Error propagation methods for LCA—a comparison

Purpose

The analysis of uncertainty in life cycle assessment (LCA) studies has been a topic for more than 10 years, and many commercial LCA programs now feature a sampling approach called Monte Carlo analysis. Yet, a full Monte Carlo analysis of a large LCA system, for instance containing the 4,000 unit processes of ecoinvent v2.2, is rarely carried out by LCA practitioners. One reason for this is computation time. An alternative faster than Monte Carlo method is analytical error propagation by means of a Taylor series expansion; however, this approach suffers from being explained in the literature in conflicting ways, hampering implementation in most software packages for LCA. The purpose of this paper is to compare the two different approaches from a theoretical and practical perspective.

Methods

In this paper, we compare the analytical and sampling approaches in terms of their theoretical background and their mathematical formulation. Using three case studies—one stylized, one real-sized, and one input–output (IO)-based—we approach these techniques from a practical perspective and compare them in terms of speed and results.

Results

Depending on the precise question, a sampling or an analytical approach provides more useful information. Whenever they provide the same indicators, an analytical approach is much faster but less reliable when the uncertainties are large.

Conclusions

For a good analysis, analytical and sampling approaches are equally important, and we recommend practitioners to use both whenever available, and we recommend software suppliers to implement both.     

On statistical methods for comparison of intrasample morphometric variability: Zalavár revisited

In studies of morphology, methods for comparing amounts of variability are often important. Three different ways of utilizing determinants of covariance matrices for testing for surplus variability in a hypothesis sample compared to a reference sample are presented: an F-test based on standardized generalized variances, a parametric bootstrap based on draws on Wishart matrices, and a nonparametric bootstrap. The F-test based on standardized generalized variances and the Wishart-based bootstrap are applicable when multivariate normality can be assumed. These methods can be applied with only summary data available. However, the nonparametric bootstrap can be applied with multivariate nonnormally distributed data as well as multivariate normally distributed data, and small sample sizes. Therefore, this method is preferable when raw data are available. Three craniometric samples are used to present the methods. A Hungarian Zalavár sample and an Austrian Berg sample are compared to a Norwegian Oslo sample, the latter employed as reference sample. In agreement with a previous study, it is shown that the Zalavár sample does not represent surplus variability, whereas the Berg sample does represent such a surplus variability.     

Which cervical sampler? A comparison of four methods

Four cytology sampling methods were compared in 1063 patients referred for colposcopy with a recent abnormal smear. A dyskaryotic smear of any grade was considered a positive result, though comparisons were limited to cases with a subsequent biopsy confirming CINII or III. There were no differences between the abilities of any of the four methods to detect higher grades of CIN (χ²₃=4.603, P >0.20). the presence or absence of endocervical cells in a smear was not significantly associated with any variation in success rate (χ²₁=0.959, P >0.30). the joint analysis of the four methods and the presence/absence of endocervical cells also showed no significant effects (χ²₇=12.768, 0.1 > P >0.05). In the latter analysis the trend towards a conventional level of significance was accounted for by the Aylesbury spatula giving a relatively high success rate when endocervical cells were present. the suggestion of advantage for the Aylesbury spatula merits further investigation.     

Responding to the threat of bioterrorism: a microbial ecology perspective – the case of anthrax

Anthrax is a disease of herbivores caused by the gram-positive bacterium Bacillus anthracis. It can affect cattle, sheep, swine, horses and various species of wildlife. The routes for the spread among wildlife are reviewed. There are three kinds of human anthrax – inhalation, cutaneous, and intestinal anthrax – which differ in their routes of infection and outcomes. In the United States, confirmation of cases is made by the isolation of B. anthracis and by biochemical tests. Vaccination is not recommended for the general public; civilians who should be vaccinated include those who, in their work places, come in contact with products potentially contaminated with B. anthracis spores, and people engaged in research or diagnostic activities. After September 11, 2001, there were bioterrorism anthrax attacks in the United States: anthrax-laced letters sent to multiple locations were the source of infectious B. anthracis. The US Postal Service issued recommendations to prevent the danger of hazardous exposure to the bacterium. B. anthracis spores can spread easily and persist for very long times, which makes decontamination of buildings very difficult. Early detection, rapid diagnosis, and well-coordinated public health response are the key to minimizing casualties. The US Government is seeking new ways to deter bioterrorism, including a tighter control of research on infectious agents, even though pathogens such as B. anthracis are widely spread in nature and easy to grow. It is necessary to define the boundary between defensive and offensive biological weapons research. Deterring bioterrorism should not restrict critical scientific research. Electronic Publication     

Can model species be used to advance the field of invasion ecology?

Hypotheses for explaining plant invasions have focused on a variety of factors that may influence invasion success, including propagule pressure, interactions of the introduced species with the biotic, abiotic, or disturbance properties of the new ecosystem, or the genetic characteristics of the invader itself. Evaluating the relative importance of these factors has been difficult because for most invaders key information about the introduced population or the introduction event is not available. We propose that natural experiments using model species is an important tool to test multiple invasion hypotheses at the same time, providing a complementary approach to meta-analysis and literature review. By focusing on a single candidate species, Pinus contorta, we explore several attributes that we propose constitute a good model, including: (a) intentional and relatively well documented introduction into a wide range of environments and countries across the world during the past century, where invasion success or failure has already occurred, (b) conspicuous growth form that simplifies assessment of growth rates, and comparisons across native and introduced ecosystems around the world, and, (c) documented and replicated variability of introduction intensity, genetic characteristics of the introduced populations, contrasting biotic communities present at sites of introduction, and abiotic conditions within and across introduced ecosystems. We propose that identifying model species with these characteristics will provide opportunities to disentangle the relative importance of different mechanisms hypothesized to influence invasion success, and thereby advance the field of invasion ecology.     

Influence of microbial activity on plant–microbial competition for organic and inorganic nitrogen

To investigate how the level of microbial activity in grassland soils affects plant–microbial competition for different nitrogen (N) forms, we established microcosms consisting of a natural soil community and a seedling of one of two co-existing grass species, Anthoxanthum odoratum or Festuca rubra. We then stimulated the soil microbial community with glucose in half of the microcosms and followed the transfer of added inorganic (¹⁵NH₄¹⁵NO₃) and organic (glycine-2-¹³C-¹⁵N) N into microbial and plant biomass. We found that microbes captured significantly more ¹⁵N in organic than in inorganic form and that glucose addition increased microbial ¹⁵N capture from the inorganic source. Shoot and root biomass, total shoot N content and shoot and root ¹⁵N contents were significantly greater for A. odoratum than F. rubra, whereas F. rubra had higher shoot and root N concentrations. Where glucose was not added, A. odoratum had higher shoot ¹⁵N content with organic than with inorganic ¹⁵N addition, whereas where glucose was added, both species had higher shoot ¹⁵N content with inorganic than with organic ¹⁵N. Glucose addition had equally negative effects on shoot growth, total shoot N content, shoot and root N concentrations and shoot and root ¹⁵N content for both species. Both N forms produced significantly more shoot biomass and higher shoot N content than the water control, but the chemical form of N had no significant effect. Our findings suggest that plant species that are better in capturing nutrients from soil are not necessarily better in tolerating increasing microbial competition for nutrients. It also appears that intense microbial competition has more adverse effects on the uptake of organic than inorganic N by plants, which may potentially have significant implications for interspecific plant–plant competition for N in ecosystems where the importance of organic N is high and some of the plant species specialize in use of organic N.     

A comparison of two methods for fitting the integrated Michaelis–Menten equation (Short Communication)

The methods of Atkins & Nimmo (1973) and Fernley (1974) for fitting the integrated Michaelis-Menten equation were compared by using the same sets of simulated experimental data. The method of Fernley (1974) is to be preferred because it gives precise and unbiased estimates of the Michaelis-Menten parameters over a wide range of substrate concentrations. However, the estimates may not be symmetrically distributed, especially at low substrate concentrations.     

Analysis of protein carbonylation — pitfalls and promise in commonly used methods

Abstract

Oxidation of proteins has received a lot of attention in the last decades due to the fact that they have been shown to accumulate and to be implicated in the progression and the pathophysiology of several diseases such as Alzheimer, coronary heart diseases, etc. This has also resulted in the fact that research scientists are becoming more eager to be able to measure accurately the level of oxidized protein in biological materials, and to determine the precise site of the oxidative attack on the protein, in order to get insights into the molecular mechanisms involved in the progression of diseases. Several methods for measuring protein carbonylation have been implemented in different laboratories around the world. However, to date no methods prevail as the most accurate, reliable, and robust. The present paper aims at giving an overview of the common methods used to determine protein carbonylation in biological material as well as to highlight the limitations and the potential. The ultimate goal is to give quick tips for a rapid decision making when a method has to be selected and taking into consideration the advantage and drawback of the methods.     

Microbial analysis of raw cows’ milk used for cheese-making: influence of storage treatments on microbial composition and other technological traits

Raw milk used to produce Grana cheese was subjected to several treatment regimes, including varying temperatures and storage times. Milk from morning and evening milking were transferred to a dairy factory separately (double delivery) or together (single delivery), after storage at the farm for 12 h; in the former case, milk was stored at 12 or 8°C, whereas, in the latter, it was kept at ambient temperature or 18°C. Values of pH of the vat milk were lower for milk samples kept at room temperature, while other physico-chemical parameters and rheological characteristics tested did not show significant differences linked to the different storage temperatures of milk used for “Grana Trentino” cheese production. Total microorganisms and several microbial groups (psychrotrophic bacteria, coliforms, mesophilic and termophilic lactic acid bacteria, including enterococci, pseudomonads and clostridia) were detected and quantified by classical (plate count and most probable number) techniques, after each technological treatment for a total of 212 milk and cream samples. The application of a culture-independent microbiological strategy, consisting of denaturing gradient gel electrophoresis, allowed the recognition of several bacterial genera and species.     

Estimates and comparisons of the effects of sampling variation using ‘national’ macroinvertebrate sampling protocols on the precision of metrics used to assess ecological status

The Water Framework Directive (WFD) of the European Union requires all member countries to provide information on the level of confidence and precision of results in their river monitoring programmes to assess the ecological status class of river sites. As part of the European Union project STAR, the overall effects of sampling variation for a wide range of commonly used metrics and sampling methods were assessed. Replicate samples were taken in each of two seasons at 2–6 sites of varying ecological status class within each of 18 stream types spread over 12 countries, using both the STAR-AQEM method and a national sampling method or, where unavailable, the RIVPACS sampling protocol. The sampling precision of a combination of sampling method and metric was estimated by expressing the replicate sampling variance as a percentage P_samp of the total variance in metric values with a stream type; low values of P_samp indicate high precision. Most metrics had percentage sampling variances less than 20% for all or most stream types and methods. Most national methods including RIVPACS had sampling precisions at least as good as those for the STAR-AQEM method as used in their country at the same sites; the main exceptions were the national methods used in Latvia and Sweden. The national methods used in the Czech Republic, Denmark, France, Poland and the RIVPACS method used in the UK and Austria all had percentage sampling variances of less than 10% for the majority of metrics assessed. In contrast, none of the metrics had percentage sampling variances less than 10% when based on either the Italian (IBE) method, which used bank-side sorting, or the Latvian national method which identifies only a limited set of taxa. P_samp was lowest on average for the two stream types sampled in the Czech Republic using either the PERLA national method or the STAR-AQEM method. Averaged over all stream types and methods, the three Saprobic-based metrics had the lowest average percentage sampling variances (3–6%) amongst the 26 metrics assessed. These estimates of sampling standard deviation can be used to help assess the uncertainty in single or multi-metric systems for estimating site ecological status using the general STAR Bioassessment Guidance Software (STARBUGS) developed within the STAR project.     

Coexistence of coral reef fishes — a lottery for living space

Synopsis Data are summarised from studies of two reef fish communities — pomacentrids territorial on rubble patches, and fishes resident in small isolated colonies of coral. In each case there is evidence that availability of living sites limits numbers of fishes, and that similar species of fish use the same kinds of spaces. Priority of arrival as recruits, rather than subtle differences in requirements or competitive abilities of adults, appears to determine which species holds each site. Faced with a limited and patchy supply of living space, most reef fishes are sedentary as adults, and produce frequent clutches of pelagic larvae over extended breeding seasons In this way they maximise their chances of getting offspring into suitable living sites as such sites appear. It is argued that by adopting this strategy, reef fishes are preadapted for forming inter-specific lotteries for living space if several species with similar requirements occur together. Such lotteries among similar species may be a feature common to many reef fish communities, and may explain the typically high within-site diversity found in them.This paper forms part of the proceedings of a mini-symposium convened at Cornell University, Ithaca, N.Y., 18–19 May 1976, entitled Patterns of Community Structure in Fishes (G. S. Helfman, ed.).     

Numerical Simulation of Plant–microbial Remediation for Petroleum-polluted Soil

This paper presents a numerical analysis of the migration and transformation mechanism of petroleum hydrocarbons (PHs) pollutants in soil. The mathematical model of the solute migration and plant–microbial remediation for PH polluted soil was established. The model was verified by field experimental data. Then, the software Hydrus-1D was employed to simulate the processes of diffusion, adsorption, desorption, microbial degradation, and plant adsorption of PHs in the soil–water system. The process of plant–microbial remediation for PH-contaminated soil was also simulated. The space-time change of PHs in soil was obtained, and the fate and remediation efficiency of PHs in soil were revealed in different remediation conditions. The results indicated that the Hydrus-1D model can adequately simulate the process of plant–microbial remediation. Plant–microbial remediation appears to be more efficient than the application of bacteria or Suaeda salsa. The majority of PH pollutants are degraded in the upper soil levels. For long-chain petro-alkane-contaminated soil, plant–microbial remediation is a more efficient method. A suitable moisture level in soil is important for improving the bioremediation effect of plant–microbial remediation technology.     

Influence of wastewater treatment on the microbial ecology of a large, temperate river system — the Danube River

In an attempt to assess the influence of tertiary-treated sewage influx on bacterial metabolism in the Danube River, bacterial abundance, ectoenzymatic activity, faecal coliforms, faecal streptococci, chlorophyll a (chl a), concentrations of dissolved (DOC) and total organic carbon (TOC) and inorganic nutrients were measured upstream of the sewage influx and compared with sampling sites downstream. Additional samples were taken near the outlet of the sewage treatment plant. Bacterial abundance as determined by epifluorescence microscopy was compared with plate counts of total heterotrophic bacteria. Significantly higher values were obtained at the stations downstream from the sewage influx only for faecal coliforms and faecal streptococci, for glucuronidase activity and bacterial biovolume. All the other parameters were not significantly different from values obtained at the upstream sampling site. Strong seasonal dependence was detectable for nitrate with high concentrations during the winter ( 250 µM) and low concentrations during summer ( 100 µM). A distinct spring phytoplankton bloom was noticeable in the river reaching chl a concentrations of 70 µg 1^–1; during the remaining seasons chl a concentrations were <20 µg 1^–1. Highly significant correlations were found between faecal coliform counts and glucuronidase activity. C:N:P ratios of 13.9:10.7:1 (for the upstream station) and 11.7:9.2:1 (for the downstream stations) of dissolved nutrients are rather low indicating severe carbon limitation of bacterioplankton. Based on our results we conclude that the heterotrophic bacterial community is not significantly effected by the input of treated sewage but faecal contamination is readily detectable over a comparatively long reach of 30 km.     

A comparison of mark–release–recapture methods for estimating colony size in the wood ant Formica lugubris

Colony size can be considered the analogue of the body size of a superorganism. Just as body size is important to the physiology of an individual animal, colony size correlates with the life-history and ecology of social insects. Although nest excavation and counting all individuals is the most accurate method for estimating colony size (or nest size), it has the major drawback of being destructive. Alternatively, mark–release–recapture (MRR) can be used repeatedly to measure the size of the same colony or nest. We compared the accuracy and feasibility of four MRR methods and a Mound-Volume method with complete counts from nest excavation for estimating the nest size of F. lugubris, a mound-building wood ant of the Formica rufa group, during the early spring in Scotland. We found that our After-Disturbing method, in which we performed marking and recapturing after gentle disturbance to the top of nest mound, has the best balance between accuracy, non-destructiveness, and time required. We also found that mound volume can be an index of ant nest size under certain conditions. Both non-destructive methods can be used on the same colony or nest repeatedly to monitor nest dynamics.     

Bias in vegetation databases? A comparison of stratified‐random and preferential sampling

Aim: Vegetation plots collected since the early 20th century and stored in large vegetation databases are an important source of ecological information. These databases are used for analyses of vegetation diversity and estimation of vegetation parameters, however such analyses can be biased due to preferential sampling of the original data. In contrast, modern vegetation survey increasingly uses stratified‐random instead of preferential sampling. To explore how these two sampling schemes affect vegetation analyses, we compare parameters of vegetation diversity based on preferentially sampled plots from a large vegetation database with those based on stratified‐random sampling. Location: Moravian Karst and Silesia, Czech Republic. Methods: We compared two parallel analyses of forest vegetation, one based on preferentially sampled plots taken from a national vegetation database and the other on plots sampled in the field according to a stratified‐random design. We repeated this comparison for two different regions in the Czech Republic. We focussed on vegetation properties commonly analysed using data from large vegetation databases, including alpha (within‐plot) diversity, cover and participation of different species groups, such as endangered and alien species within plots, total species richness of data sets, beta diversity and ordination patterns. Results: The preferentially sampled data sets obtained from the database contained more endangered species and had higher beta diversity, whereas estimates of alpha diversity and representation of alien species were not consistently different between preferentially and stratified‐randomly sampled data sets. In ordinations, plots from the preferential samples tended to be more common at margins of plot scatters. Conclusions: Vegetation data stored in large databases are influenced by researcher subjectivity in plot positioning, but we demonstrated that not all of their properties necessarily differ from data sets obtained by stratified‐random sampling. This indicates the value of vegetation databases for use in biodiversity studies; however, some analyses based on these databases are clearly biased and their results must be interpreted with caution.     

Efficiency of Plasmocin™ on various mammalian cell lines infected by mollicutes in comparison with commonly used antibiotics in cell culture: a local experience

Mycoplasma contamination is a deleterious event for cell culture laboratories. Plasmocin™ is used to prevent and eradicate mycoplasma infections from cell. In this study, 80 different mammalian cell lines from various sources; human, monkey, mice, hamster and rat were used to study and evaluate plasmocin™ efficiency and compare it to commonly used antibiotics such as BM-cyclin, ciprofloxacin and mycoplasma removal agent (MRA). It was shown that mycoplasma infections were eradicated by plasmocin™, BM-cyclin, ciprofloxacin and MRA in 65%, 66.25%, 20%, and 31.25%, respectively, of infected cell cultures. However, re-infection with mycoplasmas after the period of 4 months occurred in 10–80% of the studied cell lines. Cell cytotoxicity and culture death was observed in 25, 17.5 and 10% of the treated cells, for plasmocin™, BM-cyclin and MRA, respectively. In this study, Plasmocin™ showed strong ability to eradicate mollicutes from our cell lines with minimal percentage of regrowth. However, due to its high cell cytotoxicity it should be used with caution especially when dealing with expensive or hard-to-obtain cell lines. Amongst the antibiotics tested, BM-cyclin was shown to remove mycoplasma with the highest efficiency.     

Development,validation and comparison of LC–MS/MS and RIA methods for quantification of vertebrates-like sex-steroids in prosobranch molluscs

The role of vertebrate-like sex-steroids (testosterone, T, progesterone, P, and 17β-estradiol, E2) in molluscs is still debated, but they could represent potential biomarkers of endocrine disruption. A radioimmunoassay (RIA) and a liquid chromatography coupled to tandem mass spectrometry (LC–MS/MS) methods have been developed and compared to measure their levels in a gastropod snail Potamopyrgus antipodarum. Both methods showed a good reproducibility despite the complex matrix and the very low levels of vertebrate-like sex-steroids. Only T and P were detected using the LC–MS/MS method, while the RIA method reached lower detection limits and enabled the detection of all three steroids. Results indicated that T and P were mainly present as unconjugated forms. Both methods were compared in the analysis of snails exposed to waste water treatment plant effluents and led to the same conclusions concerning the modulation of steroids levels. Moreover, they both were in agreement concerning T measurements. On the other hand, LC–MS/MS appeared to be more suitable when analyzing P levels due to a low sensitivity of the RIA method. As E2 was not measured using the LC–MS/MS method because of a higher detection limit compared to the other steroids, the results obtained with the RIA method should be interpreted with caution. LC–MS/MS remains the gold standard for sex-steroid determinations, however a relevant and alternative method based on RIA was developed, requiring fewer organisms. RIA seems a promising method as a screening tool for experimental use, allowing comparison of sex-steroid levels in the mudsnail both in laboratory and in field experiments.     

Standardisation of data from real-time quantitative PCR methods – evaluation of outliers and comparison of calibration curves

Background  

As real-time quantitative PCR (RT-QPCR) is increasingly being relied upon for the enforcement of legislation and regulations dependent upon the trace detection of DNA, focus has increased on the quality issues related to the technique. Recent work has focused on the identification of factors that contribute towards significant measurement uncertainty in the real-time quantitative PCR technique, through investigation of the experimental design and operating procedure. However, measurement uncertainty contributions made during the data analysis procedure have not been studied in detail. This paper presents two additional approaches for standardising data analysis through the novel application of statistical methods to RT-QPCR, in order to minimise potential uncertainty in results.     

Commonly used methods for extracellular vesicles’ enrichment: Implications in downstream analyses and use

Extracellular vesicles (EVs) are becoming promising tools for clinical application, either as sources of disease-specific molecular signatures for the unraveling of disease pathophysiology and establishment of novel biomarkers, or as platforms for cell-free nanotherapy. Yet, an unsolved issue is to define standardized techniques for EV isolation allowing data comparison across laboratories worldwide. Considering the difficulties to find this necessary consensus, it has to be stressed out that the outcome of the downstream analysis might be deeply biased by the isolation method, among other variables. Thus, it is crucial that the researcher is aware of the strengths and weaknesses of each method keeping their intended use in mind, and to sufficiently report the methodology details for the results to be comparable and solid. This review aims to present the most widely used EV isolation methods, from the initial differential ultracentrifugation (dUC) to newest approaches.