Calculation and data errors require correcting. Comment on "The effect of green coffee extract supplementation on anthropometric measures in adults: A comprehensive systematic review and dose-response meta-analysis of randomized clinical trials".
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ABSTRACT:
SUBMITTER: Chen X
PROVIDER: S-EPMC8202092 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:UnlabelledBFC is a free, fast and easy-to-use sequencing error corrector designed for Illumina short reads. It uses a non-greedy algorithm but still maintains a speed comparable to implementations based on greedy methods. In evaluations on real data, BFC appears to correct more errors with fewer overcorrections in comparison to existing tools. It particularly does well in suppressing systematic sequencing errors, which helps to improve the base accuracy of de novo assemblies.Availability and implementationhttps://github.com/lh3/bfcContacthengli@broadinstitute.orgSupplementary informationSupplementary data are available at Bioinformatics online.
| S-EPMC4635656 | biostudies-literature
Project description:PurposeConsidering the present controversies on the association between green coffee supplementation and cardio metabolic risk factors, this systematic review and meta-analysis was conducted to evaluate the effect of green coffee supplementation on cardio metabolic risk factors.MethodA systematic literature search was performed throughout the PubMed, Embase, Scopus, and Web of Science databases up to October 2019. As a result, all randomized controlled trials over the effect of green coffee supplementation on fasting blood sugar (FBS), insulin, triglyceride, high-density lipoprotein (HDL), low-density lipoprotein (LDL), C - reactive protein (CRP), and homeostatic model assessment for insulin resistance (HOMA-IR) in adults were examined. Data were extracted from the relevant studies and analyzed using the random-effect or pooled model and standardized mean difference (SMD) with 95% confidence interval (CI).ResultsAfter excluding the irrelevant articles, 27 studies were included in the final analysis. Pooled results revealed that green coffee supplementation significantly reduced FBS (WMD = -2.28, 95% CI: -4.49 to -0.07, P = 0.043), insulin (WMD = -0.53, 95% CI: -0.93 to -0.14, P = 0.008), and triglyceride (WMD = -9.28, 95% CI: -14.93 to - 3.63, P = 0.001). Furthermore, green coffee supplementation increased the HDL levels (WMD = 1.33, 95% CI: 0.08 to 2.58, P = 0.037). However, the changes in HOMA-IR, LDL, and CRP levels were not significant (P > 0.05).ConclusionThis meta-analysis indicated that green coffee supplementation significantly decreased FBS, insulin, and triglyceride, but improved HDL. No statistically significant improvement was found in HOMA-IR, LDL, and CRP indices following the green coffee supplementation.
| S-EPMC7271291 | biostudies-literature
Project description:ObjectiveIn this study, we have demonstrated that supplementation of a complex of chlorogenic acid isomers (CGA-7TM) could significantly mitigate the risk of obesity in healthy overweight subjects.MethodIn a double-blind, placebo-controlled clinical study, healthy overweight (body mass index ⩾ 25 to <30 kg/m2) male and female subjects (N = 71) were randomly allocated to receive 500 mg CGA-7 or placebo daily for 12 weeks. Changes in body weight and body mass index were recorded alongside vital signs and anthropometric measurements at week 4, 8 and 12. Body composition was assessed at baseline and the end of treatment using dual-energy X-ray absorptiometry. Safety analysis included serum biochemical and haematological assessments and measurement of vital signs. In addition, any adverse or serious adverse events were recorded during the study.ResultsSixty subjects completed the study. Mean body weight and body mass index were significantly reduced in CGA-7 group as compared to placebo (p < 0.001). CGA-7 group showed significant changes in body fat (%), fat mass and lean mass in comparison with placebo group (1.38% ± 1.4% vs -0.22% ± 0.86%, 1.97 ± 1.44 kg vs -0.39 ± 1.31 kg; 0.81 ± 1.20 kg vs -0.13 ± 0.97 kg, p < 0.001). Consumption of CGA-7 significantly improved the serum lipid profile. Importantly, CGA-7 consumption in humans had no adverse effects and was well tolerated during the study. The blood biochemical and haematological parameters marginally varied in the treatment groups throughout the study.ConclusionTo conclude, this study provides scientific validation of the functionality of green coffee bean extract and recommends the safety of the supplementation in healthy individuals.
| S-EPMC7983441 | biostudies-literature
Project description:Green coffee bean extract (GCBE) provides diversified health benefits. However, its reported low bioavailability impeded its utilization in various applications. In this study, GCBE-loaded solid lipid nanoparticles (SLNs) were prepared to improve the bioavailability through enhanced intestinal absorption of GCBE. During the preparation of promising GCBE-loaded SLNs, the lipid concentration, surfactant concentration, and co-surfactant amount are crucial that were optimized using the Box-Behnken design, while particle size, polydispersity index (PDI), ζ-potential, entrapment efficiency, and cumulative drug release were the measured responses. GCBE-SLNs were successfully developed by a high shear homogenization technique using geleol as a solid lipid, tween 80 as a surfactant, and propylene glycol as Co-SAA. The optimized SLNs contained 5.8% geleol, 5.9% tween 80, and 80.4 mg PG resulting in a small particle size of 235.7 ± 12.5 nm, reasonably acceptable PDI of 0.417 ± 0.023, and ζ-potential of -15 ± 0.14 mV, with a high entrapment efficiency of 58.3 ± 0.85% and cumulative release of 7575 ± 0.78%. Furthermore, the performance of the optimized GCBE-SLN was evaluated using an ex vivo everted sac model where the intestinal permeation of GCBE was improved due to nanoencapsulation using SLN. Consequently, the results enlightened the auspicious potential of exploiting oral GCBE-SLNs for boosting intestinal absorption of chlorogenic acid.
| S-EPMC10268626 | biostudies-literature
Project description:Given its important role in human health and disease, remarkably little is known about the full-length three-dimensional (3D) molecular architecture of the breast cancer type 1 susceptibility protein (BRCA1), or its mechanisms to engage the tumor suppressor, TP53 (p53). Here, we show how a prevalent cancer-related mutation in the C-terminal region of the full-length protein, BRCA15382insC, affects its structural properties, yet can be biochemically corrected to restore its functional capacity. As a downstream consequence of restoring the ubiquitin ligase activity of mutated BRCA15382insC, the DNA repair response of p53 was enhanced in cellular extracts naturally deficient in BRCA1 protein expression. Complementary structural insights of p53 tetramers bound to DNA in different stage of the repair process support these biochemical findings in the context of human cancer cells. Equally important, we show how this knowledge can be used to lower the viability of breast cancer cells by modulating the stability of the BRCA1 protein and its associated players.
| S-EPMC6375096 | biostudies-literature
Project description:Our experiments showed that long-term coffee or green tea(GTE) extract supplementation( from 3 months old to 12 months old) ameliorates age-related hearing loss (ARHL) in mice. Then we explored the possible underlying mechanisms through comparing the cochlear transcriptome profiling (RNA-seq) of the coffee or GTE treated mice to the control mice.
2023-12-01 | GSE189798 | GEO
Project description:BackgroundDuring the last few decades, patients worldwide have been interested in using alternative medicine in treating diseases to avoid the increased side effects of chemical medications. Green coffee is unroasted coffee seeds that have higher amounts of chlorogenic acid compared to roasted coffee. Green coffee was successfully used to protect against obesity, Alzheimer disease, high blood pressure and bacterial infection.MethodsThis study aimed to investigate the probable protective activity of the green coffee methanolic extract, silymarin and their combination on CCl4-induced liver toxicity in male rats. Thirty Sprague - Dawley male albino rats were divided into 5 groups; control negative (G1) just got the vehicle (olive oil) and the other four groups received CCl4 dissolved in olive oil through an intraperitoneal injection and were divided into untreated control positive group (G2), the third group (G3) was treated with green coffee methanolic extract, the fourth group (G4) was treated with silymarin, and the fifth group (G5) was treated with a combination of green coffee methanolic extract and silymarin.ResultsIn the positive control group treated with CCl4 (G2), the CCl4-induced toxicity increased lipid peroxidation, IL-6, kidney function parameters, liver function enzymes, total cholesterol, triglycerides and low-density lipoproteins, and decreased irisin, antioxidants, CYP450 and high-density lipoprotein levels. Hepatic tissues were also injured. However, treating the injured rats in G3, G4 and G5 significantly improved the altered parameters and hepatic tissues.ConclusionsGreen coffee methanolic extract, silymarin, and their combination succeeded in protecting the male rats against CCl4 hepatotoxicity due to their antioxidant activity. Effect of green coffee methanolic extract mixed with silymarin in G5 was more efficient than that of green coffee methanolic extract in G3 or silymarin in G4.
| S-EPMC7792057 | biostudies-literature
Project description:IMRT plans generated in Eclipse use a fast algorithm to evaluate dose for optimization and a more accurate algorithm for a final dose calculation, the Analytical Anisotropic Algorithm. The use of a fast optimization algorithm introduces optimization convergence errors into an IMRT plan. Eclipse has a feature where optimization may be performed on top of an existing base plan. This feature allows for the possibility of arriving at a recursive solution to optimization that relies on the accuracy of the final dose calculation algorithm and not the optimizer algorithm. When an IMRT plan is used as a base plan for a second optimization, the second optimization can compensate for heterogeneity and modulator errors in the original base plan. Plans with the same field arrangement as the initial base plan may be added together by adding the initial plan optimal fluence to the dose correcting plan optimal fluence.A simple procedure to correct for optimization errors is presented that may be implemented in the Eclipse treatment planning system, along with an Excel spreadsheet to add optimized fluence maps together.
| S-EPMC5720570 | biostudies-literature
Project description:Although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1-3 random errors/kb of DNA. Here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic DNA. In this method, errors are revealed as mismatches by re-hybridization of the population. The DNA is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding protein (MutS). PCR assembly of the remaining fragments yields a new population of full-length sequences enriched for the consensus sequence of the input population. We show that two iterations of consensus shuffling improved a population of synthetic green fluorescent protein (GFPuv) clones from approximately 60 to >90% fluorescent, and decreased errors 3.5- to 4.3-fold to final values of approximately 1 error per 3500 bp. In addition, two iterations of consensus shuffling corrected a population of GFPuv clones where all members were non-functional, to a population where 82% of clones were fluorescent. Consensus shuffling should facilitate the rapid and accurate synthesis of long DNA sequences.
| S-EPMC1072806 | biostudies-literature
Project description:To discharge the colored effluents from industries there needs to be effective and affordable treatment options. Adsorption using reduced graphene oxide (rGO) as an adsorbent is a prominent one. In this study, green coffee bean extract (GCBE) is utilized as a safe reducing agent for the reduction of graphene oxide (GO) to synthesize rGO. The formation of rGO is confirmed by a new peak in the UV-vis spectra at 275 nm and a diffraction peak in the XRD patterns at 22°. The effective formation of rGO is further substantiated by a change in the GO peak's properties in the FTIR, EDX, and Raman spectra and a weight loss change in TGA. The SEM and TEM analyses demonstrate the effective production of the nano-sheets of rGO having exfoliated and segregated in a few layers. Furthermore, the obtained rGO exhibited outstanding efficacy in wastewater cleanup, effectively adsorbing MB as a prototype organic dye. The kinetics and isotherm study suggested that the adsorption leads by the chemisorption and monolayer formation on the homogeneous surface of rGO. The maximum adsorption capacity is found to be 89.3 mg g-1. This process offers a fresh opportunity for the economical and safe production of rGO for wastewater treatment.
| S-EPMC10784199 | biostudies-literature