bluuebunny/crossref_metadata_2025_split huggingface dataset:
Nucleocapsid-specific T cell responses associate with control of SARS-CoV-2 in the upper airways before seroconversion
Authors: Eser Tabea M. , Baranov Olga , Huth Manuel , Ahmed Mohammed I. M. , Deák Flora , Held Kathrin , Lin Luming , Pekayvaz Kami , Leunig Alexander , Nicolai Leo , Pollakis Georgios , Buggert Marcus , Price David A. , Rubio-Acero Raquel , Reich Jakob , Falk Philine , Markgraf Alissa , Puchinger Kerstin , Castelletti Noemi , Olbrich Laura , Vanshylla Kanika , Klein Florian , Wieser Andreas , Hasenauer Jan , Kroidl Inge , Hoelscher Michael , Geldmacher Christof 
Published: May 2023

AbstractDespite intensive research since the emergence of SARS-CoV-2, it has remained unclear precisely which components of the early immune response protect against the development of severe COVID-19. Here, we perform a comprehensive immunogenetic and virologic analysis of nasopharyngeal and peripheral blood samples obtained during the acute phase of infection with SARS-CoV-2. We find that soluble and transcriptional markers of systemic inflammation peak during the first week after symptom onset and correlate directly with upper airways viral loads (UA-VLs), whereas the contemporaneous frequencies of circulating viral nucleocapsid (NC)-specific CD4+ and CD8+ T cells correlate inversely with various inflammatory markers and UA-VLs. In addition, we show that high frequencies of activated CD4+ and CD8+ T cells are present in acutely infected nasopharyngeal tissue, many of which express genes encoding various effector molecules, such as cytotoxic proteins and IFN-γ. The presence of IFNG mRNA-expressing CD4+ and CD8+ T cells in the infected epithelium is further linked with common patterns of gene expression among virus-susceptible target cells and better local control of SARS-CoV-2. Collectively, these results identify an immune correlate of protection against SARS-CoV-2, which could inform the development of more effective vaccines to combat the acute and chronic illnesses attributable to COVID-19.
Redefining the role of AMPK in autophagy and the energy stress response
Authors: Park Ji-Man , Lee Da-Hye , Kim Do-Hyung 
Published: May 2023

AbstractAutophagy maintains cellular homeostasis during low energy states. According to the current understanding, glucose-depleted cells induce autophagy through AMPK, the primary energy-sensing kinase, to acquire energy for survival. However, contrary to the prevailing concept, our study demonstrates that AMPK inhibits ULK1, the kinase responsible for autophagy initiation, thereby suppressing autophagy. We found that glucose starvation suppresses amino acid starvation-induced stimulation of ULK1-Atg14-Vps34 signaling via AMPK activation. During an energy crisis caused by mitochondrial dysfunction, the LKB1-AMPK axis inhibits ULK1 activation and autophagy induction, even under amino acid starvation. Despite its inhibitory effect, AMPK protects the ULK1-associated autophagy machinery from caspase-mediated degradation during energy deficiency, preserving the cellular ability to initiate autophagy and restore homeostasis once the stress subsides. Our findings reveal that dual functions of AMPK, restraining abrupt induction of autophagy upon energy shortage while preserving essential autophagy components, are crucial to maintain cellular homeostasis and survival during energy stress.
Neural crest E-cadherin loss drives cleft lip/palate by epigenetic modulation via pro-inflammatory gene–environment interaction
Authors: Alvizi Lucas , Nani Diogo , Brito Luciano Abreu , Kobayashi Gerson Shigeru , Passos-Bueno Maria Rita , Mayor Roberto 
Published: May 2023

AbstractGene–environment interactions are believed to play a role in multifactorial phenotypes, although poorly described mechanistically. Cleft lip/palate (CLP), the most common craniofacial malformation, has been associated with both genetic and environmental factors, with little gene–environment interaction experimentally demonstrated. Here, we study CLP families harbouring CDH1/E-Cadherin variants with incomplete penetrance and we explore the association of pro-inflammatory conditions to CLP. By studying neural crest (NC) from mouse, Xenopus and humans, we show that CLP can be explained by a 2-hit model, where NC migration is impaired by a combination of genetic (CDH1 loss-of-function) and environmental (pro-inflammatory activation) factors, leading to CLP. Finally, using in vivo targeted methylation assays, we demonstrate that CDH1 hypermethylation is the major target of the pro-inflammatory response, and a direct regulator of E-cadherin levels and NC migration. These results unveil a gene–environment interaction during craniofacial development and provide a 2-hit mechanism to explain cleft lip/palate aetiology.
Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA
Authors: Liang Yufeng , Willey Sydney , Chung Yu-Chieh , Lo Yi-Meng , Miao Shiqin , Rundell Sarah , Tu Li-Chun , Bong Dennis 
Published: May 2023

AbstractThe most widely used method for intracellular RNA fluorescence labeling is MS2 labeling, which generally relies on the use of multiple protein labels targeted to multiple RNA (MS2) hairpin structures installed on the RNA of interest (ROI). While effective and conveniently applied in cell biology labs, the protein labels add significant mass to the bound RNA, which potentially impacts steric accessibility and native RNA biology. We have previously demonstrated that internal, genetically encoded, uridine-rich internal loops (URILs) comprised of four contiguous UU pairs (8 nt) in RNA may be targeted with minimal structural perturbation by triplex hybridization with 1 kD bifacial peptide nucleic acids (bPNAs). A URIL-targeting strategy for RNA and DNA tracking would avoid the use of cumbersome protein fusion labels and minimize structural alterations to the RNA of interest. Here we show that URIL-targeting fluorogenic bPNA probes in cell media can penetrate cell membranes and effectively label RNAs and RNPs in fixed and live cells. This method, which we call fluorogenic U-rich internal loop (FLURIL) tagging, was internally validated through the use of RNAs bearing both URIL and MS2 labeling sites. Notably, a direct comparison of CRISPR-dCas labeled genomic loci in live U2OS cells revealed that FLURIL-tagged gRNA yielded loci with signal to background up to 7X greater than loci targeted by guide RNA modified with an array of eight MS2 hairpins. Together, these data show that FLURIL tagging provides a versatile scope of intracellular RNA and DNA tracking while maintaining a light molecular footprint and compatibility with existing methods.
Robust cortical encoding of 3D tongue shape during feeding in macaques
Authors: Laurence-Chasen Jeffrey D. , Ross Callum F. , Arce-McShane Fritzie I. , Hatsopoulos Nicholas G. 
Published: May 2023

AbstractDexterous tongue deformation underlies eating, drinking, and speaking. The orofacial sensorimotor cortex has been implicated in the control of coordinated tongue kinematics, but little is known about how the brain encodes—and ultimately drives—the tongue’s 3D, soft-body deformation. Here we combine a biplanar x-ray video technology, multi-electrode cortical recordings, and machine-learning-based decoding to explore the cortical representation of lingual deformation. We trained long short-term memory (LSTM) neural networks to decode various aspects of intraoral tongue deformation from cortical activity during feeding in male Rhesus monkeys. We show that both lingual movements and complex lingual shapes across a range of feeding behaviors could be decoded with high accuracy, and that the distribution of deformation-related information across cortical regions was consistent with previous studies of the arm and hand.
Near-lifespan longitudinal tracking of brain microvascular morphology, topology, and flow in male mice
Authors: Walek Konrad W. , Stefan Sabina , Lee Jang-Hoon , Puttigampala Pooja , Kim Anna H. , Park Seong Wook , Marchand Paul J. , Lesage Frederic , Liu Tao , Huang Yu-Wen Alvin , Boas David A. , Moore Christopher , Lee Jonghwan 
Published: May 2023

AbstractIn age-related neurodegenerative diseases, pathology often develops slowly across the lifespan. As one example, in diseases such as Alzheimer’s, vascular decline is believed to onset decades ahead of symptomology. However, challenges inherent in current microscopic methods make longitudinal tracking of such vascular decline difficult. Here, we describe a suite of methods for measuring brain vascular dynamics and anatomy in mice for over seven months in the same field of view. This approach is enabled by advances in optical coherence tomography (OCT) and image processing algorithms including deep learning. These integrated methods enabled us to simultaneously monitor distinct vascular properties spanning morphology, topology, and function of the microvasculature across all scales: large pial vessels, penetrating cortical vessels, and capillaries. We have demonstrated this technical capability in wild-type and 3xTg male mice. The capability will allow comprehensive and longitudinal study of a broad range of progressive vascular diseases, and normal aging, in key model systems.
A positive statistical benchmark to assess network agreement
Authors: Hao Bingjie , Kovács István A. 
Published: May 2023

AbstractCurrent computational methods for validating experimental network datasets compare overlap, i.e., shared links, with a reference network using a negative benchmark. However, this fails to quantify the level of agreement between the two networks. To address this, we propose a positive statistical benchmark to determine the maximum possible overlap between networks. Our approach can efficiently generate this benchmark in a maximum entropy framework and provides a way to assess whether the observed overlap is significantly different from the best-case scenario. We introduce a normalized overlap score, Normlap, to enhance comparisons between experimental networks. As an application, we compare molecular and functional networks, resulting in an agreement network of human as well as yeast network datasets. The Normlap score can improve the comparison between experimental networks by providing a computational alternative to network thresholding and validation.
Compact optical convolution processing unit based on multimode interference
Authors: Meng Xiangyan , Zhang Guojie , Shi Nuannuan , Li Guangyi , Azaña José , Capmany José , Yao Jianping , Shen Yichen , Li Wei , Zhu Ninghua , Li Ming 
Published: May 2023

AbstractConvolutional neural networks are an important category of deep learning, currently facing the limitations of electrical frequency and memory access time in massive data processing. Optical computing has been demonstrated to enable significant improvements in terms of processing speeds and energy efficiency. However, most present optical computing schemes are hardly scalable since the number of optical elements typically increases quadratically with the computational matrix size. Here, a compact on-chip optical convolutional processing unit is fabricated on a low-loss silicon nitride platform to demonstrate its capability for large-scale integration. Three 2 × 2 correlated real-valued kernels are made of two multimode interference cells and four phase shifters to perform parallel convolution operations. Although the convolution kernels are interrelated, ten-class classification of handwritten digits from the MNIST database is experimentally demonstrated. The linear scalability of the proposed design with respect to computational size translates into a solid potential for large-scale integration.
Uncertainty analysis and performance evaluation of thermophysical property measurement of liquid Au in microgravity
Authors: Nawer Jannatun , Ishikawa Takehiko , Oda Hirohisa , Saruwatari Hideki , Koyama Chihiro , Xiao Xiao , Schneider Stephan , Kolbe Matthias , Matson Douglas M. 
Published: May 2023

AbstractA new method for quantifying facility performance has been discussed in this study that encompasses uncertainties associated with thermophysical property measurement. Four key thermophysical properties: density, volumetric thermal expansion coefficient, surface tension, and viscosity of liquid Au have been measured in microgravity environment using two different levitation facilities. Levitation experiments were conducted using the Electrostatic Levitation Furnace (ELF) onboard the ISS in Argon and air, and the TEMPUS Electromagnetic Levitation (EML) facility on a Novespace Zero-G aircraft parabolic flight in Argon. The traditional Maximum Amplitude method was augmented through the use of Frequency Crossover method to identify the natural frequency for oscillations induced on a molten sample during Faraday forcing in ESL. The EML tests were conducted using a pulse excitation method where two techniques, one imaging and one non-imaging, were used to study surface oscillations. The results from both facilities are in excellent agreement with the published literature values. A detailed study of the accuracy and precision of the measured values has also been presented in this work to evaluate facility performance.
Directly monitoring the shift in corrosion mechanisms of a model FeCrNi alloy driven by electric potential
Authors: Liu Tingkun , Li Cheng-Han , Olszta Matthew , Tao Jinhui , Devaraj Arun 
Published: May 2023

AbstractStainless steels are used in a myriad of engineering applications, including construction, automobiles, and nuclear reactors. Developing accurate, predictive mechanistic models for corrosion and electrochemical corrosion kinetics of stainless steels has been a topic of research studies over many decades. Herein, we quantified the aqueous corrosion kinetics of a model austenitic Fe–18Cr–14Ni (wt%) alloy in the presence and absence of applied potential using systematic in situ electrochemical atomic force microscopy (EC-AFM) and transmission electron microscopy (TEM). Without an applied bias, vertical dissolution of corrosion pits is controlled by the surface kinetics/diffusion hybrid mechanism, whereas lateral dissolution is diffusion controlled. When an electric bias is applied, the increase in corrosion rate is dominated by the nucleation of new pits. These insights gained by the in situ EC-AFM will allow applications of this method for a quantitative understanding of corrosion of a wider class of materials.
Influence of cementite coarsening on the corrosion resistance of high strength low alloy steel
Authors: Liu Chao , Li Can , Che Zhichao , Li Xuan , Yang Shufeng , Liu Zhiyong , Zhou Yigang , Cheng Xuequn 
Published: May 2023

AbstractThe impact of heat treatment on the initiation and progression of localized corrosion in E690 steel in a simulated marine environment was investigated systematically. The primary cause of localized corrosion was the presence of inclusions, which led to the dissolution of the distorted matrix surrounding them. In the initial stages of corrosion, localized corrosion resulting from inclusions was the predominant form. The chemical and electrochemical mechanisms underlying matrix deformation and localized corrosion caused by inclusions were meticulously elucidated. As the immersion time was extended, the galvanic contributions at the ferrite-austenite interfaces, as well as the coarsened carbides, reduced the polarization resistance in the annealed specimen, accelerating the corrosion rate compared to the lath martensite in the as-received specimen. Consequently, the heat-treated sample promoted a transition from localized to uniform corrosion. Finally, a model was established to describe the corrosion behavior of E690 steel in the marine environment.
Metagenomic insights into nutrient and hypoxic microbial communities at the macrofouling/steel interface leading to severe MIC
Authors: Wang Zhengquan , Wang Xiutong , Huang Yanliang , Hou Baorong 
Published: May 2023

AbstractAdherent macrofouling in marine environments caused complex corrosion of steel surfaces, resulting in localized corrosion at the oyster/steel interface and uniform corrosion at the ascidian/steel interface. Sulfate-reducing bacteria (SRB) have been implicated in the microbiologically influenced corrosion (MIC) process at macrofouling-covered interfaces. To better understand the role of marine biofilms as key mediators in the MIC process, metagenomic techniques were used to study microbial communities and their response to macrofouling’s coverage. Compared to ascidians, the formed local anaerobic zone at oyster/steel interface stimulated the growth of SRBs, leading to higher FeS content and severe localized corrosion. SRB Desulfovibrio and Desulfobulbus, along with the SRB-related functional gene dsr, were found to increase, while oxygen-related function genes coxC, ccoN, ccoO, ccoP, and ccoQ decreased. In contrast, steel surfaces without macrofouling coverage had the richest microbial communities, yet experienced less severe MIC, suggesting no direct connection between microbial abundance/diversity and steel corrosion promotion.
Heteromeric clusters of ubiquitinated ER-shaping proteins drive ER-phagy
Authors: Foronda Hector , Fu Yangxue , Covarrubias-Pinto Adriana , Bocker Hartmut T. , González Alexis , Seemann Eric , Franzka Patricia , Bock Andrea , Bhaskara Ramachandra M. , Liebmann Lutz , Hoffmann Marina E. , Katona Istvan , Koch Nicole , Weis Joachim , Kurth Ingo , Gleeson Joseph G. , Reggiori Fulvio , Hummer Gerhard , Kessels Michael M. , Qualmann Britta , Mari Muriel , Dikić Ivan , Hübner Christian A. 
Published: May 2023

AbstractMembrane-shaping proteins characterized by reticulon homology domains play an important part in the dynamic remodelling of the endoplasmic reticulum (ER). An example of such a protein is FAM134B, which can bind LC3 proteins and mediate the degradation of ER sheets through selective autophagy (ER-phagy)1. Mutations in FAM134B result in a neurodegenerative disorder in humans that mainly affects sensory and autonomic neurons2. Here we report that ARL6IP1, another ER-shaping protein that contains a reticulon homology domain and is associated with sensory loss3, interacts with FAM134B and participates in the formation of heteromeric multi-protein clusters required for ER-phagy. Moreover, ubiquitination of ARL6IP1 promotes this process. Accordingly, disruption of Arl6ip1 in mice causes an expansion of ER sheets in sensory neurons that degenerate over time. Primary cells obtained from Arl6ip1-deficient mice or from patients display incomplete budding of ER membranes and severe impairment of ER-phagy flux. Therefore, we propose that the clustering of ubiquitinated ER-shaping proteins facilitates the dynamic remodelling of the ER during ER-phagy and is important for neuronal maintenance.
Histone modifications regulate pioneer transcription factor cooperativity
Authors: Sinha Kalyan K. , Bilokapic Silvija , Du Yongming , Malik Deepshikha , Halic Mario 
Published: May 2023

AbstractPioneer transcription factors have the ability to access DNA in compacted chromatin1. Multiple transcription factors can bind together to a regulatory element in a cooperative way, and cooperation between the pioneer transcription factors OCT4 (also known as POU5F1) and SOX2 is important for pluripotency and reprogramming2–4. However, the molecular mechanisms by which pioneer transcription factors function and cooperate on chromatin remain unclear. Here we present cryo-electron microscopy structures of human OCT4 bound to a nucleosome containing human LIN28B or nMATN1 DNA sequences, both of which bear multiple binding sites for OCT4. Our structural and biochemistry data reveal that binding of OCT4 induces changes to the nucleosome structure, repositions the nucleosomal DNA and facilitates cooperative binding of additional OCT4 and of SOX2 to their internal binding sites. The flexible activation domain of OCT4 contacts the N-terminal tail of histone H4, altering its conformation and thus promoting chromatin decompaction. Moreover, the DNA-binding domain of OCT4 engages with the N-terminal tail of histone H3, and post-translational modifications at H3K27 modulate DNA positioning and affect transcription factor cooperativity. Thus, our findings suggest that the epigenetic landscape could regulate OCT4 activity to ensure proper cell programming.
Path loss modeling and performance evaluation of double IRSs-aided wireless communication systems based on spatial scattering channel model
Authors: Wang Jihong , Ni Hao 
Published: May 2023

AbstractIntelligent reflecting surface (IRS) is a key enabling technology to reshape the electromagnetic propagation environment and enhance the communication performance. Current single IRS-aided or multiple distributed IRSs-aided wireless communication systems leave inter-IRSs collaboration out of consideration, and as a result, the system performance may be severely restricted. For cooperative double IRSs-aided wireless communication systems, dyadic backscatter channel model is widely used in the performance analysis and optimization. However, the impact of factors such as the size and gain of IRS elements is omitted. As a result, the performance quantification and evaluation are inaccurate. In order to avoid the above limitations, spatial scattering channel model is leveraged to quantify the path loss of the double reflection link in typical application scenarios of double IRSs-aided wireless communication systems. When the near-field condition is satisfied, the electromagnetic wave signal transmitted between IRSs is a spherical wave, which leads to high-rank channel and a lower signal to noise ratio. This paper considers the rank-1 inter-IRSs equivalent channel and derives the closed-form received signal power which reveals its relationship with the deployment of IRSs and the physical and electromagnetic properties of IRSs. Taking the impact of near/far-field effects of IRS on signal propagation further into consideration, the network configurations under which double cooperative IRSs can enhance the system performance are recognized. Simulation results show that whether double IRSs should be selected to assist in the communication between the transmitter and the receiver depends on practical network configurations, and the same number of elements should be assigned to the two IRSs to maximize the system performance if they are adopted.