The helminth fauna of amphibians of open canals in meliorated regions of the Belorussian Poles'e

The helminth fauna from amphibians inhabiting open channels of different meliorated territories of the Belorussian Polesie was investigated in 1986-2000. 31 species of helminthes were found in these animals. Total infection rate with helminthes is 89.1%. A role of amphibians in a formation of natural foci of helminthoses of medical and veterinary importance is discussed.     

Epidemiological analyses on animal parasitoses: recent activity of the I.M.I.P.P.V

The paper presents a selected review of the epidemiological analyses performed in recent years (1984-1988) in the Institute of Malattie Infettive, Profilassi e Polizia Veterinaria of the University of Bologna on animal parasitoses, with special reference to the evaluation of some risk factors of bovine, swine and canine helminthoses, and to the validity of the coprological test for some parasites of the red fox.     

Cloning and characterization of RAPD markers of parasitic nematodesTrichinella spiralis andT. pseudospiralis

A RAPD analysis was carried out in parasitic nematodesTrichinella spiralis andT. pseudospiralis, which are among the most common and hazardous agents in human and animal helminthoses. Several RAPD fragments were cloned and some of them sequenced. The fragments were shown to correspond to unique or low-repetitive sequences and to contain ORFs, microsatellites, and regions homologous to various pro- and eukaryotic sequences. Several fragments can be used to distinguish betweenT. spiralis andT. pseudospiralis.     

Nonspecific immunomodulation influences resistance of mice to experimental infection with Mesocestoides corti and Ascaris suum

The influence of nonspecific immunomodulation on the course of experimental infection was examined in larval cestodosis (Mesocestoides corti) and ascaridosis (Ascaris suum) in mice. Immunosuppressive treatment (with azathioprine or hydrocortisone) resulted in a decrease of resistance in both models. The subsequent administration of T-activin to immunosuppressed mice led to the restoration of resistance to a level equal to that of untreated control mice. The administration of different immunomodulators partially protected mice against M. corti (T-activin, thymomodulin) or A. suum (T-activin, thymomodulin, thymosin fr.5, bursa-activin) infection. The protective effect of different treatments did not correlate with the level of specific antibody in the sera of infected mice. These results, which confirmed the decisive role of T-cell immunity in the resistance to the helminth infections, raise the possibility of the use of immunomodulators (thymic preparations) in the immunoprophylaxis of helminthoses.     

A comparison of three methods to assess land use impacts on biodiversity in a case study of forestry plantations in New Zealand

Purpose

The aim of this study is apply available methods to assess impacts on biodiversity from the land use caused by plantation grown radiata pine in New Zealand in a life cycle assessment framework. This is done both to quantify the impact as well as compare the results obtained by different methods.

Methods

Data on location and productivity for wood supply regions in New Zealand was assessed using three methods identified as relevant for the purpose. All data were related to a functional unit of 1 m³ of timber production.

Results and discussion

The results show both a significant difference in impact on biodiversity from land use in the different wood supply regions and a significant difference in the results from the three applied methods. Although some of the results obtained from the three methods were correlated, this was not consistent through all the results. The methodological variation emanates from the treatment of the characteristics of the wood supply regions and underlying assumptions, e.g. reference vegetation. Compared to a case study in Norway, the impact on biodiversity from plantation forestry in New Zealand is found to be relatively low following the applied methods and assumptions taken.

Conclusions

The study shows a significant variation in how impacts on biodiversity are assessed following different approaches. Research to harmonize methods to quantify impact on biodiversity is recommended, as well as exploring effects of different weighting of crucial aspects of biodiversity, such as rarity, abundance and species richness.     

Effects of Different Missing Data Imputation Techniques on the Performance of Undiagnosed Diabetes Risk Prediction Models in a Mixed-Ancestry Population of South Africa

Background

Imputation techniques used to handle missing data are based on the principle of replacement. It is widely advocated that multiple imputation is superior to other imputation methods, however studies have suggested that simple methods for filling missing data can be just as accurate as complex methods. The objective of this study was to implement a number of simple and more complex imputation methods, and assess the effect of these techniques on the performance of undiagnosed diabetes risk prediction models during external validation.

Methods

Data from the Cape Town Bellville-South cohort served as the basis for this study. Imputation methods and models were identified via recent systematic reviews. Models’ discrimination was assessed and compared using C-statistic and non-parametric methods, before and after recalibration through simple intercept adjustment.

Results

The study sample consisted of 1256 individuals, of whom 173 were excluded due to previously diagnosed diabetes. Of the final 1083 individuals, 329 (30.4%) had missing data. Family history had the highest proportion of missing data (25%). Imputation of the outcome, undiagnosed diabetes, was highest in stochastic regression imputation (163 individuals). Overall, deletion resulted in the lowest model performances while simple imputation yielded the highest C-statistic for the Cambridge Diabetes Risk model, Kuwaiti Risk model, Omani Diabetes Risk model and Rotterdam Predictive model. Multiple imputation only yielded the highest C-statistic for the Rotterdam Predictive model, which were matched by simpler imputation methods.

Conclusions

Deletion was confirmed as a poor technique for handling missing data. However, despite the emphasized disadvantages of simpler imputation methods, this study showed that implementing these methods results in similar predictive utility for undiagnosed diabetes when compared to multiple imputation.     

Critical evaluation of random mutagenesis by error-prone polymerase chain reaction protocols, Escherichia coli mutator strain, and hydroxylamine treatment

Random mutagenesis methods constitute a valuable protein modification toolbox with applications ranging from protein engineering to directed protein evolution studies. Although a variety of techniques are currently available, the field is lacking studies that would directly compare the performance parameters and operational range of different methods. In this study, we have scrutinized several of the most commonly used random mutagenesis techniques by critically evaluating popular error-prone polymerase chain reaction (PCR) protocols as well as hydroxylamine and a mutator Escherichia coli strain mutagenesis methods. Relative mutation frequencies were analyzed using a reporter plasmid that allowed direct comparison of the methods. Error-prone PCR methods yielded the highest mutation rates and the widest operational ranges, whereas the chemical and biological methods generated a low level of mutations and exhibited a narrow range of operation. The repertoire of transitions versus transversions varied among the methods, suggesting the use of a combination of methods for high-diversity full-scale mutagenesis. Using the parameters defined in this study, the evaluated mutagenesis methods can be used for controlled mutagenesis, where the intended average frequency of induced mutations can be adjusted to a desirable level.     

A systematic study of genome context methods: calibration,normalization and combination

Background  

Genome context methods have been introduced in the last decade as automatic methods to predict functional relatedness between genes in a target genome using the patterns of existence and relative locations of the homologs of those genes in a set of reference genomes. Much work has been done in the application of these methods to different bioinformatics tasks, but few papers present a systematic study of the methods and their combination necessary for their optimal use.     

Comparison of Two New Robust Parameter Estimation Methods for the Power Function Distribution

Estimation of any probability distribution parameters is vital because imprecise and biased estimates can be misleading. In this study, we investigate a flexible power function distribution and introduced new two methods such as, probability weighted moments, and generalized probability weighted methods for its parameters. We compare their results with L-moments, trimmed L-moments by a simulation study and a real data example based on performance measures such as, mean square error and total deviation. We concluded that all the methods perform well in the case of large sample size (n>30), however, the generalized probability weighted moment method performs better for small sample size.     

Evolution of Toxoplasma-PCR methods and practices: a French national survey and proposal for technical guidelines

The molecular diagnosis of toxoplasmosis lacks standardisation due to the use of numerous methods with variable performance. This diversity of methods also impairs robust performance comparisons between laboratories. The harmonisation of practices by diffusion of technical guidelines is a useful way to improve these performances. The knowledge of methods and practices used for this molecular diagnosis is an essential step to provide guidelines for Toxoplasma-PCR. In the present study, we aimed (i) to describe the methods and practices of Toxoplasma-PCR used by clinical microbiology laboratories in France and (ii) to propose technical guidelines to improve molecular diagnosis of toxoplasmosis. To do so, a yearly self-administered questionnaire-based survey was undertaken in proficient French laboratories from 2008 to 2015, and guidelines were proposed based on the results of those as well as previously published work. This period saw the progressive abandonment of conventional PCR methods, of Toxoplasma-PCR targeting the B1 gene and of the use of two concomitant molecular methods for this diagnosis. The diversity of practices persisted during the study, in spite of the increasing use of commercial kits such as PCR kits, DNA extraction controls and PCR inhibition controls. We also observed a tendency towards the automation of DNA extraction. The evolution of practices did not always go together with an improvement in those, as reported notably by the declining use of Uracil-DNA Glycosylase to avoid carry-over contamination. We here propose technical recommendations which correspond to items explored during the survey, with respect to DNA extraction, Toxoplasma-PCR and good PCR practices.     

A Comparison of Statistical Methods for Identifying Out-of-Date Systematic Reviews

Background

Systematic reviews (SRs) can provide accurate and reliable evidence, typically about the effectiveness of health interventions. Evidence is dynamic, and if SRs are out-of-date this information may not be useful; it may even be harmful. This study aimed to compare five statistical methods to identify out-of-date SRs.

Methods

A retrospective cohort of SRs registered in the Cochrane Pregnancy and Childbirth Group (CPCG), published between 2008 and 2010, were considered for inclusion. For each eligible CPCG review, data were extracted and “3-years previous” meta-analyses were assessed for the need to update, given the data from the most recent 3 years. Each of the five statistical methods was used, with random effects analyses throughout the study.

Results

Eighty reviews were included in this study; most were in the area of induction of labour. The numbers of reviews identified as being out-of-date using the Ottawa, recursive cumulative meta-analysis (CMA), and Barrowman methods were 34, 7, and 7 respectively. No reviews were identified as being out-of-date using the simulation-based power method, or the CMA for sufficiency and stability method. The overall agreement among the three discriminating statistical methods was slight (Kappa = 0.14; 95% CI 0.05 to 0.23). The recursive cumulative meta-analysis, Ottawa, and Barrowman methods were practical according to the study criteria.

Conclusion

Our study shows that three practical statistical methods could be applied to examine the need to update SRs.     

Strategies for the Genetic Manipulation of Saccharomyces cerevisiae

Abstract

The budding yeast Saccharomyces cerevisiae is now widely used as a model organism in the study of gene structure, function, and regulation in addition to its more traditional use as a workhorse of the brewing and baking industries. In this article the plethora of methods available for manipulating the genome of S. cerevisiae are reviewed. This will include a discussion of methods for manipulating individual genes and whole chromosomes, and will address both classic genetic and recombinant DNA-based methods. Furthermore, a critical evaluation of the various genetic strategies for genetically manipulating this simple eukaryote will be included, highlighting the requirements of both the new and the more traditional biotechnology industries.     

Development of free and opensource GIS software for cartographic generalisation and occupancy area calculations

The International Union for Conservation of Nature (IUCN) considers that a decrease in the area of occupancy (AOO) is a critical criterion for listing a species as rare, endemic or threatened. However, methods for the accurate measurement of changes in the area of occupancy are relatively limited, and existing methods are influenced by spatial scale and sampling methods. To overcome such cartographic problems, different cartographic methods were proposed in this study and implemented in a free and open source GIS library. A single species (Helianthemum caput-felis Boiss.), which is distributed in many countries of the western Mediterranean, was used as a case study. This plant is threatened and protected because its preferred habitat is near the sea where urban growth is high in the Mediterranean regions. Intensive field work was initially conducted to create a geodatabase with more than 13,000 GPS points. Cartographic methods were then applied to the geodatabase to obtain AOO measurements at different scales to support sustainable urban planning. Based on positive experiences with the use of the programming library, it is believed that these open source tools can be customised and extended to other similar biogeographic studies that require data analysis at different scales.     

光合细菌的分离、保存及其同化磷能力试验研究

为了研究光合细菌的保藏方法及其同化磷能力,采用液体种室内自然放置、液体种蜡封和穿刺物蜡封等方法对光合细菌进行保藏方法研究,结果表明,液体种蜡封和穿刺物蜡封可作为该菌种的长期保存方法;对两株菌的磷同化能力进行了比较,降解率分别为22%和15%。本研究为获得光合细菌的长期保存方法及其在污水净化中的应用提供参考。     

Evaluation of PCR-based methods for isolating flanking regions of genes

Several polymerase chain reaction (PCR)-based methods are available for isolation of unknown genomic fragments. In the present study, a comparative evaluation of a few methods of ligation-mediated PCR methods and a ligation-independent one were made by isolating promoter fragment for N-methyltransferase gene involved in the caffeine biosynthetic pathway of Coffea canephora. The benefits of tertiary PCR and the effects of a 4-base cutting restriction endonuclease on the size of the PCR products obtained were demonstrated in one of the ligation-mediated PCR methods. The methods adopted in this study differed in the sizes of the 5'-flanking regions obtained. The efficiencies of various methods used reflect the inherent limitations of the PCR-based methods for isolation of unknown flanking regions.     

Predicting efficiency of different chemical extraction methods in risk assessment of trace metals in sediment of the Persian Gulf

Different chemical methods have been developed to evaluate the bioavailable fraction of the trace metals. Due to the lack of a universal method for analysis of the bioavailable metal fractions, due to the differences in sediment characteristics, it is necessary to validate an appropriate chemical method for assessing the available fraction of trace metals. For this propose, in this study, different chemical extraction methods including extraction with HCl and desorption test as a single reagent leaching test as well as geochemical fractions method have been evaluated. Bushehr coastal sediments in the Persian Gulf coasts have been selected for this purpose. To validate the efficacy of these methods, a gastropod species (Trochus erithreus), as a bioindicator, has been selected and monitored for trace metals of Fe²⁺, Pb²⁺, Cu²⁺, Zn²⁺, Mn²⁺, and Ni²⁺. According to the one-way ANOVA results, all partial extraction methods for all the trace metals (except for Mn²⁺) showed no significant variation, but linear correlation coefficients were between the results of the selective chemical extraction methods and concentrations of trace metals in organism tissues. It offered that selective extraction with HCl can be used as a simple method for measuring the bioavailable fraction of the metals in the sediments.     

A guide for kernel generalized regression methods for genomic-enabled prediction

The primary objective of this paper is to provide a guide on implementing Bayesian generalized kernel regression methods for genomic prediction in the statistical software R. Such methods are quite efficient for capturing complex non-linear patterns that conventional linear regression models cannot. Furthermore, these methods are also powerful for leveraging environmental covariates, such as genotype × environment (G×E) prediction, among others. In this study we provide the building process of seven kernel methods: linear, polynomial, sigmoid, Gaussian, Exponential, Arc-cosine 1 and Arc-cosine L. Additionally, we highlight illustrative examples for implementing exact kernel methods for genomic prediction under a single-environment, a multi-environment and multi-trait framework, as well as for the implementation of sparse kernel methods under a multi-environment framework. These examples are followed by a discussion on the strengths and limitations of kernel methods and, subsequently by conclusions about the main contributions of this paper.Subject terms: Genomics, Plant sciences     

Comparison of methods for the analysis of therapeutic immunoglobulin G Fc-glycosylation profiles—Part 1: Separation-based methods

Immunoglobulin G (IgG) crystallizable fragment (Fc) glycosylation is crucial for antibody effector functions, such as antibody-dependent cell-mediated cytotoxicity, and for their pharmacokinetic and pharmacodynamics behavior. To monitor the Fc-glycosylation in bioprocess development, as well as product characterization and release analytics, reliable techniques for glycosylation analysis are needed. A wide range of analytical methods has found its way into these applications. In this study, a comprehensive comparison was performed of separation-based methods for Fc-glycosylation profiling of an IgG biopharmaceutical. A therapeutic antibody reference material was analyzed 6-fold on 2 different days, and the methods were compared for precision, accuracy, throughput and other features; special emphasis was placed on the detection of sialic acid-containing glycans. Seven, non-mass spectrometric methods were compared; the methods utilized liquid chromatography-based separation of fluorescent-labeled glycans, capillary electrophoresis-based separation of fluorescent-labeled glycans, or high-performance anion exchange chromatography with pulsed amperometric detection. Hydrophilic interaction liquid chromatography-ultra high performance liquid chromatography of 2-aminobenzamide (2-AB)-labeled glycans was used as a reference method. All of the methods showed excellent precision and accuracy; some differences were observed, particularly with regard to the detection and quantitation of minor glycan species, such as sialylated glycans.     

A comparison of methods for estimating plant population size

Assessing local population size is one of the most common tasks in biodiversity monitoring. Population size estimates are not only important for conservation management and population threat assessment; they also enter many other analyses in landscape ecology and conservation. It is therefore concerning that methods for estimating plant population sizes are not standardized. We surveyed the literature and found that the most commonly used methods are counting either all or only flowering individuals on a site, as well as counting individuals in random plots or plots on transects. Sometimes, these methods are combined in the same study, without assurance that they produce comparable results. We therefore conducted a field study, in which we obtained population size estimates from all four methods for six different calcareous grassland species at 18 study sites. Our results demonstrate not only substantial differences between overall count rates generated by the different methods, but methods that surveyed the whole population also systematically yielded lower counts when species were less visible and when the area was larger, suggesting that these methods suffer from biases that could distort species and site comparisons. We conclude that estimates from different methods should not be mixed, and that plot or transect based surveys have likely smaller biases for large areas or poorly visible individuals, and are therefore preferable.