Measurement Errors in R

Ucar, Iñaki; Pebesma, Edzer; Azcorra, Arturo

doi:10.32614/rj-2018-075

Cited by 20 publications

(15 citation statements)

References 4 publications

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“…For estimating derived variables (i.e., daily energy excretion) we used the R package "errors" (Ucar et al, 2019). This package links uncertainty metadata to quantity values (i.e., mean "daily fecal dry mass excretion", mean "fecal energy content") and this uncertainty is automatically propagated when calculating derived variables (i.e., "daily energy excretion" = "daily fecal dry mass excretion" x "fecal energy content").…”

Section: Discussionmentioning

confidence: 99%

Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle

Hoces

Lan

Sun

et al. 2021

Preprint

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Microbiota composition correlates with host metabolic health in both humans and mice. Here we investigated the extent to which a gnotobiotic microbiota can mimic the influence of a complete microbiota on mouse metabolism using an isolator-housed TSE-PhenoMaster® system. We found that energy expenditure was equivalent between germ-free (GF) and specific-opportunistic-pathogen free line (SPF) mice, and we extend this observation to the OligoMM12 microbiota (12 species across 5 phyla that are naturally abundant in a murine gut microbiota). Moreover, microbiota-released calories were well compensated by food intake in all groups. However, each group of mice have a distinctive circadian metabolic profile. OligoMM12 clustered with GF during the light phase, but with SPF during the dark phase for both RER and metabolome. Therefore, interactions between the host and a reductionist microbiota are non-uniform over the circadian cycle, revealing a promising tool to identify key microbiota species/functions that modify host metabolism.

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Section: Discussionmentioning

confidence: 99%

Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle

Hoces

Lan

Sun

et al. 2021

Preprint

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“…In order to estimate the error of soil CO 2 efflux (SR), its isotopic composition (χ( 13 C) SR ) and the amount of label recovered in soil respiration ( abs 13 C), the standard deviation of each of the measured variables in Equations (1)–(5) was propagated using first‐order Taylor expansion (Spiess, 2014; Ucar, Pebesma, & Azcorra, 2018). The coefficient of variation was calculated for SR and χ E ( 13 C) SR as ratio of propagated error and value.…”

Section: Methodsmentioning

confidence: 99%

Drought and recovery effects on belowground respiration dynamics and the partitioning of recent carbon in managed and abandoned grassland

Ingrisch

Karlowsky

Hasibeder

et al. 2020

Global Change Biology

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The supply of soil respiration with recent photoassimilates is an important and fast pathway for respiratory loss of carbon (C). To date it is unknown how drought and land‐use change interactively influence the dynamics of recent C in soil‐respired CO 2 . In an in situ common‐garden experiment, we exposed soil‐vegetation monoliths from a managed and a nearby abandoned mountain grassland to an experimental drought. Based on two 13 CO 2 pulse‐labelling campaigns, we traced recently assimilated C in soil respiration during drought, rewetting and early recovery. Independent of grassland management, drought reduced the absolute allocation of recent C to soil respiration. Rewetting triggered a respiration pulse, which was strongly fuelled by C assimilated during drought. In comparison to the managed grassland, the abandoned grassland partitioned more recent C to belowground respiration than to root C storage under ample water supply. Interestingly, this pattern was reversed under drought. We suggest that these different response patterns reflect strategies of the managed and the abandoned grassland to enhance their respective resilience to drought, by fostering their resistance and recovery respectively. We conclude that while severe drought can override the effects of abandonment of grassland management on the respiratory dynamics of recent C, abandonment alters strategies of belowground assimilate investment, with consequences for soil‐CO 2 fluxes during drought and drought‐recovery.

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“…Experimental uncertainties in the reported log K values were propagated using the first-order Taylor series method calculated by the R package errors. 41 …”

Section: Materials and Methodsmentioning

confidence: 99%

Toward an Internally Consistent Model for Hg(II) Chemical Speciation Calculations in Bacterium–Natural Organic Matter–Low Molecular Mass Thiol Systems

Song

Adediran

Jiang

et al. 2020

Environ. Sci. Technol.

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To advance the scientific understanding of bacteria-driven mercury (Hg) transformation processes in natural environments, thermodynamics and kinetics of divalent mercury Hg(II) chemical speciation need to be understood. Based on Hg L III -edge extended X-ray absorption fine structure (EXAFS) spectroscopic information, combined with competitive ligand exchange (CLE) experiments, we determined Hg(II) structures and thermodynamic constants for Hg(II) complexes formed with thiol functional groups in bacterial cell membranes of two extensively studied Hg(II) methylating bacteria: Geobacter sulfurreducens PCA and Desulfovibrio desulfuricans ND132. The Hg EXAFS data suggest that 5% of the total number of membranethiol functionalities (Mem-RS tot = 380 ± 50 μmol g –1 C) are situated closely enough to be involved in a 2-coordinated Hg(Mem-RS) 2 structure in Geobacter . The remaining 95% of Mem-RSH is involved in mixed-ligation Hg(II)-complexes, combining either with low molecular mass (LMM) thiols like Cys, Hg(Cys)(Mem-RS), or with neighboring O/N membrane functionalities, Hg(Mem-RSRO). We report log K values for the formation of the structures Hg(Mem-RS) 2 , Hg(Cys)(Mem-RS), and Hg(Mem-RSRO) to be 39.1 ± 0.2, 38.1 ± 0.1, and 25.6 ± 0.1, respectively, for Geobacter and 39.2 ± 0.2, 38.2 ± 0.1, and 25.7 ± 0.1, respectively, for ND132. Combined with results obtained from previous studies using the same methodology to determine chemical speciation of Hg(II) in the presence of natural organic matter (NOM; Suwannee River DOM) and 15 LMM thiols, an internally consistent thermodynamic data set is created, which we recommend to be used in studies of Hg transformation processes in bacterium–NOM–LMM thiol systems.

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Measurement Errors in R

Cited by 20 publications

References 4 publications

Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle

Metabolic reconstitution by a gnotobiotic microbiota varies over the circadian cycle

Drought and recovery effects on belowground respiration dynamics and the partitioning of recent carbon in managed and abandoned grassland

Toward an Internally Consistent Model for Hg(II) Chemical Speciation Calculations in Bacterium–Natural Organic Matter–Low Molecular Mass Thiol Systems

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