bluuebunny/crossref_metadata_2025_split huggingface dataset:
miRNA profiling as a complementary diagnostic tool for amyotrophic lateral sclerosis
Authors: Cheng Jack , Ho Wen-Kuang , Wu Bor-Tsang , Liu Hsin-Ping , Lin Wei-Yong 
Published: August 2023

AbstractAmyotrophic lateral sclerosis (ALS), the most prevalent motor neuron disease characterized by its complex genetic structure, lacks a single diagnostic test capable of providing a conclusive diagnosis. In order to demonstrate the potential for genetic diagnosis and shed light on the pathogenic role of miRNAs in ALS, we developed an ALS diagnostic rule by training the model using 80% of a miRNA profiling dataset consisting of 253 ALS samples and 103 control samples. Subsequently, we validated the diagnostic rule using the remaining 20% of unseen samples. The diagnostic rule we developed includes miR-205-5p, miR-206, miR-376a-5p, miR-412-5p, miR-3927-3p, miR-4701-3p, miR-6763-5p, and miR-6801-3p. Remarkably, the rule achieved an 82% true positive rate and a 73% true negative rate when predicting the unseen samples. Furthermore, the identified miRNAs target 21 genes in the PI3K-Akt pathway and 27 genes in the ALS pathway, including notable genes such as BCL2, NEFH, and OPTN. We propose that miRNA profiling may serve as a complementary diagnostic tool to supplement the clinical presentation and aid in the early recognition of ALS.
Puberty timing and relative age as predictors of physical activity discontinuation during adolescence
Authors: Gallant François , Hebert Jeff J. , Thibault Véronique , Mekari Saïd , Sabiston Catherine M. , Bélanger Mathieu 
Published: August 2023

AbstractAmong same-age adolescents, those who enter puberty relatively later and those who are relatively younger (e.g., born later in the year) might be at greater risk of physical activity discontinuation. This study aimed to (1) describe gender-specific discontinuation, re-engagement, and uptake rates in various types of physical activities from the age of 11 to 17 years, and (2) assess puberty timing and relative age as predictors of discontinuation from organized, unorganized, individual, and group-based physical activities. Longitudinal data from 781 (56% girls, age 10–13 years at study baseline) Canadian participants who self-reported puberty status, birthdate, and involvement in 36 physical activities every four months from 2011 to 2018 was analyzed. The incidence of discontinuation, re-engagement, and uptake in organized/unorganized and individual/group activities from grade 6 until grade 12 was described and Cox proportional hazard models were used to estimate associations of puberty timing and relative age with organized/unorganized and individual/group activity discontinuation. Results demonstrate that individual and unorganized activities are maintained longer than group-based and organized activities. Girls who started puberty earlier were more likely to discontinue organized activities than girls with average-puberty timing [Hazard ratio (HR) (95% confidence interval (CI)) 1.68 (1.05–2.69)]. Compared to boys born in the 4th quarter of the year, boys born in the 2nd quarter of the year were less likely to discontinue organized [HR (95% CI) 0.41 (0.23–0.74)], unorganized [HR (95% CI) 0.33 (0.16–0.70)], group [HR (95% CI) 0.58 (0.34–0.98)], and individual activities[HR (95% CI) 0.46 (0.23–0.91)], and boys born in the 3rd quarter were less likely to discontinue unorganized activities[HR (95% CI) 0.41 (0.19–0.88)]. This study illustrates the patterns of physical activity participation throughout adolescence. However, the generalizability of findings may be limited due to participant representation.
Cardamonin protects against iron overload induced arthritis by attenuating ROS production and NLRP3 inflammasome activation via the SIRT1/p38MAPK signaling pathway
Authors: Li Shaocong , He Qi , Chen Baihao , Zeng Jiaxu , Dou Xiangyun , Pan Zhaofeng , Xiao Jiacong , Li Miao , Wang Fanchen , Chen Chuyi , Lin Yuewei , Wang Xintian , Wang Haibin , Chen Jianfa 
Published: August 2023

AbstractIron homeostasis plays an essential role in joint health, while iron overload can cause damage and death of cartilage cells. Cardamonin (CAR) is a substance found in the fruit of the chasteberry plant and has anti-inflammatory and anti-tumor activities. We first administered iron dextran (500 mg/kg) intraperitoneally to establish an iron overload mouse model and surgically induced osteoarthritis. The extent of OA and iron deposition were assessed using Micro-ct, Safranin-O/fast green staining, H&E staining, and Prussian Blue 10 weeks later. We administered primary chondrocytes with Ferric Ammonium Citrate (FAC) to evaluate the chondrocyte changes. Chondrocytes were identified in vitro by toluidine blue staining, and chondrocyte viability was evaluated by CCK-8. The rate of apoptosis was determined by Annexin V-FITC/PI assay. The mechanism of action of CAR was verified by adding the SIRT1 inhibitor EX527, and the expression of SIRT1 and MAPK signaling pathways was detected by Western blot. Iron overload also promoted chondrocyte apoptosis, a process that was reversed by CAR. In addition, CAR reduced NLRP3 inflammasome production via the SIRT1-MAPK pathway, and the SIRT1 inhibitor EX527 inhibited the treatment of OA by CAR.CAR inhibited cartilage degeneration induced by iron overload both in vivo and in vitro. Besides, our study showed that iron overload not only inhibited type II collagen expression but also induced MMP expression by catalyzing the generation of NLRP3 inflammasome. Our results suggest that CAR can treat KOA by promoting SIRT1 expression and inhibiting p38MAPK pathway expression to reduce the production of NLRP3 inflammasome vesicles.
Grey hybrid normalization with period based entropy weighting and relational analysis for cities rankings
Authors: Esangbedo Moses Olabhele , Wei Jieyun 
Published: August 2023

AbstractResearchers have addressed uncertainty in multicriteria decision making from the perspective of the performance values of the alternatives, weighting of the evaluation criteria, and the evaluation methods. Still, they are yet to address the uncertainty caused by the normalization approach. In this paper, we show that different normalization methods, namely sum normalization, min–max normalization, vector normalization, and maximization normalization, can result in different rankings of the alternatives while the performance values and weights are unchanged. We applied the grey system theory to address the problem of uncertainty in this study from three aspects: alternative performance values measurement, criteria weighting, and decision matrix/table normalization within a period. The grey hybrid normalization method is proposed as the main contribution in this paper. Then, we present the rankings of 48 cities under uncertainty to decide the location of a branch office of a Chinese electric vehicle manufacturer as a practical example based on the grey entropy weighting method and grey relational analysis with positive and negative references (GRA-PNR) within the period from the year 2019 to 2021. The research results using this approach ranked New York City the best, with a stock market capitalization of economy validity as the top contributor in terms of weighting. Finally, we used simple additive weighting with grey value and the technique for order of preference by similarity to ideal solution with grey value methods to validate the study results.
TGF-β1 stimulation and VDR-dependent activation modulate calcitriol action on skeletal muscle fibroblasts and Smad signalling-associated fibrogenesis
Authors: Srikuea Ratchakrit , Hirunsai Muthita 
Published: August 2023

AbstractFibroblasts play a pivotal role in fibrogenesis after skeletal muscle injury. Excess fibrous formation can disrupt contractile functions and delay functional recovery. Although vitamin D receptor (VDR) is expressed explicitly in regenerating muscle compared with uninjured muscle, how calcitriol [1α,25(OH)2D3] directly regulates skeletal muscle primary fibroblast proliferation, the transition to myofibroblasts, and Smad signalling-associated fibrogenesis is currently unknown. Herein, the effects of calcitriol on cultured skeletal muscle primary fibroblasts of male C57BL/6 mice (aged 1 month old) were investigated. The percentage of BrdU+ nuclei in primary fibroblasts was significantly decreased after calcitriol treatment; however, the antiproliferative effect of calcitriol was diminished after TGF-β1 stimulation to induce fibroblast to myofibroblast transition. This suppressive effect was associated with significantly decreased VDR expression in TGF-β1-treated cells. In addition, Vdr siRNA transfection abolished the effects of calcitriol on the suppression of α-SMA expression and Smad2/3 signalling in myofibroblasts, supporting that its antifibrogenic effect requires VDR activation. Compared with calcitriol, the antifibrotic agent suramin could inhibit fibroblast/myofibroblast proliferation and suppress the expression of TCF-4, which regulates fibrogenic determination. Collectively, these findings suggest that profibrotic stimulation and VDR-dependent activation could modulate the effects of calcitriol on skeletal muscle fibroblast proliferation and fibrogenesis processes. Therefore, TGF-β1 and VDR expression levels are crucial determinants for the antifibrogenic effect of calcitriol on skeletal muscle after injury.
Effectiveness of the production of tissue-engineered living bone graft: a comparative study using perfusion and rotating bioreactor systems
Authors: Kazimierczak Paulina , Kalisz Grzegorz , Sroka-Bartnicka Anna , Przekora Agata 
Published: August 2023

AbstractBioreactor systems are very precious tools to generate living bone grafts in vitro. The aim of this study was to compare the effectiveness of rotating and perfusion bioreactor in the production of a living bone construct. Human bone marrow-derived mesenchymal stem cells (BMDSCs) were seeded on the surfaces of hydroxyapatite-based scaffolds and cultured for 21 days in three different conditions: (1) static 3D culture, (2) 3D culture in a perfusion bioreactor, and (3) dynamic 3D culture in a rotating bioreactor. Quantitative evaluation of cell number showed that cultivation in the perfusion bioreactor significantly reduced cell proliferation compared to the rotating bioreactor and static culture. Osteogenic differentiation test demonstrated that BMDSCs cultured in the rotating bioreactor produced significantly greater amount of osteopontin compared to the cells cultured in the perfusion bioreactor. Moreover, Raman spectroscopy showed that cultivation of BMDSCs in the rotating bioreactor enhanced extracellular matrix (ECM) mineralization that was characterized by B-type carbonated substitution of hydroxyapatite (associated with PO43− groups) and higher mineral-to-matrix ratio compared to the ECM of cells cultured in the perfusion system. Thus, it was concluded that the rotating bioreactor was much more effective than the perfusion one in the generation of bone tissue construct in vitro.
Light-absorption-driven photocatalysis and antimicrobial potential of PVP-capped zinc oxide nanoparticles
Authors: Singh Karanpal , Nancy  , Bhattu Monika , Singh Gurjinder , Mubarak Nabisab Mujawar , Singh Jagpreet 
Published: August 2023

AbstractToxic dyes in water bodies and bacterial pathogens pose serious global challenges to human health and the environment. Zinc oxide nanoparticles (ZnO NPs) demonstrate remarkable photocatalytic and antibacterial potency against reactive dyes and bacterial strains. In this work, PVP-ZnO NPs have been prepared via the co-precipitation method using polyvinylpyrrolidone (PVP) as a surfactant. The NPs’ microstructure and morphology were studied using X-ray diffraction (XRD), having a size of 22.13 nm. High-resolution transmission electron microscope (HR-TEM) and field emission scanning electron microscopy (FESEM) analysis showed spherical-shaped PVP-ZnO NPs with sizer ranging from 20 to 30 nm. Fourier Transform Infrared Spectroscopy (FT-IR) confirmed the hybrid nature of the NPs, and UV–Vis spectroscopy showed an absorption peak at 367 nm. The PVP-ZnO NPs exhibited high photocatalytic activity, achieving 88% and nearly 95% degradation of reactive red-141 azo dye with 10 mg and 20 mg catalyst dosages, respectively. The antibacterial properties of the NPs were demonstrated against Escherichia coli and Bacillus subtilis, with inhibition zones of 24 mm and 20 mm, respectively. These findings suggest that PVP-ZnO NPs can be effectively used for water treatment, targeting both dye and pathogenic contaminants.
Moderate binding of villin headpiece protein to C3N3 nanosheet reveals the suitable biocompatibility of this nanomaterial
Authors: Luo Yuqi , Gu Zonglin , Perez-Aguilar Jose Manuel , Liao Weihua , Huang Yiwen , Luo Yanbo 
Published: August 2023

AbstractSince its recent successful synthesis and due to its promising physical and chemical properties, the carbon nitrite nanomaterial, C3N3, has attracted considerable attention in various scientific areas. However, thus far, little effort has been devoted to investigating the structural influence of the direct interaction of this 2D nanomaterial and biomolecules, including proteins and biomembranes so as to understand the physical origin of its bio-effect, particularly from the molecular landscape. Such information is fundamental to correlate to the potential nanotoxicology of the C3N3 nanomaterial. In this work, we explored the potential structural influence of a C3N3 nanosheet on the prototypical globular protein, villin headpiece (HP35) using all-atom molecular dynamics (MD) simulations. We found that HP35 could maintain its native conformations upon adsorption onto the C3N3 nanosheet regardless of the diversity in the binding sites, implying the potential advantage of C3N3 in protecting the biomolecular structure. The adsorption was mediated primarily by vdW interactions. Moreover, once adsorbed on the C3N3 surface, HP35 remains relatively fixed on the nanostructure without a distinct lateral translation, which may aid in keeping the structural integrity of the protein. In addition, the porous topological structure of C3N3 and the special water layer present on the C3N3 holes conjointly contributed to the restricted motion of HP35 via the formation of a high free energy barrier and a steric hindrance to prevent the surface displacement. This work revealed for the first time the potential influence of the 2D C3N3 nanomaterial in the protein structure and provided the corresponding in-depth molecular-level mechanism, which is valuable for future applications of C3N3 in bionanomedicine.
Intraoperative neurological pupil index and postoperative delirium and neurologic adverse events after cardiac surgery: an observational study
Authors: Lee Seohee , Jung Dhong-Eun , Park Dongnyeok , Kim Tae Jung , Lee Hyung-Chul , Bae Jinyoung , Nam Karam , Jeon Yunseok , Cho Youn Joung 
Published: August 2023

AbstractNeurological pupil index (NPi) calculated by automated pupillometry predicts clinical outcomes in critically ill patients. However, there are few data on intraoperative NPi and postoperative outcome after cardiac surgery. We evaluated the relationships between intraoperative NPi and clinical outcomes, such as delirium, in cardiac surgery patients. NPi was measured at baseline, after anesthesia induction, at 30 min intervals after initiation of cardiopulmonary bypass or anastomosis of coronary artery bypass graft, and at skin closure. Abnormal NPi was defined as one or more measurements of NPi < 3.0 during surgery. The worst intraoperative NPi was recorded, then multivariate logistic regression analysis was performed to evaluate the relationship between abnormal NPi and postoperative delirium following cardiac surgery. Among 123 included patients, postoperative delirium developed in 19.5% (24/123) of patients. Intraoperative abnormal NPi was significantly associated with postoperative delirium (odds ratio 6.078; 95% confidence interval 1.845–20.025; P = 0.003) after adjustment for Society of Thoracic Surgeons Predicted Risk of Mortality score, coronary artery disease, and use of calcium channel blockers. In conclusion, abnormal intraoperative NPi independently predicted postoperative delirium following cardiac surgery. Intraoperative application of pupillometry may have prognostic value for development of postoperative delirium, thereby enabling close surveillance and early intervention in high-risk patients.Registry number: ClinicalTrials.gov (NCT04136210).
Transient vegetation degradation reinforced rapid climate change (RCC) events during the Holocene
Authors: Li Xinzhou , Liu Xiaodong , Pan Zaitao , Shi Zhengguo , Xie Xiaoning , Ma Hongyan , Zhai Jizhou , Liu Heng , Xie Xiaoxun , Dai Aona 
Published: August 2023

AbstractHigh-resolution multi-proxies from geological archives have revealed a series of rapid climate change (RCC) events during the Holocene. These events coincided with the so-called “Bond events”, which were previously linked to a weakened thermohaline circulation. However, the proposed atmosphere-ocean teleconnections associated with these events are regionally distinct, which explains why most previous studies have only explained a subset of the RCC events, depending on region and proxy type; moreover, the suggested mechanisms are much debated. Here, we present a major effort of Holocene transient simulations that identify a series of centennial-scale RCC events that are consistent with records from geological archives. All eight Holocene RCC events were captured in North China (NC) and pervasive throughout the Northern Hemisphere (NH) in experiments with active dynamic vegetation modules (DV), whereas they were largely absent in experiments without DV. These results suggest that the collapse of the terrestrial vegetation and the resulting feedback played a crucial role in RCC events. Our findings supplement or even challenge the notion that North Atlantic cooling, closely linked to ice-rafted debris (IRD) events, was the dominant driver of RCC events.
Thiol-based defect healing of WSe2 and WS2
Authors: Schwarz Aviv , Alon-Yehezkel Hadas , Levi Adi , Yadav Rajesh Kumar , Majhi Koushik , Tzuriel Yael , Hoang Lauren , Bailey Connor S. , Brumme Thomas , Mannix Andrew J. , Cohen Hagai , Yalon Eilam , Heine Thomas , Pop Eric , Cheshnovsky Ori , Naveh Doron 
Published: August 2023

AbstractRecent research on two-dimensional (2D) transition metal dichalcogenides (TMDCs) has led to remarkable discoveries of fundamental phenomena and to device applications with technological potential. Large-scale TMDCs grown by chemical vapor deposition (CVD) are now available at continuously improving quality, but native defects and natural degradation in these materials still present significant challenges. Spectral hysteresis in gate-biased photoluminescence (PL) measurements of WSe2 further revealed long-term trapping issues of charge carriers in intrinsic defect states. To address these issues, we apply here a two-step treatment with organic molecules, demonstrating the “healing” of native defects in CVD-grown WSe2 and WS2 by substituting atomic sulfur into chalcogen vacancies. We uncover that the adsorption of thiols provides only partial defect passivation, even for high adsorption quality, and that thiol adsorption is fundamentally limited in eliminating charge traps. However, as soon as the molecular backbone is trimmed and atomic sulfur is released to the crystal, both bonds of the sulfur are recruited to passivate the divalent defect and the semiconductor quality improves drastically. Time-dependent X-ray photoelectron spectroscopy (XPS) is applied here together with other methods for the characterization of defects, their healing, leading energies and occupation. First-principles calculations support a unified picture of the electronic passivation of sulfur-healed WSe2 and WS2. This work provides a simple and efficient method for improving the quality of 2D semiconductors and has the potential to impact device performance even after natural degradation.
Explainable deep learning approach for extracting cognitive features from hand-drawn images of intersecting pentagons
Authors: Tasaki Shinya , Kim Namhee , Truty Tim , Zhang Ada , Buchman Aron S. , Lamar Melissa , Bennett David A. 
Published: August 2023

AbstractHand drawing, which requires multiple neural systems for planning and controlling sequential movements, is a useful cognitive test for older adults. However, the conventional visual assessment of these drawings only captures limited attributes and overlooks subtle details that could help track cognitive states. Here, we utilized a deep-learning model, PentaMind, to examine cognition-related features from hand-drawn images of intersecting pentagons. PentaMind, trained on 13,777 images from 3111 participants in three aging cohorts, explained 23.3% of the variance in the global cognitive scores, 1.92 times more than the conventional rating. This accuracy improvement was due to capturing additional drawing features associated with motor impairments and cerebrovascular pathologies. By systematically modifying the input images, we discovered several important drawing attributes for cognition, including line waviness. Our results demonstrate that deep learning models can extract novel drawing metrics to improve the assessment and monitoring of cognitive decline and dementia in older adults.
A chromosome-scale Rhubarb (Rheum tanguticum) genome assembly provides insights into the evolution of anthraquinone biosynthesis
Authors: Li Ying , Wang Zhenyue , Zhu Mingjia , Niu Zhimin , Li Minjie , Zheng Zeyu , Hu Hongyin , Lu Zhiqiang , Zhang Jin , Wan Dongshi , Chen Qiao , Yang Yongzhi 
Published: August 2023

AbstractRhubarb is the collective name for various perennial plants from the genus Rheum L. and the Polygonaceae family. They are one of the most ancient, commonly used, and important herbs in traditional Chinese medicine. Rhubarb is a major source of anthraquinones, but how they are synthesized remains largely unknown. Here, we generate a genome sequence assembly of one important medicinal rhubarb R. tanguticum at the chromosome level, with 2.76 Gb assembled into 11 chromosomes. The genome is shaped by two recent whole-genome duplication events and recent bursts of retrotransposons. Metabolic analyses show that the major anthraquinones are mainly synthesized in its roots. Transcriptomic analysis reveals a co-expression module with a high correlation to anthraquinone biosynthesis that includes key chalcone synthase genes. One CHS, four CYP450 and two BGL genes involved in secondary metabolism show significantly upregulated expression levels in roots compared with other tissues and clustered in the co-expression module, which implies that they may also act as candidate genes for anthraquinone biosynthesis. This study provides valuable insights into the genetic bases of anthraquinone biosynthesis that will facilitate improved breeding practices and agronomic properties for rhubarb in the future.
A practical preparation of bicyclic boronates via metal-free heteroatom-directed alkenyl sp2-C‒H borylation
Authors: Peng Pei-Ying , Zhang Gui-Shan , Gong Mei-Ling , Zhang Jian-Wei , Liu Xi-Liang , Gao Dingding , Lin Guo-Qiang , Li Qing-Hua , Tian Ping 
Published: August 2023

AbstractBicyclic boronates play critical roles in the discovery of functional materials and antibacterial agents, especially against deadly bacterial pathogens. Their practical and convenient preparation is in high demand but with great challenge. Herein, we report an efficient strategy for the preparation of bicyclic boronates through metal-free heteroatom-directed alkenyl sp2-C‒H borylation. This synthetic approach exhibits good functional group compatibility, and the corresponding boronates bearing halides, aryls, acyclic and cyclic frameworks are obtained with high yields (43 examples, up to 95% yield). Furthermore, a gram-scale experiment is conducted, and downstream transformations of the bicyclic boronates are pursued to afford natural products, drug scaffolds, and chiral hemiboronic acid catalysts.