How to circumvent the limitations of open source software and orthorectify how (or better) than with commercial software

High and very high resolution satellite images are now an irreplaceable resource for earth observation in general and for the extraction of hydrogeological information in particular. In order to use them correctly and compare them with previous surveys and maps, they must be treated geometrically to removethedistortions introduced by the acquisition process. Orthorectification is not a simple georeferencing because the process must take into account the three-dimensional acquisition geometry of the sensor. For this reason orthorectification must be performed within specific commercial software with additional costs compared to image acquisition which, in some cases, is currently free of charge. Some orthorectification algorithms, mainly based on the RPC approach, are available in open source GIS software such as QGIS. OTB (Orpheus toolbox) for QGIS contains some of these algorithms but its interfaces are not clear and there are some incomprehensible limitations such as the impossibility to input three-dimensional ground control points (GCPs). This severely limits the final achievable accuracy because it does not allow to correctly estimate the influence of different ground morphologies on the acquisition geometry. To get around these limitations you can make a "pseudo DEM" and other expedients to complete the whole process obtaining absolute results comparable if not better than those of commercial software. The proposed procedure may not be the fastest but it can be a valid alternative for those who use satellite images as a tool in their research work

Vasopressin regulates the growth of the biliary epithelium in polycystic liver disease

The neurohypophysial hormone arginine vasopressin (AVP) acts by three distinct receptor subtypes: V1a, V1b, and V2. In the liver, AVP is involved in ureogenesis, glycogenolysis, neoglucogenesis and regeneration. No data exist about the presence of AVP in the biliary epithelium. Cholangiocytes are the target cells in a number of animal models of cholestasis, including bile duct ligation (BDL), and in several human pathologies, such as polycystic liver disease characterized by the presence of cysts that bud from the biliary epithelium. In vivo, liver fragments from normal and BDL mice and rats as well as liver samples from normal and ADPKD patients were collected to evaluate: (i) intrahepatic bile duct mass by immunohistochemistry for cytokeratin-19; and (ii) expression of V1a, V1b and V2 by immunohistochemistry, immunofluorescence and real-time PCR. In vitro, small and large mouse cholangiocytes, H69 (non-malignant human cholangiocytes) and LCDE (human cholangiocytes from the cystic epithelium) were stimulated with vasopressin in the absence/presence of AVP antagonists such as OPC-31260 and Tolvaptan, before assessing cellular growth by MTT assay and cAMP levels. Cholangiocytes express V2 receptor that was upregulated following BDL and in ADPKD liver samples. Administration of AVP increased proliferation and cAMP levels of small cholangiocytes and LCDE cells. We found no effect in the proliferation of large mouse cholangiocytes and H69 cells. Increases were blocked by preincubation with the AVP antagonists. These results showed that AVP and its receptors may be important in the modulation of the proliferation rate of the biliary epithelium

Guidelines for sample preparation procedures in GMO analysis

This document aims at providing guidelines for a correct sample preparation in GMO analysis on food, feed, seed, plants and propagating material samples. It has been developed by the European Network of GMO Laboratories (ENGL), specifically by the ENGL working group “sample preparation procedures” upon a mandate of the ENGL steering committee. The structure of the document is based on that of an existing ISO standard (ISO 6498:2012), dealing with sample preparation for feed; starting from this, the procedures were adapted to the needs of GMO detection and the scope concerning matrices was widen to food, feed and seeds. These guidelines cover the key steps of the sample preparation, i.e. the size of the laboratory sample, the mass reduction techniques as well as techniques for comminution and mixing; considerations about the test portion are included and some performance tests to be applied at different steps of the process are provided. While sample preparation, falling after sampling and before analytical testing for GMOs, has suffered from a lack of guidance and harmonization, this document provides detailed and practical hints on this important step, thus contributing to foster testing harmonisation.JRC.I.3-Molecular Biology and Genomic

HAX1 is a novel binding partner of Che-1/AATF. Implications in oxidative stress cell response

HAX1 is a multifunctional protein involved in the antagonism of apoptosis in cellular response to oxidative stress. In the present study we identified HAX1 as a novel binding partner for Che-1/AATF, a pro-survival factor which plays a crucial role in fundamental processes, including response to multiple stresses and apoptosis. HAX1 and Che-1 proteins show extensive colocalization in mitochondria and we demonstrated that their association is strengthened after oxidative stress stimuli. Interestingly, in MCF-7 cells, resembling luminal estrogen receptor (ER) positive breast cancer, we found that Che-1 depletion correlates with decreased HAX1 mRNA and protein levels, and this event is not significantly affected by oxidative stress induction. Furthermore, we observed an enhancement of the previously reported interaction between HAX1 and estrogen receptor alpha (ERα) upon H2O2 treatment. These results indicate the two anti-apoptotic proteins HAX1 and Che-1 as coordinated players in cellular response to oxidative stress with a potential role in estrogen sensitive breast cancer cells

Kernel Lot Distribution Assessment (KeLDA): a Comparative Study of Protein and DNA-Based Detection Methods for GMO Testing

Monitoring of market products for detection of genetically modified organisms (GMO) is needed to comply with legislation in force in many regions of the world, to enforce traceability and to allow official control along the production and the distribution chains. This objective can be more easily achieved if reliable, time and cost-effective analytical methods are available. A GMO can be detected using either DNA-based or protein-based methods; both present advantages and disadvantages. The objective of this work was to assess the performance of a protein-based (lateral flow strips—LFT) and of a DNA-based (polymerase chain reaction—PCR) detection method for GMO analysis. One thousand five hundred samples of soybean, deriving from the sampling of 15 independent bulk lots in large shipments, were analysed to assess and compare the performance of the analytical methods and evaluate their suitability for GMO testing. Several indicators were used to compare the performance of the methods, including the percentage correlation between the PCR and LFT results. The GMO content of the samples ranged from 0 up to 100 %, allowing a full assessment of both analytical approaches with respect to all possible GMO content scenarios. The study revealed a very similar performance of the two methodologies, with low false-negative and false-positive results, and a very satisfactory capacity of both methods in detecting low amounts of target. While determining the fitness for purpose of both analytical approaches, this study also underlines the importance of alternative method characteristics, like costs and time

Mice repeatedly exposed to Group-A \u3b2-Haemolytic Streptococcus show perseverative behaviors, impaired sensorimotor gating, and immune activation in rostral diencephalon

Repeated exposure to Group-A \u3b2-Haemolytic Streptococcus (GAS) may constitute a vulnerability factor in the onset and course of pediatric motor disturbances. GAS infections/colonization can stimulate the production of antibodies, which may cross the blood brain barrier, target selected brain areas (e.g. basal ganglia), and exacerbate motor alterations. Here, we exposed developing SJL male mice to four injections with a GAS homogenate and evaluated the following domains: motor coordination; general locomotion; repetitive behaviors; perseverative responses; and sensorimotor gating (pre-pulse inhibition, PPI). To demonstrate that behavioral changes were associated with immune-mediated brain alterations, we analyzed, in selected brain areas, the presence of infiltrates and microglial activation (immunohistochemistry), monoamines (HPLC), and brain metabolites (in vivo Magnetic Resonance Spectroscopy). GAS-exposed mice showed increased repetitive and perseverative behaviors, impaired PPI, and reduced concentrations of serotonin in prefrontal cortex, a brain area linked to the behavioral domains investigated, wherein they also showed remarkable elevations in lactate. Active inflammatory processes were substantiated by the observation of infiltrates and microglial activation in the white matter of the anterior diencephalon. These data support the hypothesis that repeated GAS exposure may elicit inflammatory responses in brain areas involved in motor control and perseverative behavior, and result in phenotypic abnormalities