Image Denoising using Attention-Residual Convolutional Neural Networks

During the image acquisition process, noise is usually added to the data mainly due to physical limitations of the acquisition sensor, and also regarding imprecisions during the data transmission and manipulation. In that sense, the resultant image needs to be processed to attenuate its noise without losing details. Non-learning-based strategies such as filter-based and noise prior modeling have been adopted to solve the image denoising problem. Nowadays, learning-based denoising techniques showed to be much more effective and flexible approaches, such as Residual Convolutional Neural Networks. Here, we propose a new learning-based non-blind denoising technique named Attention Residual Convolutional Neural Network (ARCNN), and its extension to blind denoising named Flexible Attention Residual Convolutional Neural Network (FARCNN). The proposed methods try to learn the underlying noise expectation using an Attention-Residual mechanism. Experiments on public datasets corrupted by different levels of Gaussian and Poisson noise support the effectiveness of the proposed approaches against some state-of-the-art image denoising methods. ARCNN achieved an overall average PSNR results of around 0.44dB and 0.96dB for Gaussian and Poisson denoising, respectively FARCNN presented very consistent results, even with slightly worsen performance compared to ARCNN.Comment: Published in: 2020 33rd SIBGRAPI Conference on Graphics, Patterns and Images (SIBGRAPI

Systems and Synthetic Biology Approaches to Engineer Fungi for Fine Chemical Production

Since the advent of systems and synthetic biology, many studies have sought to harness microbes as cell factories through genetic and metabolic engineering approaches. Yeast and filamentous fungi have been successfully harnessed to produce fine and high value-added chemical products. In this review, we present some of the most promising advances from recent years in the use of fungi for this purpose, focusing on the manipulation of fungal strains using systems and synthetic biology tools to improve metabolic flow and the flow of secondary metabolites by pathway redesign. We also review the roles of bioinformatics analysis and predictions in synthetic circuits, highlighting in silico systemic approaches to improve the efficiency of synthetic modules

The Advertisement Calls and Distribution of Two Sympatric Species of \u3cem\u3eChiasmocleis\u3c/em\u3e (Méhely 1904) (Anura, Microhylidae, Gastrophryninae) from the Atlantic Forest

The advertisement calls of Chiasmocleis cordeiroi and C. crucis are described for populations from the municipalities of Igrapiúna and Camacan, respectively, state of Bahia, Brazil. Both calls consist of multipulsed notes produced in series. Differences between the two calls are: dominant frequency, higher in C. cordeiroi (range 4500-4898 Hz; C. crucis range 4069-4435 Hz); note rate, higher in C. cordeiroi (range 6.20--7.46 s/note; C. crucis range 5.17-5.59 s/note); pulse rate, higher in C. cordeiroi (151.82-194.83 s/note; C. crucis range 125.30- 142.12 s/note); and the structure of the modulation patterns of the notes. Moreover, the advertisement calls of C. crucis and C. cordeiroi are more similar than the calls of all syntopic congeners. Furthermore, the current distribution of both species was extended

Lattice dynamics localization in low-angle twisted bilayer graphene

A low twist angle between the two stacked crystal networks in bilayer graphene enables self-organized lattice reconstruction with the formation of a periodic domain. This superlattice modulates the vibrational and electronic structures, imposing new rules for electron-phonon coupling and the eventual observation of strong correlation and superconductivity. Direct optical images of the crystal superlattice in reconstructed twisted bilayer graphene are reported here, generated by the inelastic scattering of light in a nano-Raman spectroscope. The observation of the crystallographic structure with visible light is made possible due to lattice dynamics localization, the images resembling spectral variations caused by the presence of strain solitons and topological points. The results are rationalized by a nearly-free-phonon model and electronic calculations that highlight the relevance of solitons and topological points, particularly pronounced for structures with small twist angles. We anticipate our discovery to play a role in understanding Jahn-Teller effects and electronic Cooper pairing, among many other important phonon-related effects, and it may be useful for characterizing devices in the most prominent platform for the field of twistronics.Comment: 9 pages, 8 figure

The ocean sampling day consortium.

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world's oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

Planning, Implementing, and Running a Multicentre Preterm Birth Study with Biobank Resources in Brazil: The Preterm SAMBA Study

Background. Our aim was to describe the steps in planning, implementing, and running a multicentre cohort study of maternal and perinatal health using a high-quality biobank comprised of maternal serum, plasma, and hair samples collected from five sites in Brazil. The Preterm SAMBA study, conducted by the Brazilian Network for Studies on Reproductive and Perinatal Health, was an innovative approach used to identify women at higher risk for preterm birth. It is also of great importance in the study of other maternal and perinatal complications in the context of Brazil, which is a middle-income country. Methods. We described phases of planning, implementing, and running the Preterm SAMBA study, a multicentre Brazilian cohort study of low-risk nulliparous pregnant women, to validate a set of metabolite biomarkers for preterm birth identified in an external cohort. Procedures and strategies used to plan, implement, and maintain this multicentre preterm birth study are described in detail. Barriers and experience cited in the current narrative are not usually discussed in the scientific literature or published study protocols. Results. Several barriers and strategies were identified in different phases of the Preterm SAMBA study at different levels of the study framework (steering committee; coordinating and local centres). Strategies implemented and resources used in the study are a legacy of the Brazilian Network, aimed at training collaborators in such complex settings. Conclusion. The Brazilian Network for Studies on Reproductive and Perinatal Health has gained some experience in conducting a multicentre cohort study using a resourceful biobank which may be helpful to other research groups and maternal/perinatal health networks that plan on employing a similar approach to a similar background.201

Bicistronic DNA vaccines simultaneously encoding HIV, HSV and HPV antigens promote CD8⁺ T cell responses and protective immunity

Millions of people worldwide are currently infected with human papillomavirus (HPV), herpes simplex virus (HSV) or human immunodeficiency virus (HIV). For this enormous contingent of people, the search for preventive and therapeutic immunological approaches represents a hope for the eradication of latent infection and/or virus-associated cancer. To date, attempts to develop vaccines against these viruses have been mainly based on a monovalent concept, in which one or more antigens of a virus are incorporated into a vaccine formulation. In the present report, we designed and tested an immunization strategy based on DNA vaccines that simultaneously encode antigens for HIV, HSV and HPV. With this purpose in mind, we tested two bicistronic DNA vaccines (pIRES I and pIRES II) that encode the HPV-16 oncoprotein E7 and the HIV protein p24 both genetically fused to the HSV-1 gD envelope protein. Mice i.m. immunized with the DNA vaccines mounted antigen-specific CD8⁺ T cell responses, including in vivo cytotoxic responses, against the three antigens. Under experimental conditions, the vaccines conferred protective immunity against challenges with a vaccinia virus expressing the HIV-derived protein Gag, an HSV-1 virus strain and implantation of tumor cells expressing the HPV-16 oncoproteins. Altogether, our results show that the concept of a trivalent HIV, HSV, and HPV vaccine capable to induce CD8⁺ T cell-dependent responses is feasible and may aid in the development of preventive and/or therapeutic approaches for the control of diseases associated with these viruses.CNPqINCTVFAPESPUS

The ocean sampling day consortium

Ocean Sampling Day was initiated by the EU-funded Micro B3 (Marine Microbial Biodiversity, Bioinformatics, Biotechnology) project to obtain a snapshot of the marine microbial biodiversity and function of the world’s oceans. It is a simultaneous global mega-sequencing campaign aiming to generate the largest standardized microbial data set in a single day. This will be achievable only through the coordinated efforts of an Ocean Sampling Day Consortium, supportive partnerships and networks between sites. This commentary outlines the establishment, function and aims of the Consortium and describes our vision for a sustainable study of marine microbial communities and their embedded functional traits

The Fourteenth Data Release of the Sloan Digital Sky Survey: First Spectroscopic Data from the extended Baryon Oscillation Spectroscopic Survey and from the second phase of the Apache Point Observatory Galactic Evolution Experiment

The fourth generation of the Sloan Digital Sky Survey (SDSS-IV) has been in operation since July 2014. This paper describes the second data release from this phase, and the fourteenth from SDSS overall (making this, Data Release Fourteen or DR14). This release makes public data taken by SDSS-IV in its first two years of operation (July 2014-2016). Like all previous SDSS releases, DR14 is cumulative, including the most recent reductions and calibrations of all data taken by SDSS since the first phase began operations in 2000. New in DR14 is the first public release of data from the extended Baryon Oscillation Spectroscopic Survey (eBOSS); the first data from the second phase of the Apache Point Observatory (APO) Galactic Evolution Experiment (APOGEE-2), including stellar parameter estimates from an innovative data driven machine learning algorithm known as "The Cannon"; and almost twice as many data cubes from the Mapping Nearby Galaxies at APO (MaNGA) survey as were in the previous release (N = 2812 in total). This paper describes the location and format of the publicly available data from SDSS-IV surveys. We provide references to the important technical papers describing how these data have been taken (both targeting and observation details) and processed for scientific use. The SDSS website (www.sdss.org) has been updated for this release, and provides links to data downloads, as well as tutorials and examples of data use. SDSS-IV is planning to continue to collect astronomical data until 2020, and will be followed by SDSS-V.Comment: SDSS-IV collaboration alphabetical author data release paper. DR14 happened on 31st July 2017. 19 pages, 5 figures. Accepted by ApJS on 28th Nov 2017 (this is the "post-print" and "post-proofs" version; minor corrections only from v1, and most of errors found in proofs corrected