Modelo de rentabilidade das explorações leiteiras em S. Miguel : influência dos fatores de produção : da classificação morfológica e da produção leiteira dos bovinos

Dissertação de Mestrado em Engenharia Zootécnica.Tendo presente que a situação económica das explorações leiteiras dos Açores está a atravessar grandes dificuldades económicas e financeiras, e com o aproximar do fim anunciado das quotas leiteiras e consequente liberalização total na produção de leite (PL) na Europa, a pecuária açoriana necessita de se preparar para esta nova mudança de estratégia europeia sob o risco de falência da atividade. Dessa forma, pretende-se conhecer a situação técnico-económica e a eficiência técnica das explorações, avaliar o efeito que a produção de leite aos 305 dias (PL305) e a classificação morfológica (CM) terão na rentabilidade líquida (RL), para depois criar um modelo que possa explicar a rentabilidade das explorações. Foram realizadas a análise não paramétrica de eficiência, a análise de variância, a análise cluster e a regressão linear dos registos da PL305, gordura aos 305 dias (PG305), proteína aos 305 dias (PP305) e a CM de 91 explorações que realizaram contraste leiteiro (CL) e foram inscritas em regime de contabilidade organizada no ano de 2010. Constatou-se que as explorações tinham auferindo um RL anual de 1.002,93€/ha, representando um lucro médio de 19,80%. Contudo, cada exploração recebe de subsídios por hectare (Subs/ha) 1.090,06€/ha, o que representa 22,43% do total das receitas e uma clara dependência das explorações aos subsídios (Subs), caso contrário, o lucro médio passaria a -4,20%. Com a certeza do fim anunciado das quotas leiteiras e o corte do Subs aos Produtos Lácteos, prevê-se uma quebra média dos rendimentos em 10,36%. Do lado das despesas, os custos alimentares (CAlim) são os que representam a maior percentagem da despesa com 25,32%. Após a análise não paramétrica de eficiência dos registos verificou-se, que apenas 7,69% das explorações estudadas são eficientes, baixando para os 5,49% quando se retira os Subs/ha atribuídos como forma de rendimento. Na análise de variância observou-se, que não existe qualquer efeito significativo da PL 305 e a Pontuação Final (PF) das explorações na RL das mesmas. Em contrapartida, existe uma forte correlação e um efeito significativo entre a PL305 e a PF (r=0,748, p<0,001) comprovando, que as explorações com as melhores PF são ao mesmo tempo as melhores produtoras de leite. O mesmo se passa na PG305 e na PP305. Na análise de cluster constatou-se, que as explorações mais rentáveis têm um PL305 de 9.188,56 kg, venda de leite (VL) de 5.146,29€, CAlim de 771,65€, Cabeças Normais/ha (CNha) de 3,07e PF de 82,3 pontos. A confirmar estes dados, o modelo criado pela regressão linear múltipla com R2=0,736 estabelece, que de todas as variáveis independentes somente a VL (p<0,001), Calim (p<0,001), Custos com Salários (CSalár, p<0,001), Custos com as Rendas (CRend, p<0,01) e a CNha (p<0,05) são as variáveis com efeito significativo na RL das explorações leiteiras. Assim, os dados revelam que as explorações necessitam de melhorar a qualidade morfológica das vacas leiteiras, de forma a aumentar a PL, proteína e gordura, levando a um aumento da VL, atendendo ao limite máximo dos CAlim e do CNha, de forma a melhorar a eficiência técnica e serem rentáveis sem Subs.ABSTRACT: As we know the dairy farms in Azores are crossing some economical and financial difficulties and with the announced order of milk quotas and complete liberalization of the markets, the farmers in Azores need to be well prepared to face this change in Europe. Because if they don't, they may crash. That is why, it is very important to know the real economical and technical conditions of the farms, as well as the technical efficiency of the farms, and evaluate the effect that the milk production has at 305 days (PL305) and the morphological classification (CM) will have in the net profitability (RL). After that it is important to create a model that can explain the profitability of farms. In order to do that, several things have been made such as: non-parametric analysis of efficiency, analysis of variance, analysis of the cluster, the linear regression of the records of PL305, fat at 305 days (PG305), protein at 305 days (PP305) and the CM of 91 farms that have made their milk recording (CL) and have made their proper accounting in 2010. We found that the farms have earned around 1.002,93€ per hectare, which represented an average profit of 19,80%. However, each farm receives 1.090,06€ per hectare of EU subsidies (Subs/ha), representing 22,43% of the profits and shows a clear dependence on EU subsidies (Subs), because without them, the average profit would be -4.20%. With the end of the milk quotas and the cut in subs for Dairy Products we anticipate an average break in profits around 10.36%.Speaking about the expense, the food costs (CAlim) represent the major percentage of the expense: 25,32%. After the non-parametric analysis of efficiency, we found that only 7,69% of the analyses farms are efficient, decreasing for 5,49%, if we take out the subs/ha. In the analysis of variance we noticed that there isn't any significant effect of the PL305 and the final score (PF) in the RL of the farms. On the other hand, there is a strong relation between the PL 305 and the PF (r=0,748, p<0,001) proving that the farms with the best PF are at the same time the best milk producers. The same happens at PG305 and at PP305. In the cluster analysis we observed that the most profitable farms have a 9.188,56kg of PL305, milk sales (VL) of 5.146,29€, CAlim 771,65€, normal heads /ha (CNha) of 3,07 and PF of 82,3 points. Confirming this facts, the model created by the multiple linear regression with R2=0,736 sets that between all the independent variables only the VL (p<0,001), CAlim (p<0,001), wage costs (CSalár, p<0,001), costs with rents (CRend, p<0,01) and the CNha (p<0,05) are the variables with significant effect in the RL of the farms. Therefore, data shows that the farms need to improve the morphological quality of cows, in order to increase the PL, proteins and fat, taking to an increase of VL, so that they could improve the technical efficiency and be rentable without subs

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocar

EUROCarbDB: An open-access platform for glycoinformatics

The EUROCarbDB project is a design study for a technical framework, which provides sophisticated, freely accessible, open-source informatics tools and databases to support glycobiology and glycomic research. EUROCarbDB is a relational database containing glycan structures, their biological context and, when available, primary and interpreted analytical data from high-performance liquid chromatography, mass spectrometry and nuclear magnetic resonance experiments. Database content can be accessed via a web-based user interface. The database is complemented by a suite of glycoinformatics tools, specifically designed to assist the elucidation and submission of glycan structure and experimental data when used in conjunction with contemporary carbohydrate research workflows. All software tools and source code are licensed under the terms of the Lesser General Public License, and publicly contributed structures and data are freely accessible. The public test version of the web interface to the EUROCarbDB can be found at http://www.ebi.ac.uk/eurocarb

Rearrangements of 2.5 Kilobases of Noncoding DNA from the <i>Drosophila even-skipped</i> Locus Define Predictive Rules of Genomic <i>cis</i>-Regulatory Logic

Rearrangements of about 2.5 kilobases of regulatory DNA located 5′ of the transcription start site of the Drosophila even-skipped locus generate large-scale changes in the expression of even-skipped stripes 2, 3, and 7. The most radical effects are generated by juxtaposing the minimal stripe enhancers MSE2 and MSE3 for stripes 2 and 3 with and without small “spacer” segments less than 360 bp in length. We placed these fusion constructs in a targeted transformation site and obtained quantitative expression data for these transformants together with their controlling transcription factors at cellular resolution. These data demonstrated that the rearrangements can alter expression levels in stripe 2 and the 2–3 interstripe by a factor of more than 10. We reasoned that this behavior would place tight constraints on possible rules of genomic cis-regulatory logic. To find these constraints, we confronted our new expression data together with previously obtained data on other constructs with a computational model. The model contained representations of thermodynamic protein–DNA interactions including steric interference and cooperative binding, short-range repression, direct repression, activation, and coactivation. The model was highly constrained by the training data, which it described within the limits of experimental error. The model, so constrained, was able to correctly predict expression patterns driven by enhancers for other Drosophila genes; even-skipped enhancers not included in the training set; stripe 2, 3, and 7 enhancers from various Drosophilid and Sepsid species; and long segments of even-skipped regulatory DNA that contain multiple enhancers. The model further demonstrated that elevated expression driven by a fusion of MSE2 and MSE3 was a consequence of the recruitment of a portion of MSE3 to become a functional component of MSE2, demonstrating that cis-regulatory “elements” are not elementary objects.</p

MEMOPS: Data modelling and automatic code generation

In recent years the amount of biological data has exploded to the point where much useful information can only be extracted by complex computational analyses. Such analyses are greatly facilitated by metadata standards, both in terms of the ability to compare data originating from different sources, and in terms of exchanging data in standard forms, e.g. when running processes on a distributed computing infrastructure. However, standards thrive on stability whereas science tends to constantly move, with new methods being developed and old ones modified. Therefore maintaining both metadata standards, and all the code that is required to make them useful, is a non-trivial problem. Memops is a framework that uses an abstract definition of the metadata (described in UML) to generate internal data structures and subroutine libraries for data access (application programming interfaces - APIs - currently in Python, C and Java) and data storage (in XML files or databases). For the individual project these libraries obviate the need for writing code for input parsing, validity checking or output. Memops also ensures that the code is always internally consistent, massively reducing the need for code reorganisation. Across a scientific domain a Memops-supported data model makes it easier to support complex standards that can capture all the data produced in a scientific area, share them among all programs in a complex software pipeline, and carry them forward to deposition in an archive. The principles behind the Memops generation code will be presented, along with example applications in Nuclear Magnetic Resonance (NMR) spectroscopy and structural biology

Data from: Evaluating consumptive and nonconsumptive predator effects on prey density using field times series data

Determining the degree to which predation affects prey abundance in natural communities constitutes a key goal of ecological research. Predators can affect prey through both consumptive effects (CEs) and nonconsumptive effects (NCEs), although the contributions of each mechanism to the density of prey populations remain largely hypothetical in most systems. Common statistical methods applied to time series data cannot elucidate the mechanisms responsible for hypothesized predator effects on prey density (e.g., differentiate CEs from NCEs), nor provide parameters for predictive models. State space models (SSMs) applied to time series data offer a way to meet these goals. Here, we employ SSMs to assess effects of an invasive predatory zooplankter, Bythotrephes longimanus, on an important prey species, Daphnia mendotae, in Lake Michigan. We fit mechanistic models in a SSM framework to seasonal time series (1994-2012) using a recently developed, maximum likelihood-based optimization method, iterated filtering, which can overcome challenges in ecological data (e.g. nonlinearities, measurement error, and irregular sampling intervals). Our results indicate that B. longimanus strongly influences D. mendotae dynamics, with mean annual peak densities of B. longimanus observed in Lake Michigan estimated to cause a 61% reduction in D. mendotae population growth rate and a 59% reduction in peak biomass density. Further, the mechanism underlying the B. longimanus effect is most consistent with an NCE via reduced birth rates. The SSM approach also provided estimates for key biological parameters (e.g., demographic rates) and the contribution of dynamic stochasticity and measurement error. Our study therefore highlights the utility of SSMs to enhance inference for species interactions from time series data. In particular, our findings provide evidence derived directly from survey data that the invasive zooplankter B. longimanus is affecting zooplankton demographics and offer parameter estimates needed to inform predictive models that explore the effect of B. longimanus under different scenarios such as climate change

Lake Michigan 110M Zooplankton Time Series 1994-2012

Time series data from zooplankton survey of Lake Michigan collected near Muskegon, MI, via vertical tows by NOAA GLERL researchers. Includes collection date and Julian day. Biomass density data for Daphnia mendotae (D.mendotae), Bythotrephes longimanus (Bythotrephes), and Limnocalanus macrurus (male: LimncalanusM and female: LimncalanusF). "Prior_to_1st_Daphnia_obs" indicates if the observation occurred prior to the first positive observation of D. mendotae each year

R markdown file to generate Appendix S1

R markdown file used to generate Appendix S1 (included in manuscript supplementary materials), which describes model code and details of analysis used in manuscript

Fusion constructs.

<p>(A) The 7 striped expression pattern of <i>eve</i>, visualized with antibody staining. This and other embryos are oriented dorsal up and anterior to the left. The white rectangle located in the middle of the embryo indicates a 10% strip ranging from 35 to 92% embryo length (EL). (B) Schematic view of the <i>eve</i> gene. The transcript (black box) and early acting enhancers are shown. The distance of the 5′ end of each enhancer from the TSS is specified. The colored boxes and adjacent thick lines indicate the two segments of DNA used to create various reporter constructs. (C) (left) Fluorescence <i>in situ</i> hybridization for <i>lacZ</i> mRNA. (right) Segmented image with nuclear mask. Image segmentation was carried out as described <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003243#pgen.1003243-Janssens2" target="_blank">[16]</a>. Intense and punctate fluorescent spots in the nuclei are nascent transcripts. (D) Quantitative expression data for Eve protein and 4 fusion constructs, obtained from the area shown in the white rectangle in B. Embryos were classified temporally as belonging to one of eight time classes (T1–T8) in cleavage cycle 14A (C14A), each about 6.5 min long, as described <a href="http://www.plosgenetics.org/article/info:doi/10.1371/journal.pgen.1003243#pgen.1003243-Surkova1" target="_blank">[6]</a>. T1, T6 and T8 data are shown here, with time after egg deposition (AED). The numbers in parentheses are the number of embryos used to generate the averaged expression profiles of each time class. Arrows indicate regions of major alteration in gene expression after spacer removal. (E) <i>lac</i>Z mRNA expression from individual embryos. 4 fusion constructs and their gene expression at T6 are shown.</p