IFCN Cash Crop: Benchmarking Farms Globally Oilseed Production Costs

Vegetable oil production has become one of the fastest expanding cash crop sectors in the last 50 years and it is still increasing rapidly. However the regions of expansion, the sources of plant oil and their importance vary over time. To shed light on this development it is necessary to look at the farm level production systems and their production costs for a variety of countries and oilseeds. In this paper we present the first results of the IFCN Cash Crop Network covering the international comparison of oilseed producing farms. A total of 25 farms with oilseed production have been analysed in compiling this paper. All farms produce at least one of the following oilseeds: soybeans, oilseed rape, sunflower and (two farms) mustard. The farms are located in 14 different countries/regions and represent typical oilseed producing farms in their region/country. The farm data was collected and compiled in all countries and regions by IFCN Partners according to IFCN standards to en-sure its international comparability. The most competitive farms in oilseed production worldwide can be found in South America. The farms in Ukraine also have great potential. At the moment the farms in Argentina show the highest profit margins. The farms from North America can also cover their full costs with the prices they receive for soybeans, sunflower and rape seed.Farm comparisons, Cash Crop production, International competitiveness, International Farm Comparison Network, Oilseed, Benchmarking, Crop Production/Industries,

Finite element approximation of the p(⋅)p(\cdot)-Laplacian

We study a~priori estimates for the Dirichlet problem of the $p(\cdot)$-Laplacian, $$-\mathrm{div}(|\nabla v|^{p(\cdot)-2} \nabla v) = f.$$ We show that the gradients of the finite element approximation with zero boundary data converges with rate $O(h^\alpha)$ if the exponent $p$ is $\alpha$-H\"{o}lder continuous. The error of the gradients is measured in the so-called quasi-norm, i.e. we measure the $L^2$-error of $|\nabla v|^{\frac{p-2}{2}} \nabla v$

Assessing genetic diversity of wheat genotypes from different origins by SNP markers

Genetic diversity was investigated in a set of eleven hexaploid wheat genotypes originated from CIMMYT, Turkey in comparison with some modern European mostly originated from KWS wheat breeding program using 24 wheat SNP markers. The lowest and highest genetic dissimilarities were observed between genotypes Opus and LDO 330/06, KWS Salix and LDO 330/06, respectively. Based on cluster analysis, 38 wheat genotypes were grouped in two main clusters. Although the grouping pattern is very origin heterogeneous in each group, the grouping pattern of some genotypes appeared to be associated, to some extent. Principal coordinate analysis (PCoA) was used as an alternative way of visualizing the genotypic data. The first, second and third principal components explained 17.79%, 14.39% and 12.24% of the variation, respectively. This study can also be an indicator for breeders to evolve genotypes with diverse genetic background to achieve sustainability in wheat production, to get favorable heterotic combinations in a wheat improvement program

Approximation properties of the qq-sine bases

For $q>12/11$ the eigenfunctions of the non-linear eigenvalue problem associated to the one-dimensional $q$-Laplacian are known to form a Riesz basis of $L^2(0,1)$. We examine in this paper the approximation properties of this family of functions and its dual, in order to establish non-orthogonal spectral methods for the $p$-Poisson boundary value problem and its corresponding parabolic time evolution initial value problem. The principal objective of our analysis is the determination of optimal values of $q$ for which the best approximation is achieved for a given $p$ problem.Comment: 20 pages, 11 figures and 2 tables. We have fixed a number of typos and added references. Changed the title to better reflect the conten

A framework for identifying the recent origins of mobile antibiotic resistance genes

Since the introduction of antibiotics as therapeutic agents, many bacterial pathogens have developed resistance to antibiotics. Mobile resistance genes, acquired through horizontal gene transfer, play an important role in this process. Understanding from which bacterial taxa these genes were mobilized, and whether their origin taxa share common traits, is critical for predicting which environments and conditions contribute to the emergence of novel resistance genes. This knowledge may prove valuable for limiting or delaying future transfer of novel resistance genes into pathogens. The literature on the origins of mobile resistance genes is scattered and based on evidence of variable quality. Here, we summarize, amend and scrutinize the evidence for 37 proposed origins of mobile resistance genes. Using state-of-the-art genomic analyses, we supplement and evaluate the evidence based on well-defined criteria. Nineteen percent of reported origins did not fulfill the criteria to confidently assign the respective origin. Of the curated origin taxa, >90% have been associated with infection in humans or domestic animals, some taxa being the origin of several different resistance genes. The clinical emergence of these resistance genes appears to be a consequence of antibiotic selection pressure on taxa that are permanently or transiently associated with the human/domestic animal microbiome

TNFA deletion alters apoptosis as well as caspase 3 and 4 expression during otitis media

Abstract Background Tumor necrosis factor (TNFA) is the canonical member of the TNF superfamily, which plays a major role in both inflammation and apoptosis. To evaluate the role of TNFs in otitis media (OM), the most common disease of childhood, we evaluated middle ear (ME) expression of genes encoding the TNF and TNF receptor superfamilies during bacterial OM in the mouse, characterized OM in TNFA-deficient mice, and assessed apoptosis during OM in normal versus TNF-deficient MEs. Results TNFs and TNF receptors were broadly regulated during OM, with TNFA showing the highest level of up-regulation. TNF deficient mice exhibited mucosal hyperplasia even in the absence of infection and exuberant growth of the mucosa during OM, including the formation of mucosal polyps. Mucosal recovery during OM was also delayed, in parallel with a delay in mucosal apoptosis and reduced caspase gene expression. Conclusions The TNF and TNF receptor superfamilies mediate both inflammation and apoptosis during OM. TNF appears to be critical for the maintenance of mucosal architecture in both the normal and infected ME, since excessive accumulation of mucosal tissue is seen in TNFA-/- MEs both before and after bacterial inoculation of the ME. TNFA is also required for appropriate regulation of caspase genes

Evidence for wastewaters as environments where mobile antibiotic resistance genes emerge

The emergence and spread of mobile antibiotic resistance genes (ARGs) in pathogens have become a serious threat to global health. Still little is known about where ARGs gain mobility in the first place. Here, we aimed to collect evidence indicating where such\ua0initial mobilization\ua0events of clinically relevant ARGs may have occurred. We found that the majority of previously identified origin species did not carry the mobilizing elements that likely enabled intracellular mobility of the ARGs, suggesting a necessary interplay between different bacteria. Analyses of a broad range of metagenomes revealed that wastewaters and wastewater-impacted environments had by far the highest abundance of both origin species and corresponding mobilizing elements. Most origin species were only occasionally detected in other environments. Co-occurrence of origin species and corresponding mobilizing elements were rare in human microbiota. Our results identify wastewaters and wastewater-impacted environments as plausible arenas for the initial mobilization of resistance genes

Selection of reference genes for quantitative real-time PCR in a rat asphyxial cardiac arrest model

<p>Abstract</p> <p>Background</p> <p>Cardiac arrest, and the associated arrest of blood circulation, immediately leads to permanent brain damage because of the exhaustion of oxygen, glucose and energy resources in the brain. Most hippocampal CA1 neurons die during the first week post the insult. Molecular data concerning the recovery after resuscitation are sparse and limited to the early time period. Expression analysis of marker genes via quantitative real-time RT-PCR enables to follow up the remodeling process. However, proper validation of the applied normalization strategy is a crucial prerequisite for reliable conclusions.</p> <p>Therefore, the present study aimed to determine the expression stability of ten commonly used reference genes (<it>Actb</it>, actin, beta; <it>B2m</it>, beta-2 microglobulin;<it>CypA</it>, cyclophilin A; <it>Gapdh</it>, glyceraldehyde-3-phosphate dehydrogenase; <it>Hprt</it>, hypoxanthine guanine phosphoribosyl transferase; <it>Pgk1</it>, phosphoglycerate kinase 1; <it>Rpl13a</it>, ribosomal protein L13A; <it>Sdha</it>, succinat dehydrogenase complex, subunit a, flavoprotein (Fp); <it>Tbp</it>, TATA box binding protein; <it>Ywhaz</it>, tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide) in the rat hippocampus four, seven and twenty-one days after cardiac arrest. Moreover, experimental groups treated with the anti-inflammatory and anti-apoptotic drug minocycline have been included in the study as well.</p> <p>Results</p> <p>The microglial marker <it>Mac-1</it>, used as a target gene to validate the experimental model, was found to be upregulated about 10- to 20-fold after cardiac arrest.</p> <p>Expression stability of candidate reference genes was analyzed using geNorm and NormFinder software tools. Several of these genes behave rather stable. <it>CypA </it>and <it>Pgk1 </it>were identified by geNorm as the two most stable genes 4 and 21 days after asphyxial cardiac arrest, <it>CypA </it>and <it>Gapdh </it>at 7 days post treatment. <it>B2m </it>turned out to be the most variable candidate reference gene, being about 2-fold upregulated in the cardiac arrest treatment groups.</p> <p>Conclusion</p> <p>We have validated endogenous control genes for qRT-PCR analysis of gene expression in rat hippocampus after resuscitation from cardiac arrest. For normalization purposes in gene profiling studies a combination of <it>CypA </it>and <it>Pgk1 </it>should be considered 4 and 21 days post injury, whereas <it>CypA </it>and <it>Gapdh </it>is the best combination at 7 days. <it>CypA </it>is most favorable if restriction to a single reference gene for all time points is required.</p

GEnView: a gene-centric, phylogeny-based comparative genomics pipeline for bacterial genomes and plasmids

Comparing genomic loci of a given bacterial gene across strains and species can provide insights into their evolution, including information on e.g. acquired mobility, the degree of conservation between different taxa or indications of horizontal gene transfer events. While thousands of bacterial genomes are available to date, there is no software that facilitates comparisons of individual gene loci for a large number of genomes. GEnView (Genetic Environment View) is a Python-based pipeline for the comparative analysis of gene-loci in a large number of bacterial genomes, providing users with automated, taxon-selective access to the &gt;800.000 genomes and plasmids currently available in the NCBI Assembly and RefSeq databases, and is able to process local genomes that are not deposited at NCBI, enabling searches for genomic sequences and to analyze their genetic environments through the interactive visualization and extensive metadata files created by GEnView

Adaptive FE-BE Coupling for Strongly Nonlinear Transmission Problems with Coulomb Friction

We analyze an adaptive finite element/boundary element procedure for scalar elastoplastic interface problems involving friction, where a nonlinear uniformly monotone operator such as the p-Laplacian is coupled to the linear Laplace equation on the exterior domain. The problem is reduced to a boundary/domain variational inequality, a discretized saddle point formulation of which is then solved using the Uzawa algorithm and adaptive mesh refinements based on a gradient recovery scheme. The Galerkin approximations are shown to converge to the unique solution of the variational problem in a suitable product of L^p- and L^2-Sobolev spaces.Comment: 27 pages, 3 figure