bluuebunny/crossref_metadata_2025_split huggingface dataset:
SARS-CoV-2 hijacks a cell damage response, which induces transcription of a more efficient Spike S-acyltransferase
Authors: S. Mesquita Francisco , Abrami Laurence , Bracq Lucie , Panyain Nattawadee , Mercier Vincent , Kunz Béatrice , Chuat Audrey , Carlevaro-Fita Joana , Trono Didier , van der Goot F. Gisou 
Published: November 2023

AbstractSARS-CoV-2 infection requires Spike protein-mediated fusion between the viral and cellular membranes. The fusogenic activity of Spike depends on its post-translational lipid modification by host S-acyltransferases, predominantly ZDHHC20. Previous observations indicate that SARS-CoV-2 infection augments the S-acylation of Spike when compared to mere Spike transfection. Here, we find that SARS-CoV-2 infection triggers a change in the transcriptional start site of the zdhhc20 gene, both in cells and in an in vivo infection model, resulting in a 67-amino–acid-long N-terminally extended protein with approx. 40 times higher Spike acylating activity, resulting in enhanced fusion of viruses with host cells. Furthermore, we observed the same induced transcriptional change in response to other challenges, such as chemically induced colitis and pore-forming toxins, indicating that SARS-CoV-2 hijacks an existing cell damage response pathway to optimize it fusion glycoprotein.
Topological magnons driven by the Dzyaloshinskii-Moriya interaction in the centrosymmetric ferromagnet Mn5Ge3
Authors: dos Santos Dias M. , Biniskos N. , dos Santos F. J. , Schmalzl K. , Persson J. , Bourdarot F. , Marzari N. , Blügel S. , Brückel T. , Lounis S. 
Published: November 2023

AbstractThe phase of the quantum-mechanical wave function can encode a topological structure with wide-ranging physical consequences, such as anomalous transport effects and the existence of edge states robust against perturbations. While this has been exhaustively demonstrated for electrons, properties associated with the elementary quasiparticles in magnetic materials are still underexplored. Here, we show theoretically and via inelastic neutron scattering experiments that the bulk ferromagnet Mn5Ge3 hosts gapped topological Dirac magnons. Although inversion symmetry prohibits a net Dzyaloshinskii-Moriya interaction in the unit cell, it is locally allowed and is responsible for the gap opening in the magnon spectrum. This gap is predicted and experimentally verified to close by rotating the magnetization away from the c-axis with an applied magnetic field. Hence, Mn5Ge3 realizes a gapped Dirac magnon material in three dimensions. Its tunability by chemical doping or by thin film nanostructuring defines an exciting new platform to explore and design topological magnons. More generally, our experimental route to verify and control the topological character of the magnons is applicable to bulk centrosymmetric hexagonal materials, which calls for systematic investigation.
Direct observation of intrinsic room-temperature ferroelectricity in 2D layered CuCrP2S6
Authors: Io Weng Fu , Pang Sin -Yi , Wong Lok Wing , Zhao Yuqian , Ding Ran , Mao Jianfeng , Zhao Yifei , Guo Feng , Yuan Shuoguo , Zhao Jiong , Yi Jiabao , Hao Jianhua 
Published: November 2023

AbstractMultiferroic materials have ignited enormous interest owing to their co-existence of ferroelectricity and ferromagnetism, which hold substantial promise for advanced device applications. However, the size effect, dangling bonds, and interface effect in traditional multiferroics severely hinder their potential in nanoscale device applications. Recent theoretical and experimental studies have evidenced the possibility of realizing two-dimensional (2D) multiferroicity in van der Waals (vdW) layered CuCrP2S6. However, the incorporation of magnetic Cr ions in the ferroelectric framework leads to antiferroelectric and antiferromagnetic orderings, while macroscopic spontaneous polarization is always absent. Herein, we report the direct observation of robust out-of-plane ferroelectricity in 2D vdW CuCrP2S6 at room temperature with a comprehensive investigation. Modification of the ferroelectric polarization states in 2D CuCrP2S6 nanoflakes is experimentally demonstrated. Moreover, external electric field-induced polarization switching and hysteresis loops are obtained in CuCrP2S6 down to ~2.6 nm (4 layers). By using atomically resolved scanning transmission electron microscopy, we unveil the origin of the emerged room-temperature ferroelectricity in 2D CuCrP2S6. Our work can facilitate the development of multifunctional nanodevices and provide important insights into the nature of ferroelectric ordering of this 2D vdW material.
Data-driven discovery of electrocatalysts for CO2 reduction using active motifs-based machine learning
Authors: Mok Dong Hyeon , Li Hong , Zhang Guiru , Lee Chaehyeon , Jiang Kun , Back Seoin 
Published: November 2023

AbstractThe electrochemical carbon dioxide reduction reaction (CO2RR) is an attractive approach for mitigating CO2 emissions and generating value-added products. Consequently, discovery of promising CO2RR catalysts has become a crucial task, and machine learning (ML) has been utilized to accelerate catalyst discovery. However, current ML approaches are limited to exploring narrow chemical spaces and provide only fragmentary catalytic activity, even though CO2RR produces various chemicals. Here, by merging pre-developed ML model and a CO2RR selectivity map, we establish high-throughput virtual screening strategy to suggest active and selective catalysts for CO2RR without being limited to a database. Further, this strategy can provide guidance on stoichiometry and morphology of the catalyst to researchers. We predict the activity and selectivity of 465 metallic catalysts toward four expected reaction products. During this process, we discover previously unreported and promising behavior of Cu-Ga and Cu-Pd alloys. These findings are then validated through experimental methods.
Dynamic construction of refractive index-dependent vibrations using surface plasmon-phonon polaritons
Authors: Zhou Hong , Ren Zhihao , Li Dongxiao , Xu Cheng , Mu Xiaojing , Lee Chengkuo 
Published: November 2023

AbstractOne of the fundamental hurdles in infrared spectroscopy is the failure of molecular identification when their infrared vibrational fingerprints overlap. Refractive index (RI) is another intrinsic property of molecules associated with electronic polarizability, but with limited contribution to molecular identification in mixed environments currently. Here, we investigate the coupling mode of localized surface plasmon and surface phonon polaritons for vibrational de-overlapping. The coupling mode is sensitive to the molecular refractive index, attributed to the RI-induced vibrational variations of surface phonon polaritons (SPhP) within the Reststrahlen band, referred to as RI-dependent SPhP vibrations. The RI-dependent SPhP vibrations are linked to molecular RI features. According to the deep-learning-augmented demonstration of bond-breaking-bond-making dynamic profiling in biological reaction, we substantiate that the RI-dependent SPhP vibrations effectively disentangle overlapping vibrational modes, achieving a 92% identification accuracy even for the strongly overlapping vibrational modes in the reaction. Our findings offer insights into the realm of light-matter interaction and provide a valuable toolkit for biomedicine applications.
Relational visual representations underlie human social interaction recognition
Authors: Malik Manasi , Isik Leyla 
Published: November 2023

AbstractHumans effortlessly recognize social interactions from visual input. Attempts to model this ability have typically relied on generative inverse planning models, which make predictions by inverting a generative model of agents’ interactions based on their inferred goals, suggesting humans use a similar process of mental inference to recognize interactions. However, growing behavioral and neuroscience evidence suggests that recognizing social interactions is a visual process, separate from complex mental state inference. Yet despite their success in other domains, visual neural network models have been unable to reproduce human-like interaction recognition. We hypothesize that humans rely on relational visual information in particular, and develop a relational, graph neural network model, SocialGNN. Unlike prior models, SocialGNN accurately predicts human interaction judgments across both animated and natural videos. These results suggest that humans can make complex social interaction judgments without an explicit model of the social and physical world, and that structured, relational visual representations are key to this behavior.
Virtual lesions in MEG reveal increasing vulnerability of the language network from early childhood through adolescence
Authors: Williamson Brady J. , Greiner Hansel M. , Kadis Darren S. 
Published: November 2023

AbstractIn childhood, language outcomes following brain injury are inversely related to age. Neuroimaging findings suggest that extensive representation and/or topological redundancy may confer the pediatric advantage. Here, we assess whole brain and language network resilience using in silico attacks, for 85 children participating in a magnetoencephalography (MEG) study. Nodes are targeted based on eigenvector centrality, betweenness centrality, or at random. The size of each connected component is assessed after iterated node removal; the percolation point, or moment of dis-integration, is defined as the first instance where the second largest component peaks in size. To overcome known effects of fixed thresholding on subsequent graph and resilience analyses, we study percolation across all possible network densities, within a Functional Data Analysis (FDA) framework. We observe age-related increases in vulnerability for random and betweenness centrality-based attacks for whole-brain and stories networks (adjusted-p < 0.05). Here we show that changes in topology underlie increasing language network vulnerability in development.
Genomics of soil depth niche partitioning in the Thaumarchaeota family Gagatemarchaeaceae
Authors: Sheridan Paul O. , Meng Yiyu , Williams Tom A. , Gubry-Rangin Cécile 
Published: November 2023

AbstractKnowledge of deeply-rooted non-ammonia oxidising Thaumarchaeota lineages from terrestrial environments is scarce, despite their abundance in acidic soils. Here, 15 new deeply-rooted thaumarchaeotal genomes were assembled from acidic topsoils (0-15 cm) and subsoils (30-60 cm), corresponding to two genera of terrestrially prevalent Gagatemarchaeaceae (previously known as thaumarchaeotal Group I.1c) and to a novel genus of heterotrophic terrestrial Thaumarchaeota. Unlike previous predictions, metabolic annotations suggest Gagatemarchaeaceae perform aerobic respiration and use various organic carbon sources. Evolutionary divergence between topsoil and subsoil lineages happened early in Gagatemarchaeaceae history, with significant metabolic and genomic trait differences. Reconstruction of the evolutionary mechanisms showed that the genome expansion in topsoil Gagatemarchaeaceae resulted from extensive early lateral gene acquisition, followed by progressive gene duplication throughout evolutionary history. Ancestral trait reconstruction using the expanded genomic diversity also did not support the previous hypothesis of a thermophilic last common ancestor of the ammonia-oxidising archaea. Ultimately, this study provides a good model for studying mechanisms driving niche partitioning between spatially related ecosystems.
Synthesis of dienes from pyrrolidines using skeletal modification
Authors: Qin Haitao , Guo Ting , Lin Ken , Li Guigen , Lu Hongjian 
Published: November 2023

AbstractSaturated N-heterocyclic pyrrolidines are common in natural products, medicinal compounds and agrochemicals. However, reconstruction of their skeletal structures creating new chemical space is a challenging task, and limited methods exist for this purpose. In this study, we report a skeletal modification strategy for conversion of polar cyclic pyrrolidines into nonpolar linear dienes through a N-atom removal and deconstruction process. This involves N-sulfonylazidonation followed by rearrangement of the resulting sulfamoyl azide intermediates. This can be an energetically unfavorable process, which involves the formation of active C–C π bonds, the consumption of inert C–N and C–C σ bonds and the destruction of stable five-membered rings, but we have used it here to produce versatile conjugated and nonconjugated dienes with links of varying lengths. We also studied the application of this method in late-stage skeletal modification of bioactive compounds, formal traceless C(sp2)–H functionalization and formal N-atom deletion.
Predicting early breast cancer recurrence from histopathological images in the Carolina Breast Cancer Study
Authors: Shi Yifeng , Olsson Linnea T. , Hoadley Katherine A. , Calhoun Benjamin C. , Marron J. S. , Geradts Joseph , Niethammer Marc , Troester Melissa A. 
Published: November 2023

AbstractApproaches for rapidly identifying patients at high risk of early breast cancer recurrence are needed. Image-based methods for prescreening hematoxylin and eosin (H&E) stained tumor slides could offer temporal and financial efficiency. We evaluated a data set of 704 1-mm tumor core H&E images (2–4 cores per case), corresponding to 202 participants (101 who recurred; 101 non-recurrent matched on age and follow-up time) from breast cancers diagnosed between 2008–2012 in the Carolina Breast Cancer Study. We leveraged deep learning to extract image information and trained a model to identify recurrence. Cross-validation accuracy for predicting recurrence was 62.4% [95% CI: 55.7, 69.1], similar to grade (65.8% [95% CI: 59.3, 72.3]) and ER status (66.3% [95% CI: 59.8, 72.8]). Interestingly, 70% (19/27) of early-recurrent low-intermediate grade tumors were identified by our image model. Relative to existing markers, image-based analyses provide complementary information for predicting early recurrence.
Interpass temperature effects on WAAM ER316L stainless steel corrosion using potentiostatic pulse tests
Authors: Penot Corentin , Wharton Julian , Addison Adrian , Wang Yikun , Lu Qing 
Published: November 2023

AbstractThe effect of interpass temperature on the microstructure and pit nucleation behaviour in wire and arc additive manufacturing (WAAM) deposited ER316L stainless steel is investigated. Lowering the interpass temperature increases the ferrite content and decreases the sigma phase precipitation. Potentiostatic pulse measurements show that the WAAM ER316L pits develop predominantly near sigma phases and have higher pit density compared to a wrought 316L (UNS S31600). The pitting susceptibility of WAAM ER316L increases with increasing interpass temperature due to the precipitation of larger sigma phase enhancing the elemental segregation.
Global dataset of soil organic carbon in tidal marshes
Authors: Maxwell Tania L. , Rovai André S. , Adame Maria Fernanda , Adams Janine B. , Álvarez-Rogel José , Austin William E. N. , Beasy Kim , Boscutti Francesco , Böttcher Michael E. , Bouma Tjeerd J. , Bulmer Richard H. , Burden Annette , Burke Shannon A. , Camacho Saritta , Chaudhary Doongar R. , Chmura Gail L. , Copertino Margareth , Cott Grace M. , Craft Christopher , Day John , de los Santos Carmen B. , Denis Lionel , Ding Weixin , Ellison Joanna C. , Ewers Lewis Carolyn J. , Giani Luise , Gispert Maria , Gontharet Swanne , González-Pérez José A. , González-Alcaraz M. Nazaret , Gorham Connor , Graversen Anna Elizabeth L. , Grey Anthony , Guerra Roberta , He Qiang , Holmquist James R. , Jones Alice R. , Juanes José A. , Kelleher Brian P. , Kohfeld Karen E. , Krause-Jensen Dorte , Lafratta Anna , Lavery Paul S. , Laws Edward A. , Leiva-Dueñas Carmen , Loh Pei Sun , Lovelock Catherine E. , Lundquist Carolyn J. , Macreadie Peter I. , Mazarrasa Inés , Megonigal J. Patrick , Neto Joao M. , Nogueira Juliana , Osland Michael J. , Pagès Jordi F. , Perera Nipuni , Pfeiffer Eva-Maria , Pollmann Thomas , Raw Jacqueline L. , Recio María , Ruiz-Fernández Ana Carolina , Russell Sophie K. , Rybczyk John M. , Sammul Marek , Sanders Christian , Santos Rui , Serrano Oscar , Siewert Matthias , Smeaton Craig , Song Zhaoliang , Trasar-Cepeda Carmen , Twilley Robert R. , Van de Broek Marijn , Vitti Stefano , Antisari Livia Vittori , Voltz Baptiste , Wails Christy N. , Ward Raymond D. , Ward Melissa , Wolfe Jaxine , Yang Renmin , Zubrzycki Sebastian , Landis Emily , Smart Lindsey , Spalding Mark , Worthington Thomas A. 
Published: November 2023

AbstractTidal marshes store large amounts of organic carbon in their soils. Field data quantifying soil organic carbon (SOC) stocks provide an important resource for researchers, natural resource managers, and policy-makers working towards the protection, restoration, and valuation of these ecosystems. We collated a global dataset of tidal marsh soil organic carbon (MarSOC) from 99 studies that includes location, soil depth, site name, dry bulk density, SOC, and/or soil organic matter (SOM). The MarSOC dataset includes 17,454 data points from 2,329 unique locations, and 29 countries. We generated a general transfer function for the conversion of SOM to SOC. Using this data we estimated a median (± median absolute deviation) value of 79.2 ± 38.1 Mg SOC ha−1 in the top 30 cm and 231 ± 134 Mg SOC ha−1 in the top 1 m of tidal marsh soils globally. This data can serve as a basis for future work, and may contribute to incorporation of tidal marsh ecosystems into climate change mitigation and adaptation strategies and policies.
Rapid surveillance of New York City healthcare center egress behaviors during the 2020 COVID-19 lockdown
Authors: Kirchner Thomas , Jiang Haoran , Gao Hong , Kabutaulaka Germaine , Cheong Darlene , Jiang Yungi , Khan Aseah , Qiu Weiyi , Tai Nikki , Truong Tiffany , Virk Maimunah , Gmelch Peter , Carey Chris , Laefer Debra 
Published: November 2023

AbstractThis rapid response surveillance project was funded by the National Science Foundation (NSF) to collect “perishable” data on egress behaviors and neighborhood conditions surrounding healthcare centers (HCCs) in New York City (NYC) during the initial NYC COVID-19 PAUSE ordinance from March 22nd to May 19th, 2020. Anonymized data on NYC HCC egress behaviors were collected by observational field workers using phone-based mapping applications. Each egress trip record includes the day of week, time of day, destination category type, along with an array of behavioral outcome categories, ambient weather conditions and socio-economic factors. Egress trajectories with precise estimates of distance traveled and the spatial dispersion or “spread” around each HCC were added via post-processing. The data collection and cleaning process resulted in 5,030 individual egress records from 18 facilities over a 9-week period.
Twenty-nine years of continuous monthly capture-mark-recapture data of multimammate mice (Mastomys natalensis) in Morogoro, Tanzania
Authors: Leirs Herwig , Kirkpatrick Lucinda , Sluydts Vincent , Sabuni Christopher , Borremans Benny , Katakweba Abdul , Massawe Apia , Makundi Rhodes , Mulungu Loth , Machang’u Robert , Mariën Joachim 
Published: November 2023

AbstractThe multimammate mice (Mastomys natalensis) is the most-studied rodent species in sub-Saharan Africa, where it is an important pest species in agriculture and carrier of zoonotic diseases (e.g. Lassa virus). Here, we provide a unique dataset that consists of twenty-nine years of continuous monthly capture-mark-recapture entries on one 3 ha mosaic field (MOSA) in Morogoro, Tanzania. It is one of the most accurate and long-running capture-recapture time series on a small mammal species worldwide and unique to Africa. The database can be used by ecologists to test hypotheses on the population dynamics of small mammals (e.g. to test the effect of climate change), or to validate new algorithms on real long-term field data (e.g. new survival analyses techniques). It is also useful for both scientists and decision-makers who want to optimize rodent control strategies and predict outbreaks of multimammate mice.
IDH1R132H mutation increases radiotherapy efficacy and a 4-gene radiotherapy-related signature of WHO grade 4 gliomas
Authors: Han Xuetao , Zhou Huandi , Sun Wei , Hou Liubing , Wang Yanqiang , Wang Hong , Lv Zhongqiang , Xue Xiaoying 
Published: November 2023

AbstractThe prognosis for the WHO grade 4 IDH-mutant astrocytoma is better than IDH-wildtype glioblastoma (GBM) patients. The purpose of this study is to explore the potential mechanism of how IDH1 mutation can increase the efficacy of radiotherapy and to establish a risk-score model to predict the efficacy of radiotherapy in WHO grade 4 gliomas. First, we conducted experimental study on the effect of IDH1R132H mutation on glioma cells in vitro. Radiosensitivity of glioma cells was detected by γ-H2AX after 5 Gy radiation. Cell proliferation, migration and invasion were determined respectively by CCK-8, EDU, monolayer cell migration scratch assay and Transwell assay. Then we analyzed IDH1 gene status and the survival of WHO grade 4 glioma patients received radiotherapy in our center and verified our results by analyzing CGGA and TCGA database. For the risk-score model, we use CGGA data to find genetic differences between WHO grade 4 IDH-mutant astrocytoma and IDH-wildtype GBM patients, and determined a 4-gene radiotherapy-related signature through survival analysis by R software. Evaluation and verification through different glioma validation sets and different statistical methods. For in vitro experiments, we established glioma cells stably overexpressing IDH1 wild-type and IDH1-mutant proteins. γ-H2AX assay showed that IDH1-mutant glioma cells had higher radiosensitivity than wild-type. CCK-8 and EDU assay showed that proliferation capacity of IDH1-mutant glioma cells declined. Transwell assay and monolayer cell migration scratch assay also showed that IDH1-mutant glioma cells reduced migration and invasion capabilities. Among the 83 WHO grade 4 glioma patients who received radiotherapy in our center, WHO grade 4 IDH-mutant astrocytoma patients had longer OS and PFS versus IDH-wildtype GBM (P = 0.0336, P = 0.0324, respectively). TCGA and CGGA database analysis had the similar results. Through complex analysis of CGGA and TCGA databases, we established a risk-model that can predict the efficacy of radiotherapy for WHO grade 4 glioma patients. The 4-gene radiotherapy-related signature including ADD3, GRHPR, RHBDL1 and SLC9A9. Patients in the high-risk group had worse OS compared to low-risk group (P = 0.0001). High- and low-risk groups of patients receiving radiotherapy have significant survival differences, while patients who did not receive radiotherapy have no survival difference both in CGGA and TCGA databases. WHO grade 4 IDH-mutant astrocytoma is more radiosensitive than IDH-wildtype GBM patients. Our 4-gene radiotherapy-related signature can predict the radiation efficacy of WHO grade 4 glioma patients, and it may provide some reference for clinical treatment options.