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At least 289 records · Page 16Linked to original sources
PubMed2025

Multipopulation GWAS for venous thromboembolism identifies novel loci followed by experimental validation in zebrafish.

Venous thromboembolisms (VTEs) are a leading cause of morbidity and mortality. Although many genetic risk factors have been identified, a substantial portion of the heritability remains unexplained. In this study, we employed a genome-wide association study (GWAS) for VTE across 9 international cohorts of the Global Biobank Meta-Analysis Initiative to address this question, along with in vivo functional validation. In this multipopulation GWAS (VTE cases, 27 987; controls, 1 035 290), 38 genome-wide significant loci were identified, 4 of which were potentially novel. For each autosomal locus, we performed gene prioritization using 7 independent, yet converging, lines of evidence. Through prioritization, we identified genes associated with VTE through GWAS and/or functional studies (eg, F5, F11, VWF, STAB2, PLCG2, TC2N), functionally validated those that did not have evidence other than GWAS (TC2N, TSPAN15), and discovered 1 not previously associated with coagulation (RASIP1). We evaluated the function of 6 prioritized genes with strong genetic evidence, including F7 as a positive control, using laser-mediated endothelial injury to induce thrombosis in zebrafish after CRISPR/Cas9 knockdown. From this assay, we have supportive evidence for the role of RASIP1 and TC2N in the modification of human VTE and suggestive evidence for STAB2 and TSPAN15. This study expands on the currently identified genomic architecture of VTE through biobank-based, multipopulation GWASs, in silico candidate gene predictions, and in vivo functional follow-up of candidate genes.

Zebrafish↗
PubMed2007

Experimental validation of novel genes predicted in the un-annotated regions of the Arabidopsis genome.

BACKGROUND: Several lines of evidence support the existence of novel genes and other transcribed units which have not yet been annotated in the Arabidopsis genome. Two gene prediction programs which make use of comparative genomic analysis, Twinscan and EuGene, have recently been deployed on the Arabidopsis genome. The ability of these programs to make use of sequence data from other species has allowed both Twinscan and EuGene to predict over 1000 genes that are intergenic with respect to the most recent annotation release. A high throughput RACE pipeline was utilized in an attempt to verify the structure and expression of these novel genes. RESULTS: 1,071 un-annotated loci were targeted by RACE, and full length sequence coverage was obtained for 35% of the targeted genes. We have verified the structure and expression of 378 genes that were not present within the most recent release of the Arabidopsis genome annotation. These 378 genes represent a structurally diverse set of transcripts and encode a functionally diverse set of proteins. CONCLUSION: We have investigated the accuracy of the Twinscan and EuGene gene prediction programs and found them to be reliable predictors of gene structure in Arabidopsis. Several hundred previously un-annotated genes were validated by this work. Based upon this information derived from these efforts it is likely that the Arabidopsis genome annotation continues to overlook several hundred protein coding genes.

Arabidopsis↗
PubMed2024

Integrated bioinformatics analysis and experimental validation reveal the relationship between ALOX5AP and the prognosis and immune microenvironment in glioma.

BACKGROUND: Treatment of gliomas, the most prevalent primary malignant neoplasm of the central nervous system, is challenging. Arachidonate 5-lipoxygenase activating protein (ALOX5AP) is crucial for converting arachidonic acid into leukotrienes and is associated with poor prognosis in multiple cancers. Nevertheless, its relationship with the prognosis and the immune microenvironment of gliomas remains incompletely understood. METHODS: The differential expression of ALOX5AP was evaluated based on public Databases. Kaplan-Meier, multivariate Cox proportional hazards regression analysis, time-dependent receiver operating characteristic, and nomogram were used to estimate the prognostic value of ALOX5AP. The relationship between ALOX5AP and immune infiltration was calculated using ESTIMATE and CIBERSORT algorithms. Relationships between ALOX5AP and human leukocyte antigen molecules, immune checkpoints, tumor mutation burden, TIDE score, and immunophenoscore were calculated to evaluate glioma immunotherapy response. Single gene GSEA and co-expression network-based GO and KEGG enrichment analysis were performed to explore the potential function of ALOX5AP. ALOX5AP expression was verified using multiplex immunofluorescence staining and its prognostic effects were confirmed using a glioma tissue microarray. RESULT: ALOX5AP was highly expressed in gliomas, and the expression level was related to World Health Organization (WHO) grade, age, sex, IDH mutation status, 1p19q co-deletion status, MGMTp methylation status, and poor prognosis. Single-cell RNA sequencing showed that ALOX5AP was expressed in macrophages, monocytes, and T cells but not in tumor cells. ALOX5AP expression positively correlated with M2 macrophage infiltration and poor immunotherapy response. Immunofluorescence staining demonstrated that ALOX5AP was upregulated in WHO higher-grade gliomas, localizing to M2 macrophages. Glioma tissue microarray confirmed the adverse effect of ALOX5AP in the prognosis of glioma. CONCLUSION: ALOX5AP is highly expressed in M2 macrophages and may act as a potential biomarker for predicting prognosis and immunotherapy response in patients with glioma.

Humans↗
PubMed2006

Estimating the hemodynamic impact of interventional treatments of aneurysms: numerical simulation with experimental validation: technical case report.

OBJECTIVE: The goal of this study was to use phase-contrast magnetic resonance imaging and computational fluid dynamics to estimate the hemodynamic outcome that might result from different interventional options for treating a patient with a giant fusiform aneurysm. METHODS: We followed a group of patients with giant intracranial aneurysms who have no clear surgical options. One patient demonstrated dramatic aneurysm growth and was selected for further analysis. The aneurysm geometry and input and output flow conditions were measured with contrast-enhanced magnetic resonance angiography and phase-contrast magnetic resonance imaging. The data was imported into a computational fluid dynamics program and the velocity fields and wall shear stress distributions were calculated for the presenting physiological condition and for cases in which the opposing vertebral arteries were either occluded or opened. These models were validated with in vitro flow experiments using a geometrically exact silicone flow phantom. RESULTS: Simulation indicated that altering the flow ratio in the two vertebrals would deflect the main blood jet into the aneurysm belly, and that this would likely reduce the extent of the region of low wall shear stress in the growth zone. CONCLUSIONS: Computational fluid dynamics flow simulations in a complex patient-specific aneurysm geometry were validated by in vivo and in vitro phase-contrast magnetic resonance imaging, and were shown to be useful in modeling the likely hemodynamic impact of interventional treatment of the aneurysm.

Aged↗
PubMed1992

Contributors of characteristic mitral flow velocity pattern in congestive heart failure--from clinical observations back to experimental validations.

Mitral flow velocity pattern in patients with left ventricular (LV) diastolic dysfunction usually includes decreased peak early diastolic filling velocity (E), slowed deceleration of the early diastolic filling wave and increased peak filling velocity at atrial contraction (A). However, the abnormal mitral flow velocity pattern can be normalized in the presence of concomitant congestive heart failure. In such cases E can be equal to or even higher than normal, its deceleration is normal or faster than normal value, and A can be normal or lower than normal value. Clinical observations in patients with severe heart failure showed that the mitral flow velocity pattern changes with vasodilating therapy, reflecting the changes in the left atrial (LA) to LV pressure difference rather than those in the absolute LA pressure or LV pressure alone. This was validated in the canine study in which levels of LV dysfunction were made by the injection of microspheres into the left coronary artery to study the interrelation among the mitral flow velocity pattern and LA and LV pressures. In this experiment, the changes in the mitral flow velocity pattern could not be explained by the changes in LA or LV pressure alone but was better explained by the changes in the LA to LV pressure difference. Not only LA-LV crossover pressure but also LA compliance seem to be important as determinants of LA pressure level in diastole. In addition to LV relaxation rate, incompleteness of relaxation, elastic recoil and LV passive elastic properties, extracardiac constraint is also considered to be an important determinant of the level of the LV diastolic pressure and hence of the mitral flow velocity pattern at least in the presence of congestive heart failure. Thus, mitral flow velocity pattern is determined by the interaction of LA and LV pressures, both of which are affected by chamber properties as well as loading conditions.

Animals↗
PubMed2004

Efficient testing of segmented aspherical mirrors by use of a reference plate and computer-generated holograms. II. Case study, error analysis, and experimental validation.

Segmented mirrors present unique challenges to fabrication and testing that are absent for monolithic optics. Since traditional asphere tests do not address segmented optics adequately, we validate a previously developed method to test large quantities of segments accurately, quickly, and economically. In this test, the aspheric shape of each segment is controlled to high accuracy by use of computer-generated holograms, and the radius of curvature is tightly controlled by use of the reference plate. In an adjoining paper [Appl Opt 43, 5303 (2004)] we developed the theory for this test, and now we present a complete system design and optimization for measuring the 1.4-m segments from a 30-m F/1 primary. A complete tolerance analysis predicts a test accuracy of 4.8-nm rms surface and excellent accuracy for controlling the geometry of the segment. In addition, a laboratory demonstration using 30-cm optics is presented that demonstrated 3.9-nm rms surface accuracy.

Journal Article↗
PubMed2004

Theoretical design for the optimization of a material's geometry in diode-pumped high-energy Yb3+:YAG lasers and its experimental validation at 0.5-1 J.

The geometry of ytterbium-doped active media in diode-pumped lasers can be calculated with the help of a few analytic expressions for the optimization of high-energy and high-efficiency Q-switched lasers. The first step in the optimization consists in the definition of a basic three-level model with which to estimate the energy to be extracted. In the second step, for validation purposes we use a side-pumped Yb3+:YAG slab at 2-kW peak pump power in the long-pulse mode of operation up to 1 J, and we Q switch it at reduced energies up to 100 mJ. The final step of this study provides fairly general relationships devoted the geometric sizing of optimized slabs that will be of some interest for the design of higher-energy ytterbium-doped Q-switched lasers.

Journal Article↗
PubMed2003

Experimental validation of Fourier-transform wave-front reconstruction at the Palomar Observatory.

Wave-front reconstruction with use of the Fourier transform has been validated through theory and simulation. This method provides a dramatic reduction in computational costs for large adaptive (AO) systems. Because such a reconstructor can be expressed as a matrix, it can be used as an alternative in a matrix-based AO control system. This was done with the Palomar Observatory AO system on the 200-in. Hale telescope. Results of these tests indicate that Fourier-transform wave-front reconstruction works in a real system. For both bright and dim stars, a Hudgin-geometry Fourier-transform method produced performance comparable to that of the Palomar Adaptive Optics least squares. The Fried-geometry method had a noticeable Strehl ratio performance degradation of 0.043 in the K band (165-nm rms wave-front error added in quadrature) on a dim star.

Journal Article↗
PubMed2005

Heterogeneous nucleation in sickle hemoglobin: experimental validation of a structural mechanism.

Sickle hemoglobin polymerizes by two types of nucleation: homogeneous nucleation of aggregates in solution, and heterogeneous nucleation on preexisting polymers. It has been proposed that the same contact that is made in the interior of the polymer between the mutant site beta6 and its receptor pocket on an adjacent molecule is the primary contact site for the heterogeneous nucleus. We have constructed cross-linked hybrid molecules in which one beta-subunit is from HbA with Glu at beta6, and the other is from HbS with a Val at beta6. We measured solubility (using sedimentation) and polymerization kinetics (using laser photolysis) on cross-linked hybrids, and cross-linked HbS as controls. We find approximately 4000 times less heterogeneous nucleation in the cross-linked AS molecules than in cross-linked HbS, in strong confirmation of the proposal. In addition, changes in stability of the nucleus support a further proposal that more than one beta6 contact is involved in the homogeneous nucleus.

Binding Sites↗
PubMed2006

Structural transitions of confined model proteins: molecular dynamics simulation and experimental validation.

Proteins fold in a confined space not only in vivo, i.e., folding assisted by molecular chaperons and chaperonins in a crowded cellular medium, but also in vitro as in production of recombinant proteins. Despite extensive work on protein folding in bulk, little is known about how and to what extent the thermodynamics and kinetics of protein folding are altered by confinement. In this work, we use a Gō-like off-lattice model to investigate the folding and stability of an all beta-sheet protein in spherical cages of different sizes and surface hydrophobicity. We find whereas extreme confinement inhibits correct folding, a hydrophilic cage stabilizes the protein due to restriction of the unfolded configurations. In a hydrophobic cage, however, strong attraction from the cage surface destabilizes the confined protein because of competition between self-aggregation and adsorption of hydrophobic residues. We show that the kinetics of protein collapse and folding is strongly correlated with both the cage size and the surface hydrophobicity. It is demonstrated that a cage of moderate size and hydrophobicity optimizes both the folding yield and kinetics of structural transitions. To support the simulation results, we have also investigated the refolding of hen-egg lysozyme in the presence of cetyltrimethylammoniumbromide (CTAB) surfactants that provide an effective confinement of the proteins by micellization. The influence of the surfactant hydrophobicity on the structural and biological activity of the protein is determined with circular dichroism spectrum, fluorescence emission spectrum, and biological activity assay. It is shown that, as predicted by coarse-grained simulations, CTAB micelles facilitate the collapse of denatured lysozyme, whereas the addition of beta-cyclodextrin-grafted-PNIPAAm, a weakly hydrophobic stripper, dissociates CTAB micelles and promotes the conformational rearrangement and thereby gives an improved recovery of lysozyme activity.

Acrylic Resins↗
PubMed2005

Prediction and experimental validation of acute toxicity of beta-blockers in Ceriodaphnia dubia.

Acute toxicity of beta-adrenoceptor blockers (beta-blockers) was studied with beta-blockers as single compounds or in mixture using the standardized acute 2-d Ceriodaphnia dubia immobility test. The tested compounds were selected according to their selectivity for the beta1-adrenoceptor, with three beta1-selective blockers (acebutolol, atenolol, and metoprolol) and three non-beta1-selective blockers (nadolol, oxprenolol, and propranolol). The acute toxicity (median effective concentration) of the six single compounds ranged from 1.4 mg/L for propranolol to 163 mg/L for nadolol. According to European Union directive 93/67EEC, these values range from toxic for aquatic organisms to nonclassified. The more toxic compounds, propranolol and oxprenolol, are both characterized by a membrane-stabilizing activity, a strong affinity for the beta1-adrenoceptor, and a high octanol-water partition coefficient (log Kow). The property of beta-receptor selectivity seems not to be involved in the observed acute toxicity of the single compounds for C. dubia. Nevertheless, the toxicity of the selected compounds in mixture can be defined according to the beta1-selectivity. Two main joint effects have been detected: An independent action for the beta1-selective blockers, and an additive effect when either the nonselective beta1-selective blockers or the six compounds are tested together. The concentration addition model seems to be appropriate, providing a reasonable worst-case estimation of beta-blocker mixture toxicity for regulatory purposes.

Adrenergic beta-Antagonists↗
PubMed1984

A self-instructional manual for installing low-cost/no-cost weatherization materials: Experimental validation with scouts.

In this study, we describe the development and evaluation of a self-instructional program for installing 10 low-cost/no-cost weatherization materials (e.g., weatherstripping, caulking). This program was a weatherization and retrofit manual (WARM) providing step-by-step instructions and illustrations. Boy and Girl Scouts participated and used either the WARM or existing product instructions (EPI) to apply the materials. Scouts installed the materials properly only when they used the WARM.

Journal Article↗
PubMed2025

Integrating network pharmacology and experimental validation to uncover the synergistic effects of Huangqi ()-Ezhu () with 5-fluorouracil in colorectal cancer models.

OBJECTIVE: To evaluate the effects of Huangqi (Radix Astragali Mongolici)-Ezhu (Rhizoma Curcumae Phaeocaulis) (HQEZ) on colorectal cancer therapies and to elucidate the potential mechanisms of HQEZ, especially in combination with 5-Fluorouracil (5-FU). METHODS: The anti-tumor effects of HQEZ were evaluated in colorectal cancer models both in vivo and in vitro. The network pharmacological assay was used to investigate potential mechanisms of HQEZ. Potential target genes were selected by Gene Ontology (GO) enrichment analysis, Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis, protein-protein interaction network (PPI) and molecular docking. Within key targets, potential targets related to drug sensitivity, especially the sensitivity to 5-FU, were evaluated in HCT116 in vitro by immunofluorescence, quantitative real-time polymerase chain reaction (qPCR) and Western-blot. Then, changes in potential targets were assessed in tumors from tumor-bearing mice and the expression of these targets was also evaluated in colorectal cancer (COAD) patients from the Cancer Genome Atlas Program (TCGA) database. RESULTS: HQEZ significantly enhanced the anti-tumor activity of 5-FU in vivo and inhibit the growth of HCT116 in vitro. By network pharmacological analysis, key targets, such as protein kinase B (AKT1), epidermal growth factor receptor (EGFR), adenosine triphosphate (ATP) binding cassette subfamily B member 1 (ABCB1, also named multidrug resistance protein 1, MDR1), ATP binding cassette subfamily G member 2 (ABCG2), thymidylate synthetase (TYMS, also named TS), prostaglandin-endoperoxide synthase 2 (PTGS2), matrix metallopeptidase 2 (MMP2), MMP9, toll like receptor 4 (TLR4), TLR9 and dihydropyrimidine dehydrogenase (DPYD), were identified. Additionally, 4 potential core active ingredients (Folate, Curcumin, quercetin and kaempferol) were identified to be important for the treatment of colorectal cancer with HQEZ. In key targets, chemoresistance related targets were validated to be affected by HQEZ. Furthermore, 5-FU sensitivity related targets, including MDR1, TS, EGFR, ribonucleotide reductase catalytic subunit M1, Breast and Ovarian Cancer Susceptibility Protein 1 (BRCA1) and mutl homolog 1 were also significantly reduced by HQEZ both in vitro and in vivo. Finally, these validated key targets and 5-FU sensitivity related targets were demonstrated to be up-regulated in COAD patients based on TCGA database. CONCLUSION: HQEZ has synergistic effects on the anti-tumor activity of 5-FU in the treatment of colorectal cancer both in vivo and in vitro. The beneficial effect of HQEZ results from the inhibition of the drug sensitivity targets associated with 5-FU. The combination therapy of HQEZ with 5-FU or other chemotherapeutic drugs will also improve the anti-tumor efficacy of chemotherapy.

Humans↗
PubMed2026

Exploring the mechanism of the Lianshi Jianpi formula in treating impaired glucose tolerance: a network pharmacology, molecular docking, and experimental validation study.

OBJECTIVE: To explore the bioactive constituents, key targets, signalling pathways, and molecular mechanisms of Lianshi Jianpi formula (, LSJPF) in the treatment of impaired glucose tolerance (IGT) through network pharmacology, molecular docking, and in vivo experiments. METHODS: The active ingredients and targets of LSJPF were identified using the Traditional Chinese Medicine Systems Pharmacology and HERB databases, whereas the IGT-related targets were sourced from GeneCards, DisGeNET, and PubMed. The overlap analysis identified potential targets of LSJPF. Protein-protein interaction networks and core targets were evaluated using the Search Tool for the Retrieval of Interacting Genes/Proteins and Cytoscape, and molecular docking confirmed the binding affinities. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses were performed using Metascape. The therapeutic mechanisms were validated in an animal IGT model. RESULTS: LSJPF contained 229 compounds, with 15 active compounds and 77 potential target proteins. The phosphatidylinositol-3-kinase (PI3K)-protein kinase B (AKT) signalling pathway emerged as a key IGT pathway. The KEGG enrichment analysis revealed the pivotal genes RAC-alpha serine/threonine-protein kinase (AKT1), heat shock protein 90 kDa alpha B1, and B-cell lymphoma 2 family protein, which predominantly interact with beta-sitosterol and beta-carotene, the major constituents of Semen Euryales, Semen lablab Album, Semen sojae Atricolor in LSJPF. Molecular docking revealed strong binding affinities between LSJPF and IGT-related targets. In an animal IGT model, LSJPF treatment prevented weight loss; reduced food and water intake; decreased blood glucose levels; improved insulin resistance; decreased serum triglyceride, cholesterol, and low-density lipoprotein cholesterol levels; alleviated liver pathology; and significantly increased the levels of phosphorylated adenosine 5'-monophosphate-activated protein kinase (AMPK), PI3K, and AKT, suggesting its potential role in regulating glucose and lipid metabolism. CONCLUSIONS: These findings reveal the potential of LSJPF as an IGT intervention that targets the AMPK/PI3K/AKT cascade, validating network pharmacology predictions and highlighting the role of multipathway mechanisms in metabolic diseases.

Molecular Docking Simulation↗
PubMed2026

Mechanism of Shaofu Zhuyu decoction in improving diabetic mellitus erectile dysfunction inhibition of ferroptosis based on network pharmacology and experimental validation.

OBJECTIVE: To explore the medication patterns and mechanisms of action of Shaofu Zhuyu decoction (, SFZYD) in inhibiting ferroptosis through the nuclear factor erythroid 2-related factor 2 (Nrf2)/heme oxygenase 1 (HO-1)/glutathione peroxidase 4 (GPX4) pathway to improve diabetes mellitus-induced erectile dysfunction (DMED). METHODS: Firstly, data mining was employed to identify the medication patterns of Traditional Chinese Medicine (TCM) in treating DMED. Secondly, network pharmacology combined with a ferroptosis database was used to predict the targets. Subsequently, cell counting kit-8, 4',6-diamidino-2-phenylindole staining, reverse transcription-polymerase chain reaction (RT-PCR), and reagent kits were utilized to assess the repair effects of SFZYD on corpus cavernosum endothelial cells (CCECs) induced by high glucose (HG). Metabolic indicators, hematoxylin-eosin staining, and Masson staining were performed to observe the restorative effects of SFZYD on erectile function and penile tissue in diabetic rats. Finally, using Nrf2 inhibitors, the expression of related proteins and mRNAs was detected through Western blotting and RT-PCR. Reactive oxygen species levels and mitochondrial membrane potential were detected by flow cytometry. RESULTS: Data mining revealed that the prescription rules for blood stasis-type DMED coincide with the treatment principles of SFZYD. Network pharmacology identified 48 ferroptosis-related targets, primarily heme oxygenase 1 (HMOX1) and GPX4. Kyoto Encyclopedia of Genes and Genomes enrichment analysis associated these targets with the ferroptosis pathway. SFZYD repaired HG-induced CCECs damage and restored HMOX1 and GPX4 mRNA levels. in vivo, SFZYD effectively alleviated erectile dysfunction and repaired blood sinuses and fibrosis in diabetic rats. Following Nrf2 inhibition, the expression of Nrf2, HMOX1, and GPX4 decreased, while SFZYD intervention reversed these effects, improving ferroptosis and oxidative stress indicators. CONCLUSION: This study explored the potential mechanisms and efficacy of the TCM prescription SFZYD in treating DMED through data mining, network pharmacology analysis, cellular experiments, and animal experiments. It verified its effectiveness in repairing HG-induced CCECs damage, improving the pathological state of penile tissue in diabetic rats, and restoring erectile function by regulating the Nrf2/HO-1/GPX4 signaling pathway. This provides new insights and scientific evidence for treating DMED with TCM.

Male↗
PubMed2004

Reusing microarrays within closely related species: experimental validation through phylogenetic inference.

Microarrays are generally designed for a specific set of organisms, and this poses a limitation for researchers wanting to conduct investigations on gene expression in organisms that are, in some sense, not "popular" enough. In this article, we demonstrate that microarrays may in fact be reusable for aggregate expression analysis for species that are evolutionarily related. Our validation approach is based on this assumption and draws a phylogenetic conclusion that is deemed to be true only if the assumption of reusability is valid. This article demonstrates that microarrays developed using the human transcriptome are reusable for aggregate expression analysis of primates in general.

Animals↗