bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 and its ORF3a, E and M viroporins activate inflammasome in human macrophages and induce of IL-1α in pulmonary epithelial and endothelial cells
Authors: Ambrożek-Latecka Magdalena , Kozlowski Piotr , Hoser Grażyna , Bandyszewska Magdalena , Hanusek Karolina , Nowis Dominika , Gołąb Jakub , Grzanka Małgorzata , Piekiełko-Witkowska Agnieszka , Schulz Luise , Hornung Franziska , Deinhardt-Emmer Stefanie , Kozlowska Ewa , Skirecki Tomasz 
Published: April 2024

AbstractInflammasome assembly is a potent mechanism responsible for the host protection against pathogens, including viruses. When compromised, it can allow viral replication, while when disrupted, it can perpetuate pathological responses by IL-1 signaling and pyroptotic cell death. SARS-CoV-2 infection was shown to activate inflammasome in the lungs of COVID-19 patients, however, potential mechanisms responsible for this response are not fully elucidated. In this study, we investigated the effects of ORF3a, E and M SARS-CoV-2 viroporins in the inflammasome activation in major populations of alveolar sentinel cells: macrophages, epithelial and endothelial cells. We demonstrated that each viroporin is capable of activation of the inflammasome in macrophages to trigger pyroptosis-like cell death and IL-1α release from epithelial and endothelial cells. Small molecule NLRP3 inflammasome inhibitors reduced IL-1 release but weakly affected the pyroptosis. Importantly, we discovered that while SARS-CoV-2 could not infect the pulmonary microvascular endothelial cells it induced IL-1α and IL-33 release. Together, these findings highlight the essential role of macrophages as the major inflammasome-activating cell population in the lungs and point to endothelial cell expressed IL-1α as a potential novel component driving the pulmonary immunothromobosis in COVID-19.
Multi-level, forming and filament free, bulk switching trilayer RRAM for neuromorphic computing at the edge
Authors: Park Jaeseoung , Kumar Ashwani , Zhou Yucheng , Oh Sangheon , Kim Jeong-Hoon , Shi Yuhan , Jain Soumil , Hota Gopabandhu , Qiu Erbin , Nagle Amelie L. , Schuller Ivan K. , Schuman Catherine D. , Cauwenberghs Gert , Kuzum Duygu 
Published: April 2024

AbstractCMOS-RRAM integration holds great promise for low energy and high throughput neuromorphic computing. However, most RRAM technologies relying on filamentary switching suffer from variations and noise, leading to computational accuracy loss, increased energy consumption, and overhead by expensive program and verify schemes. We developed a filament-free, bulk switching RRAM technology to address these challenges. We systematically engineered a trilayer metal-oxide stack and investigated the switching characteristics of RRAM with varying thicknesses and oxygen vacancy distributions to achieve reliable bulk switching without any filament formation. We demonstrated bulk switching at megaohm regime with high current nonlinearity, up to 100 levels without compliance current. We developed a neuromorphic compute-in-memory platform and showcased edge computing by implementing a spiking neural network for an autonomous navigation/racing task. Our work addresses challenges posed by existing RRAM technologies and paves the way for neuromorphic computing at the edge under strict size, weight, and power constraints.
Iron-catalyzed stereoselective C–H alkylation for simultaneous construction of C–N axial and C-central chirality
Authors: Zhang Zi-Jing , Jacob Nicolas , Bhatia Shilpa , Boos Philipp , Chen Xinran , DeMuth Joshua C. , Messinis Antonis M. , Jei Becky Bongsuiru , Oliveira João C. A. , Radović Aleksa , Neidig Michael L. , Wencel-Delord Joanna , Ackermann Lutz 
Published: April 2024

AbstractThe assembly of chiral molecules with multiple stereogenic elements is challenging, and, despite of indisputable advances, largely limited to toxic, cost-intensive and precious metal catalysts. In sharp contrast, we herein disclose a versatile C–H alkylation using a non-toxic, low-cost iron catalyst for the synthesis of substituted indoles with two chiral elements. The key for achieving excellent diastereo- and enantioselectivity was substitution on a chiral N-heterocyclic carbene ligand providing steric hindrance and extra represented by noncovalent interaction for the concomitant generation of C–N axial chirality and C-stereogenic center. Experimental and computational mechanistic studies have unraveled the origin of the catalytic efficacy and stereoselectivity.
Denaturing mass photometry for rapid optimization of chemical protein-protein cross-linking reactions
Authors: Gizardin-Fredon Hugo , Santo Paulo E. , Chagot Marie-Eve , Charpentier Bruno , Bandeiras Tiago M. , Manival Xavier , Hernandez-Alba Oscar , Cianférani Sarah 
Published: April 2024

AbstractChemical cross-linking reactions (XL) are an important strategy for studying protein-protein interactions (PPIs), including low abundant sub-complexes, in structural biology. However, choosing XL reagents and conditions is laborious and mostly limited to analysis of protein assemblies that can be resolved using SDS-PAGE. To overcome these limitations, we develop here a denaturing mass photometry (dMP) method for fast, reliable and user-friendly optimization and monitoring of chemical XL reactions. The dMP is a robust 2-step protocol that ensures 95% of irreversible denaturation within only 5 min. We show that dMP provides accurate mass identification across a broad mass range (30 kDa–5 MDa) along with direct label-free relative quantification of all coexisting XL species (sub-complexes and aggregates). We compare dMP with SDS-PAGE and observe that, unlike the benchmark, dMP is time-efficient (3 min/triplicate), requires significantly less material (20–100×) and affords single molecule sensitivity. To illustrate its utility for routine structural biology applications, we show that dMP affords screening of 20 XL conditions in 1 h, accurately identifying and quantifying all coexisting species. Taken together, we anticipate that dMP will have an impact on ability to structurally characterize more PPIs and macromolecular assemblies, expected final complexes but also sub-complexes that form en route.
Deep learning the cis-regulatory code for gene expression in selected model plants
Authors: Peleke Fritz Forbang , Zumkeller Simon Maria , Gültas Mehmet , Schmitt Armin , Szymański Jędrzej 
Published: April 2024

AbstractElucidating the relationship between non-coding regulatory element sequences and gene expression is crucial for understanding gene regulation and genetic variation. We explored this link with the training of interpretable deep learning models predicting gene expression profiles from gene flanking regions of the plant species Arabidopsis thaliana, Solanum lycopersicum, Sorghum bicolor, and Zea mays. With over 80% accuracy, our models enabled predictive feature selection, highlighting e.g. the significant role of UTR regions in determining gene expression levels. The models demonstrated remarkable cross-species performance, effectively identifying both conserved and species-specific regulatory sequence features and their predictive power for gene expression. We illustrated the application of our approach by revealing causal links between genetic variation and gene expression changes across fourteen tomato genomes. Lastly, our models efficiently predicted genotype-specific expression of key functional gene groups, exemplified by underscoring known phenotypic and metabolic differences between Solanum lycopersicum and its wild, drought-resistant relative, Solanum pennellii.
Ambient carbon dioxide concentration correlates with SARS-CoV-2 aerostability and infection risk
Authors: Haddrell Allen , Oswin Henry , Otero-Fernandez Mara , Robinson Joshua F. , Cogan Tristan , Alexander Robert , Mann Jamie F. S. , Hill Darryl , Finn Adam , Davidson Andrew D. , Reid Jonathan P. 
Published: April 2024

AbstractAn improved understanding of the underlying physicochemical properties of respiratory aerosol that influence viral infectivity may open new avenues to mitigate the transmission of respiratory diseases such as COVID-19. Previous studies have shown that an increase in the pH of respiratory aerosols following generation due to changes in the gas-particle partitioning of pH buffering bicarbonate ions and carbon dioxide is a significant factor in reducing SARS-CoV-2 infectivity. We show here that a significant increase in SARS-CoV-2 aerostability results from a moderate increase in the atmospheric carbon dioxide concentration (e.g. 800 ppm), an effect that is more marked than that observed for changes in relative humidity. We model the likelihood of COVID-19 transmission on the ambient concentration of CO2, concluding that even this moderate increase in CO2 concentration results in a significant increase in overall risk. These observations confirm the critical importance of ventilation and maintaining low CO2 concentrations in indoor environments for mitigating disease transmission. Moreover, the correlation of increased CO2 concentration with viral aerostability need to be better understood when considering the consequences of increases in ambient CO2 levels in our atmosphere.
Photobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization
Authors: Kim Ruth Jean Ae , Fan De , He Jiangman , Kim Keunhwa , Du Juan , Chen Meng 
Published: April 2024

AbstractPhotoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions – PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm – which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.
Cross-modality mapping using image varifolds to align tissue-scale atlases to molecular-scale measures with application to 2D brain sections
Authors: Stouffer Kaitlin M. , Trouvé Alain , Younes Laurent , Kunst Michael , Ng Lydia , Zeng Hongkui , Anant Manjari , Fan Jean , Kim Yongsoo , Chen Xiaoyin , Rue Mara , Miller Michael I. 
Published: April 2024

AbstractThis paper explicates a solution to building correspondences between molecular-scale transcriptomics and tissue-scale atlases. This problem arises in atlas construction and cross-specimen/technology alignment where specimens per emerging technology remain sparse and conventional image representations cannot efficiently model the high dimensions from subcellular detection of thousands of genes. We address these challenges by representing spatial transcriptomics data as generalized functions encoding position and high-dimensional feature (gene, cell type) identity. We map onto low-dimensional atlas ontologies by modeling regions as homogeneous random fields with unknown transcriptomic feature distribution. We solve simultaneously for the minimizing geodesic diffeomorphism of coordinates through LDDMM and for these latent feature densities. We map tissue-scale mouse brain atlases to gene-based and cell-based transcriptomics data from MERFISH and BARseq technologies and to histopathology and cross-species atlases to illustrate integration of diverse molecular and cellular datasets into a single coordinate system as a means of comparison and further atlas construction.
Collapse of carbon nanotubes due to local high-pressure from van der Waals encapsulation
Authors: Hu Cheng , Chen Jiajun , Zhou Xianliang , Xie Yufeng , Huang Xinyue , Wu Zhenghan , Ma Saiqun , Zhang Zhichun , Xu Kunqi , Wan Neng , Zhang Yueheng , Liang Qi , Shi Zhiwen 
Published: April 2024

AbstractVan der Waals (vdW) assembly of low-dimensional materials has proven the capability of creating structures with on-demand properties. It is predicted that the vdW encapsulation can induce a local high-pressure of a few GPa, which will strongly modify the structure and property of trapped materials. Here, we report on the structural collapse of carbon nanotubes (CNTs) induced by the vdW encapsulation. By simply covering CNTs with a hexagonal boron nitride flake, most of the CNTs (≈77%) convert from a tubular structure to a collapsed flat structure. Regardless of their original diameters, all the collapsed CNTs exhibit a uniform height of ≈0.7 nm, which is roughly the thickness of bilayer graphene. Such structural collapse is further confirmed by Raman spectroscopy, which shows a prominent broadening and blue shift in the Raman G-peak. The vdW encapsulation-induced collapse of CNTs is fully captured by molecular dynamics simulations of the local vdW pressure. Further near-field optical characterization reveals a metal-semiconductor transition in accompany with the CNT structural collapse. Our study provides not only a convenient approach to generate local high-pressure for fundamental research, but also a collapsed-CNT semiconductor for nanoelectronic applications.
Empowering high-dimensional optical fiber communications with integrated photonic processors
Authors: Lu Kaihang , Chen Zengqi , Chen Hao , Zhou Wu , Zhang Zunyue , Tsang Hon Ki , Tong Yeyu 
Published: April 2024

AbstractMode-division multiplexing (MDM) in optical fibers enables multichannel capabilities for various applications, including data transmission, quantum networks, imaging, and sensing. However, high-dimensional optical fiber systems, usually necessity bulk-optics approaches for launching different orthogonal fiber modes into the optical fiber, and multiple-input multiple-output digital electronic signal processing at the receiver to undo the arbitrary mode scrambling introduced by coupling and transmission in a multi-mode fiber. Here we show that a high-dimensional optical fiber communication system can be implemented by a reconfigurable integrated photonic processor, featuring kernels of multichannel mode multiplexing transmitter and all-optical descrambling receiver. Effective mode management can be achieved through the configuration of the integrated optical mesh. Inter-chip MDM optical communications involving six spatial- and polarization modes was realized, despite the presence of unknown mode mixing and polarization rotation in the circular-core optical fiber. The proposed photonic integration approach holds promising prospects for future space-division multiplexing applications.
Subgroup analyses from the phase 3 ASCENT study of sacituzumab govitecan in metastatic triple-negative breast cancer
Authors: Hurvitz Sara A. , Bardia Aditya , Punie Kevin , Kalinsky Kevin , Carey Lisa A. , Rugo Hope S. , Diéras Véronique , Phan See , Delaney Rosemary , Zhu Yanni , Tolaney Sara M. 
Published: April 2024

AbstractIn this post hoc analysis of the ASCENT study, we compared outcomes with sacituzumab govitecan (SG) vs single-agent chemotherapy in clinically important subgroups of patients with metastatic triple-negative breast cancer (mTNBC). Patients with mTNBC refractory to/relapsing after ≥2 prior chemotherapies (≥1 in the metastatic setting) were randomized 1:1 to receive SG or treatment of physician’s choice (TPC) until unacceptable toxicity/progression. The primary endpoint was progression-free survival (PFS) per RECIST 1.1 by central review in patients without brain metastases. Patients with brain metastases were allowed if metastases were stable ≥4 weeks. In the intention-to-treat (ITT) population, 19% of patients were age ≥65 years; 12% were Black, and 12% had brain metastases. SG improved PFS and overall survival (OS), respectively, vs TPC in patients age ≥65 years (7.1 vs 2.4 months and 14.7 vs 8.9 months), or of Black race (5.4 vs 2.2 months and 13.8 vs 8.5 months), consistent with outcomes in the ITT population. Patients with brain metastases had numerically higher median PFS with SG vs TPC, but median OS was similar between treatment groups. SG was well tolerated and had a manageable safety profile consistent with the full safety population across all subgroups; neutropenia and diarrhea were the most common treatment-emergent adverse events. These findings confirm the meaningful clinical benefit of SG vs standard chemotherapy in patient subgroups with high unmet needs. SG should be considered an effective and safe treatment option for patients with mTNBC eligible for second-line or later therapy. ClinicalTrials.gov Number: NCT02574455.
Passivation and corrosion of Al current collectors in lithium-ion batteries
Authors: Du Pin , Wan Jiale , Qu Jiakang , Xie Hongwei , Wang Dihua , Yin Huayi 
Published: April 2024

AbstractState-of-the-art lithium-ion batteries inevitably suffer from electrode corrosion over long-term operation, such as corrosion of Al current collectors. However, the understanding of Al corrosion and its impacts on the battery performances have not been evaluated in detail. The passivation, its breakdown, and corrosion of the Al resulted in the deterioration of the solid/solid interface and electrode integrity. Additionally, localized diffusion of F−/Al3+ brought the irreversible current detrimental to the Coulomb efficiency (1.14% loss). Eventually, the behavior led to extensive capacity damage (>20%) to battery performance until lifespan. During the battery cycling, the passivation layer greater than 20 nm was generated near the median voltage. When the charging voltage rose, the passivation layer was squeezed and deformed by the newly generated Al-F-O particles, resulting in stress corrosion cracks. The passivation layer peeled off, and the nano-passivation layer material was re-generated as the voltage continued to rise. The above results were repeated, and the Al matrix was continuously consumed. The passivity breakdown with localized corrosion was derived from ethylene carbonate adsorption, which was highly correlated to the charge voltages, especially at 4.4 V and 4.8 V. The results will serve as a benchmark for electrode corrosion of other advanced energy storage materials, which is crucial for electrode engineering and performance modulation using interfacial design.
Calcia magnesia alumino silicate (CMAS) corrosion attack on thermally sprayed thermal barrier coatings: a comprehensive review
Authors: Nair Rakesh Bhaskaran , Brabazon Dermot 
Published: April 2024

AbstractCalcia-Magnesia-Alumino Silicate (CMAS) is a form of molten siliceous residue generated at elevated temperatures within aeroengines. CMAS adheres to the surface of thermal barrier coatings (TBCs) and has the potential to cause significant damage to engine components, resulting in TBC failures. The aviation industry has long recognized CMAS as a substantial threat to aircraft engines, and this threat persists today. A substantial amount of research has been carried out, primarily focusing on gaining a fundamental understanding of the degradation mechanism of traditional TBCs manufactured using air plasma spraying (APS) and electron beam physical vapor deposition (EB-PVD) technologies after CMAS attack. A thorough understanding of why CMAS forms, its role in causing severe spallation, and how to prevent it is of significant concern both academically and industrially. This review article provides a detailed examination of the chemistry of CMAS and the resulting degradation mechanisms that the TBC may encounter throughout the aeroengine service life. This article also explores recent research, incorporating case studies, on the impact of CMAS attack on the resulting chemical and structural modifications of the ceramic topcoats. Current strategies designed to mitigate CMAS infiltration and perspectives for enhanced mitigation are discussed.
Students’ performance, attitude, and classroom observation data to assess the effect of problem-based learning approach supplemented by YouTube videos in Ugandan classroom
Authors: Gumisirizah Nicholus , Nzabahimana Joseph , Muwonge Charles M. 
Published: April 2024

AbstractIn response to global demands, Uganda’s Vision 2040 seeks to transform the country into a modern and prosperous nation by implementing Sustainable Development Goal (SDG) 4, focusing on equitable and quality education. The 21st-century workforce requires individuals who can effectively navigate complex workplace challenges. This dataset was gathered from Form-2 Ugandan secondary school students (aged 12 to 15) across 12 schools in the Sheema District. The dataset comprises three types of data: students’ performance in a physics topic (simple machines), their attitudes toward problem-solving and critical thinking when learning physics using Problem-Based Learning (PBL) supplemented by YouTube videos, and classroom observations documented with the reformed teaching observational protocol (RTOP). The intervention of teaching using PBL was executed in 2022, collecting data from 973 lower secondary school students. The intervention involved three approaches: one group (144 students) received PBL along with YouTube videos, another group of 482 students received PBL alone, and a third group (347 students) was taught using the traditional method. This data article explains the study’s data creation, collection, and analysis process. The dataset holds significance for secondary school teachers, policymakers, and researchers, offering insights into the impact of PBL with and without ICT resources on learning physics and students’ attitudes toward these learner-centered approaches.
Intra and interspecific audience effect on domestic dogs' behavioural displays and facial expressions
Authors: Pedretti Giulia , Canori Chiara , Costantini Elisa , Palme Rupert , Valsecchi Paola , Marshall-Pescini Sarah 
Published: April 2024

AbstractThe aim of the current study was to investigate the influence of both intra- and interspecific audiences on dogs' facial expressions and behaviours. Forty-six dogs were exposed to three test conditions in which a food reward, initially available, was denied when in the presence of either a human (Human condition) or a dog audience (Dog condition), or in the absence of a visible audience (Non-social condition). Salivary cortisol was collected to evaluate the stress/arousal activation in the different conditions. Compared to the Non-social condition, the presence of a conspecific evoked more facial expressions, according to the DogFACS (Facial Action Coding System, an anatomically based tool to analyze facial expressions in domestic dogs), (EAD105—Ears downward), displacement behaviours (AD137—Nose licking, AD37—Lip wiping), tail wagging, whining, and panting (AD126). When facing a conspecific, dogs assumed a more avoidant attitude, keeping a distance and not looking at the stimuli, compared to when in the presence of the human partner. Dogs also exhibited more facial expressions (EAD102—Ears Adductor, EAD104—Ears Rotator), displacement behaviours (AD137—Nose licking, AD37—Lip wiping), panting (AD126) and whining when facing the conspecific than the human partner. Post-test cortisol was not influenced by any condition, and no association between pre-test cortisol and behavioural variables was found, thus strong differences in the levels of stress/arousal were unlikely to be responsible for differences in behavior between conditions. Considering the current results in the context of the available literature, we suggest that the higher displacement behaviors exhibited with the conspecifics were likely due to an increased level of uncertainty regarding the situations.