Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain

Cell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.

Training on the use of a bespoke continuing professional development framework improves the quality of CPD records

BACKGROUND: Using continuing professional development (CPD) as part of the revalidation of pharmacy professionals has been proposed in the UK but not implemented. We developed a CPD Outcomes Framework (‘the framework’) for scoring CPD records, where the score range was -100 to +150 based on demonstrable relevance and impact of the CPD on practice. OBJECTIVE: This exploratory study aimed to test the outcome of training people to use the framework, through distance-learning material (active intervention), by comparing CPD scores before and after training. SETTING: Pharmacy professionals were recruited in the UK in Reading, Banbury, Southampton, Kingston-upon-Thames and Guildford in 2009. METHOD: We conducted a randomised, double-blinded, parallel-group, before and after study. The control group simply received information on new CPD requirements through the post; the active intervention group also received the framework and associated training. Altogether 48 participants (25 control, 23 active) completed the study. All participants submitted CPD records to the research team before and after receiving the posted resources. The records (n=226) were scored blindly by the researchers using the framework. A subgroup of CPD records (n=96) submitted first (before-stage) and rewritten (after-stage) were analysed separately. MAIN OUTCOME MEASURE: Scores for CPD records received before and after distributing group-dependent material through the post. RESULTS: Using a linear-regression model both analyses found an increase in CPD scores in favour of the active intervention group. For the complete set of records, the effect was a mean difference of 9.9 (95% CI = 0.4 to 19.3), p-value = 0.04. For the subgroup of rewritten records, the effect was a mean difference of 17.3 (95% CI = 5.6 to 28.9), p-value = 0.0048. CONCLUSION: The intervention improved participants’ CPD behaviour. Training pharmacy professionals to use the framework resulted in better CPD activities and CPD records, potentially helpful for revalidation of pharmacy professionals. IMPACT: • Using a bespoke Continuing Professional Development outcomes framework improves the value of pharmacy professionals’ CPD activities and CPD records, with the potential to improve patient care. • The CPD outcomes framework could be helpful to pharmacy professionals internationally who want to improve the quality of their CPD activities and CPD records. • Regulators and officials across Europe and beyond can assess the suitability of the CPD outcomes framework for use in pharmacy CPD and revalidation in their own setting.

Regulation of the ERK subgroup of MAP kinase cascades through G protein-coupled receptors.

The extracellularly-responsive kinase (ERK) subfamily of mitogen-activated protein kinases (MAPKs) has been implicated in the regulation of cell growth and differentiation. Activation of ERKs involves a two-step protein kinase cascade lying upstream from ERK, in which the Raf family are the MAPK kinase kinases and the MEK1/MEK2 isoforms are the MAPK kinases. The linear sequence of Raf --> MEK --> ERK constitutes the ERK cascade. Although the ERK cascade is activated through growth factor-regulated receptor protein tyrosine kinases, they are also modulated through G protein-coupled receptors (GPCRs). All four G protein subfamilies (Gq/11 Gi/o, Gs and G12/13) influence the activation state of ERKs. In this review, we describe the ERK cascade and characteristics of its activation through GPCRs. We also discuss the identity of the intervening steps that may couple agonist binding at GPCRs to activation of the ERK cascade.

Higher PUFA and omega-3 PUFA, CLA, α-tocopherol and iron, but lower iodine and selenium concentrations in organic milk: a systematic literature review and meta- and redundancy analyses

Demand for organic milk is partially driven by consumer perceptions that it is more nutritious. However, there is still considerable uncertainty over whether the use of organic production standards affects milk quality. Here we report results of meta-analyses based on 170 published studies comparing the nutrient content of organic and conventional bovine milk. There were no significant differences in total SFA and MUFA concentrations between organic and conventional milk. However, concentrations of total PUFA and n-3 PUFA were significantly higher in organic milk, by an estimated 7 (95 % CI −1, 15) % and 56 (95 % CI 38, 74) %, respectively. Concentrations of α-linolenic acid (ALA), very long-chain n-3 fatty acids (EPA+DPA+DHA) and conjugated linoleic acid were also significantly higher in organic milk, by an 69 (95 % CI 53, 84) %, 57 (95 % CI 27, 87) % and 41 (95 % CI 14, 68) %, respectively. As there were no significant differences in total n-6 PUFA and linoleic acid (LA) concentrations, the n-6:n-3 and LA:ALA ratios were lower in organic milk, by an estimated 71 (95 % CI −122, −20) % and 93 (95 % CI −116, −70) %. It is concluded that organic bovine milk has a more desirable fatty acid composition than conventional milk. Meta-analyses also showed that organic milk has significantly higher α-tocopherol and Fe, but lower I and Se concentrations. Redundancy analysis of data from a large cross-European milk quality survey indicates that the higher grazing/conserved forage intakes in organic systems were the main reason for milk composition differences.

Biases in comparative analyses of extinction risk: mind the gap

1. Comparative analyses are used to address the key question of what makes a species more prone to extinction by exploring the links between vulnerability and intrinsic species’ traits and/or extrinsic factors. This approach requires comprehensive species data but information is rarely available for all species of interest. As a result comparative analyses often rely on subsets of relatively few species that are assumed to be representative samples of the overall studied group. 2. Our study challenges this assumption and quantifies the taxonomic, spatial, and data type biases associated with the quantity of data available for 5415 mammalian species using the freely available life-history database PanTHERIA. 3. Moreover, we explore how existing biases influence results of comparative analyses of extinction risk by using subsets of data that attempt to correct for detected biases. In particular, we focus on links between four species’ traits commonly linked to vulnerability (distribution range area, adult body mass, population density and gestation length) and conduct univariate and multivariate analyses to understand how biases affect model predictions. 4. Our results show important biases in data availability with c.22% of mammals completely lacking data. Missing data, which appear to be not missing at random, occur frequently in all traits (14–99% of cases missing). Data availability is explained by intrinsic traits, with larger mammals occupying bigger range areas being the best studied. Importantly, we find that existing biases affect the results of comparative analyses by overestimating the risk of extinction and changing which traits are identified as important predictors. 5. Our results raise concerns over our ability to draw general conclusions regarding what makes a species more prone to extinction. Missing data represent a prevalent problem in comparative analyses, and unfortunately, because data are not missing at random, conventional approaches to fill data gaps, are not valid or present important challenges. These results show the importance of making appropriate inferences from comparative analyses by focusing on the subset of species for which data are available. Ultimately, addressing the data bias problem requires greater investment in data collection and dissemination, as well as the development of methodological approaches to effectively correct existing biases.

Interim analyses and sequential designs in phase III studies

Recruitment of patients to a clinical trial usually occurs over a period of time, resulting in the steady accumulation of data throughout the trial's duration. Yet, according to traditional statistical methods, the sample size of the trial should be determined in advance, and data collected on all subjects before analysis proceeds. For ethical and economic reasons, the technique of sequential testing has been developed to enable the examination of data at a series of interim analyses. The aim is to stop recruitment to the study as soon as there is sufficient evidence to reach a firm conclusion. In this paper we present the advantages and disadvantages of conducting interim analyses in phase III clinical trials, together with the key steps to enable the successful implementation of sequential methods in this setting. Examples are given of completed trials, which have been carried out sequentially, and references to relevant literature and software are provided.

Steric sea level variability (1993-2010) in an ensemble of ocean reanalyses and objective analyses

Quantifying the effect of the seawater density changes on sea level variability is of crucial importance for climate change studies, as the sea level cumulative rise can be regarded as both an important climate change indicator and a possible danger for human activities in coastal areas. In this work, as part of the Ocean Reanalysis Intercomparison Project, the global and regional steric sea level changes are estimated and compared from an ensemble of 16 ocean reanalyses and 4 objective analyses. These estimates are initially compared with a satellite-derived (altimetry minus gravimetry) dataset for a short period (2003–2010). The ensemble mean exhibits a significant high correlation at both global and regional scale, and the ensemble of ocean reanalyses outperforms that of objective analyses, in particular in the Southern Ocean. The reanalysis ensemble mean thus represents a valuable tool for further analyses, although large uncertainties remain for the inter-annual trends. Within the extended intercomparison period that spans the altimetry era (1993–2010), we find that the ensemble of reanalyses and objective analyses are in good agreement, and both detect a trend of the global steric sea level of 1.0 and 1.1 ± 0.05 mm/year, respectively. However, the spread among the products of the halosteric component trend exceeds the mean trend itself, questioning the reliability of its estimate. This is related to the scarcity of salinity observations before the Argo era. Furthermore, the impact of deep ocean layers is non-negligible on the steric sea level variability (22 and 12 % for the layers below 700 and 1500 m of depth, respectively), although the small deep ocean trends are not significant with respect to the products spread.

Genetic diversity at the Dhn3 locus in Turkish Hordeum spontaneum populations with comparative structural analyses

We analysed Hordeum spontaneum accessions from 21 different locations to understand the genetic diversity of HsDhn3 alleles and effects of single base mutations on the intrinsically disordered structure of the resulting polypeptide (HsDHN3). HsDHN3 was found to be YSK2-type with a low-frequency 6-aa deletion in the beginning of Exon 1. There is relatively high diversity in the intron region of HsDhn3 compared to the two exon regions. We have found subtle differences in K segments led to changes in amino acids chemical properties. Predictions for protein interaction profiles suggest the presence of a protein-binding site in HsDHN3 that coincides with the K1 segment. Comparison of DHN3 to closely related cereals showed that all of them contain a nuclear localization signal sequence flanking to the K1 segment and a novel conserved region located between the S and K1 segments [E(D/T)DGMGGR]. We found that H. vulgare, H. spontaneum, and Triticum urartu DHN3s have a greater number of phosphorylation sites for protein kinase C than other cereal species, which may be related to stress adaptation. Our results show that the nature and extent of mutations in the conserved segments of K1 and K2 are likely to be key factors in protection of cells.

abctools: an R package for tuning approximate Bayesian computation analyses

Approximate Bayesian computation (ABC) is a popular family of algorithms which perform approximate parameter inference when numerical evaluation of the likelihood function is not possible but data can be simulated from the model. They return a sample of parameter values which produce simulations close to the observed dataset. A standard approach is to reduce the simulated and observed datasets to vectors of summary statistics and accept when the difference between these is below a specified threshold. ABC can also be adapted to perform model choice. In this article, we present a new software package for R, abctools which provides methods for tuning ABC algorithms. This includes recent dimension reduction algorithms to tune the choice of summary statistics, and coverage methods to tune the choice of threshold. We provide several illustrations of these routines on applications taken from the ABC literature.

A regionally informed abundance index for supporting integrative analyses across butterfly monitoring schemes

1. The rapid expansion of systematic monitoring schemes necessitates robust methods to reliably assess species' status and trends. Insect monitoring poses a challenge where there are strong seasonal patterns, requiring repeated counts to reliably assess abundance. Butterfly monitoring schemes (BMSs) operate in an increasing number of countries with broadly the same methodology, yet they differ in their observation frequency and in the methods used to compute annual abundance indices. 2. Using simulated and observed data, we performed an extensive comparison of two approaches used to derive abundance indices from count data collected via BMS, under a range of sampling frequencies. Linear interpolation is most commonly used to estimate abundance indices from seasonal count series. A second method, hereafter the regional generalized additive model (GAM), fits a GAM to repeated counts within sites across a climatic region. For the two methods, we estimated bias in abundance indices and the statistical power for detecting trends, given different proportions of missing counts. We also compared the accuracy of trend estimates using systematically degraded observed counts of the Gatekeeper Pyronia tithonus (Linnaeus 1767). 3. The regional GAM method generally outperforms the linear interpolation method. When the proportion of missing counts increased beyond 50%, indices derived via the linear interpolation method showed substantially higher estimation error as well as clear biases, in comparison to the regional GAM method. The regional GAM method also showed higher power to detect trends when the proportion of missing counts was substantial. 4. Synthesis and applications. Monitoring offers invaluable data to support conservation policy and management, but requires robust analysis approaches and guidance for new and expanding schemes. Based on our findings, we recommend the regional generalized additive model approach when conducting integrative analyses across schemes, or when analysing scheme data with reduced sampling efforts. This method enables existing schemes to be expanded or new schemes to be developed with reduced within-year sampling frequency, as well as affording options to adapt protocols to more efficiently assess species status and trends across large geographical scales.

Influence of implant positioning in extraction sockets on osseointegration: histomorphometric analyses in dogs

Aim To evaluate the influence of implant positioning into extraction sockets on osseointegration. Material and methods Implants were installed immediately into extraction sockets in the mandibles of six Labrador dogs. In the control sites, the implants were positioned in the center of the alveolus, while in the test sites, the implants were positioned 0.8 mm deeper and more lingually. After 4 months of healing, the resorptive patterns of the alveolar crest were evaluated histomorphometrically. Results All implants were integrated in mineralized bone, mainly composed of mature lamellar bone. The alveolar crest underwent resorption at the control as well as at the test sites. After 4 months of healing, at the buccal aspects of the control and test sites, the location of the implant rough/smooth limit to the alveolar crest was 2 +/- 0.9 mm and 0.6 +/- 0.9 mm, respectively (P < 0.05). At the lingual aspect, the bony crest was located 0.4 mm apically and 0.2 mm coronally to the implant rough/smooth limit at the control and test sites, respectively (NS). Conclusions From a clinical point of view, implants installed into extraction sockets should be positioned approximately 1 mm deeper than the level of the buccal alveolar crest and in a lingual position in relation to the center of the alveolus in order to reduce or eliminate the exposure above the alveolar crest of the endosseous (rough) portion of the implant. To cite this article:Caneva M, Salata LA, de Souza SS, Baffone G, Lang NP, Botticelli D. Influence of implant positioning in extraction sockets on osseointegration: histomorphometric analyses in dogs.Clin. Oral Impl. Res. 21, 2010; 43-49.

Phylogenetic relationships among species of Anopheles (Nyssorhynchus) (Diptera, Culicidae) based on nuclear and mitochondrial gene sequences

Phylogenetic relationships among 21 species of mosquitoes in subgenus Nyssorhynchus were inferred from the nuclear white and mitochondrial NADH dehydrogenase subunit 6 (ND6) genes. Bayestan phylogenetic methods found that none of the three Sections within Nyssorhynchus (Albimanus, Argyritarsis, Myzorhynchella) were supported in all analyses, although Myzorhynchella was found to be monophyletic at the combined genes Within the Albimanus Section the monophyly of the Stroder Subgroup was strongly supported and within the Myzorhynchella Section Anopheles anrunesi and An lutzu formed a strongly supported monophyletic group The epidemiologically significant Albitarsis Complex showed evidence of paraphyly (relative to An lanet-Myzorhynchella) and discordance across gene trees, and the previously synonomized species of An. dunhami and An goeldii were recovered as sister species Finally, there was evidence of complexes in several species, including An antunesi, An deaneorum, and An. strodei (c) 2010 Elsevier B.V. All rights reserved

Detection of a New Yellow Fever Virus Lineage Within the South American Genotype I in Brazil

Nucleotide sequences of two regions of the genomes of 11 yellow fever virus (YFV) samples isolated from monkeys or humans with symptomatic yellow fever (YF) in Brazil in 2000,2004, and 2008 were determined with the objective of establishing the genotypes and studying the genetic variation. Results of the Bayesian phylogenetic analysis showed that sequences generated from strains from 2004 and 2008 formed a new subclade within the clade 1 of the South American genotype I. The new subgroup is here designated as 1E. Sequences of YFV strains recovered in 2000 belong to the subclade 1D, which comprises previously characterized YFV strains from Brazil. Molecular dating analyses suggested that the new subclade 1E started diversifying from 1D about 1975 and that the most recent 2004-2008 isolates arose about 1985. J. Med. Virol. 82:175-185, 2010. (C) 2009 Wiley-Liss, Inc.

Analyses of cataract surgery performed by the Unified Health System in Brazil, 2006-2007

Objective. Estimate cataract surgical rates (CSR) for Brazil and each federal unit in 2006 and 2007 based on the number of surgeries performed by the Unified Health System to help plan a comprehensive ophthalmology network in order to eliminate cataract blindness in compliance with the target set by the World Health Organization (WHO) of 3 000 cataract surgeries per million inhabitants per year. Methods. This descriptive study calculates CSR by using the number of cataract surgeries carried out by the Brazilian Unified Health System for each federal unit and estimates the need for cataract surgery in Brazil for 2006-2007, with official population data provided by the Brazilian Institute of Geography and Statistics. The number of cataract surgeries was compared with the WHO target. Results. To reach the WHO goal for eliminating age-related cataract blindness in Brazil, 560 312 cataract surgeries in 2006 and 568 006 surgeries in 2007 needed to be done. In 2006, 179 121 cataract surgeries were done by the Unified Health System, corresponding to a CSR of 959 per million population; in 2007, 223 317 were performed, with a CSR of 1 179. With the Brazilian Council of Ophthalmology estimation of 165 000 surgeries each year by the non-public services, the CSR for Brazil would be 1 842 for 2006 and 2 051 for 2007. The proportions needed to achieve the proposed target were 38.6% in 2006 and 31.6% in 2007. Conclusions. Human resources, technical expertise, and equipment are crucial to reach the WHO goal. Brazil has enough ophthalmologists but needs improved planning and infrastructure in order to eliminate the problem, aspects that require greater financial investment and stronger political commitment.

Physical analyses of compost from composting plants in Brazil

Nowadays the composting process has shown itself to be an alternative in the treatment of municipal solid wastes by composting plants. However, although more than 50% of the waste generated by the Brazilian population is composed of matter susceptible to organic composting, this process is, still today, insufficiently developed in Brazil, due to low compost quality and lack of investments in the sector. The objective of this work was to use physical analyses to evaluate the quality of the compost produced at 14 operative composting plants in the Sao Paulo State in Brazil. For this purpose, size distribution and total inert content tests were done. The results were analyzed by grouping the plants according to their productive processes: plants with a rotating drum, plants with shredders or mills, and plants without treatment after the sorting conveyor belt. Compost quality was analyzed considering the limits imposed by the Brazilian Legislation and the European standards for inert contents. The size distribution tests showed the influence of the machinery after the sorting conveyer on the granule sizes as well as the inert content, which contributes to the presence of materials that reduce the quality of the final product. (C) 2007 Elsevier Ltd. All rights reserved.