bluuebunny/crossref_metadata_2025_split huggingface dataset:
In vivo neuroprotective capacity of a Dunaliella salina extract - comprehensive transcriptomics and metabolomics study
Authors: Valdés Alberto , Sánchez-Martínez José David , Gallego Rocío , Ibáñez Elena , Herrero Miguel , Cifuentes Alejandro 
Published: January 2024

AbstractIn this study, an exhaustive chemical characterization of a Dunaliella salina (DS) microalga extract obtained using supercritical fluids has been performed, and its neuroprotective capacity has been evaluated in vivo using an Alzheimer’s disease (AD) transgenic model of Caenorhabditis elegans (strain CL4176). More than 350 compounds were annotated in the studied DS extract, with triacylglycerols, free fatty acids (FAs), carotenoids, apocarotenoids and glycerol being the most abundant. DS extract significantly protects C. elegans in a dose-dependent manner against Aβ-peptide paralysis toxicity, after 32 h, 53% of treated worms at 50 µg/mL were not paralyzed. This concentration was selected to further evaluate the transcriptomics and metabolomics changes after 26 h by using advanced analytical methodologies. The RNA-Seq data showed an alteration of 150 genes, mainly related to the stress and detoxification responses, and the retinol and lipid metabolism. The comprehensive metabolomics and lipidomics analyses allowed the identification of 793 intracellular metabolites, of which 69 were significantly altered compared to non-treated control animals. Among them, different unsaturated FAs, lysophosphatidylethanolamines, nucleosides, dipeptides and modified amino acids that have been previously reported as beneficial during AD progression, were assigned. These compounds could explain the neuroprotective capacity observed, thus, providing with new evidences of the protection mechanisms of this promising extract.
Catalytic asymmetric cationic shifts of aliphatic hydrocarbons
Authors: Wakchaure Vijay N. , DeSnoo William , Laconsay Croix J. , Leutzsch Markus , Tsuji Nobuya , Tantillo Dean J. , List Benjamin 
Published: January 2024

AbstractAsymmetric catalysis is an advanced area of chemical synthesis, but the handling of abundantly available, purely aliphatic hydrocarbons has proven to be challenging. Typically, heteroatoms or aromatic substructures are required in the substrates and reagents to facilitate an efficient interaction with the chiral catalyst. Confined acids have recently been introduced as tools for homogenous asymmetric catalysis, specifically to enable the processing of small unbiased substrates1. However, asymmetric reactions in which both substrate and product are purely aliphatic hydrocarbons have not previously been catalysed by such super strong and confined acids. We describe here an imidodiphosphorimidate-catalysed asymmetric Wagner–Meerwein shift of aliphatic alkenyl cycloalkanes to cycloalkenes with excellent regio- and enantioselectivity. Despite their long history and high relevance for chemical synthesis and biosynthesis, Wagner–Meerwein reactions utilizing purely aliphatic hydrocarbons, such as those originally reported by Wagner and Meerwein, had previously eluded asymmetric catalysis.
Adding α,α-disubstituted and β-linked monomers to the genetic code of an organism
Authors: Dunkelmann Daniel L. , Piedrafita Carlos , Dickson Alexandre , Liu Kim C. , Elliott Thomas S. , Fiedler Marc , Bellini Dom , Zhou Andrew , Cervettini Daniele , Chin Jason W. 
Published: January 2024

AbstractThe genetic code of living cells has been reprogrammed to enable the site-specific incorporation of hundreds of non-canonical amino acids into proteins, and the encoded synthesis of non-canonical polymers and macrocyclic peptides and depsipeptides1–3. Current methods for engineering orthogonal aminoacyl-tRNA synthetases to acylate new monomers, as required for the expansion and reprogramming of the genetic code, rely on translational readouts and therefore require the monomers to be ribosomal substrates4–6. Orthogonal synthetases cannot be evolved to acylate orthogonal tRNAs with non-canonical monomers (ncMs) that are poor ribosomal substrates, and ribosomes cannot be evolved to polymerize ncMs that cannot be acylated onto orthogonal tRNAs—this co-dependence creates an evolutionary deadlock that has essentially restricted the scope of translation in living cells to α-l-amino acids and closely related hydroxy acids. Here we break this deadlock by developing tRNA display, which enables direct, rapid and scalable selection for orthogonal synthetases that selectively acylate their cognate orthogonal tRNAs with ncMs inEscherichia coli, independent of whether the ncMs are ribosomal substrates. Using tRNA display, we directly select orthogonal synthetases that specifically acylate their cognate orthogonal tRNA with eight non-canonical amino acids and eight ncMs, including several β-amino acids, α,α-disubstituted-amino acids and β-hydroxy acids. We build on these advances to demonstrate the genetically encoded, site-specific cellular incorporation of β-amino acids and α,α-disubstituted amino acids into a protein, and thereby expand the chemical scope of the genetic code to new classes of monomers.
Profiling of RNA-binding protein binding sites by in situ reverse transcription-based sequencing
Authors: Xiao Yu , Chen Yan-Ming , Zou Zhongyu , Ye Chang , Dou Xiaoyang , Wu Jinjun , Liu Chang , Liu Shun , Yan Hao , Wang Pingluan , Zeng Tie-Bo , Liu Qinzhe , Fei Jingyi , Tang Weixin , He Chuan 
Published: January 2024

AbstractRNA-binding proteins (RBPs) regulate diverse cellular processes by dynamically interacting with RNA targets. However, effective methods to capture both stable and transient interactions between RBPs and their RNA targets are still lacking, especially when the interaction is dynamic or samples are limited. Here we present an assay of reverse transcription-based RBP binding site sequencing (ARTR-seq), which relies on in situ reverse transcription of RBP-bound RNAs guided by antibodies to identify RBP binding sites. ARTR-seq avoids ultraviolet crosslinking and immunoprecipitation, allowing for efficient and specific identification of RBP binding sites from as few as 20 cells or a tissue section. Taking advantage of rapid formaldehyde fixation, ARTR-seq enables capturing the dynamic RNA binding by RBPs over a short period of time, as demonstrated by the profiling of dynamic RNA binding of G3BP1 during stress granule assembly on a timescale as short as 10 minutes.
A tablet-based multi-dimensional drawing system can effectively distinguish patients with amnestic MCI from healthy individuals
Authors: Zhang Xiaonan , Lv Liangliang , Shen Jiani , Chen Jinyu , Zhang Hui , Li Yang 
Published: January 2024

AbstractThe population with dementia is expected to rise to 152 million in 2050 due to the aging population worldwide. Therefore, it is significant to identify and intervene in the early stage of dementia. The Rey-Osterreth complex figure (ROCF) test is a visuospatial test scale. Its scoring methods are numerous, time-consuming, and inconsistent, which is unsuitable for wide application as required by the high number of people at risk. Therefore, there is an urgent need for a rapid, objective, and sensitive digital scoring method to detect cognitive dysfunction in the early stage accurately. This study aims to clarify the organizational strategy of aMCI patients to draw complex figures through a multi-dimensional digital evaluation system. At the same time, a rapid, objective, and sensitive digital scoring method is established to replace traditional scoring. The data of 64 subjects (38 aMCI patients and 26 NC individuals) were analyzed in this study. All subjects completed the tablet's Geriatric Complex Figure (GCF) test, including copying, 3-min recall, and 20-min delayed recall, and also underwent a standardized neuropsychological test battery and classic ROCF test. Digital GCF (dGCF) variables and conventional GCF (cGCF) scores were input into the forward stepwise logistic regression model to construct classification models. Finally, ROC curves were made to visualize the difference in the diagnostic value of dGCF variables vs. cGCF scores in categorizing the diagnostic groups. In 20-min delayed recall, aMCI patients' time in air and pause time were longer than NC individuals. Patients with aMCI had more short strokes and poorer ability of detail integration (all p < 0.05). The diagnostic sensitivity of dGCF variables for aMCI patients was 89.47%, slightly higher than cGCF scores (sensitivity: 84.21%). The diagnostic accuracy of both was comparable (dGCF: 70.3%; cGCF: 73.4%). Moreover, combining dGCF variables and cGCF scores could significantly improve the diagnostic accuracy and specificity (accuracy: 78.1%, specificity: 84.62%). At the same time, we construct the regression equations of the two models. Our study shows that dGCF equipment can quantitatively evaluate drawing performance, and its performance is comparable to the time-consuming cGCF score. The regression equation of the model we constructed can well identify patients with aMCI in clinical application. We believe this new technique can be a highly effective screening tool for patients with MCI.
The impact of the size and angle of the cochlear basal turn on translocation of a pre-curved mid-scala cochlear implant electrode
Authors: Pai Irumee , Connor Steve , Komninos Charalampos , Ourselin Sebastien , Bergeles Christos 
Published: January 2024

AbstractScalar translocation is a severe form of intra-cochlear trauma during cochlear implant (CI) electrode insertion. This study explored the hypothesis that the dimensions of the cochlear basal turn and orientation of its inferior segment relative to surgically relevant anatomical structures influence the scalar translocation rates of a pre-curved CI electrode. In a cohort of 40 patients implanted with the Advanced Bionics Mid-Scala electrode array, the scalar translocation group (40%) had a significantly smaller mean distance A of the cochlear basal turn (p < 0.001) and wider horizontal angle between the inferior segment of the cochlear basal turn and the mastoid facial nerve (p = 0.040). A logistic regression model incorporating distance A (p = 0.003) and horizontal facial nerve angle (p = 0.017) explained 44.0–59.9% of the variance in scalar translocation and correctly classified 82.5% of cases. Every 1mm decrease in distance A was associated with a 99.2% increase in odds of translocation [95% confidence interval 80.3%, 100%], whilst every 1-degree increase in the horizontal facial nerve angle was associated with an 18.1% increase in odds of translocation [95% CI 3.0%, 35.5%]. The study findings provide an evidence-based argument for the development of a navigation system for optimal angulation of electrode insertion during CI surgery to reduce intra-cochlear trauma.
On the complexity of quantum link prediction in complex networks
Authors: Moutinho João P. , Magano Duarte , Coutinho Bruno 
Published: January 2024

AbstractLink prediction methods use patterns in known network data to infer which connections may be missing. Previous work has shown that continuous-time quantum walks can be used to represent path-based link prediction, which we further study here to develop a more optimized quantum algorithm. Using a sampling framework for link prediction, we analyze the query access to the input network required to produce a certain number of prediction samples. Considering both well-known classical path-based algorithms using powers of the adjacency matrix as well as our proposed quantum algorithm for path-based link prediction, we argue that there is a polynomial quantum advantage on the dependence on N, the number of nodes in the network. We further argue that the complexity of our algorithm, although sub-linear in N, is limited by the complexity of performing a quantum simulation of the network’s adjacency matrix, which may prove to be an important problem in the development of quantum algorithms for network science in general.
Sensing of heavy metal Pb2+ ions in water utilizing the photonic structure of highly controlled hexagonal TiON/TiO2 nanotubes
Authors: Elsayed Asmaa M. , Ahmed Ashour M. , Tammam M. T. , Eissa M. F. , Aly Arafa H. 
Published: January 2024

AbstractThe detection of heavy metals in water, especially Pb2+ ions, is important due to their severe hazardous effects. To address this issue, a highly controlled hexagonal TiON/TiO2 heterostructure has been synthesized in this study. The fabrication process involved the utilization of atomic layer deposition and direct current sputtering techniques to deposit TiO2 and TiON layers onto a porous Al2O3 membrane used as a template. The resulting heterostructure exhibits a well-ordered hollow tube structure with a diameter of 345 nm and a length of 1.2 µm. The electrochemical sensing of Pb2+ ions in water is carried out using a cyclic voltammetry technique under both light and dark conditions. The concentration range for the Pb2+ ions ranges from 10–5 to 10–1 M. The sensitivity values obtained for the sensor are 1.0 × 10–6 in dark conditions and 1.0 × 10–4 in light conditions. The remarkable enhancement in sensitivity under light illumination can be attributed to the increased activity and electron transfer facilitated by the presence of light. The sensor demonstrates excellent reproducibility, highlighting its reliability and consistency. These findings suggest that the proposed sensor holds great promise for the detection of Pb2+ ions in water, thereby facilitating environmental monitoring, water quality assessment, and safety regulation across various industries. Furthermore, the eco-friendly and straightforward preparation techniques employed in its fabrication provide a significant advantage for practical and scalable implementation.
Network-based pharmacology-based research on the effect and mechanism of the Hedyotis diffusa–Scutellaria Barbata pair in the treatment of hepatocellular carcinoma
Authors: Hou Changmiao , Wen Xiao , Yan Shifan , Gu Xiaoxiao , Jiang Yu , Chen Fang , Liu Yanjuan , Zhu Yimin , Liu Xiehong 
Published: January 2024

AbstractThe Hedyotis diffusa–Scutellaria officinalis pair (HD–SB) has therapeutic effects on a variety of cancers. Our study was to explore the mechanism of HD–SB in the treatment of hepatocellular carcinoma (HCC). A total of 217 active ingredients of HD–SB and 1196 HCC-related targets were reserved from the TCMSP and the SwissTarget Prediction database, and we got 63 intersection targets from GeneCards. We used a Venn diagram, and Cytoscape found that the three core ingredients were quercetin, luteolin, and baicalein. The PPI analysis showed that the core targets were TP53, CDK2, XPO1, and APP. Molecular docking results showed that these core ingredients had good binding potential with the core targets. HD–SB acts simultaneously on various HCC-related signaling pathways, including proteoglycans in cancer and the P53 signaling pathway. In vitro experiments confirmed that HD–SB can inhibit HepG2 cell proliferation by increasing TP53 and APP levels and decreasing XPO1 and CDK2 levels. This study analyzed active ingredients, core targets, and central mechanisms of HD–SB in the treatment of HCC. It reveals the role of HD–SB in targeting the P53 signaling pathway in the treatment of HCC. We hope that our research could provide a new perspective to the therapy of HCC and find new anticancer drugs.
Optical coupling control of isolated mechanical resonators
Authors: Onah F. E. , Jaramillo-Ávila B. R. , Maldonado-Villamizar F. H. , Rodríguez-Lara B. M. 
Published: January 2024

AbstractWe present a Hamiltonian model describing two pairs of mechanical and optical modes under standard optomechanical interaction. The vibrational modes are mechanically isolated from each other and the optical modes couple evanescently. We recover the ranges for variables of interest, such as mechanical and optical resonant frequencies and naked coupling strengths, using a finite element model for a standard experimental realization. We show that the quantum model, under this parameter range and external optical driving, may be approximated into parametric interaction models for all involved modes. As an example, we study the effect of detuning in the optical resonant frequencies modes and optical driving resolved to mechanical sidebands and show an optical beam splitter with interaction strength dressed by the mechanical excitation number, a mechanical bidirectional coupler, and a two-mode mechanical squeezer where the optical state mediates the interaction strength between the mechanical modes.
Machine learning assisted rational design of antimicrobial peptides based on human endogenous proteins and their applications for cosmetic preservative system optimization
Authors: Yue Lizhi , Song Liya , Zhu Siyu , Fu Xiaolei , Li Xuhui , He Congfen , Li Junxiang 
Published: January 2024

AbstractPreservatives are essential components in cosmetic products, but their safety issues have attracted widespread attention. There is an urgent need for safe and effective alternatives. Antimicrobial peptides (AMPs) are part of the innate immune system and have potent antimicrobial properties. Using machine learning-assisted rational design, we obtained a novel antibacterial peptide, IK-16-1, with significant antibacterial activity and maintaining safety based on β-defensins. IK-16-1 has broad-spectrum antimicrobial properties against Escherichia coli, Staphylococcus aureus, Pseudomonas aeruginosa, and Candida albicans, and has no haemolytic activity. The use of IK-16-1 holds promise in the cosmetics industry, since it can serve as a preservative synergist to reduce the amount of other preservatives in cosmetics. This study verified the feasibility of combining computational design with artificial intelligence prediction to design AMPs, achieving rapid screening and reducing development costs.
Effect of diet supplemented with functional amino acids and polyphenols on gut health in broilers subjected to a corticosterone-induced stress
Authors: Yvon Sophie , Beaumont Martin , Dayonnet Alix , Eutamène Hélène , Lambert William , Tondereau Valérie , Chalvon-Demersay Tristan , Belloir Pauline , Paës Charlotte 
Published: January 2024

AbstractTo address the overuse of antimicrobials in poultry production, new functional feed ingredients, i.e. ingredients with benefits beyond meeting basic nutritional requirements, can play a crucial role thanks to their prophylactic effects. This study evaluated the effects of the supplementation of arginine, threonine and glutamine together with grape polyphenols on the gut integrity and functionality of broilers facing a stress condition. 108 straight-run newly hatched Ross PM3 chicks were kept until 35 days and were allocated to 3 treatments. Broilers in the control group were raised in standard conditions. In experimental groups, birds were administered with corticosterone in drinking water (CORT groups) to impair the global health of the animal and were fed a well-balanced diet supplemented or not with a mix of functional amino acids together with grape extracts (1 g/kg of diet—CORT + MIX group). Gut permeability was significantly increased by corticosterone in non-supplemented birds. This corticosterone-induced stress effect was alleviated in the CORT + MIX group. MIX supplementation attenuated the reduction of crypt depth induced by corticosterone. Mucin 2 and TNF-α gene expression was up-regulated in the CORT + MIX group compared to the CORT group. Caecal microbiota remained similar between the groups. These findings indicate that a balanced diet supplemented with functional AA and polyphenols can help to restore broiler intestinal barrier after a stress exposure.
Isotherms, kinetics and thermodynamic mechanism of methylene blue dye adsorption on synthesized activated carbon
Authors: El Jery Atef , Alawamleh Heba Saed Kariem , Sami Mustafa Humam , Abbas Hussein Abdullah , Sammen Saad Sh. , Ahsan Amimul , Imteaz M. A. , Shanableh Abdallah , Shafiquzzaman Md. , Osman Haitham , Al-Ansari Nadhir 
Published: January 2024

AbstractThe treatment of methylene blue (MB) dye wastewater through the adsorption process has been a subject of extensive research. However, a comprehensive understanding of the thermodynamic aspects of dye solution adsorption is lacking. Previous studies have primarily focused on enhancing the adsorption capacity of methylene blue dye. This study aimed to develop an environmentally friendly and cost-effective method for treating methylene blue dye wastewater and to gain insights into the thermodynamics and kinetics of the adsorption process for optimization. An adsorbent with selective methylene blue dye adsorption capabilities was synthesized using rice straw as the precursor. Experimental studies were conducted to investigate the adsorption isotherms and models under various process conditions, aiming to bridge gaps in previous research and enhance the understanding of adsorption mechanisms. Several adsorption isotherm models, including Langmuir, Temkin, Freundlich, and Langmuir–Freundlich, were applied to theoretically describe the adsorption mechanism. Equilibrium thermodynamic results demonstrated that the calculated equilibrium adsorption capacity (qe) aligned well with the experimentally obtained data. These findings of the study provide valuable insights into the thermodynamics and kinetics of methylene blue dye adsorption, with potential applications beyond this specific dye type. The utilization of rice straw as an adsorbent material presents a novel and cost-effective approach for MB dye removal from wastewater.
Quantifying changes in individual-specific template-based representations of center-of-mass dynamics during walking with ankle exoskeletons using Hybrid-SINDy
Authors: Rosenberg Michael C. , Proctor Joshua L. , Steele Katherine M. 
Published: January 2024

AbstractAnkle exoskeletons alter whole-body walking mechanics, energetics, and stability by altering center-of-mass (CoM) motion. Controlling the dynamics governing CoM motion is, therefore, critical for maintaining efficient and stable gait. However, how CoM dynamics change with ankle exoskeletons is unknown, and how to optimally model individual-specific CoM dynamics, especially in individuals with neurological injuries, remains a challenge. Here, we evaluated individual-specific changes in CoM dynamics in unimpaired adults and one individual with post-stroke hemiparesis while walking in shoes-only and with zero-stiffness and high-stiffness passive ankle exoskeletons. To identify optimal sets of physically interpretable mechanisms describing CoM dynamics, termedtemplate signatures, we leveraged hybrid sparse identification of nonlinear dynamics (Hybrid-SINDy), an equation-free data-driven method for inferring sparse hybrid dynamics from a library of candidate functional forms. In unimpaired adults, Hybrid-SINDy automatically identified spring-loaded inverted pendulum-like template signatures, which did not change with exoskeletons (p > 0.16), except for small changes in leg resting length (p < 0.001). Conversely, post-stroke paretic-leg rotary stiffness mechanisms increased by 37–50% with zero-stiffness exoskeletons. While unimpaired CoM dynamics appear robust to passive ankle exoskeletons, how neurological injuries alter exoskeleton impacts on CoM dynamics merits further investigation. Our findings support Hybrid-SINDy’s potential to discover mechanisms describing individual-specific CoM dynamics with assistive devices.