bluuebunny/crossref_metadata_2025_split huggingface dataset:
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

AbstractThis 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

Abstract
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

AbstractWith 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

AbstractReliable 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

AbstractGut-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

AbstractMetastasis 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

AbstractGas 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

AbstractUnderstanding 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

AbstractCAR (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

AbstractEcosystem 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

AbstractIn 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

AbstractAnimal 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

AbstractDrug 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

AbstractGaussian 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

AbstractMotors 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.