scholarly journals Compositional data analysis (CoDA) as a tool to evaluate a new low-cost settling-based PM<sub>10</sub> sampling head in a desert dust source region

2021 ◽  
Vol 14 (12) ◽  
pp. 7657-7680
Author(s):  
Yangjunjie Xu-Yang ◽  
Rémi Losno ◽  
Fabrice Monna ◽  
Jean-Louis Rajot ◽  
Mohamed Labiadh ◽  
...  
Keyword(s):  
Data Analysis ◽  
Compositional Data ◽  
Low Cost ◽  
Source Region ◽  
Vertical Tube ◽  
Compositional Data Analysis ◽  
Size Segregation ◽  
Field Campaign ◽  
Paired Samples ◽  
Semi Arid Region

Abstract. This paper presents a new sampling head design and the method used to evaluate it. The elemental composition of aerosols collected by two different sampling devices in a semi-arid region of Tunisia is compared by means of compositional perturbation vectors and biplots. This set of underused mathematical tools belongs to a family of statistics created specifically to deal with compositional data. The two sampling devices operate at a flow rate in the range of 1 m3 h−1, with a cut-off diameter of 10 µm. The first device is a low-cost laboratory-made system, where the largest particles are removed by gravitational settling in a vertical tube. This new system will be compared to the second device, a brand-new standard commercial PM10 sampling head, where size segregation is achieved by particle impaction on a metal surface. A total of 44 elements (including rare earth elements, REEs, together with Al, As, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Rb, S, Sc, Se, Sr, Ti, Tl, U, V, Zn, and Zr) were analysed in 16 paired samples, collected during a 2-week field campaign in Tunisian dry lands, close to source areas, with high levels of large particles. The contrasting meteorological conditions encountered during the field campaign allowed a broad range of aerosol compositions to be collected, with very different aerosol mass concentrations. The compositional data analysis (CoDA) tools show that no compositional differences were observed between samples collected simultaneously by the two devices. The mass concentration of the particles collected was estimated through chemical analysis. Results for the two sampling devices were very similar to those obtained from an online aerosol weighing system, TEOM (tapered element oscillating microbalance), installed next to them. These results suggest that the commercial PM10 impactor head can therefore be replaced by the decanter, without any measurable bias, for the determination of chemical composition and for further assessment of PM10 concentrations in source regions.

scholarly journals Compositional data analysis (CoDA) as a tool to evaluate a new low-cost settling-based PM<sub>10</sub> sampling head in a desert dust source region

2021 ◽  
Author(s):  
Yangjunjie Xu-Yang ◽  
Rémi Losno ◽  
Fabrice Monna ◽  
Jean-Louis Rajot ◽  
Mohamed Labiadh ◽  
...  
Keyword(s):  
Compositional Data ◽  
Low Cost ◽  
Source Region ◽  
Vertical Tube ◽  
Compositional Data Analysis ◽  
Size Segregation ◽  
Field Campaign ◽  
Paired Samples ◽  
Aerosol Mass ◽  
Semi Arid Region

Abstract. This paper presents a new sampling head design and the method used to evaluate it. The elemental composition of aerosols collected by two different sampling devices in a semi-arid region of Tunisia is compared by means of compositional perturbation vectors and biplots. This set of underused mathematical tools belongs to a family of statistics created specifically to deal with compositional data. The two sampling devices operate at a flow rate of about 17 L min−1, with a cut-off diameter of 10 µm. The first device is a low-cost laboratory-made system, where the largest particles are removed by gravitational settling in a vertical tube. This new system will be compared to the second device, a brand-new standard commercial PM10 sampling head, where size segregation is achieved by particle impaction on a metal surface. A total of 44 elements (including rare earth elements or REE, together with Al, As, Ba, Be, Ca, Cd, Co, Cr, Cu, Fe, K, Li, Mg, Mn, Mo, Na, Ni, P, Pb, Rb, S, Sc, Se, Sr, Ti, Tl, U, V, Zn, and Zr), was analysed in sixteen paired samples, collected during a two-week field campaign in Tunisian dry lands, close to source areas, with high levels of large particles. The contrasting meteorological conditions encountered during the field campaign allowed a broad range of aerosol compositions to be collected, with very different aerosol mass concentrations. No compositional differences were observed between samples collected simultaneously by the two devices. The mass concentration of the particles collected was estimated through chemical analysis, and results for the two sampling devices were also very similar to those obtained from an on-line aerosol weighing system, TEOM (tapered element oscillating micro-balance), installed next to them. Results suggest that the commercial PM10 impactor head can therefore be replaced by the decanter, without any measurable bias, for the determination of chemical composition, and for further assessment of PM10 concentrations in source regions.

scholarly journals Tree-Aggregated Predictive Modeling of Microbiome Data

2020 ◽  
Author(s):  
Jacob Bien ◽  
Xiaohan Yan ◽  
Léo Simpson ◽  
Christian L. Müller
Keyword(s):  
Data Analysis ◽  
Predictive Modeling ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Compositional Data ◽  
Low Cost ◽  
Primary Data ◽  
Compositional Data Analysis ◽  
Taxonomic Rank ◽  
Microbiome Data

AbstractModern high-throughput sequencing technologies provide low-cost microbiome survey data across all habitats of life at unprecedented scale. At the most granular level, the primary data consist of sparse counts of amplicon sequence variants or operational taxonomic units that are associated with taxonomic and phylogenetic group information. In this contribution, we leverage the hierarchical structure of amplicon data and propose a data-driven, parameter-free, and scalable tree-guided aggregation framework to associate microbial subcompositions with response variables of interest. The excess number of zero or low count measurements at the read level forces traditional microbiome data analysis workflows to remove rare sequencing variants or group them by a fixed taxonomic rank, such as genus or phylum, or by phylogenetic similarity. By contrast, our framework, which we call trac (tree-aggregation of compositional data), learns data-adaptive taxon aggregation levels for predictive modeling making user-defined aggregation obsolete while simultaneously integrating seamlessly into the compositional data analysis framework. We illustrate the versatility of our framework in the context of large-scale regression problems in human-gut, soil, and marine microbial ecosystems. We posit that the inferred aggregation levels provide highly interpretable taxon groupings that can help microbial ecologists gain insights into the structure and functioning of the underlying ecosystem of interest.

scholarly journals Tree-aggregated predictive modeling of microbiome data

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Jacob Bien ◽  
Xiaohan Yan ◽  
Léo Simpson ◽  
Christian L. Müller
Keyword(s):  
Data Analysis ◽  
Predictive Modeling ◽  
Large Scale ◽  
High Throughput Sequencing ◽  
Compositional Data ◽  
Low Cost ◽  
Primary Data ◽  
Compositional Data Analysis ◽  
Taxonomic Rank ◽  
Microbiome Data

AbstractModern high-throughput sequencing technologies provide low-cost microbiome survey data across all habitats of life at unprecedented scale. At the most granular level, the primary data consist of sparse counts of amplicon sequence variants or operational taxonomic units that are associated with taxonomic and phylogenetic group information. In this contribution, we leverage the hierarchical structure of amplicon data and propose a data-driven and scalable tree-guided aggregation framework to associate microbial subcompositions with response variables of interest. The excess number of zero or low count measurements at the read level forces traditional microbiome data analysis workflows to remove rare sequencing variants or group them by a fixed taxonomic rank, such as genus or phylum, or by phylogenetic similarity. By contrast, our framework, which we call  (ee-ggregation of ompositional data), learns data-adaptive taxon aggregation levels for predictive modeling, greatly reducing the need for user-defined aggregation in preprocessing while simultaneously integrating seamlessly into the compositional data analysis framework. We illustrate the versatility of our framework in the context of large-scale regression problems in human gut, soil, and marine microbial ecosystems. We posit that the inferred aggregation levels provide highly interpretable taxon groupings that can help microbiome researchers gain insights into the structure and functioning of the underlying ecosystem of interest.

scholarly journals Effects of Two Randomized and Controlled Multi-Component Interventions Focusing On 24-Hour Movement Behavior among Office Workers: A Compositional Data Analysis

2021 ◽  
Vol 18 (8) ◽  
pp. 4191
Author(s):  
Lisa-Marie Larisch ◽  
Emil Bojsen-Møller ◽  
Carla F. J. Nooijen ◽  
Victoria Blom ◽  
Maria Ekblom ◽  
...  
Keyword(s):  
Physical Activity ◽  
Data Analysis ◽  
Cardiorespiratory Fitness ◽  
Leisure Time ◽  
Compositional Data ◽  
Office Workers ◽  
Movement Behavior ◽  
Compositional Data Analysis ◽  
Intervention Effects ◽  
Time In Bed

Intervention studies aiming at changing movement behavior have usually not accounted for the compositional nature of time-use data. Compositional data analysis (CoDA) has been suggested as a useful strategy for analyzing such data. The aim of this study was to examine the effects of two multi-component interventions on 24-h movement behavior (using CoDA) and on cardiorespiratory fitness among office workers; one focusing on reducing sedentariness and the other on increasing physical activity. Office workers (n = 263) were cluster randomized into one of two 6-month intervention groups, or a control group. Time spent in sedentary behavior, light-intensity, moderate and vigorous physical activity, and time in bed were assessed using accelerometers and diaries, both for 24 h in total, and for work and leisure time separately. Cardiorespiratory fitness was estimated using a sub-maximal cycle ergometer test. Intervention effects were analyzed using linear mixed models. No intervention effects were found, either for 24-h behaviors in total, or for work and leisure time behaviors separately. Cardiorespiratory fitness did not change significantly. Despite a thorough analysis of 24-h behaviors using CoDA, no intervention effects were found, neither for behaviors in total, nor for work and leisure time behaviors separately. Cardiorespiratory fitness did not change significantly. Although the design of the multi-component interventions was based on theoretical frameworks, and included cognitive behavioral therapy counselling, which has been proven effective in other populations, issues related to implementation of and compliance with some intervention components may have led to the observed lack of intervention effect.

scholarly journals The Gut Microbiota of Healthy Aged Chinese Is Similar to That of the Healthy Young

mSphere ◽  
2017 ◽  
Vol 2 (5) ◽  
Author(s):  
Gaorui Bian ◽  
Gregory B. Gloor ◽  
Aihua Gong ◽  
Changsheng Jia ◽  
Wei Zhang ◽  
...  
Keyword(s):  
Data Analysis ◽  
Gut Microbiota ◽  
Large Scale ◽  
Compositional Data ◽  
Healthy Lifestyle ◽  
Compositional Data Analysis ◽  
Surprising Result ◽  
Microbiota Composition ◽  
Cross Sectional ◽  
Age Cohorts

ABSTRACT We report the large-scale use of compositional data analysis to establish a baseline microbiota composition in an extremely healthy cohort of the Chinese population. This baseline will serve for comparison for future cohorts with chronic or acute disease. In addition to the expected difference in the microbiota of children and adults, we found that the microbiota of the elderly in this population was similar in almost all respects to that of healthy people in the same population who are scores of years younger. We speculate that this similarity is a consequence of an active healthy lifestyle and diet, although cause and effect cannot be ascribed in this (or any other) cross-sectional design. One surprising result was that the gut microbiota of persons in their 20s was distinct from those of other age cohorts, and this result was replicated, suggesting that it is a reproducible finding and distinct from those of other populations. The microbiota of the aged is variously described as being more or less diverse than that of younger cohorts, but the comparison groups used and the definitions of the aged population differ between experiments. The differences are often described by null hypothesis statistical tests, which are notoriously irreproducible when dealing with large multivariate samples. We collected and examined the gut microbiota of a cross-sectional cohort of more than 1,000 very healthy Chinese individuals who spanned ages from 3 to over 100 years. The analysis of 16S rRNA gene sequencing results used a compositional data analysis paradigm coupled with measures of effect size, where ordination, differential abundance, and correlation can be explored and analyzed in a unified and reproducible framework. Our analysis showed several surprising results compared to other cohorts. First, the overall microbiota composition of the healthy aged group was similar to that of people decades younger. Second, the major differences between groups in the gut microbiota profiles were found before age 20. Third, the gut microbiota differed little between individuals from the ages of 30 to >100. Fourth, the gut microbiota of males appeared to be more variable than that of females. Taken together, the present findings suggest that the microbiota of the healthy aged in this cross-sectional study differ little from that of the healthy young in the same population, although the minor variations that do exist depend upon the comparison cohort. IMPORTANCE We report the large-scale use of compositional data analysis to establish a baseline microbiota composition in an extremely healthy cohort of the Chinese population. This baseline will serve for comparison for future cohorts with chronic or acute disease. In addition to the expected difference in the microbiota of children and adults, we found that the microbiota of the elderly in this population was similar in almost all respects to that of healthy people in the same population who are scores of years younger. We speculate that this similarity is a consequence of an active healthy lifestyle and diet, although cause and effect cannot be ascribed in this (or any other) cross-sectional design. One surprising result was that the gut microbiota of persons in their 20s was distinct from those of other age cohorts, and this result was replicated, suggesting that it is a reproducible finding and distinct from those of other populations.

Compositional Data Analysis (CoDA) as a tool to study the (paleo)ecology of coccolithophores from coastal-neritic settings off central Portugal

2015 ◽  
Vol 319 ◽  
pp. 134-146 ◽  
Author(s):  
Catarina Guerreiro ◽  
Mário Cachão ◽  
Vera Pawlowsky-Glahn ◽  
Anabela Oliveira ◽  
Aurora Rodrigues
Keyword(s):  
Data Analysis ◽  
Compositional Data ◽  
Compositional Data Analysis ◽  
Central Portugal

scholarly journals Compositional data analysis and zeros in micro data

2000 ◽  
Vol 32 (8) ◽  
pp. 953-959 ◽  
Author(s):  
Jane M. Fry ◽  
Tim R. L. Fry ◽  
Keith R. McLaren
Keyword(s):  
Data Analysis ◽  
Compositional Data ◽  
Compositional Data Analysis ◽  
Micro Data
Sign in / Sign up

Export Citation Format

Share Document