DES science portal: Computing photometric redshifts

A significant challenge facing photometric surveys for cosmological purposes is the need to produce reliable redshift estimates. The estimation of photometric redshifts (photo-zs) has been consolidated as the standard strategy to bypass the high production costs and incompleteness of spectroscopic redshift samples. Training-based photo-z methods require the preparation of a high-quality list of spectroscopic redshifts, which needs to be constantly updated. The photo-z training, validation, and estimation must be performed in a consistent and reproducible way in order to accomplish the scientific requirements. To meet this purpose, we developed an integrated web-based data interface that not only provides the framework to carry out the above steps in a systematic way, enabling the ease testing and comparison of different algorithms, but also addresses the processing requirements by parallelizing the calculation in a transparent way for the user. This framework called the Science Portal (hereafter Portal) was developed in the context the Dark Energy Survey (DES) to facilitate scientific analysis. In this paper, we show how the Portal can provide a reliable environment to access vast datasets, provide validation algorithms and metrics, even in the case of multiple photo-zs methods. It is possible to maintain the provenance between the steps of a chain of workflows while ensuring reproducibility of the results. We illustrate how the Portal can be used to provide photo-z estimates using the DES first year (Y1A1) data. While the DES collaboration is still developing techniques to obtain more precise photo-zs, having a structured framework like the one presented here is critical for the systematic vetting of DES algorithmic improvements and the consistent production of photo-zs in future DES releases

The Dark Energy Survey Data Release 2

We present the second public data release of the Dark Energy Survey, DES DR2, based on optical/near-infrared imaging by the Dark Energy Camera mounted on the 4 m Blanco telescope at Cerro Tololo Inter-American Observatory in Chile. DES DR2 consists of reduced single-epoch and coadded images, a source catalog derived from coadded images, and associated data products assembled from 6 yr of DES science operations. This release includes data from the DES wide-area survey covering ∼5000 deg2 of the southern Galactic cap in five broad photometric bands, grizY. DES DR2 has a median delivered point-spread function FWHM of g = 1.11′′, r = 0.95′′, i = 0.88′′, z = 0.83′′, and Y = 0.′′90, photometric uniformity with a standard deviation of < 3 mmag with respect to Gaia DR2 G band, a photometric accuracy of ∼11 mmag, and a median internal astrometric precision of ∼27 mas. The median coadded catalog depth for a 1.′′95 diameter aperture at signal-to-noise ratio = 10 is g = 24.7, r = 24.4, i = 23.8, z = 23.1, and Y = 21.7 mag. DES DR2 includes ∼691 million distinct astronomical objects detected in 10,169 coadded image tiles of size 0.534 deg2 produced from 76,217 single-epoch images. After a basic quality selection, benchmark galaxy and stellar samples contain 543 million and 145 million objects, respectively. These data are accessible through several interfaces, including interactive image visualization tools, web-based query clients, image cutout servers, and Jupyter notebooks. DES DR2 constitutes the largest photometric data set to date at the achieved depth and photometric precision

DES science portal:computing photometric redshifts

A significant challenge facing photometric surveys for cosmological purposes is the need to produce reliable redshift estimates. The estimation of photometric redshifts (photo-s) has been consolidated as the standard strategy to bypass the high production costs and incompleteness of spectroscopic redshift samples. Training-based photo- methods require the preparation of a high-quality list of spectroscopic redshifts, which needs to be constantly updated. The photo- training, validation, and estimation must be performed in a consistent and reproducible way in order to accomplish the scientific requirements. To meet this purpose, we developed an integrated web-based data interface that not only provides the framework to carry out the above steps in a systematic way, enabling the ease testing and comparison of different algorithms, but also addresses the processing requirements by parallelizing the calculation in a transparent way for the user. This framework called the Science Portal (hereafter Portal) was developed in the context the Dark Energy Survey (DES) to facilitate scientific analysis. In this paper, we show how the Portal can provide a reliable environment to access vast datasets, provide validation algorithms and metrics, even in the case of multiple photo-s methods. It is possible to maintain the provenance between the steps of a chain of workflows while ensuring reproducibility of the results. We illustrate how the Portal can be used to provide photo- estimates using the DES first year (Y1A1) data. While the DES collaboration is still developing techniques to obtain more precise photo-s, having a structured framework like the one presented here is critical for the systematic vetting of DES algorithmic improvements and the consistent production of photo-zs in future DES releases

Stress-compensating MEMS sensor assembly

In this work, a system assembly technology will be presented that allows an effective mechanical decoupling of the MEMS element from the environment while maintaining minimal package footprint and cost. It utilizes a Si interposer with planar spring structures for an independent suspension of all interconnects to the MEMS element. The design of the planar springs was optimized for maximum stability and effectiveness using finite element analysis. The MEMS die is arranged below the interposer for mechanical protection during assembly and operation. The required clearance to the substrate is provided only by industry standard solder balls. The interposer is manufactured on a temporary carrier wafer by deep reactiveion etching, the interconnect to the MEMS die is realized by thermo-compression bonding. The effectiveness of this approach is demonstrated through the example of a high accuracy pressure sensor, although beyond that it has the potential to provide a functional package platform for MEMS sensors in a multitude of applications

Applications of Invertebrate Animal Models to Dimorphic Fungal Infections

Dimorphic fungi can be found in the yeast form during infection and as hyphae in the environment and are responsible for a large number of infections worldwide. Invertebrate animals have been shown to be convenient models in the study of fungal infections. These models have the advantages of being low cost, have no ethical issues, and an ease of experimentation, time-efficiency, and the possibility of using a large number of animals per experiment compared to mammalian models. Invertebrate animal models such as Galleria mellonella, Caenorhabditis elegans, and Acanthamoeba castellanii have been used to study dimorphic fungal infections in the context of virulence, innate immune response, and the efficacy and toxicity of antifungal agents. In this review, we first summarize the features of these models. In this aspect, the growth temperature, genome sequence, availability of different strains, and body characteristics should be considered in the model choice. Finally, we discuss the contribution and advances of these models, with respect to dimorphic fungi Paracoccidioides spp., Histoplasma capsulatum, Blastomyces dermatitidis, Sporothrix spp., and Talaromyces marneffei (Penicillium marneffei)

Evaluation of cytotoxicity features of antimicrobial peptides with potential to control bacterial diseases of citrus.

considered an alternative for pesticides used to control plant pathogens, including those affecting citrus. Brazil is the largest producer and exporter of frozen concentrated orange juice in the world. However, the citrus industry has been affected by several diseases such as citrus canker and huanglongbing (HLB), caused by the bacteria Xanthomonas citri subsp. citri (X.citri) and Candidatus Liberibacter asiaticus (CaLas), respectively. In order to control these pathogens, putative AMPs were prospected in databases containing citrus sequences. Furthermore, AMPs already reported in the literature were also used for in vitro and in vivo assays against X.citri. Since CaLas cannot be cultivated in vitro, surrogates as Sinorhizobium meliloti and Agrobacterium tumefaciens were used. This study reports the evaluation of six AMPs obtained from different sources, two of them from Citrus spp. (citrus-amp1 and citrus-amp2), three from amphibians (Hylin-a1, K0-W6-Hy-a1 and Ocellatin 4-analogue) and one from porcine (Tritrpticin). Peptides K0-W6-Hy-a1, Ocellatin 4-analogue, and citrus-amp1 showed bactericidal activity against X.citri and S. meliloti and bacteriostatic effect on A. tumefaciens. These results were confirmed for X.citri in planta. In addition cytotoxicity evaluations of these molecules were performed. The AMPs that showed the lowest hemolytic activities were Triptrpticin, citrus-amp1 and citrus-amp2. Citrus-amp1 and citrus-amp2 not presented toxicity in experiments using in vivo model, G. mellonella and U87 MG cells. To verify the interaction of these AMPs with bacteria and erythrocyte cell membranes, vesicles mimicking these cells were built. Citrus-amp1 and Tritrpticin exhibited higher affinity to bacterial membranes, while Ocellatin 4-analogue and Hylin-a1 showed higher affinity to erythrocyte membranes; exclude their use in citrus. This work demonstrates an essential alternative, trough AMPs obtained from Citrus spp., which can be feasibly used to control bacterial pathogens.Made available in DSpace on 2018-09-12T00:39:41Z (GMT). No. of bitstreams: 1 InuiKishietal2018journal.pone.0203451.pdf: 10553282 bytes, checksum: b9f3b7c302bb6f0ff780278ba3c99893 (MD5) Previous issue date: 2018-09-11bitstream/item/182724/1/Inui-Kishi-et-al-2018-journal.pone.0203451.pd

DES science portal: Computing photometric redshifts

A significant challenge facing photometric surveys for cosmological purposes is the need to produce reliable redshift estimates. The estimation of photometric redshifts (photo-zs) has been consolidated as the standard strategy to bypass the high production costs and incompleteness of spectroscopic redshift samples. Training-based photo-z methods require the preparation of a high-quality list of spectroscopic redshifts, which needs to be constantly updated. The photo-z training, validation, and estimation must be performed in a consistent and reproducible way in order to accomplish the scientific requirements. To meet this purpose, we developed an integrated web-based data interface that not only provides the framework to carry out the above steps in a systematic way, enabling the ease testing and comparison of different algorithms, but also addresses the processing requirements by parallelizing the calculation in a transparent way for the user. This framework called the Science Portal (hereafter Portal) was developed in the context the Dark Energy Survey (DES) to facilitate scientific analysis. In this paper, we show how the Portal can provide a reliable environment to access vast datasets, provide validation algorithms and metrics, even in the case of multiple photo-zs methods. It is possible to maintain the provenance between the steps of a chain of workflows while ensuring reproducibility of the results. We illustrate how the Portal can be used to provide photo-z estimates using the DES first year (Y1A1) data. While the DES collaboration is still developing techniques to obtain more precise photo-zs, having a structured framework like the one presented here is critical for the systematic vetting of DES algorithmic improvements and the consistent production of photo-zs in future DES releases

Alkyl Protocatechuate-Loaded Nanostructured Lipid Systems as a Treatment Strategy for Paracoccidioides brasiliensis and Paracoccidioides lutzii In Vitro

Dodecyl protocatechuate (dodecyl) is a derivative of protocatechuic acid (3,4-dihydroxybenzoic acid) that possesses anti-oxidant and antifungal properties. Nanostructured lipid systems (NLS) can potentiate the action of many antifungal agents, reducing the required dose and side effects by improving their activity. This work aimed to evaluate dodecyl protocatechuate loaded into a NLS (NLS+dodecyl) as a strategy for the treatment of Paracoccidioides brasiliensis and P. lutzii in vitro. Antifungal activity against P. brasiliensis and P. lutzii was evaluated using the microdilution technique. NLS+dodecyl showed high antifungal activity with a minimum inhibitory concentration ranging from 0.06 to 0.03 μg/mL; 4- to 16-fold higher than that of free dodecyl. NLS+dodecyl was able to inhibit fungal adhesion of the extracellular artificial matrix proteins (laminin and fibronectin), resulting in 82.4 and 81% inhibition, respectively, an increase of 8–17% compared with free dodecyl. These findings corroborate previous results demonstrating 65 and 74% inhibition of fungal adhesion in pulmonary fibroblast cells by dodecyl and NLS+dodecyl, respectively, representing a 9% increase in inhibition for NLS+dodecyl. Subsequently, cytotoxicity was evaluated using the 0.4% sulforhodamine B assay. NLS+dodecyl did not exhibit cytotoxicity in MRC5 (human pneumocyte) and HepG2 (human hepatic carcinoma) cells, thus increasing the selectivity index for NLS+dodecyl. In addition, cytotoxicity was evaluated in vivo using the Caenorhabditis elegans model; neither dodecyl nor NLS+dodecyl exhibited any toxic effects. Taken together, these results suggest that NLS can be used as a strategy to improve the activity of dodecyl against P. brasiliensis and P. lutzii because it improves antifungal activity, increases the inhibition of fungal adhesion in lung cells and the extracellular matrix in vitro, and does not exhibit any toxicity both in vitro and in vivo