bluuebunny/crossref_metadata_2025_split huggingface dataset:
The role of memory-dependent friction and solvent viscosity in isomerization kinetics in viscogenic media
Authors: Dalton Benjamin A. , Kiefer Henrik , Netz Roland R. 
Published: May 2024

AbstractMolecular isomerization kinetics in liquid solvent depends on a complex interplay between the solvent friction acting on the molecule, internal dissipation effects (also known as internal friction), the viscosity of the solvent, and the dihedral free energy profile. Due to the absence of accurate techniques to directly evaluate isomerization friction, it has not been possible to explore these relationships in full. By combining extensive molecular dynamics simulations with friction memory-kernel extraction techniques we consider a variety of small, isomerising molecules under a range of different viscogenic conditions and directly evaluate the viscosity dependence of the friction acting on a rotating dihedral. We reveal that the influence of different viscogenic media on isomerization kinetics can be dramatically different, even when measured at the same viscosity. This is due to the dynamic solute-solvent coupling, mediated by time-dependent friction memory kernels. We also show that deviations from the linear dependence of isomerization rates on solvent viscosity, which are often simply attributed to internal friction effects, are due to the simultaneous violation of two fundamental relationships: the Stokes-Einstein relation and the overdamped Kramers prediction for the barrier-crossing rate, both of which require explicit knowledge of friction.
Symmetry breaking in optimal transport networks
Authors: Patwardhan Siddharth , Barthelemy Marc , Erkol Şirag , Fortunato Santo , Radicchi Filippo 
Published: May 2024

AbstractEngineering multilayer networks that efficiently connect sets of points in space is a crucial task in all practical applications that concern the transport of people or the delivery of goods. Unfortunately, our current theoretical understanding of the shape of such optimal transport networks is quite limited. Not much is known about how the topology of the optimal network changes as a function of its size, the relative efficiency of its layers, and the cost of switching between layers. Here, we show that optimal networks undergo sharp transitions from symmetric to asymmetric shapes, indicating that it is sometimes better to avoid serving a whole area to save on switching costs. Also, we analyze the real transportation networks of the cities of Atlanta, Boston, and Toronto using our theoretical framework and find that they are farther away from their optimal shapes as traffic congestion increases.
Arabidopsis SBT5.2 and SBT1.7 subtilases mediate C-terminal cleavage of flg22 epitope from bacterial flagellin
Authors: Matsui Sayaka , Noda Saki , Kuwata Keiko , Nomoto Mika , Tada Yasuomi , Shinohara Hidefumi , Matsubayashi Yoshikatsu 
Published: May 2024

AbstractPlants initiate specific defense responses by recognizing conserved epitope peptides within the flagellin proteins derived from bacteria. Proteolytic cleavage of epitope peptides from flagellin by plant apoplastic proteases is thought to be crucial for the perception of the epitope by the plant receptor. However, the identity of the plant proteases involved in this process remains unknown. Here, we establish an efficient identification system for the target proteases in Arabidopsis apoplastic fluid; the method employs native two-dimensional electrophoresis followed by an in-gel proteolytic assay using a fluorescence-quenching peptide substrate. We designed a substrate to specifically detect proteolytic activity at the C-terminus of the flg22 epitope in flagellin and identified two plant subtilases, SBT5.2 and SBT1.7, as specific proteases responsible for the C-terminal cleavage of flg22. In the apoplastic fluid of Arabidopsis mutant plants deficient in these two proteases, we observe a decrease in the C-terminal cleavage of the flg22 domain from flagellin, leading to a decrease in the efficiency of flg22 epitope liberation. Consequently, defensive reactive oxygen species (ROS) production is delayed in sbt5.2 sbt1.7 double-mutant leaf disks compared to wild type following flagellin exposure.
Facilitating the dry reforming of methane with interfacial synergistic catalysis in an Ir@CeO2−x catalyst
Authors: Wang Hui , Cui Guoqing , Lu Hao , Li Zeyang , Wang Lei , Meng Hao , Li Jiong , Yan Hong , Yang Yusen , Wei Min 
Published: May 2024

AbstractThe dry reforming of methane provides an attractive route to convert greenhouse gases (CH4 and CO2) into valuable syngas, so as to resolve the carbon cycle and environmental issues. However, the development of high-performance catalysts remains a huge challenge. Herein, we report a 0.6% Ir/CeO2−x catalyst with a metal-support interface structure which exhibits high CH4 (~72%) and CO2 (~82%) conversion and a CH4 reaction rate of ~973 μmolCH4 gcat−1 s−1 which is stable over 100 h at 700 °C. The performance of the catalyst is close to the state-of-the-art in this area of research. A combination of in situ spectroscopic characterization and theoretical calculations highlight the importance of the interfacial structure as an intrinsic active center to facilitate the CH4 dissociation (the rate-determining step) and the CH2* oxidation to CH2O* without coke formation, which accounts for the long-term stability. The catalyst in this work has a potential application prospect in the field of high-value utilization of carbon resources.
IL-17C is a driver of damaging inflammation during Neisseria gonorrhoeae infection of human Fallopian tube
Authors: Garcia Erin M. , Lenz Jonathan D. , Schaub Ryan E. , Hackett Kathleen T. , Salgado-Pabón Wilmara , Dillard Joseph P. 
Published: May 2024

AbstractThe human pathogen Neisseria gonorrhoeae ascends into the upper female reproductive tract to cause damaging inflammation within the Fallopian tubes and pelvic inflammatory disease (PID), increasing the risk of infertility and ectopic pregnancy. The loss of ciliated cells from the epithelium is thought to be both a consequence of inflammation and a cause of adverse sequelae. However, the links between infection, inflammation, and ciliated cell extrusion remain unresolved. With the use of ex vivo cultures of human Fallopian tube paired with RNA sequencing we defined the tissue response to gonococcal challenge, identifying cytokine, chemokine, cell adhesion, and apoptosis related transcripts not previously recognized as potentiators of gonococcal PID. Unexpectedly, IL-17C was one of the most highly induced genes. Yet, this cytokine has no previous association with gonococcal infection nor pelvic inflammatory disease and thus it was selected for further characterization. We show that human Fallopian tubes express the IL-17C receptor on the epithelial surface and that treatment with purified IL-17C induces pro-inflammatory cytokine secretion in addition to sloughing of the epithelium and generalized tissue damage. These results demonstrate a previously unrecognized but critical role of IL-17C in the damaging inflammation induced by gonococci in a human explant model of PID.
A multicenter proof-of-concept study on deep learning-based intraoperative discrimination of primary central nervous system lymphoma
Authors: Zhang Xinke , Zhao Zihan , Wang Ruixuan , Chen Haohua , Zheng Xueyi , Liu Lili , Lan Lilong , Li Peng , Wu Shuyang , Cao Qinghua , Luo Rongzhen , Hu Wanming , lyu Shanshan , Zhang Zhengyu , Xie Dan , Ye Yaping , Wang Yu , Cai Muyan 
Published: May 2024

AbstractAccurate intraoperative differentiation of primary central nervous system lymphoma (PCNSL) remains pivotal in guiding neurosurgical decisions. However, distinguishing PCNSL from other lesions, notably glioma, through frozen sections challenges pathologists. Here we sought to develop and validate a deep learning model capable of precisely distinguishing PCNSL from non-PCNSL lesions, especially glioma, using hematoxylin and eosin (H&E)-stained frozen whole-slide images. Also, we compared its performance against pathologists of varying expertise. Additionally, a human-machine fusion approach integrated both model and pathologic diagnostics. In external cohorts, LGNet achieved AUROCs of 0.965 and 0.972 in distinguishing PCNSL from glioma and AUROCs of 0.981 and 0.993 in differentiating PCNSL from non-PCNSL lesions. Outperforming several pathologists, LGNet significantly improved diagnostic performance, further augmented to some extent by fusion approach. LGNet’s proficiency in frozen section analysis and its synergy with pathologists indicate its valuable role in intraoperative diagnosis, particularly in discriminating PCNSL from glioma, alongside other lesions.
Hot Cordilleran hinterland promoted lower crust mobility and decoupling of Laramide deformation
Authors: Vlaha Dominik R. , Zuza Andrew V. , Chen Lin , Harlaux Matthieu 
Published: May 2024

AbstractThe Late Cretaceous to Paleogene Laramide orogen in the North American Cordillera involved deformation >1,000 km from the plate margin that has been attributed to either plate-boundary end loading or basal traction exerted on the upper plate from the subducted Farallon flat slab. Prevailing tectonic models fail to explain the relative absence of Laramide-aged (ca. 90–60 Ma) contractional deformation within the Cordillera hinterland. Based on Raman spectroscopy of carbonaceous material thermometry and literature data from the restored upper 15–20 km of the Cordilleran crust we reconstruct the Late Cretaceous thermal architecture of the hinterland. Interpolation of compiled temperature data (n = 200) through a vertical crustal column reveals that the hinterland experienced a continuous but regionally elevated, upper-crustal geothermal gradient of >40 °C/km during Laramide orogenesis, consistent with peak metamorphic conditions and synchronous peraluminous granitic plutonism. The hot and partially melted hinterland promoted lower crust mobility and crust-mantle decoupling during flat-slab traction.
Ozone as an environmental driver of influenza
Authors: Guo Fang , Zhang Pei , Do Vivian , Runge Jakob , Zhang Kun , Han Zheshen , Deng Shenxi , Lin Hongli , Ali Sheikh Taslim , Chen Ruchong , Guo Yuming , Tian Linwei 
Published: May 2024

AbstractUnder long-standing threat of seasonal influenza outbreaks, it remains imperative to understand the drivers of influenza dynamics which can guide mitigation measures. While the role of absolute humidity and temperature is extensively studied, the possibility of ambient ozone (O3) as an environmental driver of influenza has received scant attention. Here, using state-level data in the USA during 2010–2015, we examined such research hypothesis. For rigorous causal inference by evidence triangulation, we applied 3 distinct methods for data analysis: Convergent Cross Mapping from state-space reconstruction theory, Peter-Clark-momentary-conditional-independence plus as graphical modeling algorithms, and regression-based Generalised Linear Model. The negative impact of ambient O3 on influenza activity at 1-week lag is consistently demonstrated by those 3 methods. With O3 commonly known as air pollutant, the novel findings here on the inhibition effect of O3 on influenza activity warrant further investigations to inform environmental management and public health protection.
Targeting adipocyte ESRRA promotes osteogenesis and vascular formation in adipocyte-rich bone marrow
Authors: Huang Tongling , Lu Zhaocheng , Wang Zihui , Cheng Lixin , Gao Lu , Gao Jun , Zhang Ning , Geng Chang-An , Zhao Xiaoli , Wang Huaiyu , Wong Chi-Wai , Yeung Kelvin W. K. , Pan Haobo , Lu William Weijia , Guan Min 
Published: May 2024

Abstract
Excessive bone marrow adipocytes (BMAds) accumulation often occurs under diverse pathophysiological conditions associated with bone deterioration. Estrogen-related receptor α (ESRRA) is a key regulator responding to metabolic stress. Here, we show that adipocyte-specific ESRRA deficiency preserves osteogenesis and vascular formation in adipocyte-rich bone marrow upon estrogen deficiency or obesity. Mechanistically, adipocyte ESRRA interferes with E2/ESR1 signaling resulting in transcriptional repression of secreted phosphoprotein 1 (Spp1); yet positively modulates leptin expression by binding to its promoter. ESRRA abrogation results in enhanced SPP1 and decreased leptin secretion from both visceral adipocytes and BMAds, concertedly dictating bone marrow stromal stem cell fate commitment and restoring type H vessel formation, constituting a feed-forward loop for bone formation. Pharmacological inhibition of ESRRA protects obese mice against bone loss and high marrow adiposity. Thus, our findings highlight a therapeutic approach via targeting adipocyte ESRRA to preserve bone formation especially in detrimental adipocyte-rich bone milieu.
Giant dielectric tunability in ferroelectric ceramics with ultralow loss by ion substitution design
Authors: Li Ruitao , Xu Diming , Du Chao , Ma Qianqian , Zhang Feng , Liang Xu , Wang Dawei , Shi Zhongqi , Liu Wenfeng , Zhou Di 
Published: May 2024

AbstractDue to their responsiveness to modulation by external direct current fields, dielectric tunable materials are extensively utilized in integrated components, such as ferroelectric phase shifters. Barium strontium titanate ceramics have been considered the most potential tunable materials for a long time. However, the significant dielectric loss and high voltage drive have limited their further applications. Recently, Bi6Ti5WO22 ceramic has regained attention for its high dielectric tunability with low loss. In this study, we judiciously introduce Nb5+ with a larger ionic radius, replacing Ti4+ and W6+. This successful substitution enables the modulation of the phase transition temperature of Bi6Ti5WO22 ceramics to room temperature, resulting in superior tunable properties. Specifically, the 0.7Bi6Ti5WO22−0.3Bi6Ti4Nb2O22 ceramics exhibit giant tunability (~75.6%) with ultralow loss (<0.002) under a low electric field (1.5 kV/mm). This tunability is twice that of barium strontium titanate ceramics with a similar dielectric constant and only one-tenth of the loss. Neutron powder diffraction and transmission-electron-microscopy illustrate the nanodomains and micro-strains influenced by ion substitution. Density functional theory simulation calculations reveal the contribution of ion substitution to polarization. The research provides an ideal substitute for tunable material and a general strategy for adjusting phase transition temperature to improve dielectric properties.
Effect of hydrogen embrittlement on mechanical characteristics of DLC-coating for hydrogen valves of FCEVs
Authors: Shin Dong-Ho , Kim Seong-Jong 
Published: May 2024

AbstractDiamond-like carbon (DLC) coating is a surface coating technology with excellent hydrogen permeation resistance and wear resistance. However, it is difficult to completely prevent hydrogen permeation, and when hydrogen penetrates into the coating layer, the DLC coating is adversely affected. Therefore, we investigated the effect of hydrogen embrittlement on the adhesion strength and wear resistance of the DLC coating layer. As the results of the research, the surface roughness of the DLC coating was increased by a maximum of 3.8 times with hydrogen charging, and the delamination ratio of the DLC coating reached about 58%. In addition, the Lc3, which refers to the adhesion strength corresponding to the complete delamination of the DLC coating, was decreased by a maximum of 2.0 N due to hydrogen permeation. In addition, the wear resistance decreased due to hydrogen permeation, and the exposed width of the substrate due to wear increased by more than 4 times. It was also determined that hydrogen blistering or hydrogen-induced cracking occurred at the interface between the DLC coating and the chromium buffer layer due to hydrogen permeation, which decreased the durability of the DLC coating.
Dense Al2O3 sealing inhibited high hydrostatic pressure corrosion of Cr/GLC coating
Authors: Li Shuyu , Li Hao , Zhang Yan , Yang Wei , Guo Peng , Li Xiaowei , Nishimura Kazuhito , Ke Peiling , Wang Aiying 
Published: May 2024

AbstractThe corrosion failure of amorphous carbon (a-C) coatings is commonly ascribed to the existence of growth microdefects, which serve as pathways for corrosive fluids to permeate the substrate. Atomic layer deposition (ALD) is renowned for its ability to augment the corrosion resistance of metallic materials. Graphite-like carbon (GLC) is one of the amorphous carbon materials dominated by hybridized sp2-C bonds. In this study, an ALD-deposited Al2O3 layer is specially introduced on the Cr/GLC multilayer coating to solve the aforementioned corrosion risk of a-C by taking the sealing conception for defects. Compared to the as-deposited Cr/GLC coating, the coating encapsulated with Al2O3 layer depicts the reduction of corrosion current density over two orders of magnitude under a wide pressure range of 0.1 ~ 15 MPa. Particularly, the presence of released Crn+ and Fen+ in the corrosion solution is significantly diminished, accompanying with a small quantity of Aln+ generated in sealed coating during corrosion. Microstructural analysis and electrochemical results identified that both the dense Al2O3 layer offered strong safeguard for Cr elements released from multilayers, whilst amorphous carbon network inhibited the likelihood chloride penetration induced by partially infiltrated Al2O3, which made the synergistic contributions to the enhancement of corrosion resistance for Cr/GLC coating for deep-sea applications.
High-risk clones of Pseudomonas aeruginosa contaminate the drinking water networks of French cities
Authors: Horikian Ani , Jeanvoine Audrey , Amarache Abdallah , Tourtet Morgane , Ory Jérôme , Boulestreau Hélène , Van der Mee Marquet Nathalie , Lemaitre Nadine , Eveillard Matthieu , Lepelletier Didier , Bertrand Xavier , Valot Benoît , Hocquet Didier 
Published: May 2024

AbstractPseudomonas aeruginosa is a major opportunistic pathogen responsible for severe infections in immunocompromised patients. The contamination of drinking water networks (DWNs) with this pathogen is underestimated, as it is mostly in the state of persister cells undetected by the recommended monitoring technique. We collected water samples from eight cities distant from each other and searched for P. aeruginosa using a culture-based method that resuscitates persister cells. The genomes of isolates were sequenced. Five DWNs of the eight tested (62.5%) were contaminated with P. aeruginosa, of which four were contaminated with high-risk clones (ST308, ST395). Surprisingly, the ST308 isolates retrieved from the four independent and distant DWNs were clonal. Most P. aeruginosa isolates shared a genomic island conferring tolerance to copper-ions. The population structure of the collection may result from both a common source of contamination by plumbing supplies and the selection of clones sharing genetic elements that presumably aided their propagation in DWNs.
Chromosome-level genome assembly of Odontothrips loti Haliday (Thysanoptera: Thripidae)
Authors: Yingning Luo , Shuhua Wei , Wenting Dai , Miao Miao , Ying Wang , Rong Zhang , Liping Ban 
Published: May 2024

AbstractAs the predominant pest of alfalfa, Odontothrips loti Haliday causes great damages over the major alfalfa-growing regions of China. The characteristics of strong mobility and fecundity make them develop rapidly in the field and hard to be controlled. There is a shortage of bioinformation and limited genomic resources available of O. loti for us to develop novel pest management strategies. In this study, we constructed a chromosome-level reference genome assembly of O. loti with a genome size of 346.59 Mb and scaffold N50 length of 18.52 Mb, anchored onto 16 chromosomes and contained 20128 genes, of which 93.59% were functionally annotated. The results of 99.20% complete insecta_odb10 genes in BUSCO analysis, 91.11% short reads mapped to the ref-genome, and the consistent tendency among the thrips in the distribution of gene length reflects the quality of genome. Our study provided the first report of genome for the genus Odontothrips, which offers a genomic resource for further investigations on evolution and molecular biology of O. loti, contributing to pest management.
An improved chromosome-level genome assembly and annotation of Echeneis naucrates
Authors: Gao Tianxiang , Liu Kai , Liu Qi , Wang Danyang 
Published: May 2024

AbstractEcheneis naucrates, as known as live sharksucker, is famous for the behavior of attaching to hosts using a highly modified dorsal fin with oval-shaped sucking disc. Here, we generated an improved high-quality chromosome-level genome assembly of E. naucrates using Illumina short reads, PacBio long reads and Hi-C data. Our assembled genome spans 572.85 Mb with a contig N50 of 23.19 Mb and is positioned to 24 pseudo-chromosomes. Additionally, at least one telomere was identified for 23 out of 24 chromosomes. Furthermore, we identified a total of 22,161 protein-coding genes, of which 21,402 genes (96.9%) were annotated successfully with functions. The combination of ab initio predictions and Repbase-based searches revealed that 15.57% of the assembled E. naucrates genome was identified as repetitive sequences. The completeness of the genome assembly and the gene annotation were estimated to be 97.5% and 95.4% with BUSCO analyses. This work enhances the utility of the live sharksucker genome and provides a valuable groundwork for the future study of genomics, biology and adaptive evolution in this species.
Analysis of quantum key distribution based on unified model of sequential state discrimination strategy
Authors: Namkung Min , Kwon Younghun 
Published: May 2024

AbstractThe quantum key distribution for multiparty is one of the essential subjects of study. Especially, without using entangled states, performing the quantum key distribution for multiparty is a critical area of research. For this purpose, sequential state discrimination, which provides multiparty quantum communication and quantum key distribution for multiple receivers, has recently been introduced. Moreover, the sequential state discrimination is applicable for the security analysis against an eavesdropper’s attack. In this work, we provide the security analysis of quantum key distribution by proposing a unified model of sequential state discrimination including an eavesdropper. In this model, the success probability of eavesdropping is used as a figure of merit for the security analysis. Moreover, we obtain a non-zero secret key rate between the sender and receiver, which implies that the sender and receiver can share a secret key despite the eavesdropper’s scheme that optimizing the success probability of eavesdropping. Further, we propose an experimental methodology for the proposed model, which is implementable with linear optics. We observe that the secret key between the sender and receiver can be non-zero, even with imperfections.