EVALUATING EXTENSIVE SHEEP FARMING SYSTEMS

Data from each of 5 commercial, extensive sheep farms in Cumbria, UK were used as parameters in a linear program (LP) representing labour and grazing management in such farming systems. The LP maximised ewe enterprise gross margin subject to constraints dictated by the labour availability and land types on each farm. Under the assumptions used, labour availability and price restricted ewe numbers well below those observed in practice on 2 farms i.e. land resources were adequate for the farming system practiced. On two other farms stocking levels and hence returns were limited by the availability of forage and hence feed input prices relative to output. On one farm, greater grassland productivity was the key determinant of system performance. It was concluded that a holistic systems approach was needed to properly evaluate these farming systems in terms of their potential contribution to animal welfare, land use, profit and hence their sustainabilityLivestock Production/Industries, Extensive, Sheep, Economics, LP,

Impacts of labour on interactions between economics and animal welfare in extensive sheep farms

This study quantified interactions between animal welfare and farm profitability in British extensive sheep farming systems. Qualitative welfare assessment methodology was used to assess welfare from the animal's perspective in 20 commercial extensive sheep farms and to estimate labour demand for welfare, based on the assessed welfare scores using data collected from farm inventories. The estimated labour demand was then used as a coefficient in a linear program based model to establish the gross margin maximising farm management strategy for given farm situations, subject to constraints that reflected current resource limitations including labour supply. Regression analysis showed a significant relationship between the qualitative welfare assessment scores and labour supply on the inventoried farms but there was no significant relationship between current gross margin and assessed welfare scores. However, to meet the labour demand of the best welfare score, a reduction in flock size and in the average maximum farm gross margin was often required. These findings supported the hypothesis that trade-offs between animal welfare and farm profitability are necessary in providing maximum animal welfare via on-farm labour and sustainable British extensive sheep farming systems.Sheep, Labour, Animal Welfare, Linear Programme, Livestock Production/Industries, C6, Q10, Q19, Q57,

Artificial Sequences and Complexity Measures

In this paper we exploit concepts of information theory to address the fundamental problem of identifying and defining the most suitable tools to extract, in a automatic and agnostic way, information from a generic string of characters. We introduce in particular a class of methods which use in a crucial way data compression techniques in order to define a measure of remoteness and distance between pairs of sequences of characters (e.g. texts) based on their relative information content. We also discuss in detail how specific features of data compression techniques could be used to introduce the notion of dictionary of a given sequence and of Artificial Text and we show how these new tools can be used for information extraction purposes. We point out the versatility and generality of our method that applies to any kind of corpora of character strings independently of the type of coding behind them. We consider as a case study linguistic motivated problems and we present results for automatic language recognition, authorship attribution and self consistent-classification.Comment: Revised version, with major changes, of previous "Data Compression approach to Information Extraction and Classification" by A. Baronchelli and V. Loreto. 15 pages; 5 figure

A standard tag set expounding traditional morphological features for Arabic language part-of-speech tagging

The SALMA Morphological Features Tag Set (SALMA, Sawalha Atwell Leeds Morphological Analysis tag set for Arabic) captures long-established traditional morphological features of grammar and Arabic, in a compact yet transparent notation. First, we introduce Part-of-Speech tagging and tag set standards for English and other European languages, and then survey Arabic Part-of-Speech taggers and corpora, and long-established Arabic traditions in analysis of morphology. A range of existing Arabic Part-of-Speech tag sets are illustrated and compared; and we review generic design criteria for corpus tag sets. For a morphologically-rich language like Arabic, the Part-of-Speech tag set should be defined in terms of morphological features characterizing word structure. We describe the SALMA Tag Set in detail, explaining and illustrating each feature and possible values. In our analysis, a tag consists of 22 characters; each position represents a feature and the letter at that location represents a value or attribute of the morphological feature; the dash ‘-’ represents a feature not relevant to a given word. The first character shows the main Parts of Speech, from: noun, verb, particle, punctuation, and Other (residual); these last two are an extension to the traditional three classes to handle modern texts. ‘Noun’ in Arabic subsumes what are traditionally referred to in English as ‘noun’ and ‘adjective’. The characters 2, 3, and 4 are used to represent subcategories; traditional Arabic grammar recognizes 34 subclasses of noun (letter 2), 3 subclasses of verb (letter 3), 21 subclasses of particle (letter 4). Others (residuals) and punctuation marks are represented in letters 5 and 6 respectively. The next letters represent traditional morphological features: gender (7), number (8), person (9), inflectional morphology (10) case or mood (11), case and mood marks (12), definiteness (13), voice (14), emphasized and non-emphasized (15), transitivity (16), rational (17), declension and conjugation (18). Finally there are four characters representing morphological information which is useful in Arabic text analysis, although not all linguists would count these as traditional features: unaugmented and augmented (19), number of root letters (20), verb root (21), types of nouns according to their final letters (22). The SALMA Tag Set is not tied to a specific tagging algorithm or theory, and other tag sets could be mapped onto this standard, to simplify and promote comparisons between and reuse of Arabic taggers and tagged corpora

Characterisation of Human Embryonic Stem Cells Conditioning Media by 1H-Nuclear Magnetic Resonance Spectroscopy

BACKGROUND: Cell culture media conditioned by human foreskin fibroblasts (HFFs) provide a complex supplement of protein and metabolic factors that support in vitro proliferation of human embryonic stem cells (hESCs). However, the conditioning process is variable with different media batches often exhibiting differing capacities to maintain hESCs in culture. While recent studies have examined the protein complement of conditioned culture media, detailed information regarding the metabolic component of this media is lacking. METHODOLOGY/PRINCIPAL FINDINGS: Using a (1)H-Nuclear Magnetic Resonance ((1)H-NMR) metabonomics approach, 32 metabolites and small compounds were identified and quantified in media conditioned by passage 11 HFFs (CMp11). A number of metabolites were secreted by HFFs with significantly higher concentration of lactate, alanine, and formate detected in CMp11 compared to non-conditioned media. In contrast, levels of tryptophan, folate and niacinamide were depleted in CMp11 indicating the utilisation of these metabolites by HFFs. Multivariate statistical analysis of the (1)H-NMR data revealed marked age-related differences in the metabolic profile of CMp11 collected from HFFs every 24 h over 72 h. Additionally, the metabolic profile of CMp11 was altered following freezing at -20°C for 2 weeks. CM derived from passage 18 HFFs (CMp18) was found to be ineffective at supporting hESCs in an undifferentiated state beyond 5 days culture. Multivariate statistical comparison of CMp11 and CMp18 metabolic profiles enabled rapid and clear discrimination between the two media with CMp18 containing lower concentrations of lactate and alanine as well as higher concentrations of glucose and glutamine. CONCLUSIONS/SIGNIFICANCE: (1)H-NMR-based metabonomics offers a rapid and accurate method of characterising hESC conditioning media and is a valuable tool for monitoring, controlling and optimising hESC culture media preparation

Differences between Human Plasma and Serum Metabolite Profiles

BACKGROUND: Human plasma and serum are widely used matrices in clinical and biological studies. However, different collecting procedures and the coagulation cascade influence concentrations of both proteins and metabolites in these matrices. The effects on metabolite concentration profiles have not been fully characterized. METHODOLOGY/PRINCIPAL FINDINGS: We analyzed the concentrations of 163 metabolites in plasma and serum samples collected simultaneously from 377 fasting individuals. To ensure data quality, 41 metabolites with low measurement stability were excluded from further analysis. In addition, plasma and corresponding serum samples from 83 individuals were re-measured in the same plates and mean correlation coefficients (r) of all metabolites between the duplicates were 0.83 and 0.80 in plasma and serum, respectively, indicating significantly better stability of plasma compared to serum (p = 0.01). Metabolite profiles from plasma and serum were clearly distinct with 104 metabolites showing significantly higher concentrations in serum. In particular, 9 metabolites showed relative concentration differences larger than 20%. Despite differences in absolute concentration between the two matrices, for most metabolites the overall correlation was high (mean r = 0.81±0.10), which reflects a proportional change in concentration. Furthermore, when two groups of individuals with different phenotypes were compared with each other using both matrices, more metabolites with significantly different concentrations could be identified in serum than in plasma. For example, when 51 type 2 diabetes (T2D) patients were compared with 326 non-T2D individuals, 15 more significantly different metabolites were found in serum, in addition to the 25 common to both matrices. CONCLUSIONS/SIGNIFICANCE: Our study shows that reproducibility was good in both plasma and serum, and better in plasma. Furthermore, as long as the same blood preparation procedure is used, either matrix should generate similar results in clinical and biological studies. The higher metabolite concentrations in serum, however, make it possible to provide more sensitive results in biomarker detection

Evaluation and Characterization of Bacterial Metabolic Dynamics with a Novel Profiling Technique, Real-Time Metabolotyping

BACKGROUND: Environmental processes in ecosystems are dynamically altered by several metabolic responses in microorganisms, including intracellular sensing and pumping, battle for survival, and supply of or competition for nutrients. Notably, intestinal bacteria maintain homeostatic balance in mammals via multiple dynamic biochemical reactions to produce several metabolites from undigested food, and those metabolites exert various effects on mammalian cells in a time-dependent manner. We have established a method for the analysis of bacterial metabolic dynamics in real time and used it in combination with statistical NMR procedures. METHODOLOGY/PRINCIPAL FINDINGS: We developed a novel method called real-time metabolotyping (RT-MT), which performs sequential (1)H-NMR profiling and two-dimensional (2D) (1)H, (13)C-HSQC (heteronuclear single quantum coherence) profiling during bacterial growth in an NMR tube. The profiles were evaluated with such statistical methods as Z-score analysis, principal components analysis, and time series of statistical TOtal Correlation SpectroScopY (TOCSY). In addition, using 2D (1)H, (13)C-HSQC with the stable isotope labeling technique, we observed the metabolic kinetics of specific biochemical reactions based on time-dependent 2D kinetic profiles. Using these methods, we clarified the pathway for linolenic acid hydrogenation by a gastrointestinal bacterium, Butyrivibrio fibrisolvens. We identified trans11, cis13 conjugated linoleic acid as the intermediate of linolenic acid hydrogenation by B. fibrisolvens, based on the results of (13)C-labeling RT-MT experiments. In addition, we showed that the biohydrogenation of polyunsaturated fatty acids serves as a defense mechanism against their toxic effects. CONCLUSIONS: RT-MT is useful for the characterization of beneficial bacterium that shows potential for use as probiotic by producing bioactive compounds