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1.
Nat Prod Res ; : 1-8, 2024 Jul 04.
Article in English | MEDLINE | ID: mdl-38962949

ABSTRACT

The phytochemical investigation on the rhizomes of Paris yunnanensis Franch. resulted in the discovery and characterisation of six compounds, including two new saponins named parisyunnanosides M-N (1-2), and four known ones (3-6). The structures of isolated compounds were determined by spectroscopic data analysis and chemical methods. Compound 2 is a pregnane-type saponin with a special α,ß-unsaturated carboxylic acid moiety at C-17, which is first discovered in genus Paris. The anti-inflammatory activity of the isolated compounds was assessed in vitro. The results demonstrated that compounds 3 and 4 could significantly inhibit the production of NO which was induced by LPS in RAW 264.7 cells with IC50 values of 0.67 ± 0.17 µM and 0.85 ± 0.12 µM, respectively.

2.
J Bioinform Comput Biol ; : 2450007, 2024 Jul 20.
Article in English | MEDLINE | ID: mdl-39036848

ABSTRACT

For sequencing-based spatial transcriptomics data, the gene-spot count matrix is highly sparse. This feature is similar to scRNA-seq. The goal of this paper is to identify whether there exist genes that are frequently under-detected in Visium compared to bulk RNA-seq, and the underlying potential mechanism of under-detection in Visium. We collected paired Visium and bulk RNA-seq data for 28 human samples and 19 mouse samples, which covered diverse tissue sources. We compared the two data types and observed that there indeed exists a collection of genes frequently under-detected in Visium compared to bulk RNA-seq. We performed a motif search to examine the last 350 bp of the frequently under-detected genes, and we observed that the poly (T) motif was significantly enriched in genes identified from both human and mouse data, which matches with our previous finding about frequently under-detected genes in scRNA-seq. We hypothesized that the poly (T) motif may be able to form a hairpin structure with the poly (A) tails of their mRNA transcripts, making it difficult for their mRNA transcripts to be captured during Visium library preparation.

3.
Int J Biol Macromol ; 274(Pt 1): 132917, 2024 Jun 06.
Article in English | MEDLINE | ID: mdl-38851612

ABSTRACT

The development of a multifunctional wound dressing that can adapt to the shape of wounds and provide controlled drug release is crucial for diabetic patients. This study developed a carboxymethyl chitosan-based hydrogel dressing with enhanced mechanical properties and tissue adherence that were achieved by incorporating pectin (PE) and polydopamine (PDA) and loading the hydrogel with recombinant human epidermal growth factor (rhEGF). This EGF@PDA-CMCS-PE hydrogel demonstrated robust tissue adhesion, enhanced mechanical properties, and superior water retention and vapor permeability. It also exhibited significant antioxidant capacity. The results showed that EGF@PDA-CMCS-PE could effectively scavenge 2,2'-Azinobis-(3-ethylbenzthiazoline-6-sulphonate), (1,1-diphenyl-2-picrylhydrazyl), and superoxide anions and increase superoxide dismutase and catalase levels in vivo. In vitro cytotoxicity and antibacterial assays showed good biocompatibility and antimicrobial properties. The sustained release of EGF by the hydrogel was confirmed, with a gradual release profile over 120 h. In vivo studies in diabetic mice showed that the hydrogel significantly accelerated wound healing, with a wound contraction rate of 97.84% by day 14. Histopathological analysis revealed that the hydrogel promoted fibroblast proliferation, neovascularization, and orderly connective tissue formation, leading to a more uniform and compact wound-healing process. Thus, EGF@PDA-CMCS-PE hydrogel presents a promising tool for managing chronic diabetic wounds, offering a valuable strategy for future clinical applications.

4.
Front Aging Neurosci ; 16: 1407423, 2024.
Article in English | MEDLINE | ID: mdl-38934018

ABSTRACT

Background: Amid the backdrop of global aging, the increasing prevalence of cognitive decline among the elderly, particularly within the female demographic, represents a considerable public health concern. Physical activity (PA) is recognized as an effective non-pharmacological intervention for mitigating cognitive decline in older adults. However, the relationship between different PA patterns and cognitive function (CF) in elderly women remains unclear. Methods: This study utilized data from National Health and Nutrition Examination Survey (NHANES) 2011-2014 to investigate the relationships between PA, PA patterns [inactive, Weekend Warrior (WW), and Regular Exercise (RE)], and PA intensity with CF in elderly women. Multivariate regression analysis served as the primary analytical method. Results: There was a significant positive correlation between PA and CF among elderly women (ß-PA: 0.003, 95% CI: 0.000-0.006, P = 0.03143). Additionally, WW and RE activity patterns were associated with markedly better cognitive performance compared to the inactive group (ß-WW: 0.451, 95% CI: 0.216-0.685, P = 0.00017; ß-RE: 0.153, 95% CI: 0.085-0.221, P = 0.00001). Furthermore, our results indicate a progressive increase in CF with increasing PA intensity (ß-MPA- dominated: 0.16, 95% CI: 0.02-0.09, P = 0.0208; ß-VPA-dominated: 0.21, 95% CI: 0.09-0.34, P = 0.0011; ß-Total VPA: 0.31, 95% CI: -0.01-0.63, P = 0.0566). Conclusion: Our study confirms a positive association between PA and CF in elderly women, with even intermittent but intensive PA models like WW being correlated with improved CF. These findings underscore the significant role that varying intensities and patterns of PA play in promoting cognitive health among older age groups, highlighting the need for adaptable PA strategies in public health initiatives targeting this population.

5.
Appl Opt ; 63(14): 3910-3915, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38856354

ABSTRACT

This research introduces a compact, auto-aligning interferometer engineered for measuring translations with a wide angular working range and picometer precision above 1H z. It presents a design ensuring automatic beam alignment during movement through secondary reflection from a corner reflector. The sensor head, a 20×10×10m m 3 all-glass quasi-monolithic structure, exhibits a displacement sensitivity below 1p m/H z 1/2 above 1H z and a wide angular working range of ±200m r a d. This versatile optical design holds promise to improve the sensitivity in applications such as laser ranging, optical seismometers, precision manufacturing, and metrology.

6.
Front Endocrinol (Lausanne) ; 15: 1407503, 2024.
Article in English | MEDLINE | ID: mdl-38836234

ABSTRACT

Background: Type 2 diabetes mellitus (T2DM) and hearing loss (HL) constitute significant public health challenges worldwide. Recently, the association between T2DM and HL has aroused attention. However, possible residual confounding factors and other biases inherent to observational study designs make this association undetermined. In this study, we performed univariate and multivariable Mendelian Randomization (MR) analysis to elucidate the causal association between T2DM and common hearing disorders that lead to HL. Methods: Our study employed univariate and multivariable MR analyses, with the Inverse Variance Weighted method as the primary approach to assessing the potential causal association between T2DM and hearing disorders. We selected 164 and 9 genetic variants representing T2DM from the NHGRI-EBI and DIAGRAM consortium, respectively. Summary-level data for 10 hearing disorders were obtained from over 500,000 participants in the FinnGen consortium and MRC-IEU. Sensitivity analysis revealed no significant heterogeneity of instrumental variables or pleiotropy was detected. Results: In univariate MR analysis, genetically predicted T2DM from both sources was associated with an increased risk of acute suppurative otitis media (ASOM) (In NHGRI-EBI: OR = 1.07, 95% CI: 1.02-1.13, P = 0.012; In DIAGRAM: OR = 1.14, 95% CI: 1.02-1.26, P = 0.016). Multivariable MR analysis, adjusting for genetically predicted sleep duration, alcohol consumption, body mass index, and smoking, either individually or collectively, maintained these associations. Sensitivity analyses confirmed the robustness of the results. Conclusion: T2DM was associated with an increased risk of ASOM. Strict glycemic control is essential for the minimization of the effects of T2DM on ASOM.


Subject(s)
Diabetes Mellitus, Type 2 , Mendelian Randomization Analysis , Otitis Media, Suppurative , Humans , Diabetes Mellitus, Type 2/genetics , Diabetes Mellitus, Type 2/complications , Diabetes Mellitus, Type 2/epidemiology , Otitis Media, Suppurative/genetics , Otitis Media, Suppurative/complications , Otitis Media, Suppurative/epidemiology , Polymorphism, Single Nucleotide , Risk Factors , Acute Disease , Hearing Loss/genetics , Hearing Loss/epidemiology , Hearing Loss/etiology , Female , Male , Genetic Predisposition to Disease
7.
Adv Sci (Weinh) ; : e2306237, 2024 Jun 23.
Article in English | MEDLINE | ID: mdl-38922800

ABSTRACT

Abdominal aortic aneurysm (AAA) is a common and potentially life-threatening condition. Chronic aortic inflammation is closely associated with the pathogenesis of AAA. Nerve injury-induced protein 1 (NINJ1) is increasingly acknowledged as a significant regulator of the inflammatory process. However, the precise involvement of NINJ1 in AAA formation remains largely unexplored. The present study finds that the expression level of NINJ1 is elevated, along with the specific expression level in macrophages within human and angiotensin II (Ang II)-induced murine AAA lesions. Furthermore, Ninj1flox/flox and Ninj1flox/floxLyz2-Cre mice on an ApoE-/- background are generated, and macrophage NINJ1 deficiency inhibits AAA formation and reduces macrophage infiltration in mice infused with Ang II. Consistently, in vitro suppressing the expression level of NINJ1 in macrophages significantly restricts macrophage adhesion and migration, while attenuating macrophage pro-inflammatory responses. Bulk RNA-sequencing and pathway analysis uncover that NINJ1 can modulate macrophage infiltration through the TLR4/NF-κB/CCR2 signaling pathway. Protein-protein interaction analysis indicates that NINJ1 can activate TLR4 by competitively binding with ANXA2, an inhibitory interacting protein of TLR4. These findings reveal that NINJ1 can modulate AAA formation by promoting macrophage infiltration and pro-inflammatory responses, highlighting the potential of NINJ1 as a therapeutic target for AAA.

8.
Article in English | MEDLINE | ID: mdl-38925603

ABSTRACT

This study utilizes natural language processing techniques and panel vector autoregression methodology, to delve into the perceived attitudes of social media users towards the digital transformation of agriculture, and to assess its impact on total agricultural output and agricultural science and technology inputs. Data related to agricultural digital transformation were collected from Sina Weibo using web crawlers. The SnowNLP model was employed to infer users' attitudes, encompassing both positive and negative aspects. Furthermore, the study delves into the specific themes capturing users' positive attitudes and explores regional variations in focus. The findings reveal a sustained increase in users' interest in agricultural digital transformation since 2013. Positive attitudes primarily center around green development, agricultural intelligence, and global cooperation and innovation. Moreover, the study establishes a significant positive impact of users' positive attitudes on both total agricultural output value and agricultural science and technology investment, highlighting the constructive influence of user support on the agricultural industry's development.

9.
Heliyon ; 10(9): e30726, 2024 May 15.
Article in English | MEDLINE | ID: mdl-38765164

ABSTRACT

Objectives: Glioma, the most common and aggressive form of brain cancer, possesses a complex biology, which makes elucidating its underlying mechanisms and developing effective treatment strategies challenging. Lactylation is a recently discovered post-translational modification and has emerged as a novel research target to understand its role in various biological processes and diseases. Herein, we explored the role of lactylation in gliomas. Methods: Single-cell RNA-sequencing (scRNA-seq) data were downloaded from the Tumour Immune Single-Cell Hub database. The R package 'Seurat' was used for processing the scRNA-seq data. Lactylation-related genes were identified from published literature and the Molecular Signatures Database. An unsupervised clustering method was used to identify glioma subtypes based on identified lactylation-related genes. Differences among the various clusters were examined, including clinical features, differentially expressed genes (DEGs), enriched pathways and immune cell infiltrates. A lactylation score was generated to predict the overall survival (OS) of patients with glioma using DEGs between the two clusters. Results: The lactylation-related genes were obtained from the scRNA-seq data, identifying two molecular subtypes, and a prognostic signature was established to stratify patients with glioma into high- and low-score groups. Analysis of the tumour immune microenvironment revealed that patients in the high-score group exhibited increased immune cell infiltration, chemokine expression and immune checkpoint expression but exhibited worse OS and better response to immunotherapy. Conclusions: Altogether, we established a novel signature based on lactylation-related clusters for robust survival prediction and immunotherapeutic response in gliomas.

10.
Theriogenology ; 225: 33-42, 2024 Sep 01.
Article in English | MEDLINE | ID: mdl-38788627

ABSTRACT

The in vitro maturation (IVM) quality of oocytes is directly related to the subsequent developmental potential of embryos and a fundamental of in vitro embryo production. However, conventional IVM methods fail to maintain the gap-junction intercellular communication (GJIC) between cumulus-oocyte complexes (COCs), which leads to insufficient oocyte maturation. Herein, we investigated the effects of three different three-dimensional (3D) culture methods on oocyte development in vitro, optimized of the alginate-hydrogel embedding method, and assessed the effects of the alginate-hydrogel embedding method on subsequent embryonic developmental potential of oocytes after IVM and parthenogenetic activation (PA). The results showed that Matrigel embedding and alginate-hydrogel embedding benefited the embryonic developmental potential of oocytes after IVM and PA. With the further optimization of alginate-hydrogel embedding, including crosslinking and decrosslinking of parameters, we established a 3D culture system that can significantly increase oocyte maturation and the blastocyst rate of embryos after PA (27.2 ± 1.5 vs 36.7 ± 2.8, P < 0.05). This 3D culture system produced oocytes with markedly increased mitochondrial intensity and membrane potential, which reduced the abnormalities of spindle formation and cortical granule distribution. The alginate-hydrogel embedding system can also remarkably enhance the GJIC between COCs. In summary, based on alginate-hydrogel embedding, we established a 3D culture system that can improve the IVM quality of porcine oocytes, possibly by enhancing GJIC.


Subject(s)
Alginates , Hydrogels , In Vitro Oocyte Maturation Techniques , Oocytes , Animals , In Vitro Oocyte Maturation Techniques/veterinary , In Vitro Oocyte Maturation Techniques/methods , Alginates/pharmacology , Oocytes/physiology , Swine , Cell Culture Techniques, Three Dimensional/methods , Glucuronic Acid/pharmacology , Parthenogenesis , Hexuronic Acids/pharmacology , Female , Embryo Culture Techniques/veterinary , Embryo Culture Techniques/methods
11.
Vascular ; : 17085381241249288, 2024 Apr 26.
Article in English | MEDLINE | ID: mdl-38670962

ABSTRACT

BACKGROUND: Endovenous interventions and minimally invasive procedures are effective in the management of varicose veins. However, they can cause postoperative discomfort. OBJECTIVE: To evaluate the clinical efficacy of sodium aescinate (SA) in improving edema, pain, vein-specific symptoms, and quality of life in patients following endovenous laser ablation (EVLA) for varicose veins. METHODS: In this single-center randomized controlled trial (RCT), patients were allocated into two groups: in Group A, 60 mg SA was administered twice daily for 20 days, and in Group B (control), no venoactive drug was prescribed. The Clinical-Etiology-Anatomy-Pathophysiology (CEAP) classification system for chronic venous disorders was used to assess the varicose veins. The circumferences of the calf and ankle were recorded for evaluating edema. The 10-point Visual Analog Scale (VAS), Venous Clinical Severity Score (VCSS), and Aberdeen Varicose Veins Questionnaire (AVVQ) were used to measure the pain intensity, overall varicose vein severity, and patient's quality of life, respectively. RESULTS: The study included 87 patients (mean age, 59.9 ± 10.7 years; 54 men) with CEAP class C2-C5 varicose veins who underwent EVLA and phlebectomy or foam sclerotherapy. The calf circumference recovered quicker in Group A than in Group B by days 10, 21, and 30 (difference from baseline was 1.04 ± 0.35 vs 2.39 ± 1.15 [p < .001], 0.48 ± 0.42 vs1.73 ± 1.00 [p < .001], and 0.18 ± 0.64 vs 0.82 ± 0.96 [p < .001], respectively). The ankle circumference recovered quicker in Group A than in Group B by days 10 and 21 (the difference from baseline was 1.37 ± 0.52 vs 2.36 ± 0.93 [p < .001] and 0.58 ± 0.60 vs 1.14 ± 0.88 [p = .002], respectively). Pain relief was achieved quicker in Group A than in Group B (0.257 ± 1.097 [p = .0863] vs 0.506 ± 1.250 [p = .0168] by day 21). There were no significant differences in the VCSS and AVVQ scores between both groups. There were no drug-related adverse effects. CONCLUSIONS: SA, in combination with compression therapy, can relieve edema and alleviate pain in patients following EVLA for varicose veins.

12.
BMJ Open ; 14(3): e074547, 2024 Mar 28.
Article in English | MEDLINE | ID: mdl-38548369

ABSTRACT

INTRODUCTION: Prevention of recurrence after an episode of venous thromboembolism (VTE), and also the post-thrombotic syndrome (PTS), is still a recognised challenge. In this meta-analysis, we will summarise existing evidence to compare intelligent system follow-up and routine follow-up for patients with VTE. METHODS AND ANALYSIS: Relevant randomised controlled trials (RCTs) and cohort studies will be included from the following databases: MEDLINE/PubMed, Web of Science and the Cochrane Library. The last search time will be 31 March 2024. Two reviewers will independently identify RCTs and cohort studies according to eligibility and exclusion criteria. The risk of bias of included cohort studies will be assessed with the Newcastle-Ottawa Scale, Methodological Index of Non-Randomised Studies, and the risk of bias of RCTs will be assessed with and Cochrane Collaboration's tool. The primary outcomes include overall survival rate and PTS incidence rate. The Grades of Recommendations, Assessment, Development and Evaluation tool will be used to assess the level of evidence for outcome from RCTs. RevMan V.5.4 software will be used to pool outcomes. ETHICS AND DISSEMINATION: Ethical approval was obtained from Shanghai Ninth People's Hospital, Shanghai JiaoTong University School of Medicine Science Research Ethics Committee (SH9H-2023-T466-1). The findings will be disseminated to the public through conference presentations and publication in peer-reviewed scientific journals. PROSPERO REGISTRATION NUMBER: CRD42023410644.

13.
Front Psychol ; 15: 1284787, 2024.
Article in English | MEDLINE | ID: mdl-38390413

ABSTRACT

Background: Cognitive-Motor Dual Task (CMDT) training has been widely utilized in rehabilitation and sports practice. However, whether CMDT training can better enhance athletes' cognitive-motor performance compared to traditional single-task (ST) training remains unclear. Method: A systematic review that complied with PRISMA was carried out (Prospero registration number: CRD42023443594). The electronic databases used for the systematic literature search from the beginning through 13 June 2023, included Web of Science, Embase, PubMed, and the Cochrane Library. After obtaining the initial literature, two researchers independently assessed it based on inclusion and exclusion criteria. Finally, the included literature was analyzed to compare the differences between ST training and CMDT training. Results: After screening 2,094 articles, we included 10 acute studies and 7 chronic studies. Conclusion: This systematic review shows that athletes typically show a degradation of performance in CMDT situations as opposed to ST when evaluated transversally. However, this performance decline is notably reduced following longitudinal training in CMDT, indicating the effectiveness of sustained CMDT training in enhancing cognitive-motor performance under dual-task conditions. Our study provides new insights into the application of CMDT in the field of sports training. Practitioners can utilize CMDT to assess athletic skill levels or optimize cognitive-motor performance of athletes, taking into account the specific needs of each sport. Systematic review registration: https://www.crd.york.ac.uk/prospero, identifier CRD42023443594.

14.
Comput Biol Med ; 170: 108071, 2024 Mar.
Article in English | MEDLINE | ID: mdl-38325212

ABSTRACT

BACKGROUND: Thoracic aortic aneurysm (TAA) refers to dilation and enlargement of the thoracic aorta caused by various reasons. Most patients have no apparent symptoms in the early stage and are subject to a poor prognosis once the aneurysm ruptures. It is crucial to identify individuals who are predisposed to TAA and to discover effective therapeutic targets for early intervention. METHODS: We conducted a label-free quantitative proteomic analysis among aorta tissue samples from TAA patients to screen differentially expressed proteins (DEPs) and key co-expression modules. Two datasets from Gene Expression Omnibus (GEO) database were included for integrative analysis, and the identified genes were subjected to immunohistochemistry (IHC) validation. Detailed vesicle transport related enrichment analysis was conducted and two FDA-approved drugs, chlorpromazine (CPZ) and chloroquine (CQ), were selected for in vivo inhibition of vesicle transport in mice TAA model. The diameter of thoracic aorta, mortality and histological differences after interventions were evaluated. RESULTS: We found significant enrichments in functions involved with vesicle transport, extracellular matrix organizing, and infection diseases in TAA. Endocytosis was the most essential vesicle transport process in TAA formation. Interventions with CPZ and CQ significantly reduced the aneurysm diameter and elastin degradation in vivo and enhanced the survival rates of TAA mice. CONCLUSIONS: We systematically screened the aberrantly regulated bioprocesses in TAA based on integrative multi-omics analyses, identified and demonstrated the importance of vesicle transport in the TAA formation. Our study provided pilot evidence that vesicular transport was a potential and promising target for the treatment of TAA.


Subject(s)
Aortic Aneurysm, Thoracic , Multiomics , Humans , Animals , Mice , Proteomics , Aortic Aneurysm, Thoracic/genetics , Aortic Aneurysm, Thoracic/pathology , Disease Models, Animal
15.
ACS Appl Mater Interfaces ; 16(6): 7297-7309, 2024 Feb 14.
Article in English | MEDLINE | ID: mdl-38305856

ABSTRACT

Serious open-circuit voltage (Voc) loss originating from nonradiative recombination and mismatch energy level at TiO2/perovskite buried interface dramatically limits the photovoltaic performance of all-inorganic CsPbIxBr3-x (x = 1, 2) perovskite solar cells (PSCs) fabricated through low-temperature methods. Here, an ionic liquid (IL) bridge is constructed by introducing 1-butyl-3-methylimidazolium acetate (BMIMAc) IL to treat the TiO2/perovskite buried interface, bilaterally passivate defects and modulate energy alignment. Therefore, the Voc of all-inorganic CsPbIBr2 PSCs modified by BMIMAc (Target-1) significantly increases by 148 mV (from 1.213 to 1.361 V), resulting in the efficiency increasing to 10.30% from 7.87%. Unsealed Target-1 PSCs show outstanding long-term and thermal stability. During the accelerated degradation process (85 °C, RH: 50∼60%), the Target-1 PSCs achieve a champion PCE of 11.94% with a remarkable Voc of 1.403 V, while the control PSC yields a promising PCE of 10.18% with a Voc of 1.319 V. In particular, the Voc of 1.403 V is the highest Voc reported so far in carbon-electrode-based CsPbIBr2 PSCs. Moreover, this strategy enables the modified all-inorganic CsPbI2Br PSCs to achieve a Voc of 1.295 V and a champion efficiency of 15.20%, which is close to the reported highest PCE of 15.48% for all-inorganic CsPbI2Br PSCs prepared by a low-temperature process. This study provides a simple BMIMAc IL bridge to assist bifacial defect passivation and elevate the photovoltaic performance of all-inorganic CsPbIxBr3-x (x = 1, 2) PSCs.

16.
ACS Appl Mater Interfaces ; 16(8): 9768-9786, 2024 Feb 28.
Article in English | MEDLINE | ID: mdl-38349802

ABSTRACT

This study aims to overcome the drawbacks associated with hydroxyapatite (HAP) dense structures after sintering, which often result in undesirable features such as large grain size, reduced porosity, high crystallinity, and low specific surface area. These characteristics hinder osseointegration and limit the clinical applicability of the material. To address these issues, a new method involving the preparation of hollow hydroxyapatite (hHAP) microspheres has been proposed. These microspheres exhibit distinctive traits including weak crystallization, high specific surface area, and increased porosity. The weak crystallization aligns more closely with early mineralization products found in the human body and animals. Moreover, the microspheres' high specific surface area and porosity offer advantages for protein loading and facilitating osteoblast attachment. This innovative approach not only mitigates the limitations of conventional HAP structures but also holds the potential for improving the effectiveness of hydroxyapatite in biomedical applications, particularly in enhancing osseointegration. Three-dimensional printed hHAP/chitosan (CS) scaffolds with different hHAP concentration gradients were manufactured, and the physical and biological properties of each group were systematically evaluated. In vitro and in vivo experiments show that the hHAP/CS scaffold has excellent performance in bone remodeling. Furthermore, in-scaffold components, hHAP and CS were cocultured with bone marrow mesenchymal stem cells to explore the regulatory role of hHAP and CS in the process of bone healing and to reveal the cell-level specific regulatory network activated by hHAP. Enrichment analysis showed that hHAP can promote bone regeneration and reconstruction by recruiting calcium ions and regulating inflammatory reactions.


Subject(s)
Chitosan , Durapatite , Animals , Humans , Durapatite/pharmacology , Durapatite/chemistry , Tissue Scaffolds/chemistry , Calcium , Osteogenesis , Bone Regeneration/physiology , Chitosan/chemistry , Printing, Three-Dimensional , Porosity , Ions
17.
PLoS Comput Biol ; 20(2): e1011866, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38416795

ABSTRACT

Among existing computational algorithms for single-cell RNA-seq analysis, clustering and trajectory inference are two major types of analysis that are routinely applied. For a given dataset, clustering and trajectory inference can generate vastly different visualizations that lead to very different interpretations of the data. To address this issue, we propose multiple scores to quantify the "clusterness" and "trajectoriness" of single-cell RNA-seq data, in other words, whether the data looks like a collection of distinct clusters or a continuum of progression trajectory. The scores we introduce are based on pairwise distance distribution, persistent homology, vector magnitude, Ripley's K, and degrees of connectivity. Using simulated datasets, we demonstrate that the proposed scores are able to effectively differentiate between cluster-like data and trajectory-like data. Using real single-cell RNA-seq datasets, we demonstrate the scores can serve as indicators of whether clustering analysis or trajectory inference is a more appropriate choice for biological interpretation of the data.


Subject(s)
Single-Cell Analysis , Single-Cell Gene Expression Analysis , Sequence Analysis, RNA , Algorithms , Cluster Analysis , Gene Expression Profiling
18.
Nat Commun ; 15(1): 912, 2024 Jan 30.
Article in English | MEDLINE | ID: mdl-38291052

ABSTRACT

Single-cell RNA-sequencing (scRNA-seq) has been widely used for disease studies, where sample batches are collected from donors under different conditions including demographic groups, disease stages, and drug treatments. It is worth noting that the differences among sample batches in such a study are a mixture of technical confounders caused by batch effect and biological variations caused by condition effect. However, current batch effect removal methods often eliminate both technical batch effect and meaningful condition effect, while perturbation prediction methods solely focus on condition effect, resulting in inaccurate gene expression predictions due to unaccounted batch effect. Here we introduce scDisInFact, a deep learning framework that models both batch effect and condition effect in scRNA-seq data. scDisInFact learns latent factors that disentangle condition effect from batch effect, enabling it to simultaneously perform three tasks: batch effect removal, condition-associated key gene detection, and perturbation prediction. We evaluate scDisInFact on both simulated and real datasets, and compare its performance with baseline methods for each task. Our results demonstrate that scDisInFact outperforms existing methods that focus on individual tasks, providing a more comprehensive and accurate approach for integrating and predicting multi-batch multi-condition single-cell RNA-sequencing data.


Subject(s)
Algorithms , Single-Cell Analysis , Sequence Analysis, RNA/methods , Single-Cell Analysis/methods , Exome Sequencing , RNA , Gene Expression Profiling/methods
19.
Oncol Lett ; 27(2): 63, 2024 Feb.
Article in English | MEDLINE | ID: mdl-38192681

ABSTRACT

[This retracts the article DOI: 10.3892/ol.2017.7431.].

20.
Food Chem X ; 21: 101095, 2024 Mar 30.
Article in English | MEDLINE | ID: mdl-38268840

ABSTRACT

Chitosan, derived from the deacetylation of chitin, is an abundant natural biopolymer on earth. Chitosan and its derivatives have become promising biological materials because of their unique molecular structure and excellent biological activities. The reactive functional groups of chitosan such as the amino and hydroxyl groups play a crucial role in facilitating the synthesis of three-dimensional hydrogel. Chitosan-based hydrogels have been widely used in medical, pharmaceutical, and environmental fields for years. Nowadays, chitosan-based hydrogels have been found in a wide range of applications in the food industry such as food sensors, dye adsorbents and nutrient carriers. In this review, recently developed methods for the preparation of chitosan-based hydrogels were given, and the biological activities of chitosan-based hydrogels were systematically introduced. Additionally, the recent progress in food sensors, packaging, dye adsorbents, and nutrient carriers was discussed. Finally, the challenges and prospects for the future development of chitosan-based hydrogels were discussed.

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