Decreasing time consumption of microscopy image segmentation through parallel processing on the GPU

The computational performance of graphical processing units (GPUs) has improved significantly. Achieving speedup factors of more than 50x compared to single-threaded CPU execution are not uncommon due to parallel processing. This makes their use for high throughput microscopy image analysis very appealing. Unfortunately, GPU programming is not straightforward and requires a lot of programming skills and effort. Additionally, the attainable speedup factor is hard to predict, since it depends on the type of algorithm, input data and the way in which the algorithm is implemented. In this paper, we identify the characteristic algorithm and data-dependent properties that significantly relate to the achievable GPU speedup. We find that the overall GPU speedup depends on three major factors: (1) the coarse-grained parallelism of the algorithm, (2) the size of the data and (3) the computation/memory transfer ratio. This is illustrated on two types of well-known segmentation methods that are extensively used in microscopy image analysis: SLIC superpixels and high-level geometric active contours. In particular, we find that our used geometric active contour segmentation algorithm is very suitable for parallel processing, resulting in acceleration factors of 50x for 0.1 megapixel images and 100x for 10 megapixel images

Clastic vs. primary precipitated evaporites in the Messinian sicilian Basins

The Messinian stratigraphy of Sicily has a particular importance for the comprehension ofthe Messinian salinity crisis as its successions bear the greatest similarity with those of thedeep Mediterranean basins. Despite the large number of studies carried out in the last 30years, we believe that the true time and genetic relationships between the different evaporiticand non evaporitic rock bodies are still not well established. This is probably due to thelimited, partial view offered by the central Sicilian basin, despite its complete Messinianstratigraphic record.Clastic and chaotic evaporitic deposits emplaced by tectonically-driven small to largescaleresedimentation processes form an important part of the MSC record of Sicily in theBelice and Caltanissetta basins. Facies characteristics of clastic evaporites, the stratigraphicrelationships with the other Messinian deposits, their possible significance in the regionalgeological evolution and the implications at a Mediterranean scale will be discussed in thefield. Attention also will be paid to primary precipitated facies of Lower and UpperEvaporites.The main aim of this field trip is to visit and discuss, beside some of the classic localitiesof the Caltanissetta basin, other less known outcrops of western Sicily (Belice basin), inorder to have a more complete regional geological framework of the MSC events in Sicily.This will give the participants the opportunity to discuss many of the still open problemsconcerning the MSC. In this section we suggest some topics for discussion during the fieldtrip

Field Evaluation of the Photo-induced Electron Transfer Fluorogenic Primers (PET) Real-time PCR for the Detection of Plasmodium falciparum in Tanzania.

Accurate diagnosis of malaria infections remains challenging, especially in the identification of submicroscopic infections. New molecular diagnostic tools that are inexpensive, sensitive enough to detect low-level infections and suitable in laboratory settings of resource-limited countries are required for malaria control and elimination programmes. Here the diagnostic potential of a recently developed photo-induced electron transfer fluorogenic primer (PET) real-time polymerase chain reaction (PCR) called PET-PCR was investigated. This study aimed to (i) evaluate the use of this assay as a method for the detection of both Plasmodium falciparum and other Plasmodium species infections in a developing country's diagnostic laboratory; and, (ii) determine the assay's sensitivity and specificity compared to a nested 18S rRNA PCR. Samples used in this study were obtained from a previous study conducted in the region of Iringa, Tanzania. A total of 303 samples from eight health facilities in Tanzania were utilized for this evaluation. All samples were screened using the multiplex PET-PCR assay designed to detect Plasmodium genus and P. falciparum initially in laboratory in Tanzania and then repeated at a reference laboratory at the CDC in the USA. Microscopy data was available for all the 303 samples. A subset of the samples were tested in a blinded fashion to find the sensitivity and specificity of the PET-PCR compared to the nested 18S rRNA PCR. Compared to microscopy, the PET-PCR assay was 59% more sensitive in detecting P. falciparum infections. The observed sensitivity and specificity were 100% (95% confidence interval (CI0.95) = 94-100%) and (CI0.95 = 96-100%), respectively, for the PET-PCR assay when compared to nested 18S rRNA PCR. When compared to 18S rRNA PCR, microscopy had a low sensitivity of 40% (CI0.95 = 23-61%) and specificity of 100% (CI0.95 = 96-100%). The PET-PCR results performed in the field laboratory in Tanzania were in 100% concordance with the results obtained at the reference laboratory in the USA. The PET-PCR is a new molecular diagnostic tool with similar performance characteristics as commonly used PCR methods that is less expensive, easy to use, and amiable to large scale-surveillance studies in developing country settings

Massive pneumoencephalus of late onset after an en bloc resection for lung cancer

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Involvement of PPAR\u3b3 in the anticonvulsant activity of EP-80317, a ghrelin receptor antagonist

Ghrelin, des-acyl ghrelin and other related peptides possess anticonvulsant activities. Although ghrelin and cognate peptides were shown to physiologically regulate only the ghrelin receptor, some of them were pharmacologically proved to activate the peroxisome proliferator-activated receptor gamma (PPAR\u3b3) through stimulation of the scavenger receptor CD36 in macrophages. In our study, we challenged the hypothesis that PPAR\u3b3 could be involved in the anticonvulsant effects of EP-80317, a ghrelin receptor antagonist. For this purpose, we used the PPAR\u3b3 antagonist GW9662 to evaluate the modulation of EP-80317 anticonvulsant properties in two different models. Firstly, the anticonvulsant effects of EP-80317 were studied in rats treated with pilocarpine to induce status epilepticus (SE). Secondly, the anticonvulsant activity of EP-80317 was ascertained in the repeated 6-Hz corneal stimulation model in mice. Behavioral and video electrocorticographic (ECoG) analyses were performed in both models. We also characterized levels of immunoreactivity for PPAR\u3b3 in the hippocampus of 6-Hz corneally stimulated mice. EP-80317 predictably antagonized seizures in both models. Pre-treatment with GW9662 counteracted almost all EP-80317 effects both in mice and rats. Only the effects of EP-80317 on power spectra of ECoGs recorded during repeated 6-Hz corneal stimulation were practically unaffected by GW9662 administration. Moreover, GW9662 alone produced a decrease in the latency of tonic-clonic seizures and accelerated the onset of SE in rats. Finally, in the hippocampus of mice treated with EP-80317 we found increased levels of PPAR\u3b3 immunoreactivity. Overall, these results support the hypothesis that PPAR\u3b3 is able to modulate seizures and mediates the anticonvulsant effects of EP-80317

Size Matters: Microservices Research and Applications

In this chapter we offer an overview of microservices providing the introductory information that a reader should know before continuing reading this book. We introduce the idea of microservices and we discuss some of the current research challenges and real-life software applications where the microservice paradigm play a key role. We have identified a set of areas where both researcher and developer can propose new ideas and technical solutions.Comment: arXiv admin note: text overlap with arXiv:1706.0735

Modelling of Natural Convective Heating of a Standard Wet Brick for Oven Energy Consumption Tests

The environmental impact of buildings is directly influenced by low-efficiency appliances like electric ovens. Their energy class is estimated through a test prescribed by the EN 60350 European standard, where a wet clay brick is heated under set conditions and the energy consumption is measured; throughout the test, particular attention is devoted to the control of air temperature. In this work, a transient model of the oven suitable for control design was realized including the heat and mass transfer within the brick. A lumped-parameter approach was used to ensure good predictive properties and low computational cost. The dynamics of the cavity air and the Pt500, which is used in normal operation to maintain the desired set point, was also included in the model. Model parameters were determined through an optimization procedure based on the experimental data collected during energy consumption tests with the oven in natural convective heating mode. The model was then validated. Good results were obtained in the prediction of both temperature and heating time

Rapid and sensitive detection of mycobacterium ulcerans by use of a loop-mediated isothermal amplification test

This work reports the design and evaluation of a rapid loop-mediated isothermal amplification test for detecting Mycobacterium ulcerans DNA based on the multicopy insertion sequence IS2404. The test is robust and specific with a detection limit equivalent to 20 copies of the target sequence (0.01 to 0.1 genome). The test has potential for the diagnosis of Buruli ulcer under field conditions