bluuebunny/crossref_metadata_2025 huggingface dataset:
Logic program proportions
Authors: Antić Christian
Published: December 2023

The purpose of this paper is to present a fresh idea on how symbolic learning might be realized via analogical reasoning. For this, we introduce directed analogical proportions between logic programs of the form “P transforms into Q as R transforms into S” as a mechanism for deriving similar programs by analogy-making. The idea is to instantiate a fragment of a recently introduced abstract algebraic framework of analogical proportions in the domain of logic programming. Technically, we define proportions in terms of modularity where we derive abstract forms of concrete programs from a “known” source domain which can then be instantiated in an “unknown” target domain to obtain analogous programs. To this end, we introduce algebraic operations for syntactic logic program composition and concatenation. Interestingly, our work suggests a close relationship between modularity, generalization, and analogy which we believe should be explored further in the future. In a broader sense, this paper is a further step towards a mathematical theory of logic-based analogical reasoning and learning with potential applications to open AI-problems like commonsense reasoning and computational learning and creativity.
First detection of a potentially invasive species using a multi-threat early detection trap network
Authors: Herrera Cayetano , Hervías-Parejo Sandra , Traveset Anna , Leza Mar
Published: December 2023

In this study we implemented an early detection and rapid response trapping network in the entry and distribution areas of plant material for 20 species on the island of Mallorca (the Balearic Islands, Westernmost Mediterranean Archipelago). Through this system we have detected the European hornet Vespa crabro, an exotic species, which despite not being included among the 20 target species. The European hornet is naturally present in Eurasia and absent in the Balearic and Canary Islands (Spain). It was detected in a port in the north of the island and based on the precautionary principle, the biosecurity administration in the control of species decided to classify it as potential invasive species and proceeded to search for the nest.
APR4Vul: an empirical study of automatic program repair techniques on real-world Java vulnerabilities
Authors: Bui Quang-Cuong , Paramitha Ranindya , Vu Duc-Ly , Massacci Fabio , Scandariato Riccardo
Published: December 2023

Security vulnerability fixes could be a promising research avenue for Automated Program Repair (APR) techniques. In recent years, APR tools have been thoroughly developed for fixing generic bugs. However, the area is still relatively unexplored when it comes to fixing security bugs or vulnerabilities. In this paper, we evaluate nine state-of-the-art APR tools and one vulnerability-specific repair tool. In particular, we investigate their ability to generate patches for 79 real-world Java vulnerabilities in the Vul4J dataset, as well as the level of trustworthiness of these patches. We evaluate the tools with respect to their ability to generate security patches that are (i) testable, (ii) having the positive effect of closing the vulnerability, and (iii) not having side effects from a functional point of view. Our results show that the evaluated APR tools were able to generate testable patches for around 20% of the considered vulnerabilities. On average, nearly 73% of the testable patches indeed eliminate the vulnerabilities, but only 44% of them could actually fix security bugs while maintaining the functionalities. To understand the root cause of this phenomenon, we conduct a detailed comparative study of the general bug fix patterns in Defect4J and the vulnerability fix patterns in ExtraVul (which we extend from Vul4J). Our investigation shows that, although security patches are short in terms of lines of code, they contain unique characteristics in their fix patterns compared to general bugs. For example, many security fixes require adding method calls. These method calls contain specific input validation-related keywords, such asencode,normalize, andtrim. In this regard, our study suggests that additional repair patterns should be implemented for existing APR tools to fix more types of security vulnerabilities.
Moving Past Conventionalism About Multilevel Selection
Authors: Bourrat Pierrick
Published: December 2023

The formalism used to describe evolutionary change in a multilevel setting can be used equally to re-describe the situation as one where all the selection occurs at the individual level. Thus, whether multilevel or individual-level selection occurs seems to be a matter of convention rather than fact. Yet, group selection is regarded by some as an important concept with factual rather than conventional elements. I flesh out an alternative position that regards groups as a target of selection in a way that is not merely definitional fiat and provide a theoretical basis for this position.
Children with cancer and their cardiorespiratory fitness and physical function—the long-term effects of a physical activity program during treatment: a multicenter non-randomized controlled trial
Authors: Fridh Martin Kaj , Schmidt-Andersen Peter , Andrés-Jensen Liv , Thorsteinsson Troels , Wehner Peder Skov , Hasle Henrik , Schmiegelow Kjeld , Larsen Hanne Bækgaard
Published: December 2023

Purpose

We aimed to determine the effects of a classmate-supported, supervised, in-hospital physical activity program during treatment primarily on cardiorespiratory fitness and secondarily on physical function.

Methods

A multicenter non-randomized controlled intervention study including children diagnosed with cancer, 6–18 years at diagnosis treated with chemo-/radiotherapy. The intervention comprised (i) an educational session on cancer in the child’s school class; (ii) selection of two “ambassadors”—classmates who were co-admitted, supporting the child’s everyday hospital life; and (iii) supervised in-hospital physical activity from diagnosis and throughout intensive treatment. One-year post-treatment, physical testing included cardiorespiratory fitness (primary outcome), Sit-to-Stand test, Timed-Up-and-Go, and Handgrip Strength.

Results

The intervention group included 75 of 120 children (61% boys, 13.4 ± 3.1 years); the control groups included 33 of 58 children with cancer (58% boys, 13.5 ± 2.5 years), and 94 age- and sex-matched children without a cancer history. One-year post-treatment, cardiorespiratory fitness tended to be higher in the intervention group (37.0 ± 6.0 mL/kg/min) than in the patient control group with cancer (32.3 ± 9.7 mL/kg/min) (mean difference 4.7 [0.4 to 9.1], p = 0.034). The intervention group performed better in the secondary outcomes. Compared with community controls, both patient groups had lower cardiorespiratory fitness. The patient control group had lower Sit-to-Stand, Timed Up and Go, and Handgrip Strength, while the intervention group had strength comparable to that of the community controls.

Conclusions

Peer-supported, supervised, in-hospital physical activity during treatment may improve cardiorespiratory fitness and muscle strength 1-year post-treatment in children with cancer; however, survivors continue to have lower cardiorespiratory fitness than community controls.

Implications for Cancer Survivors

Children with cancer may benefit from in-hospital physical activity in improving long-term cardiorespiratory fitness and muscle strength.
Fortification of an Innovative Tomato Cold Soup with High Bioaccessible Sulforaphene from UV-B–Treated Radish Seeds
Authors: Martínez-Zamora Lorena , Castillejo Noelia , Artés-Hernández Francisco
Published: December 2023

The aim of this work was to develop an innovative tomato cold soup fortified in bioactive compounds through the incorporation of UV-B–treated radish seeds. After a 20 kJ m−2 UV-B treatment, radish seeds increased their sulforaphene content by 30%. Different concentrations of UV-B–treated seeds (0, 0.5, 1.5, 3, and 5 g kg−1) were added to a chopped vegetables cold soup, mainly made of Kumato® cherry tomatoes as novelty, including pepper, cucumber, and garlic, which was stored for 8 days at 4 °C. Added seeds did not affect physicochemical quality attributes, microbial growth, nor sensory perception. Nevertheless, a dose-dependent behaviour was shown in glucoraphenin and sulforaphene content, according to concentrations of UV-B–treated seeds added. It was also appreciated after an in vitro digestion that the bioaccessible fraction of glucosinolates and isothiocyanates was kept constant throughout the refrigerated storage. The sulforaphene content of the soup increased by ~ 19% after 2 days at 4 °C, of which the 33% was bioaccessible (measured in vitro), and subsequently was degraded by ~ 20% after 8 days at 4 °C.
Excessive Ethanol Oxidation Versus Efficient Chain Elongation Processes
Authors: Quintela Cesar , Peshkepia Evi , Grimalt-Alemany Antonio , Nygård Yvonne , Olsson Lisbeth , Skiadas Ioannis V. , Gavala Hariklia N.
Published: December 2023

Purpose

Chain elongation is a metabolic feature that consists of the elongation of short-chain fatty acids to longer and more valuable acids when ethanol is available. To lower the operational costs, the process can also be performed using mixed microbial cultures. However, certain microorganisms in the mixed cultures can use the ethanol provided in competing reactions, which is usually termed excessive ethanol oxidation (EEO). Although minimizing ethanol use is essential, there is a lack of studies analyzing the extent, causes, and solutions to excessive ethanol oxidation processes.

Methods

To address this knowledge gap, ethanol, and acetic acid mixtures, at a molar ratio of 5 to 2, were fermented, and the following were analyzed: the fermentation profile at different (1) pH and (2) headspace gas compositions, (3) a 16S analysis of the headspace gas composition fermentations, and (4) a thermodynamic analysis of the reactions involved.

Results and Conclusions: All fermentations, except the ones at the lowest pH (5.3), exhibited a significant EEO activity that reduced the yield of chain-elongated products. It was demonstrated that neither the inhibition of methanogenic activity nor the increased H2 partial pressure is an efficient method to inhibit EEO. It was also shown that CO2 can act as an electron acceptor for EEO, promoting the growth of acetogenic bacteria. In the absence of CO2, sulfate was used as an electron acceptor by sulfate-reducing bacteria to facilitate EEO. Methods such as low pH operation with in-line extraction, and the use of alternative sulfur salts, are proposed to increase the ethanol use efficiency in chain elongation processes.

Graphical Abstract
A flocking control algorithm of multi-agent systems based on cohesion of the potential function
Authors: Li Chenyang , Yang Yonghui , Jiang Guanjie , Chen Xue-Bo
Published: December 2023

Flocking cohesion is critical for maintaining a group’s aggregation and integrity. Designing a potential function to maintain flocking cohesion unaffected by social distance is challenging due to the uncertainty of real-world conditions and environments that cause changes in agents’ social distance. Previous flocking research based on potential functions has primarily focused on agents’ same social distance and the attraction–repulsion of the potential function, ignoring another property affecting flocking cohesion: well depth, as well as the effect of changes in agents’ social distance on well depth. This paper investigates the effect of potential function well depths and agent’s social distances on the multi-agent flocking cohesion. Through the analysis, proofs, and classification of these potential functions, we have found that the potential function well depth is proportional to the flocking cohesion. Moreover, we observe that the potential function well depth varies with the agents’ social distance changes. Therefore, we design a segmentation potential function and combine it with the flocking control algorithm in this paper. It enhances flocking cohesion significantly and has good robustness to ensure the flocking cohesion is unaffected by variations in the agents’ social distance. Meanwhile, it reduces the time required for flocking formation. Subsequently, the Lyapunov theorem and the LaSalle invariance principle prove the stability and convergence of the proposed control algorithm. Finally, this paper adopts two subgroups with different potential function well depths and social distances to encounter for simulation verification. The corresponding simulation results demonstrate and verify the effectiveness of the flocking control algorithm.
Evolution of the magnetic field and flows of solar active regions with persistent magnetic bipoles before emergence
Authors: Alley C.S. , Schunker H.
Published: December 2023

Magnetic active regions on the Sun are harbingers of space weather. Understanding the physics of how they form and evolve will improve space weather forecasting. Our aim is to characterise the surface magnetic field and flows for a sample of active regions with persistent magnetic bipoles prior to emergence. We identified 42 emerging active regions (EARs), in the Solar Dynamics Observatory Helioseismic Emerging Active Region survey (Schunker et al. 2016, A&A. 595, A107), associated with small magnetic bipoles at least one day before the time of emergence. We then identified a contrasting sample of 42 EARs that emerge more abruptly without bipoles before emergence. We computed the supergranulation-scale surface flows using helioseismic holography. We averaged the flow maps and magnetic field maps over all active regions in each sample at each time interval from 2 d before emergence to 1 d after. We found that EARs associated with a persistent pre-emergence bipole evolve to be, on average, lower flux active regions than EARs that emerge more abruptly. Further, we found that the EARs that emerge more abruptly do so with a diverging flow of

$(3\pm 0.6) \times 10^{-6}$

s

$^{-1}$

on the order of 50–100 ms

$^{-1}$

. Our results show that there is a statistical dependence of the surface flow signature throughout the emergence process on the maximum magnetic flux of the active region.
The probiotic Lacticaseibacillus rhamnosus HN001 influences the architecture and gene expression of small intestine tissue in a piglet model
Authors: Montoya Carlos A. , Young Wayne , Ryan Leigh , Dunstan Kelly , Peters Jason , Dewhurst Hilary , Dekker James , Haggarty Neill , Dilger Ryan N. , Roy Nicole C.
Published: December 2023

This study investigated the effects of Lacticaseibacillus rhamnosus HN001 supplementation on the architecture and gene expression in small intestinal tissues of piglets used as an animal model for infant humans. Twenty-four 10-d-old entire male piglets (4·3 (sd 0·59) kg body weight) were fed an infant formula (IF) (control) or IF supplemented with 1·3 × 105 (low dose) or 7·9 × 106 (high dose) colony-forming units HN001 per ml of reconstituted formula (n 8 piglets/treatment). After 24 d, piglets were euthanised. Samples were collected to analyse the histology and gene expression (RNAseq and qPCR) in the jejunal and ileal tissues, blood cytokine concentrations, and blood and faecal calprotectin concentrations. HN001 consumption altered (false discovery rate < 0·05) gene expression (RNAseq) in jejunal tissues but not in ileal tissues. The number of ileal goblet cells and crypt surface area increased quadratically (P < 0·05) as dietary HN001 levels increased, but no increase was observed in the jejunal tissues. Similarly, blood plasma concentrations of IL-10 and calprotectin increased linearly (P < 0·05) as dietary HN001 levels increased. In conclusion, supplementation of IF with HN001 affected the architecture and gene expression of small intestine tissue, blood cytokine concentration and frequencies, and blood calprotectin concentrations, indicating that HN001 modulated small intestinal tissue maturation and immunity in the piglet model.
Abha Arabic
Authors: Al Malwi Ibrahim , Herrero de Haro Alfredo , Baker Amanda
Published: December 2023

Abha Arabic is a dialect of Arabic (ISO 693-3: ara), belonging to the Semitic language family group, and spoken primarily in Abha city. Abha Arabic can be broadly classified as a variety of Arabic from the Arabian Peninsula group (Versteegh, 2014), and further sub-classified as a south (-west) Arabian dialect (Ingham, 1982). Abha city is the administrative capital of the province of Asir, in south-west Saudi Arabia (Figure 1). The population of Abha is approximately 290,185 and that of the Asir province is 1,601,725, according to the most recent data on the population (General Authority for Statistics, 2010). The province is named after the Asir tribe, who first inhabited Abha and the surrounding regions. The present day Abha Arabic dialect thus represents a blending of Bedouin and urban dialects. The first settlers to Abha were the Bani-Mghed tribe (an Asir tribe) followed by three additional Asir tribes (Alkam, Rabiah w Rufeda, Bani-Malik) and other nearby tribes such as the Gahtaːn, Bal-lahmir, Bal-lasmir, Shahran, Rejal Alma’, all of which had distinct dialects (Al-Azraqi, 1998). These dialects merged to varying degrees and were further influenced by urban education and mass media, which were and continue to be dominated by Modern Standard Arabic (henceforth MSA) (Al-Azraqi, 1998).1
Let's move forward: Image-computable models and a common model evaluation scheme are prerequisites for a scientific understanding of human vision
Authors: DiCarlo James J. , Yamins Daniel L. K. , Ferguson Michael E. , Fedorenko Evelina , Bethge Matthias , Bonnen Tyler , Schrimpf Martin
Published: December 2023

In the target article, Bowers et al. dispute deep artificial neural network (ANN) models as the currently leading models of human vision without producing alternatives. They eschew the use of public benchmarking platforms to compare vision models with the brain and behavior, and they advocate for a fragmented, phenomenon-specific modeling approach. These are unconstructive to scientific progress. We outline how the Brain-Score community is moving forward to add new model-to-human comparisons to its community-transparent suite of benchmarks.
Improved gray wolf optimization algorithm integrating A* algorithm for path planning of mobile charging robots
Authors: Liu Shangjunnan , Liu Shuhai , Xiao Huaping
Published: December 2023

With the popularization of electric vehicles, early built parking lots cannot solve the charging problem of a large number of electric vehicles. Mobile charging robots have autonomous navigation and complete charging functions, which make up for this deficiency. However, there are static obstacles in the parking lot that are random and constantly changing their position, which requires a stable and fast iterative path planning method. The gray wolf optimization (GWO) algorithm is one of the optimization algorithms, which has the advantages of fast iteration speed and stability, but it has the drawback of easily falling into local optimization problems. This article first addresses this issue by improving the fitness function and position update of the GWO algorithm and then optimizing the convergence factor. Subsequently, the fitness function of the improved gray wolf optimization (IGWO) algorithm was further improved based on the minimum cost equation of the A* algorithm. The key coefficients AC1 and AC2 of two different fitness functions, Fitness1 and Fitness2, were discussed. The improved gray wolf optimization algorithm integrating A* algorithm (A*-IGWO) has improved the number of iterations and path length compared to the GWO algorithm in parking lots path planning problems.
Surface Turbulent Fluxes From the MOSAiC Campaign Predicted by Machine Learning
Authors: Cummins Donald P. , Guemas Virginie , Cox Christopher J. , Gallagher Michael R. , Shupe Matthew D.
Published: December 2023

Reliable boundary‐layer turbulence parametrizations for polar conditions are needed to reduce uncertainty in projections of Arctic sea ice melting rate and its potential global repercussions. Surface turbulent fluxes of sensible and latent heat are typically represented in weather/climate models using bulk formulae based on the Monin‐Obukhov Similarity Theory, sometimes finely tuned to high stability conditions and the potential presence of sea ice. In this study, we test the performance of new, machine‐learning (ML) flux parametrizations, using an advanced polar‐specific bulk algorithm as a baseline. Neural networks, trained on observations from previous Arctic campaigns, are used to predict surface turbulent fluxes measured over sea ice as part of the recent MOSAiC expedition. The ML parametrizations outperform the bulk at the MOSAiC sites, with RMSE reductions of up to 70 percent. We provide a plug‐in Fortran implementation of the neural networks for use in models.
Gut liver brain axis in diseases: the implications for therapeutic interventions
Authors: Yan Mengyao , Man Shuli , Sun Benyue , Ma Long , Guo Lanping , Huang Luqi , Gao Wenyuan
Published: December 2023

Gut-liver-brain axis is a three-way highway of information interaction system among the gastrointestinal tract, liver, and nervous systems. In the past few decades, breakthrough progress has been made in the gut liver brain axis, mainly through understanding its formation mechanism and increasing treatment strategies. In this review, we discuss various complex networks including barrier permeability, gut hormones, gut microbial metabolites, vagus nerve, neurotransmitters, immunity, brain toxic metabolites, β-amyloid (Aβ) metabolism, and epigenetic regulation in the gut-liver-brain axis. Some therapies containing antibiotics, probiotics, prebiotics, synbiotics, fecal microbiota transplantation (FMT), polyphenols, low FODMAP diet and nanotechnology application regulate the gut liver brain axis. Besides, some special treatments targeting gut-liver axis include farnesoid X receptor (FXR) agonists, takeda G protein-coupled receptor 5 (TGR5) agonists, glucagon-like peptide-1 (GLP-1) receptor antagonists and fibroblast growth factor 19 (FGF19) analogs. Targeting gut-brain axis embraces cognitive behavioral therapy (CBT), antidepressants and tryptophan metabolism-related therapies. Targeting liver-brain axis contains epigenetic regulation and Aβ metabolism-related therapies. In the future, a better understanding of gut-liver-brain axis interactions will promote the development of novel preventative strategies and the discovery of precise therapeutic targets in multiple diseases.
Identification of multiple organ metastasis-associated hub mRNA/miRNA signatures in non-small cell lung cancer
Authors: Zu Lingling , He Jinling , Zhou Ning , Tang Quanying , Liang Maoli , Xu Song
Published: December 2023

Metastasis remains major cause of treatment failure in non-small cell lung cancer (NSCLC). A comprehensive characterization of the transcriptomic landscape of NSCLC-cells with organ-specific metastatic potentials would advance our understanding of NSCLC metastasis process. In this study, we established NSCLC bone-metastatic (BoM), brain-metastatic (BrM), and lymph-metastatic (LnM) cells by an in vivo spontaneous metastatic model. Subsequently, by analyzing the entire transcriptomic profiles of BoM, BrM, LnM, LuM, in comparison with their parental cell line L9981, we identified miR-660-5p as a key driver that is associated with NSCLC progression and distant metastasis, potentially through its targeting of LIMCH1, SMARCA5 and TPP2. In addition, a six-gene signature (ADRB2, DPYSL2, IL7R, LIMCH1, PIK3R1, and SOX2) was subsequently established to predict NSCLC metastasis based on differentially expressed genes, three of which (DPYSL2, PIK3R1, LIMCH1) along with the transcriptional factors RB1 and TP63, were ultimately validated by experiments. Taken together, aberrant gene signature and miRNA can serve as biomarkers for predicting NSCLC distant metastasis, and targeting them could potentially contribute to the development of novel therapeutic strategies.
Enhanced formation of methane hydrate from active ice with high gas uptake
Authors: Xiao Peng , Li Juan-Juan , Chen Wan , Pang Wei-Xin , Peng Xiao-Wan , Xie Yan , Wang Xiao-Hui , Deng Chun , Sun Chang-Yu , Liu Bei , Zhu Yu-Jie , Peng Yun-Lei , Linga Praveen , Chen Guang-Jin
Published: December 2023

Gas hydrates provide alternative solutions for gas storage & transportation and gas separation. However, slow formation rate of clathrate hydrate has hindered their commercial development. Here we report a form of porous ice containing an unfrozen solution layer of sodium dodecyl sulfate, here named active ice, which can significantly accelerate gas hydrate formation while generating little heat. It can be readily produced via forming gas hydrates with water containing very low dosage (0.06 wt% or 600 ppm) of surfactant like sodium dodecyl sulfate and dissociating it below the ice point, or by simply mixing ice powder or natural snow with the surfactant. We prove that the active ice can rapidly store gas with high storage capacity up to 185 VgVw−1 with heat release of ~18 kJ mol−1 CH4 and the active ice can be easily regenerated by depressurization below the ice point. The active ice undergoes cyclic ice−hydrate−ice phase changes during gas uptake/release, thus removing most critical drawbacks of hydrate-based technologies. Our work provides a green and economic approach to gas storage and gas separation and paves the way to industrial application of hydrate-based technologies.
Direct identification of interfacial degradation in blue OLEDs using nanoscale chemical depth profiling
Authors: Trindade Gustavo F. , Sul Soohwan , Kim Joonghyuk , Havelund Rasmus , Eyres Anya , Park Sungjun , Shin Youngsik , Bae Hye Jin , Sung Young Mo , Matjacic Lidija , Jung Yongsik , Won Jungyeon , Jeon Woo Sung , Choi Hyeonho , Lee Hyo Sug , Lee Jae-Cheol , Kim Jung-Hwa , Gilmore Ian S.
Published: December 2023

Understanding the degradation mechanism of organic light-emitting diodes (OLED) is essential to improve device performance and stability. OLED failure, if not process-related, arises mostly from chemical instability. However, the challenges of sampling from nanoscale organic layers and interfaces with enough analytical information has hampered identification of degradation products and mechanisms. Here, we present a high-resolution diagnostic method of OLED degradation using an Orbitrap mass spectrometer equipped with a gas cluster ion beam to gently desorb nanometre levels of materials, providing unambiguous molecular information with 7-nm depth resolution. We chemically depth profile and analyse blue phosphorescent and thermally-activated delayed fluorescent (TADF) OLED devices at different degradation levels. For OLED devices with short operational lifetimes, dominant chemical degradation mainly relate to oxygen loss of molecules that occur at the interface between emission and electron transport layers (EML/ETL) where exciton distribution is maximised, confirmed by emission zone measurements. We also show approximately one order of magnitude increase in lifetime of devices with slightly modified host materials, which present minimal EML/ETL interfacial degradation and show the method can provide insight for future material and device architecture development.
Systemically administered wound-homing peptide accelerates wound healing by modulating syndecan-4 function
Authors: Maldonado Horacio , Savage Bryan D. , Barker Harlan R. , May Ulrike , Vähätupa Maria , Badiani Rahul K. , Wolanska Katarzyna I. , Turner Craig M. J. , Pemmari Toini , Ketomäki Tuomo , Prince Stuart , Humphries Martin J. , Ruoslahti Erkki , Morgan Mark R. , Järvinen Tero A. H.
Published: December 2023

CAR (CARSKNKDC) is a wound-homing peptide that recognises angiogenic neovessels. Here we discover that systemically administered CAR peptide has inherent ability to promote wound healing: wounds close and re-epithelialise faster in CAR-treated male mice. CAR promotes keratinocyte migration in vitro. The heparan sulfate proteoglycan syndecan-4 regulates cell migration and is crucial for wound healing. We report that syndecan-4 expression is restricted to epidermis and blood vessels in mice skin wounds. Syndecan-4 regulates binding and internalisation of CAR peptide and CAR-mediated cytoskeletal remodelling. CAR induces syndecan-4-dependent activation of the small GTPase ARF6, via the guanine nucleotide exchange factor cytohesin-2, and promotes syndecan-4-, ARF6- and Cytohesin-2-mediated keratinocyte migration. Finally, we show that genetic ablation of syndecan-4 in male mice eliminates CAR-induced wound re-epithelialisation following systemic administration. We propose that CAR peptide activates syndecan-4 functions to selectively promote re-epithelialisation. Thus, CAR peptide provides a therapeutic approach to enhance wound healing in mice; systemic, yet target organ- and cell-specific.
Shorebirds-driven trophic cascade helps restore coastal wetland multifunctionality
Authors: Li Chunming , Chen Jianshe , Liao Xiaolin , Ramus Aaron P. , Angelini Christine , Liu Lingli , Silliman Brian R. , Bertness Mark D. , He Qiang
Published: December 2023

Ecosystem restoration has traditionally focused on re-establishing vegetation and other foundation species at basal trophic levels, with mixed outcomes. Here, we show that threatened shorebirds could be important to restoring coastal wetland multifunctionality. We carried out surveys and manipulative field experiments in a region along the Yellow Sea affected by the invasive cordgrass Spartina alterniflora. We found that planting native plants alone failed to restore wetland multifunctionality in a field restoration experiment. Shorebird exclusion weakened wetland multifunctionality, whereas mimicking higher predation before shorebird population declines by excluding their key prey – crab grazers – enhanced wetland multifunctionality. The mechanism underlying these effects is a simple trophic cascade, whereby shorebirds control crab grazers that otherwise suppress native vegetation recovery and destabilize sediments (via bioturbation). Our findings suggest that harnessing the top-down effects of shorebirds – through habitat conservation, rewilding, or temporary simulation of consumptive or non-consumptive effects – should be explored as a nature-based solution to restoring the multifunctionality of degraded coastal wetlands.
N1-methylpseudouridylation of mRNA causes +1 ribosomal frameshifting
Authors: Mulroney Thomas E. , Pöyry Tuija , Yam-Puc Juan Carlos , Rust Maria , Harvey Robert F. , Kalmar Lajos , Horner Emily , Booth Lucy , Ferreira Alexander P. , Stoneley Mark , Sawarkar Ritwick , Mentzer Alexander J. , Lilley Kathryn S. , Smales C. Mark , von der Haar Tobias , Turtle Lance , Dunachie Susanna , Klenerman Paul , Thaventhiran James E. D. , Willis Anne E.
Published: December 2023

In vitro-transcribed (IVT) mRNAs are modalities that can combat human disease, exemplified by their use as vaccines for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). IVT mRNAs are transfected into target cells, where they are translated into recombinant protein, and the biological activity or immunogenicity of the encoded protein exerts an intended therapeutic effect1,2. Modified ribonucleotides are commonly incorporated into therapeutic IVT mRNAs to decrease their innate immunogenicity3–5, but their effects on mRNA translation fidelity have not been fully explored. Here we demonstrate that incorporation of N1-methylpseudouridine into mRNA results in +1 ribosomal frameshifting in vitro and that cellular immunity in mice and humans to +1 frameshifted products from BNT162b2 vaccine mRNA translation occurs after vaccination. The +1 ribosome frameshifting observed is probably a consequence of N1-methylpseudouridine-induced ribosome stalling during IVT mRNA translation, with frameshifting occurring at ribosome slippery sequences. However, we demonstrate that synonymous targeting of such slippery sequences provides an effective strategy to reduce the production of frameshifted products. Overall, these data increase our understanding of how modified ribonucleotides affect the fidelity of mRNA translation, and although there are no adverse outcomes reported from mistranslation of mRNA-based SARS-CoV-2 vaccines in humans, these data highlight potential off-target effects for future mRNA-based therapeutics and demonstrate the requirement for sequence optimization.
Organ aging signatures in the plasma proteome track health and disease
Authors: Oh Hamilton Se-Hwee , Rutledge Jarod , Nachun Daniel , Pálovics Róbert , Abiose Olamide , Moran-Losada Patricia , Channappa Divya , Urey Deniz Yagmur , Kim Kate , Sung Yun Ju , Wang Lihua , Timsina Jigyasha , Western Dan , Liu Menghan , Kohlfeld Pat , Budde John , Wilson Edward N. , Guen Yann , Maurer Taylor M. , Haney Michael , Yang Andrew C. , He Zihuai , Greicius Michael D. , Andreasson Katrin I. , Sathyan Sanish , Weiss Erica F. , Milman Sofiya , Barzilai Nir , Cruchaga Carlos , Wagner Anthony D. , Mormino Elizabeth , Lehallier Benoit , Henderson Victor W. , Longo Frank M. , Montgomery Stephen B. , Wyss-Coray Tony
Published: December 2023

Animal studies show aging varies between individuals as well as between organs within an individual1–4, but whether this is true in humans and its effect on age-related diseases is unknown. We utilized levels of human blood plasma proteins originating from specific organs to measure organ-specific aging differences in living individuals. Using machine learning models, we analysed aging in 11 major organs and estimated organ age reproducibly in five independent cohorts encompassing 5,676 adults across the human lifespan. We discovered nearly 20% of the population show strongly accelerated age in one organ and 1.7% are multi-organ agers. Accelerated organ aging confers 20–50% higher mortality risk, and organ-specific diseases relate to faster aging of those organs. We find individuals with accelerated heart aging have a 250% increased heart failure risk and accelerated brain and vascular aging predict Alzheimer’s disease (AD) progression independently from and as strongly as plasma pTau-181 (ref. 5), the current best blood-based biomarker for AD. Our models link vascular calcification, extracellular matrix alterations and synaptic protein shedding to early cognitive decline. We introduce a simple and interpretable method to study organ aging using plasma proteomics data, predicting diseases and aging effects.
The OREGANO knowledge graph for computational drug repurposing
Authors: Boudin Marina , Diallo Gayo , Drancé Martin , Mougin Fleur
Published: December 2023

Drug repositioning is a faster and more affordable solution than traditional drug discovery approaches. From this perspective, computational drug repositioning using knowledge graphs is a very promising direction. Knowledge graphs constructed from drug data and information can be used to generate hypotheses (molecule/drug - target links) through link prediction using machine learning algorithms. However, it remains rare to have a holistically constructed knowledge graph using the broadest possible features and drug characteristics, which is freely available to the community. The OREGANO knowledge graph aims at filling this gap. The purpose of this paper is to present the OREGANO knowledge graph, which includes natural compounds related data. The graph was developed from scratch by retrieving data directly from the knowledge sources to be integrated. We therefore designed the expected graph model and proposed a method for merging nodes between the different knowledge sources, and finally, the data were cleaned. The knowledge graph, as well as the source codes for the ETL process, are openly available on the GitHub of the OREGANO project (https://gitub.u-bordeaux.fr/erias/oregano).
Practical, high-speed Gaussian coherent state continuous variable quantum key distribution with real-time parameter monitoring, optimised slicing, and post-processed key distillation
Authors: Weerasinghe Amanda , Alhussein Muataz , Alderton Adam , Wonfor Adrian , Penty Richard
Published: December 2023

Gaussian coherent state continuous variable quantum key distribution has gained interest owing to its security and compatibility with classical coherent optical fibre networks. For successful system deployment it is necessary to implement practical high speed systems which distil keys efficiently. Here, we demonstrate a Gaussian coherent state continuous variable quantum key distribution system at a 50 MHz symbol rate. Unlike most demonstrations to date which measure excess noise and infer key rates from this, we record signals in real time and distil keys. We also demonstrate, for the first time, slice reconciliation with optimised guard bands to maximise achievable secret key rates. Using this optimisation with multilevel slicing, a record 5 Mb/s secret key rate after a transmission distance of 25 km is achieved. This is a significant improvement on the 3 Mb/s secret key rate which is achieved with single level optimised slice reconciliation.
Wirelessly powered motor operation in dynamic scenarios using non-Hermitian parity-time symmetry
Authors: Esaki Muthu Pandara Kone Shrinathan , Yatsugi Kenichi , Iizuka Hideo
Published: December 2023

Motors arise as a heart of the mobility society, and wirelessly operated motors may improve our standard of living. Wireless power transfer in the kilohertz and megahertz range has been extensively explored, finding various potential applications in consumer electronics, electric vehicles, and medical implants. However, stable operation of wirelessly powered motors remains challenging due to voltage fluctuations for motors occurring in dynamic scenarios, e.g., the rotating speed of the motors is varied. Here, we theoretically and experimentally demonstrate the operation of a motor, where the power is wirelessly transferred via coils, is robust against the rotating speed by employing the analogy with non-Hermitian parity-time (PT) symmetry. In addition, our system is robust for misalignment of the coils. Our results open up opportunities for the robust operation of motors via wireless power transfer in dynamic scenarios towards autonomous vehicles.
Enhancing supply chain management in the physical internet: a hybrid SAGA approach
Authors: Yan Weiqi , Li Nan , Zhang Xin
Published: December 2023

This paper introduces an advanced inventory replenishment optimization approach tailored for the Physical Internet (PI), addressing the dynamic and complex nature of this environment. We propose a hybrid Simulated Annealing–Genetic Algorithm (SA–GA), engineered to optimize the balance between exploration and exploitation, ensuring adaptability and efficiency in a variety of PI contexts. The study also presents an enriched mathematical model integrating dynamic demand, and multi-objective optimization. The SA–GA algorithm emerges as a novel contribution, characterized by its computational efficiency and adaptability, marking an advancement in PI inventory management. The incorporation of real-time data analytics in our dynamic inventory replenishment strategy enhances adaptability and responsiveness, while the robust mathematical model offers a versatile tool for both theoretical analysis and practical application. Collectively, these innovations help bridge existing gaps in PI inventory management and serve as a reference for other similar studies.
Contrasting structures of the Southern Benue trough and the contiguous crystalline basement as observed from high-resolution aeromagnetic data
Authors: Adebiyi Leke Sunday , Eluwole Akinola Bolaji , Fajana Akindeji Opeyemi , Salawu Naheem Banji , Saleh Aliyu
Published: December 2023

The present study investigated crustal structures and geological bodies within selected areas of the southern Benue trough and the adjacent crystalline basement. It utilized high-resolution aeromagnetic data to provide original insights into the contrasting structures and geological bodies within the area, while also identifying promising areas for further mineral and hydrocarbon investigations. The aeromagnetic anomaly data were analyzed using various techniques, including total gradient magnitude, pseudo-gravity transformation, tilt derivative, and source parameter imaging. The total gradient magnitude anomalies revealed a considerable component of the basin affected by block faulting which may have resulted from severe tectonic and structural deformation of the metamorphic basement and the subsequent injection into the sedimentary sequence, a few intrusions. The pseudo-gravity transformation identified a large igneous body in the sedimentary basin which is characterized by positive pseudo-gravity anomalies and surrounded on both sides by linear negative anomalies that signify a rift zone. The positive amplitude of the tilt derivative identified subtle linear magnetic minerals associated with the geologic structure and igneous bodies that suggest considerable mineral exploration prospects. A two-dimensional model of the source parameter imaging reveals the basement below the sedimentary basin to be intensely fragmented and variably subsided with the floor of the basin forming irregular upward and downward folds. In conclusion, the findings suggest promising prospects for mineral exploration along the margin of the sedimentary basin and potential hydrocarbon resources in the northeastern segment of the basin, which is characterized by fewer intrusions.
Non-immobilized GO-SELEX screening of aptamers against cyclosporine A and its application in a AuNPs colorimetric aptasensor
Authors: Yang Jie , Lu Xiaoling , Chen Meilun , Tang Chunhua , Wei Zheng , Liu Yijie , Jiang Hanbing , Yu Peng
Published: December 2023

Scheme of non-immobilized GO-SELEX screening of aptamers against cyclosporine A and the development of AuNPs colorimetric aptasensor.
Zn(002)-preferred and pH-buffering triethanolamine as electrolyte additive for dendrite-free Zn anodes
Authors: Ge Wenjing , Peng Huili , Dong Jingjing , Wang Gulian , Cui Lifeng , Sun Wei , Ma Xiaojian , Yang Jian
Published: December 2023

TEOA as an electrolyte additive preferentially adsorbs on Zn(002) and enhances Zn(002) exposure, suppressing dendrite growth and side reactions. Meanwhile, it diminishes the change in pH near Zn anode, reducing the formation of byproducts.
Two biocompatible iron-based CPMs for high-capacity adsorption and pH-responsive sustained release of diclofenac sodium
Authors: Zou Xin , Li Xu-shan , Sun Qian , Gao En-qing
Published: December 2023

This study focused on synthesizing two iron-based crystalline porous materials (CPMs) with cationic framework and their loading capacities and sustained release behavior for diclofenac sodium (DS), an anionic drug.
The effects of water, substrate, and intermediate adsorption on the photocatalytic decomposition of air pollutants over nano-TiO2 photocatalysts
Authors: Lin Zhifeng , Jiang Xueding , Xu Weicheng , Li Fuhua , Chen Xin , Wang Hailong , Liu Si , Lu Xihong
Published: December 2023

The progress and challenges in the experimental and theoretical studies to explore the effects of water, substrate, and intermediate adsorption over nano-TiO2 photocatalysts during air treatment are comprehensively summarized and discussed.
A magnetic microneedle to isolate single immunomagnetically labeled cells
Authors: Stevens Michiel , Harder Philip , Terstappen Leon W. M. M.
Published: December 2023

Single target cells are picked up from immunomagnetically enriched samples by means of a magnetic microneedle. This allows cell isolation as well as precise placement of the target cells.
DPP-bridged narrow band gap oligomer-like donor materials: significant effect of molecular structure regulation on photovoltaic performance
Authors: Liu Chang , Yin Lunxiang , Guo Yanli , Xie Bao , Wang Xu , Li Yanqin
Published: December 2023

A series of novel oligomer-like molecules were synthesized. Cz(DPPCz)2 achieved the most satisfactory regulation with the band gap of 1.32 eV and the PCE was 6.12%, which is three times higher than the small molecule counterpart DPP(Cz)2.
Overcoming barriers with non-covalent interactions: supramolecular recognition of adamantyl cucurbit[n]uril assemblies for medical applications
Authors: Alešković Marija , Šekutor Marina
Published: December 2023

Supramolecular host–guest systems consisting of adamantanes and cucurbit[n]urils have found medicinal applications in drug delivery, controlled drug release, bioanalytics, sensing assays, bioimaging, diagnostics, hybrid nanostructures and beyond.
Comparison of the penetration depth in mouse brain in vivo through 3PF imaging using AIE nanoparticle labeling and THG imaging within the 1700 nm window
Authors: Zhang Yingxian , Zhong Jincheng , Cheng Hui , Huang Jie , Li Zhenhui , Zhang Chi , Gao Zhiang , Xu Zhourui , Xu Gaixia , Qiu Ping , Wang Ke
Published: December 2023

Herein, we systematically studied 3PF imaging and THG imaging in living mice at different excitation wavelengths within the 1700 nm window, thus exploring the optimal wavelength for the excitation of MPM within the 1700 nm window.
Camptothecin-loaded supramolecular nanodelivery system based on amphiphilic calix[4]arene for targeted tumor therapy
Authors: Zheng Han-yuan , Liu Yu-dun , Zhang Yu-lei , Shi Qing-hua , Hou Xue-li , An Lin
Published: December 2023

To decrease the potential side effects of the quinoline alkaloid camptothecin (CPT) in the treatment of malignant tumors, a supramolecular drug delivery based on synthesized biotin–PEG-linked calix[4]arene (PDCA) has been successfully developed.
Preparation and optical properties of Eu2+–Pr3+/Nd3+ co-doped CaAl2O4 long afterglow luminescent materials
Authors: Zhang Ning , Zeng Qingling , Yin Chunhua , Guo Dongcai
Published: December 2023

A long afterglow material, CaAl2O4:Eu2+,Pr3+/Nd3+, emitting blue light has been synthesized by a high-temperature solid-phase method.
Correction: Developing a biocatalyst showcasing the synergistic effect of rice husk biochar and bacterial cells for the removal of heavy metals
Authors: Manikandan Soumya Koippully , Nair Vaishakh
Published: December 2023

Correction for ‘Developing a biocatalyst showcasing the synergistic effect of rice husk biochar and bacterial cells for the removal of heavy metals’ by Soumya Koippully Manikandan et al., New J. Chem., 2023, https://doi.org/10.1039/d3nj02889e.
Correction: Kinetics and mechanism of halide exchange in reactions of CpRu(PPh3)2Cl with alkyl halides: evidence for radical pairs
Authors: Carney Katherine , Polito Lauren , Reid Kamilya , Srinivas Surbhi , Blake Gabrielle , Chintala Nithin , Dong Sijia S. , Kirss Rein U.
Published: December 2023

Correction for ‘Kinetics and mechanism of halide exchange in reactions of CpRu(PPh3)2Cl with alkyl halides: evidence for radical pairs’ by Katherine Carney et al., New J. Chem., 2023, 47, 21404–21410, https://doi.org/10.1039/D3NJ03839D.
Ferroelectricity of ice nanotube forests grown in three-dimensional graphene: the electric field effect
Authors: Zhang Tengfei , Han Yang , Luo Chuan-fu , Liu Xiaochuang , Zhang Xiaowei , Song Yuhan , Chen Yi-Tung , Du Shiyu
Published: December 2023

Different kinds of ice nanotube forests (i.e. (5, 0), fully polarized (5, 0) and spiral (5, 1) ones) can grow inside three dimensional graphene in a single cooling process. An electric field can help significantly improve their ferroelectricity.
Correction: MXenes vs. clays: emerging and traditional 2D layered nanoarchitectonics
Authors: Ruiz-Hitzky Eduardo , Ruiz-Garcia Cristina
Published: December 2023

Correction for ‘MXenes vs. clays: emerging and traditional 2D layered nanoarchitectonics’ by Eduardo Ruiz-Hitzky et al., Nanoscale, 2023, https://doi.org/10.1039/d3nr03037g.
PolyNC: a natural and chemical language model for the prediction of unified polymer properties
Authors: Qiu Haoke , Liu Lunyang , Qiu Xuepeng , Dai Xuemin , Ji Xiangling , Sun Zhao-Yan
Published: December 2023

PolyNC directly infers properties based on human prompts and polymer structures, enabling an end-to-end learning that encourages the model to autonomously acquire fundamental polymer knowledge, in a multi-task, multi-type unified model manner.