bluuebunny/crossref_metadata_2025_split huggingface dataset:
Size-dependent deformation behavior in nanosized amorphous metals suggesting transition from collective to individual atomic transport
Authors: Liu Naijia , Sohn Sungwoo , Na Min Young , Park Gi Hoon , Raj Arindam , Liu Guannan , Kube Sebastian A. , Yuan Fusen , Liu Yanhui , Chang Hye Jung , Schroers Jan 
Published: September 2023

AbstractThe underlying atomistic mechanism of deformation is a central problem in mechanics and materials science. Whereas deformation of crystalline metals is fundamentally understood, the understanding of deformation of amorphous metals lacks behind, particularly identifying the involved temporal and spatial scales. Here, we reveal that at small scales the size-dependent deformation behavior of amorphous metals significantly deviates from homogeneous flow, exhibiting increasing deformation rate with reducing size and gradually shifted composition. This transition suggests the deformation mechanism changes from collective atomic transport by viscous flow to individual atomic transport through interface diffusion. The critical length scale of the transition is temperature dependent, exhibiting a maximum at the glass transition. While viscous flow does not discriminate among alloy constituents, diffusion does and the constituent element with higher diffusivity deforms faster. Our findings yield insights into nano-mechanics and glass physics and may suggest alternative processing methods to epitaxially grow metallic glasses.
Bifidobacteria shape antimicrobial T-helper cell responses during infancy and adulthood
Authors: Vogel Katrin , Arra Aditya , Lingel Holger , Bretschneider Dirk , Prätsch Florian , Schanze Denny , Zenker Martin , Balk Silke , Bruder Dunja , Geffers Robert , Hachenberg Thomas , Arens Christoph , Brunner-Weinzierl Monika C. 
Published: September 2023

AbstractMicrobial infections early in life are challenging for the unexperienced immune system. The SARS-CoV-2 pandemic again has highlighted that neonatal, infant, child, and adult T-helper(Th)-cells respond differently to infections, and requires further understanding. This study investigates anti-bacterial T-cell responses against Staphylococcus aureus aureus, Staphylococcus epidermidis and Bifidobacterium longum infantis in early stages of life and adults and shows age and pathogen-dependent mechanisms. Beside activation-induced clustering, T-cells stimulated with Staphylococci become Th1-type cells; however, this differentiation is mitigated in Bifidobacterium-stimulated T-cells. Strikingly, prestimulation of T-cells with Bifidobacterium suppresses the activation of Staphylococcus-specific T-helper cells in a cell-cell dependent manner by inducing FoxP3+CD4+ T-cells, increasing IL-10 and galectin-1 secretion and showing a CTLA-4-dependent inhibitory capacity. Furthermore Bifidobacterium dampens Th responses of severely ill COVID-19 patients likely contributing to resolution of harmful overreactions of the immune system. Targeted, age-specific interventions may enhance infection defence, and specific immune features may have potential cross-age utilization.
Structure of the peroxisomal Pex1/Pex6 ATPase complex bound to a substrate
Authors: Rüttermann Maximilian , Koci Michelle , Lill Pascal , Geladas Ermis Dionysios , Kaschani Farnusch , Klink Björn Udo , Erdmann Ralf , Gatsogiannis Christos 
Published: September 2023

AbstractThe double-ring AAA+ ATPase Pex1/Pex6 is required for peroxisomal receptor recycling and is essential for peroxisome formation. Pex1/Pex6 mutations cause severe peroxisome associated developmental disorders. Despite its pathophysiological importance, mechanistic details of the heterohexamer are not yet available. Here, we report cryoEM structures of Pex1/Pex6 from Saccharomyces cerevisiae, with an endogenous protein substrate trapped in the central pore of the catalytically active second ring (D2). Pairs of Pex1/Pex6(D2) subdomains engage the substrate via a staircase of pore-1 loops with distinct properties. The first ring (D1) is catalytically inactive but undergoes significant conformational changes resulting in alternate widening and narrowing of its pore. These events are fueled by ATP hydrolysis in the D2 ring and disengagement of a “twin-seam” Pex1/Pex6(D2) heterodimer from the staircase. Mechanical forces are propagated in a unique manner along Pex1/Pex6 interfaces that are not available in homo-oligomeric AAA-ATPases. Our structural analysis reveals the mechanisms of how Pex1 and Pex6 coordinate to achieve substrate translocation.
TAGET: a toolkit for analyzing full-length transcripts from long-read sequencing
Authors: Xia Yuchao , Jin Zijie , Zhang Chengsheng , Ouyang Linkun , Dong Yuhao , Li Juan , Guo Lvze , Jing Biyang , Shi Yang , Miao Susheng , Xi Ruibin 
Published: September 2023

AbstractSingle-molecule Real-time Isoform Sequencing (Iso-seq) of transcriptomes by PacBio can generate very long and accurate reads, thus providing an ideal platform for full-length transcriptome analysis. We present an integrated computational toolkit named TAGET for Iso-seq full-length transcript data analyses, including transcript alignment, annotation, gene fusion detection, and quantification analyses such as differential expression gene analysis and differential isoform usage analysis. We evaluate the performance of TAGET using a public Iso-seq dataset and newly sequenced Iso-seq datasets from tumor patients. TAGET gives significantly more precise novel splice site prediction and enables more accurate novel isoform and gene fusion discoveries, as validated by experimental validations and comparisons with RNA-seq data. We identify and experimentally validate a differential isoform usage gene ECM1, and further show that its isoform ECM1b may be a tumor-suppressor in laryngocarcinoma. Our results demonstrate that TAGET provides a valuable computational toolkit and can be applied to many full-length transcriptome studies.
Non-uniform temporal scaling of developmental processes in the mammalian cortex
Authors: Paolino Annalisa , Haines Elizabeth H. , Bailey Evan J. , Black Dylan A. , Moey Ching , García-Moreno Fernando , Richards Linda J. , Suárez Rodrigo , Fenlon Laura R. 
Published: September 2023

AbstractThe time that it takes the brain to develop is highly variable across animals. Although staging systems equate major developmental milestones between mammalian species, it remains unclear how distinct processes of cortical development scale within these timeframes. Here, we compare the timing of cortical development in two mammals of similar size but different developmental pace: eutherian mice and marsupial fat-tailed dunnarts. Our results reveal that the temporal relationship between cell birth and laminar specification aligns to equivalent stages between these species, but that migration and axon extension do not scale uniformly according to the developmental stages, and are relatively more advanced in dunnarts. We identify a lack of basal intermediate progenitor cells in dunnarts that likely contributes in part to this timing difference. These findings demonstrate temporal limitations and differential plasticity of cortical developmental processes between similarly sized Therians and provide insight into subtle temporal changes that may have contributed to the early diversification of the mammalian brain.
Ultra-durable superhydrophobic cellular coatings
Authors: Gu Wancheng , Li Wanbo , Zhang Yu , Xia Yage , Wang Qiaoling , Wang Wei , Liu Ping , Yu Xinquan , He Hui , Liang Caihua , Ban Youxue , Mi Changwen , Yang Sha , Liu Wei , Cui Miaomiao , Deng Xu , Wang Zuankai , Zhang Youfa 
Published: September 2023

AbstractDeveloping versatile, scalable, and durable coatings that resist the accretion of matters (liquid, vapor, and solid phases) in various operating environments is important to industrial applications, yet has proven challenging. Here, we report a cellular coating that imparts liquid-repellence, vapor-imperviousness, and solid-shedding capabilities without the need for complicated structures and fabrication processes. The key lies in designing basic cells consisting of rigid microshells and releasable nanoseeds, which together serve as a rigid shield and a bridge that chemically bonds with matrix and substrate. The durability and strong resistance to accretion of different matters of our cellular coating are evidenced by strong anti-abrasion, enhanced anti-corrosion against saltwater over 1000 h, and maintaining dry in complicated phase change conditions. The cells can be impregnated into diverse matrixes for facile mass production through scalable spraying. Our strategy provides a generic design blueprint for engineering ultra-durable coatings for a wide range of applications.
Mechanical metamaterials and beyond
Authors: Jiao Pengcheng , Mueller Jochen , Raney Jordan R. , Zheng Xiaoyu , Alavi Amir H. 
Published: September 2023

AbstractMechanical metamaterials enable the creation of structural materials with unprecedented mechanical properties. However, thus far, research on mechanical metamaterials has focused on passive mechanical metamaterials and the tunability of their mechanical properties. Deep integration of multifunctionality, sensing, electrical actuation, information processing, and advancing data-driven designs are grand challenges in the mechanical metamaterials community that could lead to truly intelligent mechanical metamaterials. In this perspective, we provide an overview of mechanical metamaterials within and beyond their classical mechanical functionalities. We discuss various aspects of data-driven approaches for inverse design and optimization of multifunctional mechanical metamaterials. Our aim is to provide new roadmaps for design and discovery of next-generation active and responsive mechanical metamaterials that can interact with the surrounding environment and adapt to various conditions while inheriting all outstanding mechanical features of classical mechanical metamaterials. Next, we deliberate the emerging mechanical metamaterials with specific functionalities to design informative and scientific intelligent devices. We highlight open challenges ahead of mechanical metamaterial systems at the component and integration levels and their transition into the domain of application beyond their mechanical capabilities.
Tensorial stress-plastic strain fields in α - ω Zr mixture, transformation kinetics, and friction in diamond-anvil cell
Authors: Levitas Valery I. , Dhar Achyut , Pandey K. K. 
Published: September 2023

AbstractVarious phenomena (phase transformations (PTs), chemical reactions, microstructure evolution, strength, and friction) under high pressures in diamond-anvil cell are strongly affected by fields of stress and plastic strain tensors. However, they could not be measured. Here, we suggest coupled experimental-analytical-computational approaches utilizing synchrotron X-ray diffraction, to solve an inverse problem and find fields of all components of stress and plastic strain tensors and friction rules before, during, and after α-ω PT in strongly plastically predeformed Zr. Results are in good correspondence with each other and experiments. Due to advanced characterization, the minimum pressure for the strain-induced α-ω PT is changed from 1.36 to 2.7 GPa. It is independent of the plastic strain before PT and compression-shear path. The theoretically predicted plastic strain-controlled kinetic equation is verified and quantified. Obtained results open opportunities for developing quantitative high-pressure/stress science, including mechanochemistry, synthesis of new nanostructured materials, geophysics, astrogeology, and tribology.
Grinding-induced supramolecular charge-transfer assemblies with switchable vapochromism toward haloalkane isomers
Authors: Wu Jia-Rui , Wu Gengxin , Li Dongxia , Li Meng-Hao , Wang Yan , Yang Ying-Wei 
Published: September 2023

AbstractSynthetic macrocycles have proved to be of great application value in functional charge-transfer systems in the solid state in recent years. Here we show a switchable on-off type vapochromic system toward 1-/2-bromoalkane isomers by constructing solid-state charge-transfer complexes between electron-rich perethylated pillar[5]arene and electron-deficient aromatic acceptors including 4-nitrobenzonitrile and 1,4-dinitrobenzene. These charge-transfer complexes with different colors show opposite color changes upon exposure to the vapors of 1-bromoalkanes (fading) and 2-bromoalkanes (deepening). Single-crystal structures incorporating X-ray powder diffraction and spectral analyses demonstrate that this on-off type vapochromic behavior is mainly attributed to the destruction (off) and reconstruction (on) of the charge-transfer interactions between perethylated pillar[5]arene and the acceptors, for which the competitive host-guest binding of 1-bromoalkanes and the solid-state structural transformation triggered by 2-bromoalkanes are respectively responsible. This work provides a simple colorimetric method for distinguishing positional isomers with similar physical and chemical properties.
Single-chain dimers from de novo immunoglobulins as robust scaffolds for multiple binding loops
Authors: Roel-Touris Jorge , Nadal Marta , Marcos Enrique 
Published: September 2023

AbstractAntibody derivatives have sought to recapitulate the antigen binding properties of antibodies, but with improved biophysical attributes convenient for therapeutic, diagnostic and research applications. However, their success has been limited by the naturally occurring structure of the immunoglobulin dimer displaying hypervariable binding loops, which is hard to modify by traditional engineering approaches. Here, we devise geometrical principles for de novo designing single-chain immunoglobulin dimers, as a tunable two-domain architecture that optimizes biophysical properties through more favorable dimer interfaces. Guided by these principles, we computationally designed protein scaffolds that were hyperstable, structurally accurate and robust for accommodating multiple functional loops, both individually and in combination, as confirmed through biochemical assays and X-ray crystallography. We showcase the modularity of this architecture by deep-learning-based diversification, opening up the possibility for tailoring the number, positioning, and relative orientation of ligand-binding loops targeting one or two distal epitopes. Our results provide a route to custom-design robust protein scaffolds for harboring multiple functional loops.
The leaderless communication peptide (LCP) class of quorum-sensing peptides is broadly distributed among Firmicutes
Authors: Aggarwal Shifu , Huang Elaine , Do Hackwon , Makthal Nishanth , Li Yanyan , Bapteste Eric , Lopez Philippe , Bernard Charles , Kumaraswami Muthiah 
Published: September 2023

AbstractThe human pathogen Streptococcus pyogenes secretes a short peptide (leaderless communication peptide, LCP) that mediates intercellular communication and controls bacterial virulence through interaction with its receptor, RopB. Here, we show that LCP and RopB homologues are present in other Firmicutes. We experimentally validate that LCPs with distinct peptide communication codes act as bacterial intercellular signals and regulate gene expression in Streptococcus salivarius, Streptococcus porcinus, Enterococcus malodoratus and Limosilactobacillus reuteri. Our results indicate that LCPs are more widespread than previously thought, and their characterization may uncover new signaling mechanisms and roles in coordinating diverse bacterial traits.
Monolithic 3D integration of 2D transistors and vertical RRAMs in 1T–4R structure for high-density memory
Authors: Xie Maosong , Jia Yueyang , Nie Chen , Liu Zuheng , Tang Alvin , Fan Shiquan , Liang Xiaoyao , Jiang Li , He Zhezhi , Yang Rui 
Published: September 2023

AbstractEmerging data-intensive computation has driven the advanced packaging and vertical stacking of integrated circuits, for minimized latency and energy consumption. Yet a monolithic three-dimensional (3D) integrated structure with interleaved logic and high-density memory layers has been difficult to achieve due to challenges in managing the thermal budget. Here we experimentally demonstrate a monolithic 3D integration of atomically-thin molybdenum disulfide (MoS2) transistors and 3D vertical resistive random-access memories (VRRAMs), with the MoS2transistors stacked between the bottom-plane and top-plane VRRAMs. The whole fabrication process is integration-friendly (below 300 °C), and the measurement results confirm that the top-plane fabrication does not affect the bottom-plane devices. The MoS2transistor can drive each layer of VRRAM into four resistance states. Circuit-level modeling of the monolithic 3D structure demonstrates smaller area, faster data transfer, and lower energy consumption than a planar memory. Such platform holds a high potential for energy-efficient 3D on-chip memory systems.
Towards interoperability in infection control: a standard data model for microbiology
Authors: Rinaldi Eugenia , Drenkhahn Cora , Gebel Benjamin , Saleh Kutaiba , Tönnies Hauke , von Loewenich Friederike D. , Thoma Norbert , Baier Claas , Boeker Martin , Hinske Ludwig Christian , Diaz Luis Alberto Peña , Behnke Michael , Ingenerf Josef , Thun Sylvia 
Published: September 2023

AbstractThe COVID-19 pandemic has made it clear: sharing and exchanging data among research institutions is crucial in order to efficiently respond to global health threats. This can be facilitated by defining health data models based on interoperability standards. In Germany, a national effort is in progress to create common data models using international healthcare IT standards. In this context, collaborative work on a data set module for microbiology is of particular importance as the WHO has declared antimicrobial resistance one of the top global public health threats that humanity is facing. In this article, we describe how we developed a common model for microbiology data in an interdisciplinary collaborative effort and how we make use of the standard HL7 FHIR and terminologies such as SNOMED CT or LOINC to ensure syntactic and semantic interoperability. The use of international healthcare standards qualifies our data model to be adopted beyond the environment where it was first developed and used at an international level.
Improved accuracy in colorectal cancer tissue decomposition through refinement of established deep learning solutions
Authors: Prezja Fabi , Äyrämö Sami , Pölönen Ilkka , Ojala Timo , Lahtinen Suvi , Ruusuvuori Pekka , Kuopio Teijo 
Published: September 2023

AbstractHematoxylin and eosin-stained biopsy slides are regularly available for colorectal cancer patients. These slides are often not used to define objective biomarkers for patient stratification and treatment selection. Standard biomarkers often pertain to costly and slow genetic tests. However, recent work has shown that relevant biomarkers can be extracted from these images using convolutional neural networks (CNNs). The CNN-based biomarkers predicted colorectal cancer patient outcomes comparably to gold standards. Extracting CNN-biomarkers is fast, automatic, and of minimal cost. CNN-based biomarkers rely on the ability of CNNs to recognize distinct tissue types from microscope whole slide images. The quality of these biomarkers (coined ‘Deep Stroma’) depends on the accuracy of CNNs in decomposing all relevant tissue classes. Improving tissue decomposition accuracy is essential for improving the prognostic potential of CNN-biomarkers. In this study, we implemented a novel training strategy to refine an established CNN model, which then surpassed all previous solutions . We obtained a 95.6% average accuracy in the external test set and 99.5% in the internal test set. Our approach reduced errors in biomarker-relevant classes, such as Lymphocytes, and was the first to include interpretability methods. These methods were used to better apprehend our model’s limitations and capabilities.
Urban intelligent assistant on the example of the escalator passenger safety management at the subway stations
Authors: Tianxing Man , Vodyaho Alexander , Zhukova Nataly , Subbotin Alexey , Shichkina Yulia 
Published: September 2023

AbstractIntelligent assistants often struggle with the complexity of spatiotemporal models used for understanding objects and environments. The construction and usage of such models demand significant computational resources. This article introduces a novel multilevel spatiotemporal model and a computationally efficient construction method. To facilitate model construction on different levels, we employ a meta-mining technique. Furthermore, the proposed model is specifically designed to excel in foggy environments. As a practical application, we develop an intelligent assistant focused on enhancing subway passenger safety. We present case examples involving jammed objects, such as shoes, in escalator combs. Our results demonstrate the effectiveness of the proposed model and method. Specifically, the accuracy of breakdown detection has improved by 10% compared to existing information systems used in subways. Moreover, the time required to build a spatiotemporal model is reduced by 2.3 times, further highlighting the efficiency of our approach. Our research offers a promising solution for intelligent assistants dealing with complex spatiotemporal modeling, with practical applications in ensuring subway passenger safety.
Early weaning and biological sex shape long-term immune and metabolic responses in pigs
Authors: Fardisi Mahsa , Thelen Kyan , Groenendal Allegra , Rajput Mrigendra , Sebastian Kimberly , Contreras G. Andres , Moeser Adam J. 
Published: September 2023

AbstractDuring the early pre and postnatal life, host and environmental factors can impart a major influence on immune development, thus shaping lifelong disease resistance. Two major factors known to influence immune function and mortality in animals and people are early life stress and biological sex. How these two factors interact to shape long-term immune development and later life disease risk is poorly understood. Here we investigated how early weaning, a common early life stressor in pigs, and biological sex impacts long-term systemic inflammatory responses and hypothalamic–pituitary–adrenal axis (HPA axis) activation later in life. Ten-week-old female (F), intact-male (IM) and castrated-male (CM) pigs that were randomly assigned to early weaning (EW) and later weaning (LW) (at 15 or 28 days of age, respectively) were intramuscularly injected with either saline vehicle or lipopolysaccharide (LPS) to induce a systemic inflammatory response. Complete blood counts (CBC), proinflammatory cytokines, cortisol, testosterone, estradiol, and rectal temp were measured at 0 h, 2 h, and 4 h post-LPS challenge. At 4 h post-LPS, peritoneal fluid (PF) and white blood cells (WBC) were collected for differential analysis. LPS challenge significantly increased rectal temp and plasma cortisol level in all treatment groups. Together, the CBC results and immune cell counts in peritoneal cavity indicated that EW-F exhibited greater systemic immune response characterized by increased neutrophils to lymphocytes ratio (NLR) and enhanced neutrophil trafficking to the peritoneal cavity. Early weaning had an opposite effect on IM and CM pigs, which exhibited a suppressed LPS-induced neutrophil migration. Early weaning induced significantly greater cortisol responses only in IM pigs indicating a heightened HPA axis responses in EW-IM. how early weaning and biological sex affect immune and stress responses in pigs. Together, these results demonstrate that early weaning and biological sex and castration shape later life immune responses in pigs and provides insight into potential mechanisms driving sex differences in later life inflammatory disease risk and mortality.