scholarly journals Binary Simplification as an Effective Tool in Metabolomics Data Analysis

Metabolites ◽  
2021 ◽  
Vol 11 (11) ◽  
pp. 788
Author(s):  
Francisco Traquete ◽  
João Luz ◽  
Carlos Cordeiro ◽  
Marta Sousa Silva ◽  
António E. N. Ferreira
Keyword(s):  
Data Analysis ◽  
Small Molecules ◽  
Background Noise ◽  
Treatment Method ◽  
Metabolomics Data ◽  
Benchmark Datasets ◽  
Clustering And Classification ◽  
Pre Treatment ◽  
Treatment Procedures ◽  
Better Than

Metabolomics aims to perform a comprehensive identification and quantification of the small molecules present in a biological system. Due to metabolite diversity in concentration, structure, and chemical characteristics, the use of high-resolution methodologies, such as mass spectrometry (MS) or nuclear magnetic resonance (NMR), is required. In metabolomics data analysis, suitable data pre-processing, and pre-treatment procedures are fundamental, with subsequent steps aiming at highlighting the significant biological variation between samples over background noise. Traditional data analysis focuses primarily on the comparison of the features’ intensity values. However, intensity data are highly variable between experimental batches, instruments, and pre-processing methods or parameters. The aim of this work was to develop a new pre-treatment method for MS-based metabolomics data, in the context of sample profiling and discrimination, considering only the occurrence of spectral features, encoding feature presence as 1 and absence as 0. This “Binary Simplification” encoding (BinSim) was used to transform several benchmark datasets before the application of clustering and classification methods. The performance of these methods after the BinSim pre-treatment was consistently as good as and often better than after different combinations of traditional, intensity-based, pre-treatments. Binary Simplification is, therefore, a viable pre-treatment procedure that effectively simplifies metabolomics data-analysis pipelines.

scholarly journals A comparison framework and guideline of clustering methods for mass cytometry data

2019 ◽  
Vol 20 (1) ◽  
Author(s):  
Xiao Liu ◽  
Weichen Song ◽  
Brandon Y. Wong ◽  
Ting Zhang ◽  
Shunying Yu ◽  
...  
Keyword(s):  
Data Analysis ◽  
Sample Size ◽  
Performance Measures ◽  
Clustering Methods ◽  
Mass Cytometry ◽  
Internal Evaluation ◽  
Linear Discriminant ◽  
Benchmark Datasets ◽  
Supervised Methods ◽  
Better Than

Abstract Background With the expanding applications of mass cytometry in medical research, a wide variety of clustering methods, both semi-supervised and unsupervised, have been developed for data analysis. Selecting the optimal clustering method can accelerate the identification of meaningful cell populations. Result To address this issue, we compared three classes of performance measures, “precision” as external evaluation, “coherence” as internal evaluation, and stability, of nine methods based on six independent benchmark datasets. Seven unsupervised methods (Accense, Xshift, PhenoGraph, FlowSOM, flowMeans, DEPECHE, and kmeans) and two semi-supervised methods (Automated Cell-type Discovery and Classification and linear discriminant analysis (LDA)) are tested on six mass cytometry datasets. We compute and compare all defined performance measures against random subsampling, varying sample sizes, and the number of clusters for each method. LDA reproduces the manual labels most precisely but does not rank top in internal evaluation. PhenoGraph and FlowSOM perform better than other unsupervised tools in precision, coherence, and stability. PhenoGraph and Xshift are more robust when detecting refined sub-clusters, whereas DEPECHE and FlowSOM tend to group similar clusters into meta-clusters. The performances of PhenoGraph, Xshift, and flowMeans are impacted by increased sample size, but FlowSOM is relatively stable as sample size increases. Conclusion All the evaluations including precision, coherence, stability, and clustering resolution should be taken into synthetic consideration when choosing an appropriate tool for cytometry data analysis. Thus, we provide decision guidelines based on these characteristics for the general reader to more easily choose the most suitable clustering tools.

scholarly journals A Study of the Effects of Waste Egg and Shrimp Shells on the Toxicity Immobilisation of Chemicals

2018 ◽  
Vol 34 (4) ◽  
pp. 1926-1929
Author(s):  
Boontida Uapipatanakul
Keyword(s):  
Zeta Potential ◽  
Surface Charge ◽  
Copper Sulfate ◽  
Biological Treatment ◽  
Treatment Method ◽  
Toxic Compounds ◽  
Shrimp Shells ◽  
Pre Treatment ◽  
Positively Charged ◽  
Better Than

Natural resources are declining rapidly. Water scarcity is one of the biggest crises that the world faces. Even though there are many treatment methods, it still leaves a large carbon footprint. Hence, biological treatment is desired. However, there are many toxic compounds that contaminate wastewater, which inhibit biological treatment. Therefore, waste egg and shrimp shells were introduced as adsorbents to immobilize toxicity as a pre-treatment method. Egg and shrimp shells were tested for their surface charge with zeta potential. Then, Escherichia coli (E.coli) cells were exposed to the toxic compounds, copper sulfate and carbonyl phenol, for 15 minutes. Subsequently, E.coli cells were regrown on the agar plates to determine the recuperation rate of the colonies. It was found that eggshells decreased the toxicity of the tried concoction to E.coli, and enabled the colonies to recover by up to 62%. Moreover, it has proved that there is potential that the surface charge has an effect on the adsorption process. Eggshells, which have -21.85 zeta potential, adsorb copper sulfate, which is positively charged, better than carbonyl phenol, which is negatively charged; and vice versa for shrimp shells.

EELS characterization of “Smut” layer films on steel surface prepared for chrome plating by anodic etching

1995 ◽  
Vol 53 ◽  
pp. 538-539
Author(s):  
E Y. Wang ◽  
J. T. Cherian ◽  
A. Madsen ◽  
R. M. Fisher
Keyword(s):  
Steel Surface ◽  
Surface Preparation ◽  
Treatment Method ◽  
Chrome Plating ◽  
Transmission Electron ◽  
Alloy Steels ◽  
Pre Treatment ◽  
Hard Chrome ◽  
Electron Energy Loss

Many steel parts are electro-plated with chromium to protect them against corrosion and to improve their wear-resistance. Good adhesion of the chrome plate to the steel surface, which is essential for long term durability of the part, is extremely dependent on surface preparation prior to plating. Recently, McDonnell Douglas developed a new pre-treatment method for chrome plating in which the steel is anodically etched in a sulfuric acid and hydrofluoric acid solution. On carbon steel surfaces, this anodic pre-treatment produces a dark, loosely adhering material that is commonly called the “smut” layer. On stainless steels and nickel alloys, the surface is only darkened by the anodic pre-treatment and little residue is produced. Anodic pre-treatment prior to hard chrome plating results in much better adherence to both carbon and alloy steels.We have characterized the anodic pre-treated steel surface and the resulting “smut” layer using various techniques including electron spectroscopy for chemical analysis (ESCA) on bulk samples and transmission electron microscopy (TEM) and electron energy-loss spectroscopy (EELS) on stripped films.

Motilitas dan Vabilitas Spermatozoa Ayam Kampung pada Suhu 5°C Menggunakan Pengencer dan Lama Simpan yang Berbeda

2018 ◽  
Vol 5 (2) ◽  
pp. 102
Author(s):  
Enike Dwi Kusumawati ◽  
Selvinus Lawu Woli ◽  
Aju Tjatur Nugroho Krisnaningsih ◽  
Waluyo Edi Susanto ◽  
Syam Rahadi
Keyword(s):  
Data Analysis ◽  
Storage Temperature ◽  
Coconut Water ◽  
Laboratory Research ◽  
Ringer Lactate ◽  
Randomized Design ◽  
Native Chicken ◽  
Lactate Solution ◽  
Better Than

ABSTRAKPenelitian ini dilakukan untuk mengetahui motilitas dan viabilitas spermatozoa ayam kampung pada suhu 5oC menggunakan pengencer dan lama simpan yang berbeda. Metode yang digunakan dalam penelitian ini adalah penelitian laboratorium menggunakan Rancangan Acak Lengkap (RAL) Faktorial dengan pengencer ringer lactat solution, air kelapa dan tanpa pengencer serta lama simpan 0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30, masing-masing diulang 10 kali. Variabel yang diamati yaitu motilitas dan viabilitas spermatozoa. Analisa data yang digunakan adalah analisis varian. Hasil analisis data menunjukkan bahwa motilitas dan viabilitas spermatozoa menggunakan pengencer ringer lactat solution lebih tinggi (P<0,01) serta dapat bertahan sampai lama simpan 24 jam dibandingkan air kelapa dan tanpa pengencer. Adapun nilai motilitas ringer lactat solution, air kelapa dan tanpa pengencer pada lama simpan 24 jam masing-masing sebesar 43,5±17,17%; 8±4,83%; 6,5±2,4%, sedangkan nilai viabilitasnya sebesar 83,2±7,25%; 64,6±3,20%; dan 63,1±2,33%. Kesimpulan dari hasil penelitian ini adalah ringer lactat solution lebih baik dibandingkan air kelapa dan tanpa pengencer dalam mempertahankan kualitas semen ayam kampung pada suhu simpan 5oC sampai lama simpan 24 jam.Kata Kunci : air kelapa, ayam kampung, motilitas, spermatozoa, viabilitas  ABSTRACTThis study was conducted to determine the motility and viability of spermatozoa of Native chickens at 5oC using different diluents and time storage. The method used in this study was laboratory research using Factorial Completely Randomized Design with ringer lactate solution, coconut water and without diluent at 0, 3, 6, 9, 12, 15, 18, 21, 24, 27, 30 hours of time storage each repeated 10 times. The variables observed were motility and viability of sperm. Data analysis used is variance analysis. The results of data analysis showed that the motility and viability of spermatozoa using ringer lactate solution diluents was higher (P <0.05) than coconut water and without diluents. The motility values of ringer lactat solution, coconut water and without diluents were 43,5±17,17%; 8±4,83%; 6,5±2,4% respectively, while the viability values were 83,2±7,25%; 64,6±3,20% and 63,1±2,33%. The conclusion of this study is that ringer lactat solution is better than coconut water an without diluents in maintaining the quality of Native chicken semen at a storage temperature of 5oC until 24 hours.Keywords: coconut water, motility, native chicken, sperm, viability

Isolation of an Anti-fatigue Preparation from Cellulase-treated Maca by Hydroalcoholic Extraction

2017 ◽  
Vol 17 (1) ◽  
pp. 93-98
Author(s):  
Zheng Yue ◽  
Zhang Wen-Cheng ◽  
Wu Ze-Yu ◽  
Fu Chuan-Xiang ◽  
Gao Han ◽  
...  
Keyword(s):  
Positive Control ◽  
Glycogen Storage ◽  
Hepatic Glycogen ◽  
Time To Exhaustion ◽  
High Dose ◽  
Hydroalcoholic Extract ◽  
Swimming Time ◽  
Significant Difference ◽  
Pre Treatment ◽  
Better Than

The purpose of this study was to evaluate the anti-fatigue activity of maca hydroalcoholic extract (ME), which mainly contains macamides and polysaccharides. ME was prepared by circumfluence extraction with enzymatic pre-treatment. Anti-fatigue activity of ME was investigated in weight-loaded forced swimming mice, with pure macamides and commercially available maca tablet as positive control. Compared with normal group, pure macamides treatment group could prolong the swimming time to exhaustion, but there was no statistically significant difference (P > 0.05); while ME (middle-dose and high-dose groups) could effectively prolong the swimming durations (P < 0.05). Supplementation with pure macamides significantly decreased blood lactic acid (BLA), whereas ME significantly increased hepatic glycogen (HG), decreased BLA, and blood urea nitrogen (BUN) compared with those in normal control (P < 0.05). The results suggested that the anti-fatigue effect of ME was better than that of pure macamides, which can be explained by the increase of glycogen storage and the reduction of metabolites accumulation.

scholarly journals Therapeutic efficacy of artemether–lumefantrine and artesunate–amodiaquine for the treatment of uncomplicated Plasmodium falciparum malaria in Mali, 2015–2016

2021 ◽  
Vol 20 (1) ◽  
Author(s):  
Youssouf Diarra ◽  
Oumar Koné ◽  
Lansana Sangaré ◽  
Lassina Doumbia ◽  
Dade Bouye Ben Haidara ◽  
...  
Keyword(s):  
Plasmodium Falciparum ◽  
Uncomplicated Malaria ◽  
Artemisinin Resistance ◽  
National Malaria Control Programme ◽  
Plasmodium Falciparum Malaria ◽  
Control Programme ◽  
Malaria Control Programme ◽  
Pre Treatment ◽  
Better Than

Abstract Background The current first-line treatments for uncomplicated malaria recommended by the National Malaria Control Programme in Mali are artemether–lumefantrine (AL) and artesunate–amodiaquine (ASAQ). From 2015 to 2016, an in vivo study was carried out to assess the clinical and parasitological responses to AL and ASAQ in Sélingué, Mali. Methods Children between 6 and 59 months of age with uncomplicated Plasmodium falciparum infection and 2000–200,000 asexual parasites/μL of blood were enrolled, randomly assigned to either AL or ASAQ, and followed up for 42 days. Uncorrected and PCR-corrected efficacy results at days 28 and 42. were calculated. Known markers of resistance in the Pfk13, Pfmdr1, and Pfcrt genes were assessed using Sanger sequencing. Results A total of 449 patients were enrolled: 225 in the AL group and 224 in the ASAQ group. Uncorrected efficacy at day 28 was 83.4% (95% CI 78.5–88.4%) in the AL arm and 93.1% (95% CI 89.7–96.5%) in the ASAQ arm. The per protocol PCR-corrected efficacy at day 28 was 91.0% (86.0–95.9%) in the AL arm and 97.1% (93.6–100%) in the ASAQ arm. ASAQ was significantly (p < 0.05) better than AL for each of the aforementioned efficacy outcomes. No mutations associated with artemisinin resistance were identified in the Pfk13 gene. Overall, for Pfmdr1, the N86 allele and the NFD haplotype were the most common. The NFD haplotype was significantly more prevalent in the post-treatment than in the pre-treatment isolates in the AL arm (p < 0.01) but not in the ASAQ arm. For Pfcrt, the CVIET haplotype was the most common. Conclusions The findings indicate that both AL and ASAQ remain effective for the treatment of uncomplicated malaria in Sélingué, Mali.

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