Typification of farming systems for constructing representative farm models: two illustrations of the application of multi-variate analyses in Chile and Pakistan

If the fundamental precepts of Farming Systems Research were to be taken literally then it would imply that for each farm 'unique' solutions should be sought. This is an unrealistic expectation, but it has led to the idea of a recommendation domain, implying creating a taxonomy of farms, in order to increase the general applicability of recommendations. Mathematical programming models are an established means of generating recommended solutions, but for such models to be effective they have to be constructed for 'truly' typical or representative situations. The multi-variate statistical techniques provide a means of creating the required typologies, particularly when an exhaustive database is available. This paper illustrates the application of this methodology in two different studies that shared the common purpose of identifying types of farming systems in their respective study areas. The issues related with the use of factor and cluster analyses for farm typification prior to building representative mathematical programming models for Chile and Pakistan are highlighted. (C) 2003 Elsevier Science Ltd. All rights reserved.

Near infrared reflectance spectroscopy (NIRS) to predict biological parameters of maize silage: effects of particle comminution, oven drying temperature and the presence of residual moisture

Maize silage nutritive quality is routinely determined by near infrared reflectance spectroscopy (NIRS). However, little is known about the impact of sample preparation on the accuracy of the calibration to predict biological traits. A sample population of 48 maize silages representing a wide range of physiological maturities was used in a study to determine the impact of different sample preparation procedures (i.e., drying regimes; the presence or absence of residual moisture; the degree of particle comminution) on resultant NIR prediction statistics. All silages were scanned using a total of 12 combinations of sample pre-treatments. Each sample preparation combination was subjected to three multivariate regression techniques to give a total of 36 predictions per biological trait. Increased sample preparations procedure, relative to scanning the unprocessed whole plant (WP) material, always resulted in a numerical minimisation of model statistics. However, the ability of each of the treatments to significantly minimise the model statistics differed. Particle comminution was the most important factor, oven-drying regime was intermediate, and residual moisture presence was the least important. Models to predict various biological parameters of maize silage will be improved if material is subjected to a high degree of particle comminution (i.e., having been passed through a 1 mm screen) and developed on plant material previously dried at 60 degrees C. The extra effort in terms of time and cost required to remove sample residual moisture cannot be justified. (c) 2005 Elsevier B.V. All rights reserved.

Using near infrared reflectance spectroscopy (NIRS) to predict the biological parameters of maize silage

The microbial fermentability, ruminal degradability and digestibility of 48 maize silages were determined using in vitro gas production (GP), in situ degradability and in vitro digestibility procedures. The silages were produced from forage maize harvested throughout the summer of 1998, and represent a wide range of physiological maturities. Large variations among samples were observed for all biological parameters, with the exception of in vitro digestibility and the asymptote of in vitro GP. The potential of near infrared reflectance spectroscopy (NIRS) to predict the biological parameters measured was determined by regression of the biological data against the respective spectral profile. NIRS demonstrated only a moderate ability (R-2 > 0.60-0.80) to predict in vitro digestibility, modelled kinetics of gas production (excluding the asymptote of gas production) and the modelled ruminally soluble dry matter (DM) fraction. Calibration statistics for remaining biological parameters were unacceptably poor (R-2 = 0.60). (C) 2004 Elsevier B.V. All rights reserved.

Elusive relationships within order fabales: phylogenetic analyses using matK and rbcL sequence data

The order Fabales, including Leguminosae, Polygalaceae, Quillajaceae and Surianaceae, represents a novel hypothesis emerging from angiosperm molecular phylogenies. Despite good support for the order, molecular studies to date have suggested contradictory, poorly supported interfamilial relationships. Our reappraisal of relationships within Fabales addresses past taxon sampling deficiencies, and employs parsimony and Bayesian approaches using sequences from the plastid regions rbcL (166 spp.) and matK (78 spp.). Five alternative hypotheses for interfamilial relationships within Fabales were recovered. The Shimodaira-Hasegawa test found the likelihood of a resolved topology significantly higher than the one calculated for a polytomy, but did not favour any of the alternative hypotheses of relationship within Fabales. In the light of the morphological evidence available and the comparative behavior of rbcL and matK, the topology recovering Polygalaceae as sister to the rest of the order Fabales with Leguminosae more closely related to Quillajaceae + Surianaceae, is considered the most likely hypothesis of interfamilial relationships of the order. Dating of selected crown clades in the Fabales phylogeny using penalized likelihood suggests rapid radiation of the Leguminosae, Polygalaceae, and (Quillajaceae + Surianaceae) crown clades.

Genomic and genetic analyses of diversity and plant interactions of Pseudomonas fluorescens

Background: Pseudomonas fluorescens are common soil bacteria that can improve plant health through nutrient cycling, pathogen antagonism and induction of plant defenses. The genome sequences of strains SBW25 and Pf0-1 were determined and compared to each other and with P. fluorescens Pf-5. A functional genomic in vivo expression technology (IVET) screen provided insight into genes used by P. fluorescens in its natural environment and an improved understanding of the ecological significance of diversity within this species. Results: Comparisons of three P. fluorescens genomes (SBW25, Pf0-1, Pf-5) revealed considerable divergence: 61% of genes are shared, the majority located near the replication origin. Phylogenetic and average amino acid identity analyses showed a low overall relationship. A functional screen of SBW25 defined 125 plant-induced genes including a range of functions specific to the plant environment. Orthologues of 83 of these exist in Pf0-1 and Pf-5, with 73 shared by both strains. The P. fluorescens genomes carry numerous complex repetitive DNA sequences, some resembling Miniature Inverted-repeat Transposable Elements (MITEs). In SBW25, repeat density and distribution revealed 'repeat deserts' lacking repeats, covering approximately 40% of the genome. Conclusions: P. fluorescens genomes are highly diverse. Strain-specific regions around the replication terminus suggest genome compartmentalization. The genomic heterogeneity among the three strains is reminiscent of a species complex rather than a single species. That 42% of plant-inducible genes were not shared by all strains reinforces this conclusion and shows that ecological success requires specialized and core functions. The diversity also indicates the significant size of genetic information within the Pseudomonas pan genome.

Strategies to prevent falls and fractures in hospitals and care homes and effect of cognitive impairment: systematic review and meta-analyses

OBJECTIVES: To evaluate the evidence for strategies to prevent falls or fractures in residents in care homes and hospital inpatients and to investigate the effect of dementia and cognitive impairment. DESIGN: Systematic review and meta-analyses of studies grouped by intervention and setting (hospital or care home). Meta-regression to investigate the effects of dementia and of study quality and design. DATA SOURCES: Medline, CINAHL, Embase, PsychInfo, Cochrane Database, Clinical Trials Register, and hand searching of references from reviews and guidelines to January 2005. RESULTS: 1207 references were identified, including 115 systematic reviews, expert reviews, or guidelines. Of the 92 full papers inspected, 43 were included. Meta-analysis for multifaceted interventions in hospital (13 studies) showed a rate ratio of 0.82 (95% confidence interval 0.68 to 0.997) for falls but no significant effect on the number of fallers or fractures. For hip protectors in care homes (11 studies) the rate ratio for hip fractures was 0.67 (0.46 to 0.98), but there was no significant effect on falls and not enough studies on fallers. For all other interventions (multifaceted interventions in care homes; removal of physical restraints in either setting; fall alarm devices in either setting; exercise in care homes; calcium/vitamin D in care homes; changes in the physical environment in either setting; medication review in hospital) meta-analysis was either unsuitable because of insufficient studies or showed no significant effect on falls, fallers, or fractures, despite strongly positive results in some individual studies. Meta-regression showed no significant association between effect size and prevalence of dementia or cognitive impairment. CONCLUSION: There is some evidence that multifaceted interventions in hospital reduce the number of falls and that use of hip protectors in care homes prevents hip fractures. There is insufficient evidence, however, for the effectiveness of other single interventions in hospitals or care homes or multifaceted interventions in care homes.

Predicting functional gene links from phylogenetic-statistical analyses of whole genomes

An important element of the developing field of proteomics is to understand protein-protein interactions and other functional links amongst genes. Across-species correlation methods for detecting functional links work on the premise that functionally linked proteins will tend to show a common pattern of presence and absence across a range of genomes. We describe a maximum likelihood statistical model for predicting functional gene linkages. The method detects independent instances of the correlated gain or loss of pairs of proteins on phylogenetic trees, reducing the high rates of false positives observed in conventional across-species methods that do not explicitly incorporate a phylogeny. We show, in a dataset of 10,551 protein pairs, that the phylogenetic method improves by up to 35% on across-species analyses at identifying known functionally linked proteins. The method shows that protein pairs with at least two to three correlated events of gain or loss are almost certainly functionally linked. Contingent evolution, in which one gene's presence or absence depends upon the presence of another, can also be detected phylogenetically, and may identify genes whose functional significance depends upon its interaction with other genes. Incorporating phylogenetic information improves the prediction of functional linkages. The improvement derives from having a lower rate of false positives and from detecting trends that across-species analyses miss. Phylogenetic methods can easily be incorporated into the screening of large-scale bioinformatics datasets to identify sets of protein links and to characterise gene networks.

Inter-simple sequence repeat and aggressiveness analyses revealed high genetic diversity, recombination and long-range dispersal in Fusarium culmorum

Inter-simple sequence repeat (ISSR) analysis and aggressiveness assays were used to investigate genetic variability within a global collection of Fusarium culmorum isolates. A set of four ISSR primers were tested, of which three primers amplified a total of 37 bands out of which 30 (81%) were polymorphic. The intraspecific diversity was high, ranging from four to 28 different ISSR genotypes for F. culmorum depending on the primer. The combined analysis of ISSR data revealed 59 different genotypes clustered into seven distinct clades amongst 75 isolates of F. culmorum examined. All the isolates were assayed to test their aggressiveness on a winter wheat cv. 'Armada'. A significant quantitative variation for aggressiveness was found among the isolates. The ISSR and aggressiveness variation existed on a macro- as well as micro-geographical scale. The data suggested a long-range dispersal of F. culmorum and indicated that this fungus may have been introduced into Canada from Europe. In addition to the high level of intraspecific diversity observed in F. culmorum, the index of multilocus association calculated using ISSR data indicated that reproduction in F. culmorum cannot be exclusively clonal and recombination is likely to occur.

A study by high energy transfer inelastic neutron scattering spectroscopy of the mineral fraction of ox femur bone

We have used high energy transfer (HET) inelastic neutron scattering spectroscopy to measure the vibrational modes in the spectra of hydroxyapatite, bone and brushite to confirm our earlier work that only a fraction of the hydroxyl groups in bone mineral are substituted. The HET spectra are better observed due to the higher scattering cross section of hydrogen compared with the other elements in the calcium phosphate compounds. (C) 2003 Elsevier Science B.V. All rights reserved.

In situ observation of lithium hydride hydrolysis by DRIFT spectroscopy

Polycrystalline LiH was studied in situ using diffuse reflectance infrared Fourier transform (DRIFT) spectroscopy to investigate the effect water vapour has on the rate of production of the corrosion products, particularly LiOH. The reaction rate of the formation of surface LiOH was monitored by measurement of the hydroxyl (OH) band at 3676 cm(-1). The initial hydrolysis rate of LiH exposed to water vapour at 50% relative humidity was found to be almost two times faster than LiH exposed to water vapour at 2% relative humidity. The hydrolysis rate was shown to be initially very rapid followed by a much slower, almost linear rate. The change in hydrolysis rate was attributed to the formation of a coherent layer of LiOH on the LiH surface. Exposure to lower levels of water vapour appeared to result in the formation of a more coherent corrosion product, resulting in effective passivation of the surface to further attack from water. Crown Copyright (c) 2007 Published by Elsevier B.V. All rights reserved.

13C-2H correlation NMR spectroscopy studies of the in vivo transformations of natural products from Artemisia annua

13C-2H correlation NMR spectroscopy (13C-2H COSY) permits the identification of 13C and 2H nuclei which are connected to one another by a single chemical bond via the sizeable 1JCD coupling constant. The practical development of this technique is described using a 13C-2H COSY pulse sequence which is derived from the classical 13C-1H correlation experiment. An example is given of the application of 13C-2H COSY to the study of the biogenesis of natural products from the anti-malarial plant Artemisia annua, using a doubly-labelled precursor molecule. Although the biogenesis of artemisinin, the anti-malarial principle from this species, has been extensively studied over the past twenty years there is still no consensus as to the true biosynthetic route to this important natural product – indeed, some published experimental results are directly contradictory. One possible reason for this confusion may be the ease with which some of the metabolites from A. annua undergo spontaneous autoxidation, as exemplified by our recent in vitro studies of the spontaneous autoxidation of dihydroartemisinic acid, and the application of 13C-2H COSY to this biosynthetic problem has been important in helping to mitigate against such processes. In this in vivo application of 13C-2H COSY, [15-13C2H3]-dihydroartemisinic acid (the doubly-labelled analogue of the natural product from this species which was obtained through synthesis) was fed to A. annua plants and was shown to be converted into several natural products which have been described previously, including artemisinin. It is proposed that all of these transformations occurred via a tertiary hydroperoxide intermediate, which is derived from dihyroartemisinic acid. This intermediate was observed directly in this feeding experiment by the 13C-2H COSY technique; its observation by more traditional procedures (e.g., chromatographic separation, followed by spectroscopic analysis of the purified product) would have been difficult owing to the instability of the hydroperoxide group (as had been established previously by our in vitro studies of the spontaneous autoxidation of dihydroartemisinic acid). This same hydroperoxide has been reported as the initial product of the spontaneous autoxidation of dihydroartemisinic acid in our previous in vitro studies. Its observation in this feeding experiment by the 13C-2H COSY technique, a procedure which requires the minimum of sample manipulation in order to achieve a reliable identification of metabolites (based on both 13C and 2H chemical shifts at the 15-position), provides the best possible evidence for its status as a genuine biosynthetic intermediate, rather than merely as an artifact of the experimental procedure.

Syntheses and spectroscopy of diamine complexes of Zn(II) and Cd(II) ethylxanthates and the molecular structures of [M(S2COEt)(2)TMEDA]: formation of US nanoparticles from [Cd(S2COEt)(2)] and [Cd(S2COEt)(2)TMEDA]

The zinc and cadmium ethylxanthate complexes of N,N,N',N'-tetramethylethylenediamine (TMEDA), [M(S2COEt)(2)TMEDA], were synthesized and characterized with infrared, H-1 and C-13 NMR spectroscopy, mass spectrometry and X-ray crystallography. Whereas the cadmium complex has a six-coordinate {CdS4N2} centre with bidentate xanthate ligands, the zinc complex contains four coordinate {ZnS2N2} zinc with two monodentate xanthate groups. The cadmium species [Cd(S2COEt)(2)(diamine)] (where diamine = N,N-dimethylethylenediamine or N,N'-diisopropylethylenediamine) were also synthesized. The surfactant-assisted formation of nanoparticles from [Cd(S2COEt)(2)] and [Cd(S2COEt)(2)TMEDA] was studied with TEM, XRD and XRF techniques. From [Cd(S2COEt)(2)], spherical nanoparticle aggregates 140-200 nm in diameter were obtained but from [Cd(S2COEt)(2)TMEDA], single nanoparticles were produced with estimated diameters in the range of 4-7 nm and almost no aggregation. (C) 2004 Elsevier Ltd. All rights reserved.

Argon predissociation spectroscopy of the OH-center dot H2O and Cl-center dot H2O complexes in the 1000-1900 cm(-1) region: Intramolecular bending transitions and the search for the shared-proton fundamental in the hydroxide monohydrate

We present argon predissociation vibrational spectra of the OH-.H2O and Cl-.H2O complexes in the 1000-1900 cm(-1) energy range, far below the OH stretching region reported in previous studies. This extension allows us to explore the fundamental transitions of the intramolecular bending vibrations associated with the water molecule, as well as that of the shared proton inferred from previous assignments of overtones in the higher energy region. Although the water bending fundamental in the Cl-.H2O spectrum is in very good agreement with expectations, the OH-.H2O spectrum is quite different than anticipated, being dominated by a strong feature at 1090 cm(-1). New full-diniensionality calculations of the OH-.H2O vibrational level structure using diffusion Monte Carlo and the VSCF/CI methods indicate this band arises from excitation of the shared proton.

The gas-phase reactions Of SiCl4 and Si2Cl6 with CH3OH and C2H5OH: an investigation by mass spectrometry and matrix-isolation infrared spectroscopy

The gas phase reactions Of SiCl4 and Si2Cl6 With CH3OH and C2H5OH have been investigated using both mass spectrometry and matrix isolation techniques. SiCl4 reacts with both CH3OH and C2H5OH upon mixing of the vapours for times in excess of 3 h to generate the HCl-elimination products SiCl3OR (R = CH3 or C2H5). The identity of these products is confirmed by deuteration experiments and by ab initio calculations at the HF/6-31G(d) level. Further products are generated when the mixture is passed through a tube heated to 750degreesC. Si2Cl6 reacts with CH3OH and C2H5OH via a different mechanism in which the Si-Si bond is cleaved to yield SiCl3OR and HCl. Other products of the type SiCl4-n(OCH3)(n) are tentatively identified by a combination of mass spectrometric and matrix isolation measurements. These latter products indicate further replacement of Cl atoms by OR groups as a result of reaction of CH3OH or C2H5OH with the initial product.