Despite their importance, the structure and molecular basis for K+-selectivity is poorly understood. Here, we report ~3.1 Å resolution cryo-EM structures of the Escherichia coli glutathione (GSH)-gated K+ efflux transporter KefC in complex with AMP, AMP/GSH and an ion-binding variant. KefC forms a homodimer similar to the inward-facing conformation of Na+/H+ antiporter NapA. By structural assignment of a coordinated K+ ion, MD simulations, and SSM-based electrophysiology, we demonstrate how ion-binding in KefC is adapted for binding a dehydrated K+ ion. KefC harbors C-terminal regulator of K+ conductance (RCK) domains, as present in some bacterial K+-ion channels. The domain-swapped helices in the RCK domains bind AMP and GSH and they inhibit transport by directly interacting with the ion-transporter module. Taken together, we propose that KefC is activated by detachment of the RCK domains and that ion selectivity exploits the biophysical properties likewise adapted by K+-ion-channels.
How liquids charge the superhydrophobic surfaces
Authors: Jin Yuankai , Yang Siyan , Sun Mingzi , Gao Shouwei , Cheng Yaqi , Wu Chenyang , Xu Zhenyu , Guo Yunting , Xu Wanghuai , Gao Xuefeng , Wang Steven , Huang Bolong , Wang Zuankai 
Published: June 2024

AbstractLiquid-solid contact electrification (CE) is essential to diverse applications. Exploiting its full implementation requires an in-depth understanding and fine-grained control of charge carriers (electrons and/or ions) during CE. Here, we decouple the electrons and ions during liquid-solid CE by designing binary superhydrophobic surfaces that eliminate liquid and ion residues on the surfaces and simultaneously enable us to regulate surface properties, namely work function, to control electron transfers. We find the existence of a linear relationship between the work function of superhydrophobic surfaces and the as-generated charges in liquids, implying that liquid-solid CE arises from electron transfer due to the work function difference between two contacting surfaces. We also rule out the possibility of ion transfer during CE occurring on superhydrophobic surfaces by proving the absence of ions on superhydrophobic surfaces after contact with ion-enriched acidic, alkaline, and salt liquids. Our findings stand in contrast to existing liquid-solid CE studies, and the new insights learned offer the potential to explore more applications.
A combined experimental and computational study of ligand-controlled Chan-Lam coupling of sulfenamides
Authors: Han Kaiming , Liu Hong , Rotella Madeline E. , Xu Zeyu , Tao Lizhi , Chen Shufeng , Kozlowski Marisa C. , Jia Tiezheng 
Published: June 2024

AbstractThe unique features of the sulfenamides’ S(II)-N bond lead to interesting stereochemical properties and significant industrial functions. Here we present a chemoselective Chan–Lam coupling of sulfenamides to prepare N-arylated sulfenamides. A tridentate pybox ligand governs the chemoselectivity favoring C–N bond formation, and overrides the competitive C-S bond formation by preventing the S,N-bis-chelation of sulfenamides to copper center. The Cu(II)-derived resting state of catalyst is captured by UV-Vis spectra and EPR technique, and the key intermediate is confirmed by the EPR isotope response using 15N-labeled sulfenamide. A computational mechanistic study reveals that N-arylation is both kinetically and thermodynamically favorable, with deprotonation of the sulfenamide nitrogen atom occurring prior to reductive elimination. The origin of ligand-controlled chemoselectivity is explored, with the interaction between the pybox ligand and the sulfenamide substrate controlling the energy of the S-arylation and the corresponding product distribution, in agreement with the EPR studies and kinetic results.
Changes in planned and unplanned canopy openings are linked in Europe’s forests
Authors: Seidl Rupert , Senf Cornelius 
Published: June 2024

AbstractCanopy openings are increasing in Europe’s forests, yet the contributions of anthropogenic and ecological agents of disturbance to this increase remain debated. Here we attribute the root cause of all stand-replacing canopy disturbances identified for Europe in the period 1986–2020 from Landsat data (417,000 km²), distinguishing between planned and unplanned canopy openings (i.e., disturbance by human land use versus by wind, bark beetles, and wildfire). We show that canopy openings by humans dominate the European forest disturbance regime, accounting for 82% of the area disturbed. Both planned and unplanned canopy openings increased in the early 21st century (+24% and +30% relative to the late 20th century). Their changes are linked, with simultaneous increases in planned and unplanned canopy openings on 68% of Europe’s forest area. We conclude that an important direction for tackling disturbance change in policy and management is to break the link between planned and unplanned canopy openings in Europe’s forests.
Shear force effect of the dry process on cathode contact coverage in all-solid-state batteries
Authors: Lee Dongkyu , Shim Yejin , Kim Youngsung , Kwon Guhan , Choi Seung Ho , Kim KyungSu , Yoo Dong-Joo 
Published: June 2024

AbstractThe state-of-the-art all-solid-state batteries have emerged as an alternative to the traditional flammable lithium-ion batteries, offering higher energy density and safety. Nevertheless, insufficient intimate contact at electrode-electrolyte surface limits their stability and electrochemical performance, hindering the commercialization of all-solid-state batteries. Herein, we conduct a systematic investigation into the effects of shear force in the dry electrode process by comparing binder-free hand-mixed pellets, wet-processed electrodes, and dry-processed electrodes. Through digitally processed images, we quantify a critical factor, ‘coverage’, the percentage of electrolyte-covered surface area of the active materials. The coverage of dry electrodes was significantly higher (67.2%) than those of pellets (30.6%) and wet electrodes (33.3%), enabling superior rate capability and cyclability. A physics-based electrochemical model highlights the effects of solid diffusion by elucidating the impact of coverage on active material utilization under various current densities. These results underscore the pivotal role of the electrode fabrication process, with the focus on the critical factor of coverage.