bluuebunny/crossref_metadata_2025_split huggingface dataset:
SiFT: uncovering hidden biological processes by probabilistic filtering of single-cell data
Authors: Piran Zoe , Nitzan Mor 
Published: January 2024

AbstractCellular populations simultaneously encode multiple biological attributes, including spatial configuration, temporal trajectories, and cell-cell interactions. Some of these signals may be overshadowed by others and harder to recover, despite the great progress made to computationally reconstruct biological processes from single-cell data. To address this, we present SiFT, a kernel-based projection method for filtering biological signals in single-cell data, thus uncovering underlying biological processes. SiFT applies to a wide range of tasks, from the removal of unwanted variation in the data to revealing hidden biological structures. We demonstrate how SiFT enhances the liver circadian signal by filtering spatial zonation, recovers regenerative cell subpopulations in spatially-resolved liver data, and exposes COVID-19 disease-related cells, pathways, and dynamics by filtering healthy reference signals. SiFT performs the correction at the gene expression level, can scale to large datasets, and compares favorably to state-of-the-art methods.
Elucidation of unusual biosynthesis and DnaN-targeting mode of action of potent anti-tuberculosis antibiotics Mycoplanecins
Authors: Fu Chengzhang , Liu Yunkun , Walt Christine , Rasheed Sari , Bader Chantal D. , Lukat Peer , Neuber Markus , Haeckl F. P. Jake , Blankenfeldt Wulf , Kalinina Olga V. , Müller Rolf 
Published: January 2024

AbstractDNA polymerase III sliding clamp (DnaN) was recently validated as a new anti-tuberculosis target employing griselimycins. Three (2 S,4 R)−4-methylproline moieties of methylgriselimycin play significant roles in target binding and metabolic stability. Here, we identify the mycoplanecin biosynthetic gene cluster by genome mining using bait genes from the 4-methylproline pathway. We isolate and structurally elucidate four mycoplanecins comprising scarce homo-amino acids and 4-alkylprolines. Evaluating mycoplanecin E against Mycobacterium tuberculosis surprisingly reveals an excitingly low minimum inhibition concentration at 83 ng/mL, thus outcompeting griselimycin by approximately 24-fold. We show that mycoplanecins bind DnaN with nanomolar affinity and provide a co-crystal structure of mycoplanecin A-bound DnaN. Additionally, we reconstitute the biosyntheses of the unusual l-homoleucine, l-homonorleucine, and (2 S,4 R)−4-ethylproline building blocks by characterizing in vitro the full set of eight enzymes involved. The biosynthetic study, bioactivity evaluation, and drug target validation of mycoplanecins pave the way for their further development to tackle multidrug-resistant mycobacterial infections.
An extensive disulfide bond network prevents tail contraction in Agrobacterium tumefaciens phage Milano
Authors: Sonani Ravi R. , Palmer Lee K. , Esteves Nathaniel C. , Horton Abigail A. , Sebastian Amanda L. , Kelly Rebecca J. , Wang Fengbin , Kreutzberger Mark A. B. , Russell William K. , Leiman Petr G. , Scharf Birgit E. , Egelman Edward H. 
Published: January 2024

AbstractA contractile sheath and rigid tube assembly is a widespread apparatus used by bacteriophages, tailocins, and the bacterial type VI secretion system to penetrate cell membranes. In this mechanism, contraction of an external sheath powers the motion of an inner tube through the membrane. The structure, energetics, and mechanism of the machinery imply rigidity and straightness. The contractile tail of Agrobacterium tumefaciens bacteriophage Milano is flexible and bent to varying degrees, which sets it apart from other contractile tail-like systems. Here, we report structures of the Milano tail including the sheath-tube complex, baseplate, and putative receptor-binding proteins. The flexible-to-rigid transformation of the Milano tail upon contraction can be explained by unique electrostatic properties of the tail tube and sheath. All components of the Milano tail, including sheath subunits, are crosslinked by disulfides, some of which must be reduced for contraction to occur. The putative receptor-binding complex of Milano contains a tailspike, a tail fiber, and at least two small proteins that form a garland around the distal ends of the tailspikes and tail fibers. Despite being flagellotropic, Milano lacks thread-like tail filaments that can wrap around the flagellum, and is thus likely to employ a different binding mechanism.
Structural and functional insights into the lipid regulation of human anion exchanger 2
Authors: Zhang Weiqi , Ding Dian , Lu Yishuo , Chen Hongyi , Jiang Peijun , Zuo Peng , Wang Guangxi , Luo Juan , Yin Yue , Luo Jianyuan , Yin Yuxin 
Published: January 2024

AbstractAnion exchanger 2 (AE2) is an electroneutral Na+-independent Cl-/HCO3- exchanger belongs to the SLC4 transporter family. The widely expressed AE2 participates in a variety of physiological processes, including transepithelial acid-base secretion and osteoclastogenesis. Both the transmembrane domains (TMDs) and the N-terminal cytoplasmic domain (NTD) are involved in regulation of AE2 activity. However, the regulatory mechanism remains unclear. Here, we report a 3.2 Å cryo-EM structure of the AE2 TMDs in complex with PIP2 and a 3.3 Å full-length mutant AE2 structure in the resting state without PIP2. We demonstrate that PIP2 at the TMD dimer interface is involved in the substrate exchange process. Mutation in the PIP2 binding site leads to the displacement of TM7 and further stabilizes the interaction between the TMD and the NTD. Reduced substrate transport activity and conformation similar to AE2 in acidic pH indicating the central contribution of PIP2 to the function of AE2.
Bioinspired handheld time-share driven robot with expandable DoFs
Authors: Wang Yunjiang , Hu Xinben , Cui Luhang , Xiao Xuan , Yang Keji , Zhu Yongjian , Jin Haoran 
Published: January 2024

AbstractHandheld robots offer accessible solutions with a short learning curve to enhance operator capabilities. However, their controllable degree-of-freedoms are limited due to scarce space for actuators. Inspired by muscle movements stimulated by nerves, we report a handheld time-share driven robot. It comprises several motion modules, all powered by a single motor. Shape memory alloy (SMA) wires, acting as “nerves”, connect to motion modules, enabling the selection of the activated module. The robot contains a 202-gram motor base and a 0.8 cm diameter manipulator comprised of sequentially linked bending modules (BM). The manipulator can be tailored in length and integrated with various instruments in situ, facilitating non-invasive access and high-dexterous operation at remote surgical sites. The applicability was demonstrated in clinical scenarios, where a surgeon held the robot to conduct transluminal experiments on a human stomach model and an ex vivo porcine stomach. The time-share driven mechanism offers a pragmatic approach to build a multi-degree-of-freedom robot for broader applications.
Compositional and temporal division of labor modulates mixed sugar fermentation by an engineered yeast consortium
Authors: Shin Jonghyeok , Liao Siqi , Kuanyshev Nurzhan , Xin Yongping , Kim Chanwoo , Lu Ting , Jin Yong-Su 
Published: January 2024

AbstractSynthetic microbial communities have emerged as an attractive route for chemical bioprocessing. They are argued to be superior to single strains through microbial division of labor (DOL), but the exact mechanism by which DOL confers advantages remains unclear. Here, we utilize a synthetic Saccharomyces cerevisiae consortium along with mathematical modeling to achieve tunable mixed sugar fermentation to overcome the limitations of single-strain fermentation. The consortium involves two strains with each specializing in glucose or xylose utilization for ethanol production. By controlling initial community composition, DOL allows fine tuning of fermentation dynamics and product generation. By altering inoculation delay, DOL provides additional programmability to parallelly regulate fermentation characteristics and product yield. Mathematical models capture observed experimental findings and further offer guidance for subsequent fermentation optimization. This study demonstrates the functional potential of DOL in bioprocessing and provides insight into the rational design of engineered ecosystems for various applications.
Photocatalytic ethylene production by oxidative dehydrogenation of ethane with dioxygen on ZnO-supported PdZn intermetallic nanoparticles
Authors: Wang Pu , Zhang Xingyu , Shi Run , Zhao Jiaqi , Waterhouse Geoffrey I. N. , Tang Junwang , Zhang Tierui 
Published: January 2024

AbstractThe selective oxidative dehydrogenation of ethane (ODHE) is attracting increasing attention as a method for ethylene production. Typically, thermocatalysts operating at high temperatures are needed for C–H activation in ethane. In this study, we describe a low temperature ( < 140 °C) photocatalytic route for ODHE, using O2 as the oxidant. A photocatalyst containing PdZn intermetallic nanoparticles supported on ZnO is prepared, affording an ethylene production rate of 46.4 mmol g–1 h–1 with 92.6% ethylene selectivity under 365 nm irradiation. When we employ a simulated shale gas feed, the photocatalytic ODHE system achieves nearly 20% ethane conversion while maintaining an ethylene selectivity of about 87%. The robust interface between the PdZn intermetallic nanoparticles and ZnO support plays a crucial role in ethane activation through a photo-assisted Mars-van Krevelen mechanism, followed by a rapid lattice oxygen replenishment to complete the reaction cycle. Our findings demonstrate that photocatalytic ODHE is a promising method for alkane-to-alkene conversions under mild conditions.
Direct 4D printing of ceramics driven by hydrogel dehydration
Authors: Wang Rong , Yuan Chao , Cheng Jianxiang , He Xiangnan , Ye Haitao , Jian Bingcong , Li Honggeng , Bai Jiaming , Ge Qi 
Published: January 2024

Abstract4D printing technology combines 3D printing and stimulus-responsive materials, enabling construction of complex 3D objects efficiently. However, unlike smart soft materials, 4D printing of ceramics is a great challenge due to the extremely weak deformability of ceramics. Here, we report a feasible and efficient manufacturing and design approach to realize direct 4D printing of ceramics. Photocurable ceramic elastomer slurry and hydrogel precursor are developed for the fabrication of hydrogel-ceramic laminates via multimaterial digital light processing 3D printing. Flat patterned laminates evolve into complex 3D structures driven by hydrogel dehydration, and then turn into pure ceramics after sintering. Considering the dehydration-induced deformation and sintering-induced shape retraction, we develop a theoretical model to calculate the curvatures of bent laminate and sintered ceramic part. Then, we build a design flow for direct 4D printing of various complex ceramic objects. This approach opens a new avenue for the development of ceramic 4D printing technology.
A contact-electro-catalysis process for producing reactive oxygen species by ball milling of triboelectric materials
Authors: Wang Ziming , Dong Xuanli , Li Xiao-Fen , Feng Yawei , Li Shunning , Tang Wei , Wang Zhong Lin 
Published: January 2024

AbstractBall milling is a representative mechanochemical strategy that uses the mechanical agitation-induced effects, defects, or extreme conditions to activate substrates. Here, we demonstrate that ball grinding could bring about contact-electro-catalysis (CEC) by using inert and conventional triboelectric materials. Exemplified by a liquid-assisted-grinding setup involving polytetrafluoroethylene (PTFE), reactive oxygen species (ROS) are produced, despite PTFE being generally considered as catalytically inert. The formation of ROS occurs with various polymers, such as polydimethylsiloxane (PDMS) and polypropylene (PP), and the amount of generated ROS aligns well with the polymers’ contact-electrification abilities. It is suggested that mechanical collision not only maximizes the overlap in electron wave functions across the interface, but also excites phonons that provide the energy for electron transition. We expect the utilization of triboelectric materials and their derived CEC could lead to a field of ball milling-assisted mechanochemistry using any universal triboelectric materials under mild conditions.
Thermo-optic epsilon-near-zero effects
Authors: Wu Jiaye , Clementi Marco , Huang Chenxingyu , Ye Feng , Fu Hongyan , Lu Lei , Zhang Shengdong , Li Qian , Brès Camille-Sophie 
Published: January 2024

AbstractNonlinear epsilon-near-zero (ENZ) nanodevices featuring vanishing permittivity and CMOS-compatibility are attractive solutions for large-scale-integrated systems-on-chips. Such confined systems with unavoidable heat generation impose critical challenges for semiconductor-based ENZ performances. While their optical properties are temperature-sensitive, there is no systematic analysis on such crucial dependence. Here, we experimentally report the linear and nonlinear thermo-optic ENZ effects in indium tin oxide. We characterize its temperature-dependent optical properties with ENZ frequencies covering the telecommunication O-band, C-band, and 2-μm-band. Depending on the ENZ frequency, it exhibits an unprecedented 70–93-THz-broadband 660–955% enhancement over the conventional thermo-optic effect. The ENZ-induced fast-varying large group velocity dispersion up to 0.03–0.18 fs2nm−1 and its temperature dependence are also observed for the first time. Remarkably, the thermo-optic nonlinearity demonstrates a 1113–2866% enhancement, on par with its reported ENZ-enhanced Kerr nonlinearity. Our work provides references for packaged ENZ-enabled photonic integrated circuit designs, as well as a new platform for nonlinear photonic applications and emulations.
An energy-free strategy to elevate anti-icing performance of superhydrophobic materials through interfacial airflow manipulation
Authors: Jiang Jiawei , Shen Yizhou , Xu Yangjiangshan , Wang Zhen , Tao Jie , Liu Senyun , Liu Weilan , Chen Haifeng 
Published: January 2024

AbstractSuperhydrophobic surfaces demonstrate excellent anti-icing performance under static conditions. However, they show a marked decrease in icing time under real flight conditions. Here we develop an anti-icing strategy using ubiquitous wind field to improve the anti-icing efficiency of superhydrophobic surfaces during flight. We find that the icing mass on hierarchical superhydrophobic surface with a microstructure angle of 30° is at least 40% lower than that on the conventional superhydrophobic plate, which is attributed to the combined effects of microdroplet flow upwelling induced by interfacial airflow and microdroplet ejection driven by superhydrophobic characteristic. Meanwhile, the disordered arrangement of water molecules induced by the specific 30° angle also raises the energy barriers required for nucleation, resulting in an inhibition of the nucleation process. This strategy of microdroplet movement manipulation induced by interfacial airflow is expected to break through the anti-icing limitation of conventional superhydrophobic materials in service conditions and can further reduce the risk of icing on the aircraft surface.
Global surveillance of antimicrobial resistance in food animals using priority drugs maps
Authors: Zhao Cheng , Wang Yu , Mulchandani Ranya , Van Boeckel Thomas P. 
Published: January 2024

AbstractAntimicrobial resistance (AMR) in food animals is a growing threat to animal health and potentially to human health. In resource-limited settings, allocating resources to address AMR can be guided with maps. Here, we mapped AMR prevalence in 7 antimicrobials in Escherichia coli and nontyphoidal Salmonella species across low- and middle-income countries (LIMCs), using 1088 point-prevalence surveys in combination with a geospatial model. Hotspots of AMR were predicted in China, India, Brazil, Chile, and part of central Asia and southeastern Africa. The highest resistance prevalence was for tetracycline (59% for E. coli and 54% for nontyphoidal Salmonella, average across LMICs) and lowest for cefotaxime (33% and 19%). We also identified the antimicrobial with the highest probability of resistance exceeding critical levels (50%) in the future (1.7–12.4 years) for each 10 × 10 km pixel on the map. In Africa and South America, 78% locations were associated with penicillins or tetracyclines crossing 50% resistance in the future. In contrast, in Asia, 77% locations were associated with penicillins or sulphonamides. Our maps highlight diverging geographic trends of AMR prevalence across antimicrobial classes, and can be used to target AMR surveillance in AMR hotspots for priority antimicrobial classes.
UBR5 promotes antiviral immunity by disengaging the transcriptional brake on RIG-I like receptors
Authors: Yang Duomeng , Geng Tingting , Harrison Andrew G. , Cahoon Jason G. , Xing Jian , Jiao Baihai , Wang Mark , Cheng Chao , Hill Robert E. , Wang Huadong , Vella Anthony T. , Cheng Gong , Wang Yanlin , Wang Penghua 
Published: January 2024

AbstractThe Retinoic acid-Inducible Gene I (RIG-I) like receptors (RLRs) are the major viral RNA sensors essential for the initiation of antiviral immune responses. RLRs are subjected to stringent transcriptional and posttranslational regulations, of which ubiquitination is one of the most important. However, the role of ubiquitination in RLR transcription is unknown. Here, we screen 375 definite ubiquitin ligase knockout cell lines and identify Ubiquitin Protein Ligase E3 Component N-Recognin 5 (UBR5) as a positive regulator of RLR transcription. UBR5 deficiency reduces antiviral immune responses to RNA viruses, while increases viral replication in primary cells and mice. Ubr5 knockout mice are more susceptible to lethal RNA virus infection than wild type littermates. Mechanistically, UBR5 mediates the Lysine 63-linked ubiquitination of Tripartite Motif Protein 28 (TRIM28), an epigenetic repressor of RLRs. This modification prevents intramolecular SUMOylation of TRIM28, thus disengages the TRIM28-imposed brake on RLR transcription. In sum, UBR5 enables rapid upregulation of RLR expression to boost antiviral immune responses by ubiquitinating and de-SUMOylating TRIM28.
D6PK plasma membrane polarity requires a repeated CXX(X)P motif and PDK1-dependent phosphorylation
Authors: Graf Alina , Bassukas Alkistis Eleftheria Lanassa , Xiao Yao , Barbosa Inês C. R. , Mergner Julia , Grill Peter , Michalke Bernhard , Kuster Bernhard , Schwechheimer Claus 
Published: January 2024

AbstractD6 PROTEIN KINASE (D6PK) is a polarly localized plasma-membrane-associated kinase from Arabidopsis thaliana that activates polarly distributed PIN-FORMED auxin transporters. D6PK moves rapidly to and from the plasma membrane, independent of its PIN-FORMED targets. The middle D6PK domain, an insertion between kinase subdomains VII and VIII, is required and sufficient for association and polarity of the D6PK plasma membrane. How D6PK polarity is established and maintained remains to be shown. Here we show that cysteines from repeated middle domain CXX(X)P motifs are S-acylated and required for D6PK membrane association. While D6PK S-acylation is not detectably regulated during intracellular transport, phosphorylation of adjacent serine residues, in part in dependence on the upstream 3-PHOSPHOINOSITIDE-DEPENDENT PROTEIN KINASE, promotes D6PK transport, controls D6PK residence time at the plasma membrane and prevents its lateral diffusion. We thus identify new mechanisms for the regulation of D6PK plasma membrane interaction and polarity.
A fluid biomarker reveals loss of TDP-43 splicing repression in presymptomatic ALS–FTD
Authors: Irwin Katherine E. , Jasin Pei , Braunstein Kerstin E. , Sinha Irika R. , Garret Mark A. , Bowden Kyra D. , Chang Koping , Troncoso Juan C. , Moghekar Abhay , Oh Esther S. , Raitcheva Denitza , Bartlett Dan , Miller Timothy , Berry James D. , Traynor Bryan J. , Ling Jonathan P. , Wong Philip C. 
Published: January 2024

AbstractAlthough loss of TAR DNA-binding protein 43 kDa (TDP-43) splicing repression is well documented in postmortem tissues of amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD), whether this abnormality occurs during early-stage disease remains unresolved. Cryptic exon inclusion reflects loss of function of TDP-43, and thus detection of proteins containing cryptic exon-encoded neoepitopes in cerebrospinal fluid (CSF) or blood could reveal the earliest stages of TDP-43 dysregulation in patients. Here we use a newly characterized monoclonal antibody specific to a TDP-43-dependent cryptic epitope (encoded by the cryptic exon found in HDGFL2) to show that loss of TDP-43 splicing repression occurs in ALS–FTD, including in presymptomatic C9orf72 mutation carriers. Cryptic hepatoma-derived growth factor-like protein 2 (HDGFL2) accumulates in CSF at significantly higher levels in familial ALS–FTD and sporadic ALS compared with controls and is elevated earlier than neurofilament light and phosphorylated neurofilament heavy chain protein levels in familial disease. Cryptic HDGFL2 can also be detected in blood of individuals with ALS–FTD, including in presymptomatic C9orf72 mutation carriers, and accumulates at levels highly correlated with those in CSF. Our findings indicate that loss of TDP-43 cryptic splicing repression occurs early in disease progression, even presymptomatically, and that detection of the HDGFL2 cryptic neoepitope serves as a potential diagnostic biomarker for ALS, which should facilitate patient recruitment and measurement of target engagement in clinical trials.
A multidisciplinary approach to tackling invasive species: barcoding, morphology, and metataxonomy of the leafhopper Arboridia adanae
Authors: Piccinno Riccardo , Tatti Alessia , Avosani Sabina , Galla Giulio , Lazazzara Valentina , Pedrazzoli Federico , Zadra Nicola , Rodeghiero Mirco , Seljak Gabrijel , Özgen İnanç , Hauffe Heidi C. , Verrastro Vincenzo , Stacconi Marco Valerio Rossi , Mazzoni Valerio , Rota-Stabelli Omar 
Published: January 2024

AbstractThe leafhopper genus Arboridia includes several species that feed on Vitis vinifera and cause leaf chlorosis. We report the first alien Arboridia infestation in Italy in 2021 in an Apulian vineyard. To confirm the taxonomic status of the species responsible for crop damage, and reconstruct its demographic history, we barcoded individuals from Apulia together with Arboridia spp. from Crete (Greece), A. adanae from Central Turkey and other specimens of the presumed sister species, A. dalmatina from Dalmatia (Croatia). Molecular phylogenies and barcoding gap analysis identified clades not associated with sampling locations. This result is incongruent with classical specimen assignment and is further supported by morphological analyses, which did not reveal significant differences among the populations. Therefore, we propose A. dalmatina as a junior synonym of A. adanae, which would become the only grapevine-related Arboridia species in the eastern Mediterranean. To further characterise A. adanae evolution, we performed a molecular clock analysis that suggested a radiation during the Pleistocene glaciations. Finally, to assess whether the Apulian individuals carried microorganisms of agricultural relevance, we sequenced their bacterial microbiota using 16S rRNA amplicon sequencing identifying three phytopathogens not generally associated with Arboridia activities as well as Wolbachia in one Apulian haplogroup. We discuss the agricultural implications of this infestation.