bluuebunny/crossref_metadata_2025_split huggingface dataset:
Fabricating strong and tough aramid fibers by small addition of carbon nanotubes
Authors: Luo Jiajun , Wen Yeye , Jia Xiangzheng , Lei Xudong , Gao Zhenfei , Jian Muqiang , Xiao Zhihua , Li Lanying , Zhang Jiangwei , Li Tao , Dong Hongliang , Wu Xianqian , Gao Enlai , Jiao Kun , Zhang Jin 
Published: May 2023

AbstractSynthetic high-performance fibers present excellent mechanical properties and promising applications in the impact protection field. However, fabricating fibers with high strength and high toughness is challenging due to their intrinsic conflicts. Herein, we report a simultaneous improvement in strength, toughness, and modulus of heterocyclic aramid fibers by 26%, 66%, and 13%, respectively, via polymerizing a small amount (0.05 wt%) of short aminated single-walled carbon nanotubes (SWNTs), achieving a tensile strength of 6.44 ± 0.11 GPa, a toughness of 184.0 ± 11.4 MJ m−3, and a Young’s modulus of 141.7 ± 4.0 GPa. Mechanism analyses reveal that short aminated SWNTs improve the crystallinity and orientation degree by affecting the structures of heterocyclic aramid chains around SWNTs, and in situ polymerization increases the interfacial interaction therein to promote stress transfer and suppress strain localization. These two effects account for the simultaneous improvement in strength and toughness.
An Aurora B-RPA signaling axis secures chromosome segregation fidelity
Authors: Roshan Poonam , Kuppa Sahiti , Mattice Jenna R. , Kaushik Vikas , Chadda Rahul , Pokhrel Nilisha , Tumala Brunda R. , Biswas Aparna , Bothner Brian , Antony Edwin , Origanti Sofia 
Published: May 2023

AbstractErrors in chromosome segregation underlie genomic instability associated with cancers. Resolution of replication and recombination intermediates and protection of vulnerable single-stranded DNA (ssDNA) intermediates during mitotic progression requires the ssDNA binding protein Replication Protein A (RPA). However, the mechanisms that regulate RPA specifically during unperturbed mitotic progression are poorly resolved. RPA is a heterotrimer composed of RPA70, RPA32 and RPA14 subunits and is predominantly regulated through hyperphosphorylation of RPA32 in response to DNA damage. Here, we have uncovered a mitosis-specific regulation of RPA by Aurora B kinase. Aurora B phosphorylates Ser-384 in the DNA binding domain B of the large RPA70 subunit and highlights a mode of regulation distinct from RPA32. Disruption of Ser-384 phosphorylation in RPA70 leads to defects in chromosome segregation with loss of viability and a feedback modulation of Aurora B activity. Phosphorylation at Ser-384 remodels the protein interaction domains of RPA. Furthermore, phosphorylation impairs RPA binding to DSS1 that likely suppresses homologous recombination during mitosis by preventing recruitment of DSS1-BRCA2 to exposed ssDNA. We showcase a critical Aurora B-RPA signaling axis in mitosis that is essential for maintaining genomic integrity.
Polarization patterning in ferroelectric nematic liquids via flexoelectric coupling
Authors: Sebastián Nerea , Lovšin Matija , Berteloot Brecht , Osterman Natan , Petelin Andrej , Mandle Richard J. , Aya Satoshi , Huang Mingjun , Drevenšek-Olenik Irena , Neyts Kristiaan , Mertelj Alenka 
Published: May 2023

AbstractThe recently discovered ferroelectric nematic liquids incorporate to the functional combination of fluidity, processability and anisotropic optical properties of nematic liquids, an astonishing range of physical properties derived from the phase polarity. Among them, the remarkably large values of second order optical susceptibility encourage to exploit these new materials for non-linear photonic applications. Here we show that photopatterning of the alignment layer can be used to structure polarization patterns. To do so, we take advantage of the flexoelectric effect and design splay structures that geometrically define the polarization direction. We demonstrate the creation of periodic polarization structures and the possibility of guiding polarization by embedding splay structures in uniform backgrounds. The demonstrated capabilities of polarization patterning, open a promising new route for the design of ferroelectric nematic based photonic structures and their exploitation.
Machine learning-enabled exploration of the electrochemical stability of real-scale metallic nanoparticles
Authors: Bang Kihoon , Hong Doosun , Park Youngtae , Kim Donghun , Han Sang Soo , Lee Hyuck Mo 
Published: May 2023

AbstractSurface Pourbaix diagrams are critical to understanding the stability of nanomaterials in electrochemical environments. Their construction based on density functional theory is, however, prohibitively expensive for real-scale systems, such as several nanometer-size nanoparticles (NPs). Herein, with the aim of accelerating the accurate prediction of adsorption energies, we developed a bond-type embedded crystal graph convolutional neural network (BE-CGCNN) model in which four bonding types were treated differently. Owing to the enhanced accuracy of the bond-type embedding approach, we demonstrate the construction of reliable Pourbaix diagrams for very large-size NPs involving up to 6525 atoms (approximately 4.8 nm in diameter), which enables the exploration of electrochemical stability over various NP sizes and shapes. BE-CGCNN-based Pourbaix diagrams well reproduce the experimental observations with increasing NP size. This work suggests a method for accelerated Pourbaix diagram construction for real-scale and arbitrarily shaped NPs, which would significantly open up an avenue for electrochemical stability studies.
An ancient metabolite damage-repair system sustains photosynthesis in plants
Authors: Leister Dario , Sharma Anurag , Kerber Natalia , Nägele Thomas , Reiter Bennet , Pasch Viviana , Beeh Simon , Jahns Peter , Barbato Roberto , Pribil Mathias , Rühle Thilo 
Published: May 2023

AbstractRibulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco) is the major catalyst in the conversion of carbon dioxide into organic compounds in photosynthetic organisms. However, its activity is impaired by binding of inhibitory sugars such as xylulose-1,5-bisphosphate (XuBP), which must be detached from the active sites by Rubisco activase. Here, we show that loss of two phosphatases in Arabidopsis thaliana has detrimental effects on plant growth and photosynthesis and that this effect could be reversed by introducing the XuBP phosphatase from Rhodobacter sphaeroides. Biochemical analyses revealed that the plant enzymes specifically dephosphorylate XuBP, thus allowing xylulose-5-phosphate to enter the Calvin-Benson-Bassham cycle. Our findings demonstrate the physiological importance of an ancient metabolite damage-repair system in degradation of by-products of Rubisco, and will impact efforts to optimize carbon fixation in photosynthetic organisms.
Retrosynthesis prediction using an end-to-end graph generative architecture for molecular graph editing
Authors: Zhong Weihe , Yang Ziduo , Chen Calvin Yu-Chian 
Published: May 2023

AbstractRetrosynthesis planning, the process of identifying a set of available reactions to synthesize the target molecules, remains a major challenge in organic synthesis. Recently, computer-aided synthesis planning has gained renewed interest and various retrosynthesis prediction algorithms based on deep learning have been proposed. However, most existing methods are limited to the applicability and interpretability of model predictions, and further improvement of predictive accuracy to a more practical level is still required. In this work, inspired by the arrow-pushing formalism in chemical reaction mechanisms, we present an end-to-end architecture for retrosynthesis prediction called Graph2Edits. Specifically, Graph2Edits is based on graph neural network to predict the edits of the product graph in an auto-regressive manner, and sequentially generates transformation intermediates and final reactants according to the predicted edits sequence. This strategy combines the two-stage processes of semi-template-based methods into one-pot learning, improving the applicability in some complicated reactions, and also making its predictions more interpretable. Evaluated on the standard benchmark dataset USPTO-50k, our model achieves the state-of-the-art performance for semi-template-based retrosynthesis with a promising 55.1% top-1 accuracy.
Bridging the immunogenicity of a tetravalent dengue vaccine (TAK-003) from children and adolescents to adults
Authors: LeFevre Inge , Bravo Lulu , Folschweiller Nicolas , Medina Eduardo Lopez , Moreira Edson Duarte , Nordio Francesco , Sharma Mayuri , Tharenos Leslie M. , Tricou Vianney , Watanaveeradej Veerachai , Winkle Peter J. , Biswal Shibadas 
Published: May 2023

AbstractImmunobridging is an important methodology that can be used to extrapolate vaccine efficacy estimates to populations not evaluated in clinical studies, and that has been successfully used in developing many vaccines. Dengue, caused by a mosquito-transmitted flavivirus endemic to many tropical and subtropical regions, is traditionally thought of as a pediatric disease but is now a global threat to both children and adults. We bridged immunogenicity data from a phase 3 efficacy study of a tetravalent dengue vaccine (TAK-003), performed in children and adolescents living in endemic areas, with an immunogenicity study in adults in non-endemic areas. Neutralizing antibody responses were comparable in both studies following receipt of a two-dose TAK-003 schedule (months 0 and 3). Similar immune responses were observed across exploratory assessments of additional humoral responses. These data support the potential for clinical efficacy of TAK-003 in adults.
Strong immune responses and protection of PcrV and OprF-I mRNA vaccine candidates against Pseudomonas aeruginosa
Authors: Wang Xingyun , Liu Cong , Rcheulishvili Nino , Papukashvili Dimitri , Xie Fengfei , Zhao Jiao , Hu Xing , Yu Kaiwei , Yang Nuo , Pan Xuehua , Liu Xueyan , Wang Peng George , He Yunjiao 
Published: May 2023

AbstractPseudomonas aeruginosa (PA) is a leading cause of hospital-acquired and ventilator-associated pneumonia. The multidrug-resistance (MDR) rate of PA is increasing making the management of PA a global challenge. Messenger RNA (mRNA) vaccines represent the most promising alternative to conventional vaccines and are widely studied for viral infection and cancer immunotherapy while rarely studied for bacterial infections. In this study, two mRNA vaccines encoding PcrV– the key component of the type III secretion system in Pseudomonas and the fusion protein OprF-I comprising outer membrane proteins OprF and OprI were constructed. The mice were immunized with either one of these mRNA vaccines or with the combination of both. Additionally, mice were vaccinated with PcrV, OprF, or the combination of these two proteins. Immunization with either mRNA-PcrV or mRNA-OprF-I elicited a Th1/Th2 mixed or slighted Th1-biased immune response, conferred broad protection, and reduced bacterial burden and inflammation in burn and systemic infection models. mRNA-PcrV induced significantly stronger antigen-specific humoral and cellular immune responses and higher survival rate compared with the OprF-I after challenging with all the PA strains tested. The combined mRNA vaccine demonstrated the best survival rate. Moreover, the mRNA vaccines showed the superiority over protein vaccines. These results suggest that mRNA-PcrV as well as the mixture of mRNA-PcrV and mRNA-OprF-I are promising vaccine candidates for the prevention of PA infection.
Transverse oscillations and an energy source in a strongly magnetized sunspot
Authors: Yuan Ding , Fu Libo , Cao Wenda , Kuźma Błażej , Geeraerts Michaël , Trelles Arjona Juan C. , Murawski Kris , Van Doorsselaere Tom , Srivastava Abhishek K. , Miao Yuhu , Feng Song , Feng Xueshang , Noda Carlos Quintero , Cobo Basilio Ruiz , Su Jiangtao 
Published: May 2023

AbstractThe solar corona is two to three orders of magnitude hotter than the underlying photosphere, and the energy loss of coronal plasma is extremely strong, requiring a heating flux of over 1,000 W m−2 to maintain its high temperature. Using the 1.6 m Goode Solar Telescope, we report a detection of ubiquitous and persistent transverse waves in umbral fibrils in the chromosphere of a strongly magnetized sunspot. The energy flux carried by these waves was estimated to be 7.52 × 106 W m−2, three to four orders of magnitude stronger than the energy loss rate of plasma in active regions. Two-fluid magnetohydrodynamic simulations reproduced the high-resolution observations and showed that these waves dissipate significant energy, which is vital for coronal heating. Such transverse oscillations and the associated strong energy flux may exist in a variety of magnetized regions on the Sun, and could be the observational target of next-generation solar telescopes.
Fibril formation and ordering of disordered FUS LC driven by hydrophobic interactions
Authors: Maltseva Daria , Chatterjee Sayantan , Yu Chun-Chieh , Brzezinski Mateusz , Nagata Yuki , Gonella Grazia , Murthy Anastasia C. , Stachowiak Jeanne C. , Fawzi Nicolas L. , Parekh Sapun H. , Bonn Mischa 
Published: May 2023

AbstractBiomolecular condensates, protein-rich and dynamic membrane-less organelles, play critical roles in a range of subcellular processes, including membrane trafficking and transcriptional regulation. However, aberrant phase transitions of intrinsically disordered proteins in biomolecular condensates can lead to the formation of irreversible fibrils and aggregates that are linked to neurodegenerative diseases. Despite the implications, the interactions underlying such transitions remain obscure. Here we investigate the role of hydrophobic interactions by studying the low-complexity domain of the disordered ‘fused in sarcoma’ (FUS) protein at the air/water interface. Using surface-specific microscopic and spectroscopic techniques, we find that a hydrophobic interface drives fibril formation and molecular ordering of FUS, resulting in solid-like film formation. This phase transition occurs at 600-fold lower FUS concentration than required for the canonical FUS low-complexity liquid droplet formation in bulk. These observations highlight the importance of hydrophobic effects for protein phase separation and suggest that interfacial properties drive distinct protein phase-separated structures.
Very short-lived halogens amplify ozone depletion trends in the tropical lower stratosphere
Authors: Villamayor Julián , Iglesias-Suarez Fernando , Cuevas Carlos A. , Fernandez Rafael P. , Li Qinyi , Abalos Marta , Hossaini Ryan , Chipperfield Martyn P. , Kinnison Douglas E. , Tilmes Simone , Lamarque Jean-François , Saiz-Lopez Alfonso 
Published: May 2023

AbstractIn contrast to the general stratospheric ozone recovery following international agreements, recent observations show an ongoing net ozone depletion in the tropical lower stratosphere (LS). This depletion is thought to be driven by dynamical transport accelerated by global warming, while chemical processes have been considered to be unimportant. Here we use a chemistry–climate model to demonstrate that halogenated ozone-depleting very short-lived substances (VSLS) chemistry may account for around a quarter of the observed tropical LS negative ozone trend in 1998–2018. VSLS sources include both natural and anthropogenic emissions. Future projections show the persistence of the currently unaccounted for contribution of VSLS to ozone loss throughout the twenty-first century in the tropical LS, the only region of the global stratosphere not projecting an ozone recovery by 2100. Our results show the need for mitigation strategies of anthropogenic VSLS emissions to preserve the present and future ozone layer in low latitudes.
Grooved electrodes for high-power-density fuel cells
Authors: Lee ChungHyuk , Kort-Kamp Wilton J. M. , Yu Haoran , Cullen David A. , Patterson Brian M. , Arman Tanvir Alam , Komini Babu Siddharth , Mukundan Rangachary , Borup Rod L. , Spendelow Jacob S. 
Published: May 2023

AbstractProton exchange membrane fuel cells (PEMFCs) are leading candidates to decarbonize the transport sector, but widespread deployment will require improvements in lifetime, fuel economy and cost. Here we present the grooved electrode, an alternative electrode structure that enhances PEMFC performance and durability by coupling high ionomer (ion-conducting binder) content for improved H+ transport with grooves for rapid O2 transport. Grooved electrodes provide up to 50% higher performance than state-of-the-art conventional electrodes under standard operating conditions. Fuel cell diagnostics combined with multiphysics modelling demonstrate that grooved electrodes provide facile O2 transport despite their high ionomer content, enabling improved reaction rate uniformity. Grooved electrodes also provide improved durability, with less performance loss after carbon corrosion compared with baseline electrodes. Machine learning analysis demonstrates the potential to further optimize grooved structures for next-generation PEMFCs with enhanced performance and durability, enabling smaller and cheaper fuel cell stacks with higher fuel efficiency.
IngridKG: A FAIR Knowledge Graph of Graffiti
Authors: Sherif Mohamed Ahmed , da Silva Ana Alexandra Morim , Pestryakova Svetlana , Ahmed Abdullah Fathi , Niemann Sven , Ngomo Axel-Cyrille Ngonga 
Published: May 2023

AbstractGraffiti is an urban phenomenon that is increasingly attracting the interest of the sciences. To the best of our knowledge, no suitable data corpora are available for systematic research until now. The Information System Graffiti in Germany project (Ingrid) closes this gap by dealing with graffiti image collections that have been made available to the project for public use. Within Ingrid, the graffiti images are collected, digitized and annotated. With this work, we aim to support the rapid access to a comprehensive data source on Ingrid targeted especially by researchers. In particular, we present IngridKG, an RDF knowledge graph of annotated graffiti, abides by the Linked Data and FAIR principles. We weekly update IngridKG by augmenting the new annotated graffiti to our knowledge graph. Our generation pipeline applies RDF data conversion, link discovery and data fusion approaches to the original data. The current version of IngridKG contains 460,640,154 triples and is linked to 3 other knowledge graphs by over 200,000 links. In our use case studies, we demonstrate the usefulness of our knowledge graph for different applications.
The first high-quality chromosome-level genome of the Sipuncula Sipunculus nudus using HiFi and Hi-C data
Authors: Zheng Zhe , Lai Zhuoxin , Wu Bin , Song Xinlin , Zhao Wei , Zhong Ruzhuo , Zhang Jiawei , Liao Yongshan , Yang Chuangye , Deng Yuewen , Mei Junpu , Yue Zhen , Jian Jianbo , Wang Qingheng 
Published: May 2023

AbstractSipuncula is a class of exocoelomic unsegmented animals whose evolutionary relationships are unresolved. The peanut worm Sipunculus nudus is a globally distributed, economically important species belonging to the class Sipuncula. Herein, we present the first high-quality chromosome-level assembly of S. nudus based on HiFi reads and high-resolution chromosome conformation capture (Hi-C) data. The assembled genome was 1,427 Mb, with a contig N50 length of 29.46 Mb and scaffold N50 length of 80.87 Mb. Approximately 97.91% of the genome sequence was anchored to 17 chromosomes. A BUSCO assessment showed that 97.7% of the expectedly conserved genes were present in the genome assembly. The genome was composed of 47.91% repetitive sequences, and 28,749 protein-coding genes were predicted. A phylogenetic tree demonstrated that Sipuncula belongs to Annelida and diverged from the common ancestor of Polychaeta. The high-quality chromosome-level genome of S. nudus will serve as a valuable reference for studies of the genetic diversity and evolution of Lophotrochozoa.
Magnetic DNA random access memory with nanopore readouts and exponentially-scaled combinatorial addressing
Authors: Lau Billy , Chandak Shubham , Roy Sharmili , Tatwawadi Kedar , Wootters Mary , Weissman Tsachy , Ji Hanlee P. 
Published: May 2023

AbstractThe storage of data in DNA typically involves encoding and synthesizing data into short oligonucleotides, followed by reading with a sequencing instrument. Major challenges include the molecular consumption of synthesized DNA, basecalling errors, and limitations with scaling up read operations for individual data elements. Addressing these challenges, we describe a DNA storage system called MDRAM (Magnetic DNA-based Random Access Memory) that enables repetitive and efficient readouts of targeted files with nanopore-based sequencing. By conjugating synthesized DNA to magnetic agarose beads, we enabled repeated data readouts while preserving the original DNA analyte and maintaining data readout quality. MDRAM utilizes an efficient convolutional coding scheme that leverages soft information in raw nanopore sequencing signals to achieve information reading costs comparable to Illumina sequencing despite higher error rates. Finally, we demonstrate a proof-of-concept DNA-based proto-filesystem that enables an exponentially-scalable data address space using only small numbers of targeting primers for assembly and readout.
Stochastic gradient descent for optimization for nuclear systems
Authors: Williams Austin , Walton Noah , Maryanski Austin , Bogetic Sandra , Hines Wes , Sobes Vladimir 
Published: May 2023

AbstractThe use of gradient descent methods for optimizing k-eigenvalue nuclear systems has been shown to be useful in the past, but the use of k-eigenvalue gradients have proved computationally challenging due to their stochastic nature. ADAM is a gradient descent method that accounts for gradients with a stochastic nature. This analysis uses challenge problems constructed to verify if ADAM is a suitable tool to optimize k-eigenvalue nuclear systems. ADAM is able to successfully optimize nuclear systems using the gradients of k-eigenvalue problems despite their stochastic nature and uncertainty. Furthermore, it is clearly demonstrated that low-compute time, high-variance estimates of the gradient lead to better performance in the optimization challenge problems tested here.
A network meta-analysis assessing the effectiveness of various radical and conservative surgical approaches regarding recurrence in treating solid/multicystic ameloblastomas
Authors: Hendra Faqi Nurdiansyah , Helder Marco N. , Ruslin Muhammad , Van Cann Ellen M. , Forouzanfar Tymour 
Published: May 2023

AbstractMultiple treatment approaches have been undertaken to reduce the incidence of recurrence in solid/multicystic ameloblastoma (SMA), both conservative and radical. A network meta-analysis (NMA) was conducted to assess and compare the effectiveness of these various treatment approaches concurrently. This study was reported based on the Preferred Reporting Items for Systematic Reviews for Network Meta-Analysis (PRISMA-NMA) statement. PubMed (MEDLINE), ScienceDirect, Scopus, and Web of Science were searched until August 10, 2021. The NMA was conducted using the STATA program. Of 1153 records identified in the search, seven observational studies with 180 patients were included. Six different treatment approaches were identified. Segmental resection ranked highest for reducing the recurrence rate with the highest SUCRA score (77.7), followed by curettage with cryotherapy (66.9) and marginal resection (49.3). Network inconsistencies and publication bias appeared to be absent. According to the Confidence in Network Meta-Analysis (CINeMa) method, the evidence's certainty was low for all comparisons due to imprecision and within-study bias. In conclusion, this study is the first NMA in the field of ameloblastoma. Segmental resection seemed to be the most effective treatment approach for minimizing recurrence in SMA patients. Nevertheless, weak certainty of evidence makes that the results must be regarded with caution.