Foreign acquisition and internal organization

NIPE WP 05/2016

A nutrient balance model for typical Irish farming systems

The twin objectives of the work described were to construct nutrient balance models (NBM) for a range of Irish animal production systems and to evaluate their potential as a means of estimating the nutrient composition of farm wastes. The NBM has three components. The first is the intake of nutrients in the animal's diet. The second is retention or the nutrients the animal retains for the production of milk, meat or eggs. The third is the balance or the difference between the nutrient intake and retention. Data on the intake levels and their nutrient value for dairy cows, beef cattle, pigs and poultry systems were assembled. Literature searches and interviews with National experts were the primary sources of information. NBMs were then constructed for each production system. Summary tables of the nutrient values for the common diet constituents used in Irish animal production systems, the nutrient composition of the animal products and the NBMs (nutrient intake, retention and excretion) for a range of production systems were assembled. These represent the first comprehensive data set of this type for Irish animal production systems. There was generally good agreement between the derived NBMs values and those published in the literature. The NBMs were validated on a number of farms. Data on animal numbers, fertiliser use, concentrates inputs and production output were recorded on seven farms. Using the data a nutrient input/output balance was constructed for each farm. This was compared with the NBM estimate of the farm nutrient balance. The results showed good agreement between the measured balance and the NBM estimate particularly for the pig and poultry farms. However, the validation emphasised the inherent risks associated with NBMs. The average values used for feed intake and production parameters in the NEMs may result in the under or over estimate of actual nutrient balances on individual farms where these variables are substantially different. On the grassland farms there was a poor correlation between the input/output estimate and the NBM. This possibly results from the omission of the soil's contribution to the nutrient balance. However, the results indicate that the NBMs developed are a potentially useful tool for estimating nutrient balances. They also will serve to highlight the significant fraction of the nutrient inputs into farming systems that are retained on the farm. The potential of the NBM as a means of estimating the nutrient composition of farm wastes was evaluated on two farms. Feed intake and composition, animal production, slurry production was monitored during the indoor winter feeding period. Slurry samples were taken for analysis. The appropriates NBMs were used to estimate the nutrient balance for each farm. The nutrient content of the slurry produced was calculated. There was a good agreement between the NBM estimate and the measured values. This preliminary evaluation suggests that the NBM has a potential to provide the farmer with a simple means of estimating the nutrient value of his slurry.

Multivariate Analysis for Animal Selection in Experimental Research

Background: Several researchers seek methods for the selection of homogeneous groups of animals in experimental studies, a fact justified because homogeneity is an indispensable prerequisite for casualization of treatments. The lack of robust methods that comply with statistical and biological principles is the reason why researchers use empirical or subjective methods, influencing their results. Objective: To develop a multivariate statistical model for the selection of a homogeneous group of animals for experimental research and to elaborate a computational package to use it. Methods: The set of echocardiographic data of 115 male Wistar rats with supravalvular aortic stenosis (AoS) was used as an example of model development. Initially, the data were standardized, and became dimensionless. Then, the variance matrix of the set was submitted to principal components analysis (PCA), aiming at reducing the parametric space and at retaining the relevant variability. That technique established a new Cartesian system into which the animals were allocated, and finally the confidence region (ellipsoid) was built for the profile of the animals’ homogeneous responses. The animals located inside the ellipsoid were considered as belonging to the homogeneous batch; those outside the ellipsoid were considered spurious. Results: The PCA established eight descriptive axes that represented the accumulated variance of the data set in 88.71%. The allocation of the animals in the new system and the construction of the confidence region revealed six spurious animals as compared to the homogeneous batch of 109 animals. Conclusion: The biometric criterion presented proved to be effective, because it considers the animal as a whole, analyzing jointly all parameters measured, in addition to having a small discard rate.

Recent trends in Spanish income distribution: a robust picture of falling income inequality

Income distribution in Spain has experienced a substantial improvement towards equalisation during the second half of the seventies and the eighties; a period during which most OECD countries experienced the opposite trend. In spite of the many recent papers on the Spanish income distribution, the period covered by those stops in 1990. The aim of this paper is to extent the analysis to 1996 employing the same methodology and the same data set (ECPF). Our results not only corroborate the (decreasing inequality) trend found by others during the second half of the eighties, but also suggest that this trend extends over the first half of the nineties. We also show that our main conclusions are robust to changes in the equivalence scale, to changes in the definition of income and to potential data contamination. Finally, we analyse some of the causes which may be driving the overall picture of income inequality using two decomposition techniques. From this analyses three variables emerge as the major responsible factors for the observed improvement in the income distribution: education, household composition and socioeconomic situation of the household head.

The demand elasticity on tolled motorways

This paper analyses the elasticities of demand in tolled motorways in Spain with respect to the main variables influencing it. The demand equation is estimated using a panel data set where the cross-section observations correspond to the different Spanish tolled motorways sections, and the temporal dimension ranges from the beginning of the eighties until the end of the nineties. The results show a high elasticity with respect to the economic activity level. The average elasticity with respect to petrol price falls around -0.3, while toll elasticities clearly vary across motorway sections. These motorway sections are classified into four groups according to the estimated toll elasticity with values that range from -0.21 for the most inelastic to -0.83 for the most elastic. The main factors that explain such differences are the quality of the alternative road and the length of the section. The long-term effect is about 50 per cent higher than the short term one; however, the period of adjustment is relatively short.

Material flow accounting of Mexico (1970-2003)

This technical background paper describes the methods applied and data sources used in the compilation of the 1980-2003 data set for material flow accounts of the Mexican economy and presents the data set. It is organised in four parts: the first part gives an overview of the Material Flow Accounting (MFA) methodology. The second part presents the main material flows of the Mexican economy including biomass, fossil fuels, metal ores, industrial minerals and, construction minerals. The aim of this part is to explain the procedures and methods followed, the data sources used as well as providing a brief evaluation of the quality and reliability of the information used and the accounts established. Finally, some conclusions will be provided.

Effects of competition over quality-adjusted price indexes: an application to the Spanish automobile market

Using a newly constructed data set, we calculate quality-adjusted price indexes after estimating hedonic price regressions from 1988 to 2004 in the Spanish automobile market. The increasing competition was favoured by the removal of trade restrictions and the special plans for the renewal of the Spanish automobile fleet. We find that the increasing degree of competition during those years led to an overall drop in automobile prices by 20 percent which implied considerable consumer gains thanks to higher market efficiency. Additionally, our results indicate that loyalty relevance and discrepancies in automobile reliability declined during those years. This is captured.

Restriction site-associated DNA sequencing, genotyping error estimation and de novo assembly optimization for population genetic inference.

Restriction site-associated DNA sequencing (RADseq) provides researchers with the ability to record genetic polymorphism across thousands of loci for nonmodel organisms, potentially revolutionizing the field of molecular ecology. However, as with other genotyping methods, RADseq is prone to a number of sources of error that may have consequential effects for population genetic inferences, and these have received only limited attention in terms of the estimation and reporting of genotyping error rates. Here we use individual sample replicates, under the expectation of identical genotypes, to quantify genotyping error in the absence of a reference genome. We then use sample replicates to (i) optimize de novo assembly parameters within the program Stacks, by minimizing error and maximizing the retrieval of informative loci; and (ii) quantify error rates for loci, alleles and single-nucleotide polymorphisms. As an empirical example, we use a double-digest RAD data set of a nonmodel plant species, Berberis alpina, collected from high-altitude mountains in Mexico.

Results of An International Study of Quantitative BCR/ABL Assays Using Defined RNA Samples

Molecular monitoring of BCR/ABL transcripts by real time quantitative reverse transcription PCR (qRT-PCR) is an essential technique for clinical management of patients with BCR/ABL-positive CML and ALL. Though quantitative BCR/ABL assays are performed in hundreds of laboratories worldwide, results among these laboratories cannot be reliably compared due to heterogeneity in test methods, data analysis, reporting, and lack of quantitative standards. Recent efforts towards standardization have been limited in scope. Aliquots of RNA were sent to clinical test centers worldwide in order to evaluate methods and reporting for e1a2, b2a2, and b3a2 transcript levels using their own qRT-PCR assays. Total RNA was isolated from tissue culture cells that expressed each of the different BCR/ABL transcripts. Serial log dilutions were prepared, ranging from 100 to 10-5, in RNA isolated from HL60 cells. Laboratories performed 5 independent qRT-PCR reactions for each sample type at each dilution. In addition, 15 qRT-PCR reactions of the 10-3 b3a2 RNA dilution were run to assess reproducibility within and between laboratories. Participants were asked to run the samples following their standard protocols and to report cycle threshold (Ct), quantitative values for BCR/ABL and housekeeping genes, and ratios of BCR/ABL to housekeeping genes for each sample RNA. Thirty-seven (n=37) participants have submitted qRT-PCR results for analysis (36, 37, and 34 labs generated data for b2a2, b3a2, and e1a2, respectively). The limit of detection for this study was defined as the lowest dilution that a Ct value could be detected for all 5 replicates. For b2a2, 15, 16, 4, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. For b3a2, 20, 13, and 4 labs showed a limit of detection at the 10-5, 10-4, and 10-3 dilutions, respectively. For e1a2, 10, 21, 2, and 1 lab(s) showed a limit of detection at the 10-5, 10-4, 10-3, and 10-2 dilutions, respectively. Log %BCR/ABL ratio values provided a method for comparing results between the different laboratories for each BCR/ABL dilution series. Linear regression analysis revealed concordance among the majority of participant data over the 10-1 to 10-4 dilutions. The overall slope values showed comparable results among the majority of b2a2 (mean=0.939; median=0.9627; range (0.399 - 1.1872)), b3a2 (mean=0.925; median=0.922; range (0.625 - 1.140)), and e1a2 (mean=0.897; median=0.909; range (0.5174 - 1.138)) laboratory results (Fig. 1-3)). Thirty-four (n=34) out of the 37 laboratories reported Ct values for all 15 replicates and only those with a complete data set were included in the inter-lab calculations. Eleven laboratories either did not report their copy number data or used other reporting units such as nanograms or cell numbers; therefore, only 26 laboratories were included in the overall analysis of copy numbers. The median copy number was 348.4, with a range from 15.6 to 547,000 copies (approximately a 4.5 log difference); the median intra-lab %CV was 19.2% with a range from 4.2% to 82.6%. While our international performance evaluation using serially diluted RNA samples has reinforced the fact that heterogeneity exists among clinical laboratories, it has also demonstrated that performance within a laboratory is overall very consistent. Accordingly, the availability of defined BCR/ABL RNAs may facilitate the validation of all phases of quantitative BCR/ABL analysis and may be extremely useful as a tool for monitoring assay performance. Ongoing analyses of these materials, along with the development of additional control materials, may solidify consensus around their application in routine laboratory testing and possible integration in worldwide efforts to standardize quantitative BCR/ABL testing.

Una arqueometria del canvi tecnològic: producció i consum d'àmfores durant el canvi d'era en la zona nord de la costa catalana

L’objectiu de la recerca és definir un marc teòric i metodològic per a l’estudi del canvi tecnològic en Arqueologia. Aquest model posa èmfasi en caracteritzar els compromisos que configuren una tecnologia i avaluar-los en funció dels factors de situació —tècnics, econòmics, polítics, socials i ideològics. S’ha aplicat aquest model a un cas d’estudi concret: la producció d’àmfores romanes durant el canvi d’Era en la província Tarraconensis. L’estudi tecnològic dels envasos s’ha realitzat mitjançant diverses tècniques analítiques: Fluorescència de raigs X (FRX), Difracció de raigs X (DRX), Microscòpia òptica (MO) i Microscòpia electrònica de rastreig (MER). Les dades obtingudes permeten, a més, establir els grups de referència per a cada centre productor d’àmfores i, així, identificar la provinença dels individus recuperats en els centres consumidors. Donat que les àmfores en estudi són artefactes dissenyats específicament per a ser estibats en una nau i servir com a envàs de transport, l’estudi inclou la caracterització de les propietats mecàniques de resistència a la fractura i de tenacitat. En aquest sentit, i per primera vegada, s’ha aplicat l’Anàlisi d’Elements Finits (AEF) per a conèixer el comportament dels diferents dissenys d’àmfora en ésser sotmesos a diverses forces d’ús. L’AEF permet simular per ordinador les activitats en què les àmfores haurien participat durant el seu ús i avaluar-ne el seu comportament tècnic. Els resultats mostren una gran adequació entre les formulacions teòriques i el programa analític implementat per a aquest estudi. Respecte el cas d’estudi, els resultats mostren una gran variabilitat en les eleccions tecnològiques preses pels ceramistes de diferents tallers, però també al llarg del període de funcionament d’un mateix taller. L’aplicació del model ha permès proposar una explicació al canvi de disseny de les àmfores romanes.

Evolutionary switch and genetic convergence on rbcL following the evolution of C4 photosynthesis.

Rubisco is responsible for the fixation of CO2 into organic compounds through photosynthesis and thus has a great agronomic importance. It is well established that this enzyme suffers from a slow catalysis, and its low specificity results into photorespiration, which is considered as an energy waste for the plant. However, natural variations exist, and some Rubisco lineages, such as in C4 plants, exhibit higher catalytic efficiencies coupled to lower specificities. These C4 kinetics could have evolved as an adaptation to the higher CO2 concentration present in C4 photosynthetic cells. In this study, using phylogenetic analyses on a large data set of C3 and C4 monocots, we showed that the rbcL gene, which encodes the large subunit of Rubisco, evolved under positive selection in independent C4 lineages. This confirms that selective pressures on Rubisco have been switched in C4 plants by the high CO2 environment prevailing in their photosynthetic cells. Eight rbcL codons evolving under positive selection in C4 clades were involved in parallel changes among the 23 independent monocot C4 lineages included in this study. These amino acids are potentially responsible for the C4 kinetics, and their identification opens new roads for human-directed Rubisco engineering. The introgression of C4-like high-efficiency Rubisco would strongly enhance C3 crop yields in the future CO2-enriched atmosphere.

An atlas of human gene expression from massively parallel signature sequencing (MPSS).

We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences in gene expression between cell and tissue types are largely determined by transcripts derived from a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little more than half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the idea that most human genes have been mapped, if not functionally characterized. This data set should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance. The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com.

Innovation sources and productivity in Catalonian firms: a quantile regression analysis

This paper explores the effects of two main sources of innovation -intramural and external R&D- on the productivity level in a sample of 3,267 Catalonian firms. The data set used is based on the official innovation survey of Catalonia which was a part of the Spanish sample of CIS4, covering the years 2002-2004. We compare empirical results by applying usual OLS and quantile regression techniques both in manufacturing and services industries. In quantile regression, results suggest different patterns at both innovation sources as we move across conditional quantiles. The elasticity of intramural R&D activities on productivity decreased when we move up the high productivity levels both in manufacturing and services sectors, while the effects of external R&D rise in high-technology industries but are more ambiguous in low-technology and knowledge-intensive services. JEL codes: O300, C100, O140. Keywords: Innovation sources, R&D, Productivity, Quantile regression

Molecular variation at a candidate gene implicated in the regulation of fire ant social behavior

The fire ant Solenopsis invicta and its close relatives display an important social polymorphism involving differences in colony queen number. Colonies are headed by either a single reproductive queen (monogyne form) or multiple queens (polygyne form). This variation in social organization is associated with variation at the gene Gp-9, with monogyne colonies harboring only B-like allelic variants and polygyne colonies always containing b-like variants as well. We describe naturally occurring variation at Gp-9 in fire ants based on 185 full-length sequences, 136 of which were obtained from S. invicta collected over much of its native range. While there is little overall differentiation between most of the numerous alleles observed, a surprising amount is found in the coding regions of the gene, with such substitutions usually causing amino acid replacements. This elevated coding-region variation may result from a lack of negative selection acting to constrain amino acid replacements over much of the protein, different mutation rates or biases in coding and non-coding sequences, negative selection acting with greater strength on non-coding than coding regions, and/or positive selection acting on the protein. Formal selection analyses provide evidence that the latter force played an important role in the basal b-like lineages coincident with the emergence of polygyny. While our data set reveals considerable paraphyly and polyphyly of S. invicta sequences with respect to those of other fire ant species, the b-like alleles of the socially polymorphic species are monophyletic. An expanded analysis of colonies containing alleles of this clade confirmed the invariant link between their presence and expression of polygyny. Finally, our discovery of several unique alleles bearing various combinations of b-like and B-like codons allows us to conclude that no single b-like residue is completely predictive of polygyne behavior and, thus, potentially causally involved in its expression. Rather, all three typical b-like residues appear to be necessary.

Does urban sprawl increase the costs of providing local public services? Evidence from Spanish municipalities

This paper examines the impact of urban sprawl, a phenomenon of particular interest in Spain, which is currently experiencing this process of rapid, low-density urban expansion. Many adverse consequences are attributed to urban sprawl (e.g., traffic congestion, air pollution and social segregation), though here we are concerned primarily with the rising costs of providing local public services. Our initial aim is to develop an accurate measure of urban sprawl so that we might empirically test its impact on municipal budgets. Then, we undertake an empirical analysis using a cross-sectional data set of 2,500 Spanish municipalities for the year 2003 and a piecewise linear function to account for the potentially nonlinear relationship between sprawl and local costs. The estimations derived from the expenditure equations for both aggregate and six disaggregated spending categories indicate that low-density development patterns lead to greater provision costs of local public services.