bluuebunny/crossref_metadata_2025_split huggingface dataset:
Mechanism of DNA origami folding elucidated by mesoscopic simulations
Authors: DeLuca Marcello , Duke Daniel , Ye Tao , Poirier Michael , Ke Yonggang , Castro Carlos , Arya Gaurav 
Published: April 2024

AbstractMany experimental and computational efforts have sought to understand DNA origami folding, but the time and length scales of this process pose significant challenges. Here, we present a mesoscopic model that uses a switchable force field to capture the behavior of single- and double-stranded DNA motifs and transitions between them, allowing us to simulate the folding of DNA origami up to several kilobases in size. Brownian dynamics simulations of small structures reveal a hierarchical folding process involving zipping into a partially folded precursor followed by crystallization into the final structure. We elucidate the effects of various design choices on folding order and kinetics. Larger structures are found to exhibit heterogeneous staple incorporation kinetics and frequent trapping in metastable states, as opposed to more accessible structures which exhibit first-order kinetics and virtually defect-free folding. This model opens an avenue to better understand and design DNA nanostructures for improved yield and folding performance.
Wide field-of-hearing metalens for aberration-free sound capture
Authors: Lee Dongwoo , Oh Beomseok , Park Jeonghoon , Moon Seong-Won , Shin Kilsoo , Kim Sea-Moon , Rho Junsuk 
Published: April 2024

AbstractMetalenses are instruments that manipulate waves and have exhibited remarkable capabilities to date. However, an important hurdle arises due to the severe hampering of the angular response originating from coma and field curvature aberrations, which result in a loss of focusing ability. Herein, we provide a blueprint by introducing the notion of a wide field-of-hearing (FOH) metalens, designed particularly for capturing and focusing sound with decreased aberrations. Employing an aberration-free planar-thin metalens that leverages perfect acoustic symmetry conversion, we experimentally realize a robust wide FOH capability of approximately 140∘in angular range. Moreover, our metalens features a relatively short focal length, enabling compact implementation by reducing the aperture-to-hearing plane distance. This is beneficial for space-efficient source-tracking sound sensing. Our strategy can be used across various platforms, potentially including energy harvesting, monitoring, imaging, and communication in auditory, ultrasonic, and submerged environments.
Dermal injury drives a skin to gut axis that disrupts the intestinal microbiome and intestinal immune homeostasis in mice
Authors: Dokoshi Tatsuya , Chen Yang , Cavagnero Kellen J. , Rahman Gibraan , Hakim Daniel , Brinton Samantha , Schwarz Hana , Brown Elizabeth A. , O’Neill Alan , Nakamura Yoshiyuki , Li Fengwu , Salzman Nita H. , Knight Rob , Gallo Richard L. 
Published: April 2024

AbstractThe composition of the microbial community in the intestine may influence the functions of distant organs such as the brain, lung, and skin. These microbes can promote disease or have beneficial functions, leading to the hypothesis that microbes in the gut explain the co-occurrence of intestinal and skin diseases. Here, we show that the reverse can occur, and that skin directly alters the gut microbiome. Disruption of the dermis by skin wounding or the digestion of dermal hyaluronan results in increased expression in the colon of the host defense genes Reg3 and Muc2, and skin wounding changes the composition and behavior of intestinal bacteria. Enhanced expression Reg3 and Muc2 is induced in vitro by exposure to hyaluronan released by these skin interventions. The change in the colon microbiome after skin wounding is functionally important as these bacteria penetrate the intestinal epithelium and enhance colitis from dextran sodium sulfate (DSS) as seen by the ability to rescue skin associated DSS colitis with oral antibiotics, in germ-free mice, and fecal microbiome transplantation to unwounded mice from mice with skin wounds. These observations provide direct evidence of a skin-gut axis by demonstrating that damage to the skin disrupts homeostasis in intestinal host defense and alters the gut microbiome.
Essential role of lattice oxygen in hydrogen sensing reaction
Authors: Li Jiayu , Si Wenzhe , Shi Lei , Gao Ruiqin , Li Qiuju , An Wei , Zhao Zicheng , Zhang Lu , Bai Ni , Zou Xiaoxin , Li Guo-Dong 
Published: April 2024

AbstractUnderstanding the sensing mechanism of metal oxide semiconductors is imperative to the development of high-performance sensors. The traditional sensing mechanism only recognizes the effect of surface chemisorbed oxygen from the air but ignores surface lattice oxygen. Herein, using in-situ characterizations, we provide direct experimental evidence that the surface chemisorbed oxygen participated in the sensing process can come from lattice oxygen of the oxides. Further density functional theory (DFT) calculations prove that the p-band center of O serves as a state of art for regulating the participation of lattice oxygen in gas-sensing reactions. Based on our experimental data and theoretical calculations, we discuss mechanisms that are fundamentally different from the conventional mechanism and show that the easily participation of lattice oxygen is helpful for the high response value of the materials.
p53 promotes revival stem cells in the regenerating intestine after severe radiation injury
Authors: Morral Clara , Ayyaz Arshad , Kuo Hsuan-Cheng , Fink Mardi , Verginadis Ioannis I. , Daniel Andrea R. , Burner Danielle N. , Driver Lucy M. , Satow Sloane , Hasapis Stephanie , Ghinnagow Reem , Luo Lixia , Ma Yan , Attardi Laura D. , Koumenis Constantinos , Minn Andy J. , Wrana Jeffrey L. , Lee Chang-Lung , Kirsch David G. 
Published: April 2024

AbstractIonizing radiation induces cell death in the gastrointestinal (GI) epithelium by activating p53. However, p53 also prevents animal lethality caused by radiation-induced acute GI syndrome. Through single-cell RNA-sequencing of the irradiated mouse small intestine, we find that p53 target genes are specifically enriched in regenerating epithelial cells that undergo fetal-like reversion, including revival stem cells (revSCs) that promote animal survival after severe damage of the GI tract. Accordingly, in mice with p53 deleted specifically in the GI epithelium, ionizing radiation fails to induce fetal-like revSCs. Using intestinal organoids, we show that transient p53 expression is required for the induction of revival stem cells and is controlled by an Mdm2-mediated negative feedback loop. Together, our findings reveal that p53 suppresses severe radiation-induced GI injury by promoting fetal-like reprogramming of irradiated intestinal epithelial cells.
Landslide hazard cascades can trigger earthquakes
Authors: Zhang Zhen , Liu Min , Tan Yen Joe , Walter Fabian , He Siming , Chmiel Małgorzata , Su Jinrong 
Published: April 2024

AbstractWhile earthquakes are well-known to trigger surface hazards and initiate hazard cascades, whether surface hazards can instead trigger earthquakes remains underexplored. In 2018, two landslides on the Tibetan plateau created landslide-dammed lakes which subsequently breached and caused catastrophic outburst floods. Here we build an earthquake catalog using machine-learning and cross-correlation-based methods which shows there was a statistically significant increase in earthquake activity (local magnitude ≤ 2.6) as the landslide-dammed lake approached peak water level which returned to the background level after dam breach. We further find that ~90% of the seismicity occurred where Coulomb stress increased due to the combined effect of direct loading and pore pressure diffusion. The close spatial and temporal correlation between the calculated Coulomb stress increase and earthquake activity suggests that the earthquakes were triggered by these landslide hazard cascades. Finally, our Coulomb stress modeling considering the properties of landslide-dammed lakes and reservoir-induced earthquakes globally suggests that earthquake triggering by landslide-dammed lakes and similar structures may be a ubiquitous phenomenon. Therefore, we propose that earthquake-surface hazard interaction can include bidirectional triggering which should be properly accounted for during geological hazard assessment and management in mountainous regions.
Integration of pathologic characteristics, genetic risk and lifestyle exposure for colorectal cancer survival assessment
Authors: Xin Junyi , Gu Dongying , Li Shuwei , Qian Sangni , Cheng Yifei , Shao Wei , Ben Shuai , Chen Silu , Zhu Linjun , Jin Mingjuan , Chen Kun , Hu Zhibin , Zhang Zhengdong , Du Mulong , Shen Hongbing , Wang Meilin 
Published: April 2024

AbstractThe development of an effective survival prediction tool is key for reducing colorectal cancer mortality. Here, we apply a three-stage study to devise a polygenic prognostic score (PPS) for stratifying colorectal cancer overall survival. Leveraging two cohorts of 3703 patients, we first perform a genome-wide survival association analysis to develop eight candidate PPSs. Further using an independent cohort with 470 patients, we identify the 287 variants-derived PPS (i.e., PPS287) achieving an optimal prediction performance [hazard ratio (HR) per SD = 1.99, P = 1.76 × 10−8], accompanied by additional tests in two external cohorts, with HRs per SD of 1.90 (P = 3.21 × 10−14; 543 patients) and 1.80 (P = 1.11 × 10−9; 713 patients). Notably, the detrimental impact of pathologic characteristics and genetic risk could be attenuated by a healthy lifestyle, yielding a 7.62% improvement in the 5-year overall survival rate. Therefore, our findings demonstrate the integrated contribution of pathologic characteristics, germline variants, and lifestyle exposure to the prognosis of colorectal cancer patients.
The assembly platform FimD is required to obtain the most stable quaternary structure of type 1 pili
Authors: Zyla Dawid S. , Wiegand Thomas , Bachmann Paul , Zdanowicz Rafal , Giese Christoph , Meier Beat H. , Waksman Gabriel , Hospenthal Manuela K. , Glockshuber Rudi 
Published: April 2024

AbstractType 1 pili are important virulence factors of uropathogenic Escherichia coli that mediate bacterial attachment to epithelial cells in the urinary tract. The pilus rod is comprised of thousands of copies of the main structural subunit FimA and is assembled in vivo by the assembly platform FimD. Although type 1 pilus rods can self-assemble from FimA in vitro, this reaction is slower and produces structures with lower kinetic stability against denaturants compared to in vivo-assembled rods. Our study reveals that FimD-catalysed in vitro-assembled type 1 pilus rods attain a similar stability as pilus rods assembled in vivo. Employing structural, biophysical and biochemical analyses, we show that in vitro assembly reactions lacking FimD produce pilus rods with structural defects, reducing their stability against dissociation. Overall, our results indicate that FimD is not only required for the catalysis of pilus assembly, but also to control the assembly of the most stable quaternary structure.
Exciton engineering of 2D Ruddlesden–Popper perovskites by synergistically tuning the intra and interlayer structures
Authors: Guo Songhao , Mihalyi-Koch Willa , Mao Yuhong , Li Xinyu , Bu Kejun , Hong Huilong , Hautzinger Matthew P. , Luo Hui , Wang Dong , Gu Jiazhen , Zhang Yifan , Zhang Dongzhou , Hu Qingyang , Ding Yang , Yang Wenge , Fu Yongping , Jin Song , Lü Xujie 
Published: April 2024

AbstractDesigning two-dimensional halide perovskites for high-performance optoelectronic applications requires deep understanding of the structure-property relationship that governs their excitonic behaviors. However, a design framework that considers both intra and interlayer structures modified by the A-site and spacer cations, respectively, has not been developed. Here, we use pressure to synergistically tune the intra and interlayer structures and uncover the structural modulations that result in improved optoelectronic performance. Under applied pressure, (BA)2(GA)Pb2I7 exhibits a 72-fold boost of photoluminescence and 10-fold increase of photoconductivity. Based on the observed structural change, we introduce a structural descriptor χ that describes both the intra and interlayer characteristics and establish a general quantitative relationship between χ and photoluminescence quantum yield: smaller χ correlates with minimized trapped excitons and more efficient emission from free excitons. Building on this principle, we design a perovskite (CMA)2(FA)Pb2I7 that exhibits a small χ and an impressive photoluminescence quantum yield of 59.3%.
Basal actomyosin pulses expand epithelium coordinating cell flattening and tissue elongation
Authors: Li Shun , Liu Zong-Yuan , Li Hao , Zhou Sijia , Liu Jiaying , Sun Ningwei , Yang Kai-Fu , Dougados Vanessa , Mangeat Thomas , Belguise Karine , Feng Xi-Qiao , Liu Yiyao , Wang Xiaobo 
Published: April 2024

AbstractActomyosin networks constrict cell area and junctions to alter cell and tissue shape. However, during cell expansion under mechanical stress, actomyosin networks are strengthened and polarized to relax stress. Thus, cells face a conflicting situation between the enhanced actomyosin contractile properties and the expansion behaviour of the cell or tissue. To address this paradoxical situation, we study late Drosophila oogenesis and reveal an unusual epithelial expansion wave behaviour. Mechanistically, Rac1 and Rho1 integrate basal pulsatile actomyosin networks with ruffles and focal adhesions to increase and then stabilize basal area of epithelial cells allowing their flattening and elongation. This epithelial expansion behaviour bridges cell changes to oocyte growth and extension, while oocyte growth in turn deforms the epithelium to drive cell spreading. Basal pulsatile actomyosin networks exhibit non-contractile mechanics, non-linear structures and F-actin/Myosin-II spatiotemporal signal separation, implicating unreported expanding properties. Biophysical modelling incorporating these expanding properties well simulates epithelial cell expansion waves. Our work thus highlights actomyosin expanding properties as a key mechanism driving tissue morphogenesis.
Universal inter-molecular radical transfer reactions on metal surfaces
Authors: Wang Junbo , Niu Kaifeng , Zhu Huaming , Xu Chaojie , Deng Chuan , Zhao Wenchao , Huang Peipei , Lin Haiping , Li Dengyuan , Rosen Johanna , Liu Peinian , Allegretti Francesco , Barth Johannes V. , Yang Biao , Björk Jonas , Li Qing , Chi Lifeng 
Published: April 2024

AbstractOn-surface synthesis provides tools to prepare low-dimensional supramolecular structures. Traditionally, reactive radicals are a class of single-electron species, serving as exceptional electron-withdrawing groups. On metal surfaces, however, such species are affected by conduction band screening effects that may even quench their unpaired electron characteristics. As a result, radicals are expected to be less active, and reactions catalyzed by surface-stabilized radicals are rarely reported. Herein, we describe a class of inter-molecular radical transfer reactions on metal surfaces. With the assistance of aryl halide precursors, the coupling of terminal alkynes is steered from non-dehydrogenated to dehydrogenated products, resulting in alkynyl-Ag-alkynyl bonds. Dehalogenated molecules are fully passivated by detached hydrogen atoms. The reaction mechanism is unraveled by various surface-sensitive technologies and density functional theory calculations. Moreover, we reveal the universality of this mechanism on metal surfaces. Our studies enrich the on-surface synthesis toolbox and develop a pathway for producing low-dimensional organic materials.
Stress increases hepatic release of lipocalin 2 which contributes to anxiety-like behavior in mice
Authors: Yan Lan , Yang Fengzhen , Wang Yajie , Shi Lingling , Wang Mei , Yang Diran , Wang Wenjing , Jia Yanbin , So Kwok-Fai , Zhang Li 
Published: April 2024

AbstractChronic stress induces anxiety disorders via both neural pathways and circulating factors. Although many studies have elucidated the neural circuits involved in stress-coping behaviors, the origin and regulatory mechanism of peripheral cytokines in behavioural regulation under stress conditions are not fully understood. Here, we identified a serum cytokine, lipocalin 2 (LCN2), that was upregulated in participants with anxiety disorders. Using a mouse model of chronic restraint stress (CRS), circulating LCN2 was found to be related to stress-induced anxiety-like behaviour via modulation of neural activity in the medial prefrontal cortex (mPFC). These results suggest that stress increases hepatic LCN2 via a neural pathway, leading to disrupted cortical functions and behaviour.
Immunoregulatory role of the gut microbiota in inflammatory depression
Authors: Liu Penghong , Liu Zhifen , Wang Jizhi , Wang Junyan , Gao Mingxue , Zhang Yanyan , Yang Chunxia , Zhang Aixia , Li Gaizhi , Li Xinrong , Liu Sha , Liu Lixin , Sun Ning , Zhang Kerang 
Published: April 2024

AbstractInflammatory depression is a treatment-resistant subtype of depression. A causal role of the gut microbiota as a source of low-grade inflammation remains unclear. Here, as part of an observational trial, we first analyze the gut microbiota composition in the stool, inflammatory factors and short-chain fatty acids (SCFAs) in plasma, and inflammatory and permeability markers in the intestinal mucosa of patients with inflammatory depression (ChiCTR1900025175). Gut microbiota of patients with inflammatory depression exhibits higherBacteroidesand lowerClostridium, with an increase in SCFA-producing species with abnormal butanoate metabolism. We then perform fecal microbiota transplantation (FMT) and probiotic supplementation in animal experiments to determine the causal role of the gut microbiota in inflammatory depression. After FMT, the gut microbiota of the inflammatory depression group shows increased peripheral and central inflammatory factors and intestinal mucosal permeability in recipient mice with depressive and anxiety-like behaviors.Clostridium butyricumadministration normalizes the gut microbiota, decreases inflammatory factors, and displays antidepressant-like effects in a mouse model of inflammatory depression. These findings suggest that inflammatory processes derived from the gut microbiota can be involved in neuroinflammation of inflammatory depression.
Stroma-infiltrating T cell spatiotypes define immunotherapy outcomes in adolescent and young adult patients with melanoma
Authors: Bai Xinyu , Attrill Grace H. , Gide Tuba N. , Ferguson Peter M. , Nahar Kazi J. , Shang Ping , Vergara Ismael A. , Palendira Umaimainthan , da Silva Ines Pires , Carlino Matteo S. , Menzies Alexander M. , Long Georgina V. , Scolyer Richard A. , Wilmott James S. , Quek Camelia 
Published: April 2024

AbstractThe biological underpinnings of therapeutic resistance to immune checkpoint inhibitors (ICI) in adolescent and young adult (AYA) melanoma patients are incompletely understood. Here, we characterize the immunogenomic profile and spatial architecture of the tumor microenvironment (TME) in AYA (aged ≤ 30 years) and older adult (aged 31–84 years) patients with melanoma, to determine the AYA-specific features associated with ICI treatment outcomes. We identify two ICI-resistant spatiotypes in AYA patients with melanoma showing stroma-infiltrating lymphocytes (SILs) that are distinct from the adult TME. The SILhigh subtype was enriched in regulatory T cells in the peritumoral space and showed upregulated expression of immune checkpoint molecules, while the SILlow subtype showed a lack of immune activation. We establish a young immunosuppressive melanoma score that can predict ICI responsiveness in AYA patients and propose personalized therapeutic strategies for the ICI-resistant subgroups. These findings highlight the distinct immunogenomic profile of AYA patients, and individualized TME features in ICI-resistant AYA melanoma that require patient-specific treatment strategies.
Concerted transformation of a hyper-paused transcription complex and its reinforcing protein
Authors: Zuber Philipp K. , Said Nelly , Hilal Tarek , Wang Bing , Loll Bernhard , González-Higueras Jorge , Ramírez-Sarmiento César A. , Belogurov Georgiy A. , Artsimovitch Irina , Wahl Markus C. , Knauer Stefan H. 
Published: April 2024

AbstractRfaH, a paralog of the universally conserved NusG, binds to RNA polymerases (RNAP) and ribosomes to activate expression of virulence genes. In free, autoinhibited RfaH, an α-helical KOW domain sequesters the RNAP-binding site. Upon recruitment to RNAP paused at an ops site, KOW is released and refolds into a β-barrel, which binds the ribosome. Here, we report structures of ops-paused transcription elongation complexes alone and bound to the autoinhibited and activated RfaH, which reveal swiveled, pre-translocated pause states stabilized by an ops hairpin in the non-template DNA. Autoinhibited RfaH binds and twists the ops hairpin, expanding the RNA:DNA hybrid to 11 base pairs and triggering the KOW release. Once activated, RfaH hyper-stabilizes the pause, which thus requires anti-backtracking factors for escape. Our results suggest that the entire RfaH cycle is solely determined by the ops and RfaH sequences and provide insights into mechanisms of recruitment and metamorphosis of NusG homologs across all life.
Accurately clustering biological sequences in linear time by relatedness sorting
Authors: Wright Erik 
Published: April 2024

AbstractClustering biological sequences into similar groups is an increasingly important task as the number of available sequences continues to grow exponentially. Search-based approaches to clustering scale super-linearly with the number of input sequences, making it impractical to cluster very large sets of sequences. Approaches to clustering sequences in linear time currently lack the accuracy of super-linear approaches. Here, I set out to develop and characterize a strategy for clustering with linear time complexity that retains the accuracy of less scalable approaches. The resulting algorithm, named Clusterize, sorts sequences by relatedness to linearize the clustering problem. Clusterize produces clusters with accuracy rivaling popular programs (CD-HIT, MMseqs2, and UCLUST) but exhibits linear asymptotic scalability. Clusterize generates higher accuracy and oftentimes much larger clusters than Linclust, a fast linear time clustering algorithm. I demonstrate the utility of Clusterize by accurately solving different clustering problems involving millions of nucleotide or protein sequences.