PZnet: Efficient 3D ConvNet Inference on Manycore CPUs

Convolutional nets have been shown to achieve state-of-the-art accuracy in many biomedical image analysis tasks. Many tasks within biomedical analysis domain involve analyzing volumetric (3D) data acquired by CT, MRI and Microscopy acquisition methods. To deploy convolutional nets in practical working systems, it is important to solve the efficient inference problem. Namely, one should be able to apply an already-trained convolutional network to many large images using limited computational resources. In this paper we present PZnet, a CPU-only engine that can be used to perform inference for a variety of 3D convolutional net architectures. PZNet outperforms MKL-based CPU implementations of PyTorch and Tensorflow by more than 3.5x for the popular U-net architecture. Moreover, for 3D convolutions with low featuremap numbers, cloud CPU inference with PZnet outperfroms cloud GPU inference in terms of cost efficiency

Self-Supervised Metric Learning for Alignment of Petascale Connectomics Datasets

The reconstruction of neural circuits from serial section electron microscopy(ssEM) images is being accelerated by automatic image segmentation methods. These methods are often limited by the preceding step of aligning 2D section images to create a 3D image stack. Precise and robust alignment in the presence of image artifacts is challenging, especially as datasets are attaining the petascale. The problem of 3D stack alignment can be divided into two subproblems – image pair alignment and alignment globalization. Image pair alignment is . This dissertation presents a computational pipeline for aligning ssEM images with several key elements. First, a self-supervised convolutional net are trained via metric learning to encode and align image pairs, followed by iterative finetuning of alignment. Second, a procedure called vector voting is used to remove outliers, further increasing robustness to image defects. Third, for speedup the series is divided into blocks that are distributed to computational workers for alignment. Fourth, the blocks are aligned to each other by composing transformations with decay, which achieves a global alignment without resorting to a time-consuming global optimization. The pipeline is used to align a female adult fly brain dataset, as well as a cubic millimeter of mouse visual cortex and is publicly available through two open source Python packages

Intangible cultural heritage as a resource for cultural tourism: the case of embroidery and carpet weaving in Ukraine

The purpose of the article is to present intangible cultural heritage as a resource for a special category of cultural and educational tourism, namely heritage tourism. The authors use embroidery and carpet weaving as examples of intangible cultural heritage. The methods used in the study include a review of foreign and domestic theoretical and methodological developments, analysis of best practices in the field of heritage tourism, field research, analysis of materials collected during a survey of locations and the authors’ personal experience of tourist products. The results of the study outline the development of heritage tourism based on a creative approach as well as strategic plans of the state regarding tourism development. Based on practical experience, the authors present general principles of designing tourist routes, where elements of intangible cultural heritage act as “magnets”. The analysis has indicated elements of intangible cultural heritage that can appeal to tourists under particular circumstances. The authors argue that the development of heritage tourism based on a creative approach to designing tourist products in the form of intangible cultural heritage should popularize it in the national tourism market and promote tourism destinations with intangible cultural heritage, such as embroidery and carpet weaving. These tourist destinations should be used not only to attract domestic and foreign tourists, but also to promote the Ukrainian culture

Catalytic properties of AgAlBEA and AgSiBEA zeolites in H2-promoted selective reduction of NO with ethanol

International audiencePhysicochemical properties of AgAlBEA and AgSiBEA zeolites were investigated by IR spectroscopy with pyridine, H2-TPR, XPS and diffuse reflectance UV–vis spectroscopy. Their catalytic properties were studied in the process of selective reduction of NO with ethanol and in the presence of hydrogen in reaction mixture. AgAlBEA catalysts show wider temperature range of NO-to-N2 conversion in the process of SCR with ethanol than AgSiBEA. Promoting H2-effect on the SCR of NO with ethanol is observed in the presence of AgAlBEA catalysts, whereas it is almost absent for AgSiBEA. A key factor for better performance of AgAlBEA than AgSiBEA is the presence of silver nanoclusters in close proximity of strong Lewis acidic sites

A Generalized Framework for Automatic Scripting Language Parallelization

Computational scientists are typically not expert programmers, and thus work in easy to use dynamic languages. However, they have very high performance requirements, due to their large datasets and experimental setups. Thus, the performance required for computational science must be extracted from dynamic languages in a manner that is transparent to the programmer. Current approaches to optimize and parallelize dynamic languages, such as just-in-time compilation and highly optimized interpreters, require a huge amount of implementation effort and are typically only effective for a single language. However, scientists in different fields use different languages, depending upon their needs.This paper presents techniques to enable automatic extraction of parallelism within scripts that are universally applicable across multiple different dynamic scripting languages. The key insight is that combining a script with its interpreter, through program specialization techniques, will embed any parallelism within the script into the combined program that can then be extracted via automatic parallelization techniques. Additionally, this paper presents several enhancements to existing speculative automatic parallelization techniques to handle the dependence patterns created by the specialization process. A prototype of the proposed technique, called Partial Evaluation with Parallelization (PEP), is evaluated against two open-source script interpreters with 6 input linear algebra kernel scripts each. The resulting geomean speedup of 5.10× on a 24-core machine shows the potential of the generalized approach in automatic extraction of parallelism in dynamic scripting languages

Method development for the quantitative determination of captopril from Caco-2 cell monolayers by using LC-MS/MS

Aim. Caco-2 cells are a human colon epithelial cancer cell line used as a model of human intestinal absorption of drugs and other compounds. Although compounds were used in the original Caco-2 cells monolayer assays, compounds have been replaced in most laboratories by the use of liquid chromatography-mass spectrometry (LC-MS) and LC-tandem mass spectrometry (LC-MS/MS). Mass spectrometry not only eliminates the need for compounds, but permits the simultaneous measurement of multiple compounds. The measurement of multiple compounds per assay reduces the number of incubations that need to be carried out, thereby increasing the throughput of the experiments. Furthermore, LC-MS and LC-MS-MS add another dimension to Caco-2 assays by facilitating the investigation of the metabolism of compounds by Caco-2 cells. A simple, rapid LC-MS/MS method has been developed for determination of captopril from confluent Caco-2 monolayers and from aqueous solution. Materials and methods. Chromatography was achieved on Discovery C18, 50 × 2.1 mm, 5 μm column. Samples were chromatographed in a gradient mode (eluent A (acetonitrile – water – formic acid, 5 : 95 : 0.1 v/v), eluent B (acetonitrile – formic acid, 100 : 0.1 v/v)). The initial content of the eluent B is 0%, which increases linearly by 1.0 min to 100% and to 1.01 min returns to the initial 0%. The mobile phase was delivered at a flow rate of 0.4 mL/min into the mass spectrometer ESI chamber. The sample volume was 5 μl. Results. Under these conditions, captopril was eluted at 1.42 min. A linear response function was established at 2 – 200 ng/mL. The regression equation for the analysis was y =0.0187x+0.000248 with coefficient of correction (r2) = 0.9993. According to the Caco-2 test results, captopril showed low permeability. It should be noted that the recovery value is 103.20%. The within-run coefficients of variation ranged between 0.321% and 0.541%. The within-run percentages of nominal concentrations ranged between 99.13% and 101.12%. The between-run coefficients of variation ranged between 0.314% and 0.663%. The between-run percentages of nominal concentrations ranged between 99.17% and 101.03%.The assay values on both the occasions (intra- and inter-day) were found to be within the accepted limits. Conclusion. From results of analysis, it can be concluded that developed method is simple and rapid for determination of captopril from confluent Caco-2 monolayers and from aqueous solution. Acquired results demonstrate that proposed strategy can be effortlessly and advantageously applied for examination of captopril from Caco-2 cell monolayers

Sn-BEA zeolites prepared by two-step postsynthesis method: Physicochemical properties and catalytic activity in processes based on MPV reduction

International audienceSn0.5SiBEA and Sn2.0SiBEA zeolites obtained by two-step postsynthesis method were characterized by several physicochemical techniques (namely, NMR, Mössbauer, XPS, DR UV-vis and IR spectroscopies) and used in the study of Meerwein–Ponndorf–Verley (MPV) reduction as well as with the subsequent reaction of etherification, that is, conversion of (i) cyclohexanone with 2-propanol, (ii) 4-methoxybenzaldehyde with 2-butanol, and (iii) HMF with butyl alcohols (1-butanol, 2-butanol or isobutanol). The results have shown that in the case of cyclohexanone, MPV reduction to cyclohexanol occurs on both Sn0.5SiBEA and Sn2.0SiBEA zeolite catalysts with a higher degree of conversion in the presence of Sn2.0SiBEA. For 4-methoxybenzaldehyde a tandem process was observed consisting of MPV reduction with 2-butanol to 4-methoxybenzylalcohol followed by its etherification with 2-butanol to 4-methoxybenzyl sec-butyl ether. Higher conversion of aldehyde was achieved on the catalyst with higher amount of tin. The zeolites were active in HMF conversion with butyl alcohols. However, a tandem process including MPV reduction with the next formation of furanic diether was achieved only in the presence of secondary alcohol at test conditions