A Framework for Fast Image Deconvolution with Incomplete Observations

In image deconvolution problems, the diagonalization of the underlying operators by means of the FFT usually yields very large speedups. When there are incomplete observations (e.g., in the case of unknown boundaries), standard deconvolution techniques normally involve non-diagonalizable operators, resulting in rather slow methods, or, otherwise, use inexact convolution models, resulting in the occurrence of artifacts in the enhanced images. In this paper, we propose a new deconvolution framework for images with incomplete observations that allows us to work with diagonalized convolution operators, and therefore is very fast. We iteratively alternate the estimation of the unknown pixels and of the deconvolved image, using, e.g., an FFT-based deconvolution method. This framework is an efficient, high-quality alternative to existing methods of dealing with the image boundaries, such as edge tapering. It can be used with any fast deconvolution method. We give an example in which a state-of-the-art method that assumes periodic boundary conditions is extended, through the use of this framework, to unknown boundary conditions. Furthermore, we propose a specific implementation of this framework, based on the alternating direction method of multipliers (ADMM). We provide a proof of convergence for the resulting algorithm, which can be seen as a "partial" ADMM, in which not all variables are dualized. We report experimental comparisons with other primal-dual methods, where the proposed one performed at the level of the state of the art. Four different kinds of applications were tested in the experiments: deconvolution, deconvolution with inpainting, superresolution, and demosaicing, all with unknown boundaries.Comment: IEEE Trans. Image Process., to be published. 15 pages, 11 figures. MATLAB code available at https://github.com/alfaiate/DeconvolutionIncompleteOb

A convex formulation for hyperspectral image superresolution via subspace-based regularization

Hyperspectral remote sensing images (HSIs) usually have high spectral resolution and low spatial resolution. Conversely, multispectral images (MSIs) usually have low spectral and high spatial resolutions. The problem of inferring images which combine the high spectral and high spatial resolutions of HSIs and MSIs, respectively, is a data fusion problem that has been the focus of recent active research due to the increasing availability of HSIs and MSIs retrieved from the same geographical area. We formulate this problem as the minimization of a convex objective function containing two quadratic data-fitting terms and an edge-preserving regularizer. The data-fitting terms account for blur, different resolutions, and additive noise. The regularizer, a form of vector Total Variation, promotes piecewise-smooth solutions with discontinuities aligned across the hyperspectral bands. The downsampling operator accounting for the different spatial resolutions, the non-quadratic and non-smooth nature of the regularizer, and the very large size of the HSI to be estimated lead to a hard optimization problem. We deal with these difficulties by exploiting the fact that HSIs generally "live" in a low-dimensional subspace and by tailoring the Split Augmented Lagrangian Shrinkage Algorithm (SALSA), which is an instance of the Alternating Direction Method of Multipliers (ADMM), to this optimization problem, by means of a convenient variable splitting. The spatial blur and the spectral linear operators linked, respectively, with the HSI and MSI acquisition processes are also estimated, and we obtain an effective algorithm that outperforms the state-of-the-art, as illustrated in a series of experiments with simulated and real-life data.Comment: IEEE Trans. Geosci. Remote Sens., to be publishe

The effects of emerging environmental contaminants on Stenotrophomonas maltophilia isolated from drinking water in planktonic and sessile states

Concerns on the presence of emerging contaminants (ECs) in water sources have increased in recent years. The lack of efficient technologies to remove ECs from residual waters contributes for their appearance in drinking water distribution systems (DWDS). Therefore, sessile microorganisms on DWDS pipes are continuously exposed to trace concentrations of ECs. However, no data exists on the role of ECs on the resident microbiota. The present work aims to understand the effects of prolonged exposure of a bacterial strain of Stenotrophomonas maltophilia, isolated from a DWDS, in both planktonic and biofilm states, to trace concentrations of selected ECs (antipyrineANTP; diclofenac sodium saltDCF; ibuprofenIBP; galaxolideGAL; tonalideTON; carbamazepineCBZ; clofibric acidCA; tylosinTY) on its tolerance to sodium hypochlorite (NaOCl) and resistance to antibiotics. Pre-established S. maltophilia biofilms were exposed to ECs for 26 d. Subsequently, the planktonic behaviour of the biofilm cells grown in the presence of ECS was characterized in terms of susceptibility to NaOCl and to selected antibiotics (levofloxacin and trimethoprim-sulfamethoxazole). Moreover, S.maltophilia was tested on its biofilm productivity in the presence of ECs (alone and mixed). These biofilms were challenged by NaOCl in order to assess the role of ECs on biofilm susceptibility. The results did not evidence remarkable effects of ECs on planktonic S. maltophilia susceptibility to NaOCl and antibiotics. However, S. maltophilia biofilm production and susceptibility to NaOCl was affected from ECs pre-exposure, particularly by the combination of different ECs (CA+CBZ, CA+IBP, CA+CBZ+IBP). S. maltophilia biofilms became more resistant to removal by NaOCl when developed in the presence of mixtures of CA+CBZ and CA+CBZ+IBP. Also, biofilm production was significantly affected. CA was present in all the combinations that altered biofilm behaviour. The overall results propose that exposure to ECs for 26days had not a huge impact on S. maltophilia planktonic antimicrobial susceptibility. Nevertheless, the prolonged exposure to some ECs altered biofilm production and tolerance to NaOCl, with a potential practical outcome of hindering DWDS disinfection. The simultaneous presence of different ECs in the environment may amplify biofilm resilience.This work was the result of the projects: POCI-01-0145-FEDER-030219; POCI-01-0145-FEDER-006939 (Laboratory for Process Engineering, Environment, Biotechnology and Energy – UID/EQU/00511/2013) funded by the European Regional Development Fund (ERDF), through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) and by national funds, through FCT - Fundação para a Ciência e a Tecnologia. NORTE-01-0145-FEDER-000005 – LEPABE-2-ECO-INNOVATION, supported by North Portugal Regional Operational Program (NORTE 2020), under the Portugal 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Grants attributed by Portuguese Foundation for Science and Technology – FCT – to Inês Gomes (SFRH/BD/103810/2014) and Lúcia Simões (SFRH/BPD/81982/2011).info:eu-repo/semantics/publishedVersio

The effects of sodium hypochlorite against selected drinking water-isolated bacteria in planktonic and sessile states

Chlorine is the most commonly used agent for general disinfection, particularly for microbial growth control in drinking water distribution systems. The goals of this study were to understand the effects of chlorine, as sodium hypochlorite (NaOCl), on bacterial membrane physicochemical properties (surface charge, surface tension and hydrophobicity) and on motility of two emerging pathogens isolated from drinking water, Acinetobacter calcoaceticus and Stenotrophomonas maltophilia. The effects of NaOCl on the control of single and dual-species monolayer adhered bacteria (2 h incubation) and biofilms (24 h incubation) was also assessed. NaOCl caused significant changes on the surface hydrophobicity and motility of A. calcoaceticus, but not of S. maltophilia. Planktonic and sessile S. maltophilia were significantly more resistant to NaOCl than A. calcoaceticus. Monolayer adhered co-cultures of A. calcoaceticus-S. maltophilia were more resilient than the single species. Oppositely, dual species biofilms were more susceptible to NaOCl than their single species counterparts. In general, biofilm removal and killing demonstrated to be distinct phenomena: total bacterial viability reduction was achieved even if NaOCl at the higher concentrations had a reduced removal efficacy, allowing biofilm reseed. In conclusion, understanding the antimicrobial susceptibility of microorganisms to NaOCl can contribute to the design of effective biofilm control strategies targeting key microorganisms, such as S. maltophilia, and guarantying safe and high-quality drinking water. Moreover, the results reinforce that biofilms should be regarded as chronic contaminants of drinking water distribution systems and accurate methods are needed to quantify their presence as well as strategies complementary/alternative to NaOCl are required to effectively control the microbiological quality of drinking water.This work was financially supported by: Project POCI-01-0145-FEDER-006939 (Laboratory for Process Engineering, Environment, Biotechnology and Energy – LEPABE funded by FEDER funds through COMPETE2020 - Programa Operacional Competitividade e Internacionalização (POCI) – and by national funds through FCT - Fundação para a Ciência e a Tecnologia/MEC: Project POMACEA–Inn-INDIGO/0001/2014, SFRH/BD/103810/2014 and SFRH/BPD/81982/2011

Influence of surface copper content on Stenotrophomonas maltophilia biofilm control using chlorine and mechanical stress

This work aimed to evaluate the action of materials with different copper content (0, 57, 96 and 100%) on biofilm formation and control by chlorination and mechanical stress. Stenotrophomonas maltophilia isolated from drinking water was used as a model microorganism and biofilms were developed in a rotating cylinder reactor using realism-based shear stress conditions. Biofilms were characterized phenotypically and exposed to three control strategies: 10mg l1 of free chlorine for 10min, an increased shear stress (a fluid velocity of 1.5m s1 for 30s), and a combination of both treatments. These shock treatments were not effective in biofilm control. The benefits from the use of copper surfaces was found essentially in reducing the numbers of non-damaged cells. Copper materials demonstrated better performance in biofilm prevention than chlorine. In general, copper alloys may have a positive public health impact by reducing the number of non-damaged cells in the water delivered after chlorine exposure.This work was the result of the projects: UID/EQU/00511/2019 – Laboratory for Process Engineering, Environment, Biotechnology and Energy – LEPABE funded by national funds through FCT/MCTES (PIDDAC); POCI-01-0145-FEDER-030219; POCI-01-0247-FEDER-035234; POCI-01-0247-FEDER-033298 - funded by FEDER funds through COMPETE2020 – Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) through FCT/MCTES; NORTE-01-0145-FEDER-000005 – LEPABE-2-ECO-INNOVATION, supported by Norte Portugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 Partnership Agreement, through the European Regional Development Fund (ERDF). Grant attributed by Portuguese Foundation for Science and Technology – FCT – to Inês Gomes (SFRH/BD/103810/2014) and to Manuel Simoes (SFRH/BSAB/150379/2019).info:eu-repo/semantics/publishedVersio

Copper surfaces in biofilm control

Biofilms are structures comprising microorganisms associated to surfaces and enclosed by an extracellular polymeric matrix produced by the colonizer cells. These structures protect microorganisms from adverse environmental conditions. Biofilms are typically associated with several negative impacts for health and industries and no effective strategy for their complete control/eradication has been identified so far. The antimicrobial properties of copper are well recognized among the scientific community, which increased their interest for the use of these materials in different applications. In this review the use of different copper materials (copper, copper alloys, nanoparticles and copper-based coatings) in medical settings, industrial equipment and plumbing systems will be discussed considering their potential to prevent and control biofilm formation. Particular attention is given to the mode of action of copper materials. The putative impact of copper materials in the health and/or products quality is reviewed taking into account their main use and the possible effects on the spread of antimicrobial resistance.This work was financially supported by: Base Funding—UIDB/00511/2020 of LEPABE and UIDB/00081/2020 of CIQUP funded by national funds through the FCT/MCTES (PIDDAC); Project Biocide_for_Biofilm—PTDC/BII-BTI/30219/2017—POCI-01-0145-FEDER-030219, ABFISH—PTDC/ASP-PES/28397/2017—POCI-01-0145-FEDER-028397 and ALGAVALOR—POCI-01-0247-FEDER-035234, funded by FEDER funds through COMPETE2020—Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) through FCT/MCTES; Portuguese Foundation for Science and Technology (FCT) under the scope of the strategic funding of UIDB/04469/2020 unit and BioTecNorte operation (NORTE-01-0145-FEDER-000004) funded by the European Regional Development Fund under the scope of Norte2020—Programa Operacional Regional do Norte; SFRH/BSAB/150379/2019 (Manuel Simões).info:eu-repo/semantics/publishedVersio

Influence of different copper materials on biofilm control using chlorine and mechanical stress

The selection of materials for plumbing application has potential implications on the chemical and microbiological quality of the delivered water. This work aims to evaluate the action of materials with different copper content (0, 57, 96 and 100%) on biofilm formation and control by chlorination and mechanical stress. A strain of Stenotrophomonas maltophilia isolated from drinking water was used as model microorganism and biofilms were developed in a rotating cylinder reactor (RCR) using realism-based shear stress conditions. Biofilms were characterized phenotypically and exposed to three control strategies: 10 mg/l of free chlorine for 10 min; an increased shear stress (equivalent to 1.5 m/s of fluid velocity); and the combination of both treatments. Biofilms formed on the copper materials had lower wet mass and produced significantly lower amounts of extracellular proteins than those formed on stainless steel (0% of copper content). Although, the effects of copper materials on biofilm cell density was not significant, these materials had important impact on the efficacy of chemical and/or mechanical treatments. Biofilms formed on 96 or 100% copper materials had lower content of culturable bacteria than that observed on stainless steel after exposure to chlorine or shear stress. The mechanical treatment used had no relevant effects in biofilm control. The combination of chemical and mechanical treatments only caused higher culturability reduction than chlorine in biofilms formed on 57% copper alloy. The number of viable cells present in bulk water after biofilm treatment with chlorine was lower when biofilms were formed on any of the copper surface. The overall results are of potential importance on the selection of materials for drinking water distribution systems, particularly for house and hospital plumbing systems to overcome the effects from chlorine decay. Copper alloys may have a positive public health impact by reducing the number of viable cells in the delivered water after chlorine exposure and improving the disinfection of DW systems. Moreover, the results demonstrate that residual chlorine and mechanical stress, two strategies conventionally used for disinfection of drinking water distribution systems, failed in S. maltophilia biofilm control.This work was the result of the projects: UIDB/00511/2020 of the Laboratory for ProcessEngineering, Environment, Biotechnology and Energy – LEPABE - funded by national funds throughthe FCT/MCTES(PIDDAC); PTDC/BII-BTI/30219/2017-POCI-01-0145-FEDER-030219;POCI-01-0145-FEDER-006939, funded by FEDER funds through COMPETE2020 – ProgramaOperacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) throughFCT/MCTES; NORTE-01-0145-FEDER-000005 – LEPABE-2-ECO-INNOVATION, supported by NortePortugal Regional Operational Programme (NORTE 2020), under PORTUGAL 2020 PartnershipAgreement, through the European Regional Development Fund (ERDF)info:eu-repo/semantics/publishedVersio

Emerging contaminants affect the microbiome of water systems: strategies for their mitigation

The presence of emerging contaminants (ECs) in the environment has been consistently recognized as a worldwide concern. ECs may be defined as chemicals or materials found in the environment at trace concentrations with potential, perceived, or real risk to the One Health trilogy (environment, human, and animal health). The main concern regarding pharmaceuticals and in particular antibiotics is the widespread dissemination of antimicrobial resistance. Nevertheless, non-antimicrobials also interact with microorganisms in both bulk phase and in biofilms. In fact, drugs not developed for antimicrobial chemotherapy can exert an antimicrobial action and, therefore, a selective pressure on microorganisms. This review aims to provide answers to questions typically ignored in epidemiological and environmental monitoring studies with a focus on water systems, particularly drinking water (DW): Do ECs exposure changes the behavior of environmental microorganisms? May non-antibiotic ECs affect tolerance to antimicrobials? Do ECs interfere with biofilm function? Are ECs-induced changes in microbial behavior of public health concern? Nowadays, the answers to these questions are still very limited. However, this study demonstrates that some ECs have significant effects in microbial behavior. The most studied ECs are pharmaceuticals, particularly antibiotics, carbamazepine and diclofenac. The pressure caused by antibiotic and other antimicrobial agents on the acquisition and spread of antibiotic resistance seems to be unquestionable. However, regarding the effects of ECs on the development and behavior of biofilms, the conclusions of different studies are still controversial. The dissimilar findings propose that standardized tests are needed for an accurate assessment on the effects of ECs in the microbiome of water systems. The variability of experimental conditions, combined with the presence of mixtures of ECs as well as the lack of information about the effects of non-pharmaceutical ECs constitute the main challenge to be overcome in order to improve ECs prioritization.This work was financially supported by project UIDB/EQU/00511/2020—Laboratory for Process Engineering, Environment, Biotechnology and Energy—LEPABE funded by national funds through FCT/MCTES (PIDDAC); Projects PTDC/BII-BTI/30219/2017–POCI- 01-0145-FEDER-030219, PTDC/ASP-PES/28397/2017–POCI-01-0145-FEDER-028397 and POCI-01-0247-FEDER-035234 funded by FEDER funds through COMPETE2020— Programa Operacional Competitividade e Internacionalização (POCI) and by national funds (PIDDAC) through FCT/MCTES.info:eu-repo/semantics/publishedVersio