bluuebunny/crossref_metadata_2025_split huggingface dataset:
Dislocation interactions during plastic relaxation of epitaxial colloidal crystals
Authors: Svetlizky Ilya , Kim Seongsoo , Weitz David A. , Spaepen Frans 
Published: September 2023

AbstractThe severe difficulty to resolve simultaneously both the macroscopic deformation process and the dislocation dynamics on the atomic scale limits our understanding of crystal plasticity. Here we use colloidal crystals, imaged on the single particle level by high-speed three-dimensional (3D) confocal microscopy, and resolve in real-time both the relaxation of the epitaxial misfit strain and the accompanying evolution of dislocations. We show how dislocation interactions give rise to the formation of complex dislocation networks in 3D and to unexpectedly sharp plastic relaxation. The sharp relaxation is facilitated by attractive interactions that promote the formation of new dislocations that are more efficient in mediating strain. Dislocation networks form fragmented structures, as dislocation growth is blocked by either attractive interactions, which result in the formation of sessile dislocation junctions, or by repulsion from perpendicular segments. The strength of these blocking mechanisms decreases with the thickness of the crystal film. These results reveal the critical role of dislocation interactions in plastic deformation of thin films and can be readily generalized from the colloidal to the atomic scale.
Smart dynamic hybrid membranes with self-cleaning capability
Authors: Pantuso Elvira , Ahmed Ejaz , Fontananova Enrica , Brunetti Adele , Tahir Ibrahim , Karothu Durga Prasad , Alnaji Nisreen Amer , Dushaq Ghada , Rasras Mahmoud , Naumov Panče , Di Profio Gianluca 
Published: September 2023

AbstractThe growing freshwater scarcity has caused increased use of membrane desalination of seawater as a relatively sustainable technology that promises to provide long-term solution for the increasingly water-stressed world. However, the currently used membranes for desalination on an industrial scale are inevitably prone to fouling that results in decreased flux and necessity for periodic chemical cleaning, and incur unacceptably high energy cost while also leaving an environmental footprint with unforeseeable long-term consequences. This extant problem requires an immediate shift to smart separation approaches with self-cleaning capability for enhanced efficiency and prolonged operational lifetime. Here, we describe a conceptually innovative approach to the design of smart membranes where a dynamic functionality is added to the surface layer of otherwise static membranes by incorporating stimuli-responsive organic crystals. We demonstrate a gating effect in the resulting smart dynamic membranes, whereby mechanical instability caused by rapid mechanical response of the crystals to heating slightly above room temperature activates the membrane and effectively removes the foulants, thereby increasing the mass transfer and extending its operational lifetime. The approach proposed here sets a platform for the development of a variety of energy-efficient hybrid membranes for water desalination and other separation processes that are devoid of fouling issues and circumvents the necessity of chemical cleaning operations.
Hexanematic crossover in epithelial monolayers depends on cell adhesion and cell density
Authors: Eckert Julia , Ladoux Benoît , Mège René-Marc , Giomi Luca , Schmidt Thomas 
Published: September 2023

AbstractChanges in tissue geometry during developmental processes are associated with collective migration of cells. Recent experimental and numerical results suggest that these changes could leverage on the coexistence of nematic and hexatic orientational order at different length scales. How this multiscale organization is affected by the material properties of the cells and their substrate is presently unknown. In this study, we address these questions in monolayers of Madin-Darby canine kidney cells having various cell densities and molecular repertoires. At small length scales, confluent monolayers are characterized by a prominent hexatic order, independent of the presence of E-cadherin, monolayer density, and underlying substrate stiffness. However, all three properties affect the meso-scale tissue organization. The length scale at which hexatic order transits to nematic order, the “hexanematic” crossover scale, strongly depends on cell-cell adhesions and correlates with monolayer density. Our study demonstrates how epithelial organization is affected by mechanical properties, and provides a robust description of tissue organization during developmental processes.
Discovery and pharmacophoric characterization of chemokine network inhibitors using phage-display, saturation mutagenesis and computational modelling
Authors: Vales Serena , Kryukova Jhanna , Chandra Soumyanetra , Smagurauskaite Gintare , Payne Megan , Clark Charlie J. , Hafner Katrin , Mburu Philomena , Denisov Stepan , Davies Graham , Outeiral Carlos , Deane Charlotte M. , Morris Garrett M. , Bhattacharya Shoumo 
Published: September 2023

AbstractCC and CXC-chemokines are the primary drivers of chemotaxis in inflammation, but chemokine network redundancy thwarts pharmacological intervention. Tick evasins promiscuously bind CC and CXC-chemokines, overcoming redundancy. Here we show that short peptides that promiscuously bind both chemokine classes can be identified from evasins by phage-display screening performed with multiple chemokines in parallel. We identify two conserved motifs within these peptides and show using saturation-mutagenesis phage-display and chemotaxis studies of an exemplar peptide that an anionic patch in the first motif and hydrophobic, aromatic and cysteine residues in the second are functionally necessary. AlphaFold2-Multimer modelling suggests that the peptide occludes distinct receptor-binding regions in CC and in CXC-chemokines, with the first and second motifs contributing ionic and hydrophobic interactions respectively. Our results indicate that peptides with broad-spectrum anti-chemokine activity and therapeutic potential may be identified from evasins, and the pharmacophore characterised by phage display, saturation mutagenesis and computational modelling.
Global mean nitrogen recovery efficiency in croplands can be enhanced by optimal nutrient, crop and soil management practices
Authors: You Luncheng , Ros Gerard H. , Chen Yongliang , Shao Qi , Young Madaline D. , Zhang Fusuo , de Vries Wim 
Published: September 2023

AbstractAn increase in nitrogen (N) recovery efficiency, also denoted as N use efficiency (NUEr), is crucial to reconcile food production and environmental health. This study assessed the effects of nutrient, crop and soil management on NUEr accounting for its dependency on site conditions, including mean annual temperature and precipitation, soil organic carbon, clay and pH, by meta-regression models using 2436 pairs of observations from 407 primary studies. Nutrient management increased NUEr by 3.6-11%, crop management by 4.4–8%, while reduction in tillage had no significant impact. Site conditions strongly affected management induced changes in NUEr, highlighting their relevance for site-specific practices. Data driven models showed that the global mean NUEr can increase by 30%, from the current average of 48% to 78%, using optimal combinations of nutrient (27%), crop (6.6%) and soil (0.6%) management. This increase will in most cases allow to reconcile crop production with acceptable N losses to water. The predicted increase in NUEr was below average in most high-income regions but above average in middle-income regions.
Plasma metabolomic profiles associated with mortality and longevity in a prospective analysis of 13,512 individuals
Authors: Wang Fenglei , Tessier Anne-Julie , Liang Liming , Wittenbecher Clemens , Haslam Danielle E. , Fernández-Duval Gonzalo , Heather Eliassen A. , Rexrode Kathryn M. , Tobias Deirdre K. , Li Jun , Zeleznik Oana , Grodstein Francine , Martínez-González Miguel A. , Salas-Salvadó Jordi , Clish Clary , Lee Kyu Ha , Sun Qi , Stampfer Meir J. , Hu Frank B. , Guasch-Ferré Marta 
Published: September 2023

AbstractExperimental studies reported biochemical actions underpinning aging processes and mortality, but the relevant metabolic alterations in humans are not well understood. Here we examine the associations of 243 plasma metabolites with mortality and longevity (attaining age 85 years) in 11,634 US (median follow-up of 22.6 years, with 4288 deaths) and 1878 Spanish participants (median follow-up of 14.5 years, with 525 deaths). We find that, higher levels of N2,N2-dimethylguanosine, pseudouridine, N4-acetylcytidine, 4-acetamidobutanoic acid, N1-acetylspermidine, and lipids with fewer double bonds are associated with increased risk of all-cause mortality and reduced odds of longevity; whereas L-serine and lipids with more double bonds are associated with lower mortality risk and a higher likelihood of longevity. We further develop a multi-metabolite profile score that is associated with higher mortality risk. Our findings suggest that differences in levels of nucleosides, amino acids, and several lipid subclasses can predict mortality. The underlying mechanisms remain to be determined.
Dipole field in nitrogen-enriched carbon nitride with external forces to boost the artificial photosynthesis of hydrogen peroxide
Authors: Li Zhi , Zhou Yuanyi , Zhou Yingtang , Wang Kai , Yun Yang , Chen Shanyong , Jiao Wentao , Chen Li , Zou Bo , Zhu Mingshan 
Published: September 2023

AbstractArtificial photosynthesis is a promising strategy for efficient hydrogen peroxide production, but the poor directional charge transfer from bulk to active sites restricts the overall photocatalytic efficiency. To address this, a new process of dipole field-driven spontaneous polarization in nitrogen-rich triazole-based carbon nitride (C3N5) to harness photogenerated charge kinetics for hydrogen peroxide production is constructed. Here, C3N5 achieves a hydrogen peroxide photosynthesis rate of 3809.5 µmol g−1 h−1 and a 2e− transfer selectivity of 92% under simulated sunlight and ultrasonic forces. This high performance is attributed to the introduction of rich nitrogen active sites of the triazole ring in C3N5, which brings a dipole field. This dipole field induces a spontaneous polarization field to accelerate a rapid directional electron transfer process to nitrogen active sites and therefore induces Pauling-type adsorption of oxygen through an indirect 2e− transfer pathway to form hydrogen peroxide. This innovative concept using a dipole field to harness the migration and transport of photogenerated carriers provides a new route to improve photosynthesis efficiency via structural engineering.
The impact of methane leakage on the role of natural gas in the European energy transition
Authors: Shirizadeh Behrang , Villavicencio Manuel , Douguet Sebastien , Trüby Johannes , Bou Issa Charbel , Seck Gondia Sokhna , D’herbemont Vincent , Hache Emmanuel , Malbec Louis-Marie , Sabathier Jerome , Venugopal Malavika , Lagrange Fanny , Saunier Stephanie , Straus Julian , Reigstad Gunhild A. 
Published: September 2023

AbstractDecarbonising energy systems is a prevalent topic in the current literature on climate change mitigation, but the additional climate burden caused by methane emissions along the natural gas value chain is rarely discussed at the system level. Considering a two-basket greenhouse gas neutrality objective (both CO2and methane), we model cost-optimal European energy transition pathways towards 2050. Our analysis shows that adoption of best available methane abatement technologies can entail an 80% reduction in methane leakage, limiting the additional environmental burden to 8% of direct CO2emissions (vs. 35% today). We show that, while renewable energy sources are key drivers of climate neutrality, the role of natural gas strongly depends on actions to abate both associated CO2and methane emissions. Moreover, clean hydrogen (produced mainly from renewables) can replace natural gas in a substantial proportion of its end-uses, satisfying nearly a quarter of final energy demand in a climate-neutral Europe.
Structural insights into functional properties of the oxidized form of cytochrome c oxidase
Authors: Ishigami Izumi , Sierra Raymond G. , Su Zhen , Peck Ariana , Wang Cong , Poitevin Frederic , Lisova Stella , Hayes Brandon , Moss Frank R. , Boutet Sébastien , Sublett Robert E. , Yoon Chun Hong , Yeh Syun-Ru , Rousseau Denis L. 
Published: September 2023

AbstractCytochrome c oxidase (CcO) is an essential enzyme in mitochondrial and bacterial respiration. It catalyzes the four-electron reduction of molecular oxygen to water and harnesses the chemical energy to translocate four protons across biological membranes. The turnover of the CcO reaction involves an oxidative phase, in which the reduced enzyme (R) is oxidized to the metastable OH state, and a reductive phase, in which OH is reduced back to the R state. During each phase, two protons are translocated across the membrane. However, if OH is allowed to relax to the resting oxidized state (O), a redox equivalent to OH, its subsequent reduction to R is incapable of driving proton translocation. Here, with resonance Raman spectroscopy and serial femtosecond X-ray crystallography (SFX), we show that the heme a3 iron and CuB in the active site of the O state, like those in the OH state, are coordinated by a hydroxide ion and a water molecule, respectively. However, Y244, critical for the oxygen reduction chemistry, is in the neutral protonated form, which distinguishes O from OH, where Y244 is in the deprotonated tyrosinate form. These structural characteristics of O provide insights into the proton translocation mechanism of CcO.
Genome-wide promoter responses to CRISPR perturbations of regulators reveal regulatory networks in Escherichia coli
Authors: Han Yichao , Li Wanji , Filko Alden , Li Jingyao , Zhang Fuzhong 
Published: September 2023

AbstractElucidating genome-scale regulatory networks requires a comprehensive collection of gene expression profiles, yet measuring gene expression responses for every transcription factor (TF)-gene pair in living prokaryotic cells remains challenging. Here, we develop pooled promoter responses to TF perturbation sequencing (PPTP-seq) via CRISPR interference to address this challenge. Using PPTP-seq, we systematically measure the activity of 1372 Escherichia coli promoters under single knockdown of 183 TF genes, illustrating more than 200,000 possible TF-gene responses in one experiment. We perform PPTP-seq for E. coli growing in three different media. The PPTP-seq data reveal robust steady-state promoter activities under most single TF knockdown conditions. PPTP-seq also enables identifications of, to the best of our knowledge, previously unknown TF autoregulatory responses and complex transcriptional control on one-carbon metabolism. We further find context-dependent promoter regulation by multiple TFs whose relative binding strengths determined promoter activities. Additionally, PPTP-seq reveals different promoter responses in different growth media, suggesting condition-specific gene regulation. Overall, PPTP-seq provides a powerful method to examine genome-wide transcriptional regulatory networks and can be potentially expanded to reveal gene expression responses to other genetic elements.
The phased telomere-to-telomere reference genome of Musa acuminata, a main contributor to banana cultivars
Authors: Liu Xin , Arshad Rida , Wang Xu , Li Wei-Ming , Zhou Yongfeng , Ge Xue-Jun , Huang Hui-Run 
Published: September 2023

AbstractMusa acuminata is a main wild contributor to banana cultivars. Here, we reported a haplotype-resolved and telomere-to-telomere reference genome of M. acuminata by incorporating PacBio HiFi reads, Nanopore ultra-long reads, and Hi-C data. The genome size of the two haploid assemblies was estimated to be 469.83 Mb and 470.21 Mb, respectively. Multiple assessments confirmed the contiguity (contig N50: 16.53 Mb and 18.58 Mb; LAI: 20.18 and 19.48), completeness (BUSCOs: 98.57% and 98.57%), and correctness (QV: 45.97 and 46.12) of the genome. The repetitive sequences accounted for about half of the genome size. In total, 40,889 and 38,269 protein-coding genes were annotated in the two haploid assemblies, respectively, of which 9.56% and 3.37% were newly predicted. Genome comparison identified a large reciprocal translocation involving 3 Mb and 10 Mb from chromosomes 01 and 04 within M. acuminata. This reference genome of M. acuminata provides a valuable resource for further understanding of subgenome evolution of Musa species, and precise genetic improvement of banana.
An algorithm for discovering vital nodes in regional networks based on stable path analysis
Authors: Liu Yan , Liu Yimin , Liu Fenlin , Fan Jiaxing , Tao Zhiyuan 
Published: September 2023

AbstractVital node discovery is a hotspot in network topology research. The key is using the Internet’s routing characteristics to remove noisy paths and accurately describe the network topology. In this manuscript, a vital regional routing nodes discovery algorithm based on routing characteristics is proposed. We analyze the stability of multiple rounds of measurement results to overcome the single vantage point’s path deviation. The unstable paths are eliminated from the regional network which is constructed through probing for target area, and the pruned topology is more in line with real routing rules. Finally, we weight the edge based on the actual network’s routing characteristics and discover vital nodes in combination with the weighting degree. Unlike existing algorithms, the proposed algorithm reconstructs the network topology based on communication and transforms unweighted network connections into weighted connections. We can evaluate the node importance in a more realistic network structure. Experiments on the Internet measurement data (275 million probing results collected in 107 days) demonstrate that: the proposed algorithm outperforms four existing typical algorithms. Among 15 groups of comparison in 3 cities, our algorithm found more (or the same number) backbone nodes in 10 groups and found more (or the same number) national backbone nodes in 13 groups.
Wideband parametric baseband macromodeling of linear and passive photonic circuits via complex vector fitting
Authors: Ullrick Thijs , Spina Domenico , Bogaerts Wim , Dhaene Tom 
Published: September 2023

AbstractA novel wideband parametric baseband macromodeling technique for passive photonic devices and circuits is presented. It allows to efficiently estimate the baseband scattering representations of a linear, passive photonic system as a function of a set of design variables, such as geometrical layout or substrate features. The proposed technique relies on the interpolation of macromodels computed via a complex vector fitting (CVF) algorithm, by adopting a methodology based on amplitude and frequency scaling that preserves, by construction, the physical properties of the system, such as causality, stability and passivity. For a specified combination of the design parameters, a rational CVF model is derived that can be simulated by a wide range of ordinary differential equation (ODE) solvers or circuit simulators. Additionally, time-domain simulations using the computed model can be performed at arbitrary optical carrier frequencies, thus allowing for the simulation of multi-wavelength systems. Two application examples are presented to demonstrate the flexibility and advantages of the proposed method.
Green synthesis of TiO2 for furfural production by photohydrolysis of tortilla manufacturing waste
Authors: López-Mercado Janneth , González-Domínguez Martha-Isabel , Reynoso-Marin Francisco-Javier , Acosta Brenda , Smolentseva Elena , Nambo Apolo 
Published: September 2023

AbstractCorn nixtamalization generates a waste byproduct that requires diverse environmental preservation measures depending on the country. Such measures could include catalytic and advanced oxidation processes. This study aims to exploit the hemicellulose within the nejayote (32.5%) to create added value chemicals such as furfural using photocatalytic hydrolysis. In the present work, titania (TiO2) nanoparticles (NPs) were greenly synthesized using Ricinus Communis (RC), Moringa Oleifera (MO) or Bougainvillea Spectabilis (BS) plant extracts. Obtained nanoparticles were characterized using XRD, SEM, EDS, BET, XPS and UV–vis techniques. Furthermore, the photocatalytic performance of the obtained samples was evaluated in the furfural production from nejayote. Furfural yield reached 44% in 30 min using the BS synthesized material, which is 1.6 × the yield obtained by the material synthesized with MO extract (26.4% at 45 min) and 6 × the yield obtained by the material obtained with RC (7.2% at 90 min). Such results have not been reported before in the literature and could be the groundwork for novel waste treatments in the tortilla-making industry.
A new hybrid algorithm for intelligent detection of sudden decline syndrome of date palm disease
Authors: Magsi Aurangzeb , Mahar Javed Ahmed , Maitlo Abdullah , Ahmad Muneer , Razzaq Mirza Abdur , Bhuiyan Mohammad Arif Sobhan , Yew Teh Jia 
Published: September 2023

AbstractDate palm is an important domestic cash crop in most countries. Sudden Decline Syndrome (SDS) causes a huge loss to the crop both in quality and quantity. The literature reports the significance of early detection of disease towards preventive measures to improve the quality of the crop. The number of prevailing detection methods limits to consideration of a certain aspect of disease identification. This study proposes a new hybrid fuzzy fast multi-Otsu K-Means (FFMKO) algorithm integrating the date palm image enhancement, robust thresholding, and optimal clustering for significant disease identification. The algorithm adopts a multi-operator image resizing cost function based on image energy and the dominant color descriptor, the adaptive Fuzzy noise filter, and Otsu image thresholding combined with K-Means clustering enhancements. Besides, we validate the process with histogram equalization and threshold transformation towards enhanced color feature extraction of date palm images. The algorithm authenticates findings on a local dataset of 3293 date palm images and, on a benchmarked data set as well. It achieves an accuracy of 94.175% for successful detection of SDS that outperforms the existing similar algorithms. The impactful findings of this study assure the fast and authentic detection of the disease at an earlier stage to uplift the quality and quantity of the date palm and boost the agriculture-based economy.